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Sample records for species delimitation approach

  1. A new approach to species delimitation in Septoria

    NARCIS (Netherlands)

    Verkley, G.J.M.; Quaedvlieg, W.; Shin, H.D.; Crous, P.W.

    2013-01-01

    Septoria is a large genus of asexual morphs of Ascomycota causing leaf spot diseases of many cultivated and wild plants. Host specificity has long been a decisive criterium in species delimitation in Septoria, mainly because of the paucity of useful morphological characters and the high level of

  2. Algorithmic approaches to aid species' delimitation in multidimensional morphospace

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    Pearson Paul N

    2010-06-01

    Full Text Available Abstract Background The species is a fundamental unit of biological pattern and process, but its delimitation has proven a ready source of argument and disagreement. Here, we discuss four key steps that utilize statistical thresholds to describe the morphological variability within a sample and hence assess whether there is evidence for one or multiple species. Once the initial set of biologically relevant traits on comparable individuals has been identified, there is no need for the investigator to hypothesise how specimens might be divided among groups, nor the traits on which groups might be separated. Results Principal components are obtained using robust covariance estimates and retained only if they exceed threshold amounts of explanatory power, before model-based clustering is performed on the dimension-reduced space. We apply these steps in an attempt to resolve ongoing debates among taxonomists working on the extinct Eocene planktonic foraminifera Turborotalia, providing statistical evidence for two species shortly before the lineage's extinction near the Eocene/Oligocene boundary. Conclusion By estimating variance robustly (samples containing incipient species are unlikely to be scaled optimally by means and standard deviations and identifying thresholds relevant to a particular system rather than universal standards, the steps of the framework aim to optimize the chances of delineation without imposing pre-conceived patterns onto estimates of species limits.

  3. Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

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    Andrea A. F. Mourão

    Full Text Available ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó individuals were collected in Paraná and Tietê rivers (SP, Brazil. For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

  4. Species concepts, species delimitation and the inherent limitations

    Indian Academy of Sciences (India)

    Frank Zachos

    synchrony and to sexually reproducing organisms would not be a problem anymore ... approach to species delimitation that combines genetic data with .... The datasets or algorithms could then be modified so that the groups yielded conform.

  5. Phylogenetic species delimitation for crayfishes of the genus Pacifastacus.

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    Larson, Eric R; Castelin, Magalie; Williams, Bronwyn W; Olden, Julian D; Abbott, Cathryn L

    2016-01-01

    Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genus Pacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly, Pacifastacus includes both the widely invasive signal crayfish Pacifastacus leniusculus, as well as several species of conservation concern like the Shasta crayfish Pacifastacus fortis. Our analysis used 83 individuals sampled across the four extant Pacifastacus species (omitting the extinct Pacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genus Pacifastacus as monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method. Pacifastacus leniusculus included the majority of PSHs and was not monophyletic relative to the other Pacifastacus species considered. Several of these highly distinct P. leniusculus PSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities for Pacifastacus crayfishes in western

  6. Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

    OpenAIRE

    Flot, Jean-François; Couloux, Arnaud; Tillier, Simon

    2010-01-01

    Abstract Background Usual methods for inferring species boundaries from molecular sequence data rely either on gene trees or on population genetic analyses. Another way of delimiting species, based on a view of species as "fields for recombination" (FFRs) characterized by mutual allelic exclusivity, was suggested in 1995 by Doyle. Here we propose to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring in heterozygous individuals) to visualize and...

  7. Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton.

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    Flot, Jean-François; Couloux, Arnaud; Tillier, Simon

    2010-11-30

    Usual methods for inferring species boundaries from molecular sequence data rely either on gene trees or on population genetic analyses. Another way of delimiting species, based on a view of species as "fields for recombination" (FFRs) characterized by mutual allelic exclusivity, was suggested in 1995 by Doyle. Here we propose to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring in heterozygous individuals) to visualize and delineate single-locus FFRs (sl-FFRs). Furthermore, we introduce a method to quantify the reliability of putative species boundaries according to the number of independent markers that support them, and illustrate this approach with a case study of taxonomically difficult corals of the genus Pocillopora collected around Clipperton Island (far eastern Pacific). One haploweb built from intron sequences of the ATP synthase β subunit gene revealed the presence of two sl-FFRs among our 74 coral samples, whereas a second one built from ITS sequences turned out to be composed of four sl-FFRs. As a third independent marker, we performed a combined analysis of two regions of the mitochondrial genome: since haplowebs are not suited to analyze non-recombining markers, individuals were sorted into four haplogroups according to their mitochondrial sequences. Among all possible bipartitions of our set of samples, thirteen were supported by at least one molecular dataset, none by two and only one by all three datasets: this congruent pattern obtained from independent nuclear and mitochondrial markers indicates that two species of Pocillopora are present in Clipperton. Our approach builds on Doyle's method and extends it by introducing an intuitive, user-friendly graphical representation and by proposing a conceptual framework to analyze and quantify the congruence between sl-FFRs obtained from several independent markers. Like delineation methods based on population-level statistical approaches, our method can

  8. Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

    Directory of Open Access Journals (Sweden)

    Flot Jean-François

    2010-11-01

    Full Text Available Abstract Background Usual methods for inferring species boundaries from molecular sequence data rely either on gene trees or on population genetic analyses. Another way of delimiting species, based on a view of species as "fields for recombination" (FFRs characterized by mutual allelic exclusivity, was suggested in 1995 by Doyle. Here we propose to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring in heterozygous individuals to visualize and delineate single-locus FFRs (sl-FFRs. Furthermore, we introduce a method to quantify the reliability of putative species boundaries according to the number of independent markers that support them, and illustrate this approach with a case study of taxonomically difficult corals of the genus Pocillopora collected around Clipperton Island (far eastern Pacific. Results One haploweb built from intron sequences of the ATP synthase β subunit gene revealed the presence of two sl-FFRs among our 74 coral samples, whereas a second one built from ITS sequences turned out to be composed of four sl-FFRs. As a third independent marker, we performed a combined analysis of two regions of the mitochondrial genome: since haplowebs are not suited to analyze non-recombining markers, individuals were sorted into four haplogroups according to their mitochondrial sequences. Among all possible bipartitions of our set of samples, thirteen were supported by at least one molecular dataset, none by two and only one by all three datasets: this congruent pattern obtained from independent nuclear and mitochondrial markers indicates that two species of Pocillopora are present in Clipperton. Conclusions Our approach builds on Doyle's method and extends it by introducing an intuitive, user-friendly graphical representation and by proposing a conceptual framework to analyze and quantify the congruence between sl-FFRs obtained from several independent markers. Like delineation methods based on

  9. Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota.

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    Xinli Wei

    Full Text Available Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae. In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the "Automatic Barcode Gap Discovery" (ABGD, the Poisson tree process model (PTP, the General Mixed Yule Coalescent (GMYC, and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST. The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain

  10. Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

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    Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

    2018-01-01

    The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

  11. Species delimitation in the Stenocereus griseus (Cactaceae species complex reveals a new species, S. huastecorum.

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    Hernán Alvarado-Sizzo

    Full Text Available The Stenocereus griseus species complex (SGSC has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

  12. Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura).

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    Toussaint, Emmanuel F A; Morinière, Jérôme; Müller, Chris J; Kunte, Krushnamegh; Turlin, Bernard; Hausmann, Axel; Balke, Michael

    2015-10-01

    The charismatic tropical Polyura Nawab butterflies are distributed across twelve biodiversity hotspots in the Indomalayan/Australasian archipelago. In this study, we tested an array of species delimitation methods and compared the results to existing morphology-based taxonomy. We sequenced two mitochondrial and two nuclear gene fragments to reconstruct phylogenetic relationships within Polyura using both Bayesian inference and maximum likelihood. Based on this phylogenetic framework, we used the recently introduced bGMYC, BPP and PTP methods to investigate species boundaries. Based on our results, we describe two new species Polyura paulettae Toussaint sp. n. and Polyura smilesi Toussaint sp. n., propose one synonym, and five populations are raised to species status. Most of the newly recognized species are single-island endemics likely resulting from the recent highly complex geological history of the Indomalayan-Australasian archipelago. Surprisingly, we also find two newly recognized species in the Indomalayan region where additional biotic or abiotic factors have fostered speciation. Species delimitation methods were largely congruent and succeeded to cross-validate most extant morphological species. PTP and BPP seem to yield more consistent and robust estimations of species boundaries with respect to morphological characters while bGMYC delivered contrasting results depending on the different gene trees considered. Our findings demonstrate the efficiency of comparative approaches using molecular species delimitation methods on empirical data. They also pave the way for the investigation of less well-known groups to unveil patterns of species richness and catalogue Earth's concealed, therefore unappreciated diversity. Published by Elsevier Inc.

  13. Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae: cryptic diversity in North American tarantulas.

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    Chris A Hamilton

    Full Text Available The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal "barcoding gene". An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp and ND1-16S (886 bp. Multiple species delimitation techniques (DNA tree-based methods, a "barcode gap" using percent of pairwise sequence divergence (uncorrected p-distances, and the GMYC method consistently recognized a number of divergent and genealogically exclusive groups.The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a

  14. Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data.

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    Lyra, Goia de M; Gurgel, C Frederico D; Costa, Emmanuelle da S; de Jesus, Priscila B; Oliveira, Mariana C; Oliveira, Eurico C; Davis, Charles C; Nunes, José Marcos de Castro

    2016-12-01

    Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae. © 2016 Phycological Society of America.

  15. Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography.

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    Sun, Xin; Zhang, Feng; Ding, Yinhuan; Davies, Thomas W; Li, Yu; Wu, Donghui

    2017-08-15

    Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.

  16. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

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    Justin C Bagley

    Full Text Available Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the

  17. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species

    KAUST Repository

    Arrigoni, Roberto

    2016-09-09

    Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals. (C) 2016 Elsevier Inc. All rights reserved.

  18. Species delimitation in taxonomically difficult fungi: the case of Hymenogaster.

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    Benjamin Stielow

    2011-01-01

    Full Text Available False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season. In particular, taxa described in the 19(th century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general.

  19. Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.

    Science.gov (United States)

    Lymbery, A J

    2017-01-01

    An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species

    Czech Academy of Sciences Publication Activity Database

    Kotsakiozi, P.; Jablonski, D.; Ilgaz, Ç.; Kumlutaş, Y.; Avci, A.; Meiri, S.; Itescu, Y.; Kukushkin, O.; Gvoždík, Václav; Scillitani, G.; Roussos, S. A.; Jandzik, D.; Kasapidis, P.; Lymberakis, P.; Poulakakis, N.

    2018-01-01

    Roč. 125, August (2018), s. 177-187 ISSN 1055-7903 Institutional support: RVO:68081766 Keywords : Gekkonidae * Divergence times * Species delimitation * Species complex * Systematics * Eastern Mediterranean Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 4.419, year: 2016

  1. Mating type genes in the genus Neofusicoccum: Mating strategies and usefulness in species delimitation.

    Science.gov (United States)

    Lopes, Anabela; Phillips, Alan J L; Alves, Artur

    2017-04-01

    The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed. Homothallism was the predominant mating strategy among the species tested. Furthermore, the potential of mating type gene sequences for species delimitation was evaluated. Phylogenetic analyses were performed on both MAT genes and compared with multigene genealogies using sequences of the ribosomal internal transcribed spacer region, translation elongation factor 1-alpha and beta-tubulin. Phylogenies based on mating type genes could discriminate between the species analysed and are in concordance with the results obtained with the more conventional multilocus phylogenetic analysis approach. Thus, MAT genes represent a powerful tool to delimit cryptic species in the genus Neofusicoccum. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  2. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    Science.gov (United States)

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Haplowebs as a graphical tool for delimiting species: a revival of Doyle's "field for recombination" approach and its application to the coral genus Pocillopora in Clipperton

    OpenAIRE

    Flot, J.; Couloux, A.; Tillier, S.

    2010-01-01

    BackgroundUsual methods for inferring species boundaries from molecular sequence data rely either on gene trees or on population genetic analyses. Another way of delimiting species, based on a view of species as "fields for recombination" (FFRs) characterized by mutual allelic exclusivity, was suggested in 1995 by Doyle. Here we propose to use haplowebs (haplotype networks with additional connections between haplotypes found co-occurring in heterozygous individuals) to visualize and delineate...

  4. Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)

    Science.gov (United States)

    Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d’Alençon, Emmanuelle; Kergoat, Gael J.

    2015-01-01

    Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

  5. Phylogenetic molecular species delimitations unravel potential new species in the pest genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae.

    Directory of Open Access Journals (Sweden)

    Pascaline Dumas

    Full Text Available Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence. As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae, a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808, S. frugiperda (J.E. Smith, 1797 and S. mauritia (Boisduval, 1833 and support the synonymy of S. marima (Schaus, 1904 with S. ornithogalli (Guenée, 1852. They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858 and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities.

  6. Complex patterns of speciation in cosmopolitan "rock posy" lichens - an integrative approach to discovering and delimiting fungal species in the lichen-forming rhizoplaca melanophthalma speciescomplex

    Science.gov (United States)

    A growing body of evidence indicates that morphology-based species circumspection of lichenized ascomycetes greatly misrepresents the number of existing species. Recently it has been demonstrated that population-level processes operating within diverging populations can facilitate the identification...

  7. Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

    KAUST Repository

    Terraneo, Tullia Isotta; Benzoni, Francesca; Arrigoni, Roberto; Berumen, Michael L.

    2016-01-01

    Variable skeletal morphology, genotype induced plasticity, and homoplasy of skeletal structures have presented major challenges for scleractinian coral taxonomy and systematics since the 18th century. Although the recent integration of genetic and micromorphological data is helping to clarify the taxonomic confusion within the order, phylogenetic relationships and species delimitation within most coral genera are still far from settled. In the present study, the species boundaries in the scleractinian coral genus Goniopora were investigated using 199 colonies from the Saudi Arabian Red Sea and sequencing of four molecular markers: the mitochondrial intergenic spacer between CytB and NAD2, the nuclear ribosomal ITS region, and two single-copy nuclear genes (ATPsβ and CalM). DNA sequence data were analyzed using a variety of methods and exploratory species-delimitation tools. The results were broadly congruent in identifying five distinct molecular lineages within the sequenced Goniopora samples: G. somaliensis/G. savignyi, G. djiboutiensis/G. lobata, G. stokesi, G. albiconus/G. tenuidens, and G. minor/G. gracilis. Although the traditional macromorphological characters used to identify these nine morphospecies were not able to discriminate the obtained molecular clades, informative micromorphological and microstructural features (such as the micro-ornamentation and the arrangement of the columella) were recovered among the five lineages. Moreover, unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. This study represents the first attempt to identify species boundaries within Goniopora using a combined morpho-molecular approach. The obtained data establish a basis for future taxonomic revision of the genus, which should include colonies across its entire geographical distribution in the Indo-Pacific.

  8. Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea

    KAUST Repository

    Terraneo, Tullia Isotta

    2016-06-16

    Variable skeletal morphology, genotype induced plasticity, and homoplasy of skeletal structures have presented major challenges for scleractinian coral taxonomy and systematics since the 18th century. Although the recent integration of genetic and micromorphological data is helping to clarify the taxonomic confusion within the order, phylogenetic relationships and species delimitation within most coral genera are still far from settled. In the present study, the species boundaries in the scleractinian coral genus Goniopora were investigated using 199 colonies from the Saudi Arabian Red Sea and sequencing of four molecular markers: the mitochondrial intergenic spacer between CytB and NAD2, the nuclear ribosomal ITS region, and two single-copy nuclear genes (ATPsβ and CalM). DNA sequence data were analyzed using a variety of methods and exploratory species-delimitation tools. The results were broadly congruent in identifying five distinct molecular lineages within the sequenced Goniopora samples: G. somaliensis/G. savignyi, G. djiboutiensis/G. lobata, G. stokesi, G. albiconus/G. tenuidens, and G. minor/G. gracilis. Although the traditional macromorphological characters used to identify these nine morphospecies were not able to discriminate the obtained molecular clades, informative micromorphological and microstructural features (such as the micro-ornamentation and the arrangement of the columella) were recovered among the five lineages. Moreover, unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. This study represents the first attempt to identify species boundaries within Goniopora using a combined morpho-molecular approach. The obtained data establish a basis for future taxonomic revision of the genus, which should include colonies across its entire geographical distribution in the Indo-Pacific.

  9. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data.

    Science.gov (United States)

    Tang, Cuong Q; Humphreys, Aelys M; Fontaneto, Diego; Barraclough, Timothy G; Paradis, Emmanuel

    2014-10-01

    Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.

  10. Delimiting invasive Myriophyllum aquaticum in Kashmir Himalaya using a molecular phylogenetic approach.

    Science.gov (United States)

    Shah, M A; Ali, M A; Al-Hemaid, F M; Reshi, Z A

    2014-09-12

    Myriophyllum aquaticum (Vell.) Verdc. (family Haloragaceae) is one of the most invasive and destructive South American aquatic plant species and is present in a wide range of geographic regions, including the Kashmir Himalaya. Confusion regarding the taxonomic delimitation of M. aquaticum in the Himalayan region impedes effective and targeted management. Hence, our goal was improve the identification of M. aquaticum for exclusive delimitation from other related species in the study region using a molecular phylogenetic approach. A maximum parsimony tree recovered from phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA was used to authenticate the identification of M. aquaticum. The results of this study can be used for targeted management of this tropical invader into the temperate Kashmir Himalaya.

  11. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

    OpenAIRE

    Kapli, P.; Lutteropp, S.; Zhang, J.; Kobert, K.; Pavlidis, P.; Stamatakis, A.; Flouri, T.

    2017-01-01

    Motivation: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently i...

  12. Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods.

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    Shawn R Kuchta

    Full Text Available Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC, Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr. By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population

  13. Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics.

    Science.gov (United States)

    Vitecek, Simon; Kučinić, Mladen; Previšić, Ana; Živić, Ivana; Stojanović, Katarina; Keresztes, Lujza; Bálint, Miklós; Hoppeler, Felicitas; Waringer, Johann; Graf, Wolfram; Pauls, Steffen U

    2017-06-06

    Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.

  14. Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).

    Science.gov (United States)

    Musher, Lukas J; Cracraft, Joel

    2018-01-01

    Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Integrating DNA barcodes and morphology for species delimitation in the Corynoneura group (Diptera: Chironomidae: Orthocladiinae).

    Science.gov (United States)

    Silva, F L; Wiedenbrug, S

    2014-02-01

    In this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to the Corynoneura group (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within the Corynoneura group, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.

  16. Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae

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    Johannes Bergsten

    2017-06-01

    Full Text Available The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760, are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1 was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey.

  17. Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea.

    Directory of Open Access Journals (Sweden)

    Shahan Derkarabetian

    Full Text Available Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species.

  18. A multilocus species delimitation reveals a striking number of species of coralline algae forming Maerl in the OSPAR maritime area.

    Science.gov (United States)

    Pardo, Cristina; Lopez, Lua; Peña, Viviana; Hernández-Kantún, Jazmin; Le Gall, Line; Bárbara, Ignacio; Barreiro, Rodolfo

    2014-01-01

    Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment) and plastidial (psbA gene) sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96'N) to the Canary Islands (28°64'N) that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC) to delineate 16 primary species hypotheses (PSHs) arranged into four major lineages. Second, chloroplast (psbA) sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs) that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material), six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.

  19. A multilocus species delimitation reveals a striking number of species of coralline algae forming Maerl in the OSPAR maritime area.

    Directory of Open Access Journals (Sweden)

    Cristina Pardo

    Full Text Available Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment and plastidial (psbA gene sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96'N to the Canary Islands (28°64'N that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC to delineate 16 primary species hypotheses (PSHs arranged into four major lineages. Second, chloroplast (psbA sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material, six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.

  20. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

    Science.gov (United States)

    Kapli, P; Lutteropp, S; Zhang, J; Kobert, K; Pavlidis, P; Stamatakis, A; Flouri, T

    2017-06-01

    In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . : paschalia.kapli@h-its.org or

  1. Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest.

    Science.gov (United States)

    Blair, Christopher; Méndez de la Cruz, Fausto R; Law, Christopher; Murphy, Robert W

    2015-03-01

    Methods and approaches for accurate species delimitation continue to be a highly controversial subject in the systematics community. Inaccurate assessment of species' limits precludes accurate inference of historical evolutionary processes. Recent evidence suggests that multilocus coalescent methods show promise in delimiting species in cryptic clades. We combine multilocus sequence data with coalescence-based phylogenetics in a hypothesis-testing framework to assess species limits and elucidate the timing of diversification in leaf-toed geckos (Phyllodactylus) of Mexico's dry forests. Tropical deciduous forests (TDF) of the Neotropics are among the planet's most diverse ecosystems. However, in comparison to moist tropical forests, little is known about the mode and tempo of biotic evolution throughout this threatened biome. We find increased speciation and substantial, cryptic molecular diversity originating following the formation of Mexican TDF 30-20million years ago due to orogenesis of the Sierra Madre Occidental and Mexican Volcanic Belt. Phylogenetic results suggest that the Mexican Volcanic Belt, the Rio Fuerte, and Isthmus of Tehuantepec may be important biogeographic barriers. Single- and multilocus coalescent analyses suggest that nearly every sampling locality may be a distinct species. These results suggest unprecedented levels of diversity, a complex evolutionary history, and that the formation and expansion of TDF vegetation in the Miocene may have influenced subsequent cladogenesis of leaf-toed geckos throughout western Mexico. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae)

    Science.gov (United States)

    Fossen, Erlend I.; Ekrem, Torbjørn; Nilsson, Anders N.; Bergsten, Johannes

    2016-01-01

    Abstract The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular

  3. Species delimitation and interspecific relationships of the genus Orychophragmus (Brassicaceae inferred from whole chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Huan Hu

    2016-12-01

    Full Text Available IntroductionIt is rather difficult to delimit recently diverged species and construct their interspecific relationships because of insufficient informative variations of sampled DNA fragments (Schluter, 2000; Arnold, 2006. The genome-scale sequence variations were found to increase the phylogenetic resolutions of both high- and low-taxonomic groups (e.g., Yoder et al., 2013; Lamichhaney et al., 2015. It is still expensive to collect nuclear genome variations between species for most none-model genera without the reference genome. However, chloroplast genomes (plastome are relatively easy to be assembled to examine interspecific relationships for phylogenetic analyses, especially in addressing unresolved relationship at low taxonomic levels (Wu et al., 2010; Nock et al., 2011; Yang et al., 2013; Huang et al., 2014; Carbonell-Caballero et al., 2015. Plastomes are haploid with maternal inheritance in most angiosperms (Corriveau and Coleman, 1988; Zhang and Liu, 2003; Hagemann, 2004 and are highly conservative in gene order and genome structure with rare recombinations (Jansen et al., 2007; Moore et al., 2010. In this study, we aimed to examine species delimitation and interspecific relationships in Orychophragmus through assembling chloroplast genomes of multiple individuals of tentatively delimited species (Hu et al., 2015a. Orychophragmus is a small genus in the mustard family (Brassicaceae, Cruciferae distributed in northern, central, and southeastern China (Zhou et al., 2001. Its plants have been widely cultivated as ornamentals, vegetables, or source of seed oil (Sun et al., 2011. Despite controversial species delimitations in the genus (Zhou et al., 1987; Tan et al., 1998; Wu and Zhao, 2003; Al-Shehbaz and Yang, 2000; Zhou et al., 2001; Sun et al., 2012, our recent study based on nuclear (nr ITS sequence variations suggested the recognition of seven species (Hu et al., 2015a. Orychophragmus is sister to Sinalliaria, which is a genus endemic

  4. Species delimitation and morphological divergence in the scorpion Centruroides vittatus (Say, 1821: insights from phylogeography.

    Directory of Open Access Journals (Sweden)

    Tsunemi Yamashita

    Full Text Available Scorpion systematics and taxonomy have recently shown a need for revision, partially due to insights from molecular techniques. Scorpion taxonomy has been difficult with morphological characters as disagreement exists among researchers with character choice for adequate species delimitation in taxonomic studies. Within the family Buthidae, species identification and delimitation is particularly difficult due to the morphological similarity among species and extensive intraspecific morphological diversity. The genus Centruroides in the western hemisphere is a prime example of the difficulty in untangling the taxonomic complexity within buthid scorpions. In this paper, we present phylogeographic, Ecological Niche Modeling, and morphometric analyses to further understand how population diversification may have produced morphological diversity in Centruroides vittatus (Say, 1821. We show that C. vittatus populations in the Big Bend and Trans-Pecos region of Texas, USA are phylogeographically distinct and may predate the Last Glacial Maximum (LGM. In addition, we suggest the extended isolation of Big Bend region populations may have created the C. vittatus variant once known as C. pantheriensis.

  5. Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species.

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    Mansour Aliabadian

    Full Text Available DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species.In this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species, we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob (4614 sequences, 2087 species and 16S (708 sequences, 498 species. Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob.DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.

  6. Species delimitation in congenerics of Genus Daemonorops from India using DNA barcodes

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    Senthilkumar Umapathy

    2014-10-01

    Full Text Available Daemonorops is one of the largest genus of palms, widely distributed in tropical evergreen forests of South and Southeast Asia and especially abundant in peninsular Malaysia. It shares the phylogenetic clade with genus Calamus, but distinctly characterized by the presence of the prophyllar bracts in subtribe Calaminae of family Arecaceae (Palmae. However, the species of Daemonorops are highly variable and homoplasious in their morphological characters. Indian Daemonorops has six species, of which five distributed in Andaman group of islands and one in Indo-China. The study mainly focused on the species of Indo-Myanmar (Andaman Islands because they have showed uncertainty in their stand as distinct species. Hence it was attempted to test the species delimitation in congenerics using phylogenetic and character analysis of the nuclear genes. The study indicates three species of both Griffith and Beccari (D. jenkinsiana, D. manii, and D. kurziana in India, and another three species of Renuka et al. (D. wrightmyoensis, D. aurea, and D. rarispinosa from Andaman group of islands could be the variabilities of D. manii that is colonized throughout the archipelago.

  7. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.

    Science.gov (United States)

    Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Young, Kyle; Sanzana, Jose; Orellana, Gabriel; Fowler, Daniel; Howes, Paul; Monzon-Arguello, Catalina; Consuegra, Sofia

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

  8. Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo-West Pacific

    KAUST Repository

    Titus, Benjamin M.; Daly, Marymegan; Hamilton, Natalie; Berumen, Michael L.; Baeza, J. Antonio

    2018-01-01

    Specimens of Thor amboinensis were obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals

  9. Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution.

    Science.gov (United States)

    Koehler, Samantha; Cabral, Juliano S; Whitten, W Mark; Williams, Norris H; Singer, Rodrigo B; Neubig, Kurt M; Guerra, Marcelo; Souza, Anete P; Amaral, Maria do Carmo E

    2008-10-01

    Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Six of 21 currently accepted species were recovered. The results also support recognition of the 'C. pumila' clade as a single species. Molecular phylogenetic relationships within the 'C. acicularis-C. madida' and 'C. ferdinandiana-C. neowiedii' species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic

  10. Molecular Phylogeny of the Neotropical Genus Christensonella (Orchidaceae, Maxillariinae): Species Delimitation and Insights into Chromosome Evolution

    Science.gov (United States)

    Koehler, Samantha; Cabral, Juliano S.; Whitten, W. Mark; Williams, Norris H.; Singer, Rodrigo B.; Neubig, Kurt M.; Guerra, Marcelo; Souza, Anete P.; Amaral, Maria do Carmo E.

    2008-01-01

    Background and Aims Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Methods Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Key Results Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. Conclusions The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent

  11. Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America.

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    Leavitt, Steven D; Johnson, Leigh; St Clair, Larry L

    2011-02-01

    Accurate species delimitation is important for understanding the diversification of biota and has critical implications for ecological and conservation studies. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized fungi misrepresents fungal diversity. The foliose lichen genus Xanthoparmelia includes over 800 species displaying a complex array of morphological and secondary metabolite diversity. We used a multifaceted approach, applying phylogenetic, population genetic, and genealogical analyses to delimit species in a single well-supported monophyletic clade containing 10 morphologically and chemically diverse Xanthoparmelia species in western North America. Sequence data from four ribosomal and two low-copy, protein-coding markers, along with chemical and morphological data were used to assess species diversity. We found that traditionally circumscribed species are not supported by molecular data. Rather, all sampled taxa were better represented by three polymorphic population clusters. Our results suggest that secondary metabolite variation may have limited utility in diagnosing lineages within this group, while identified populations clusters did not reflect major phylogeographic or ecological patterns. In contrast to studies revealing previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical concepts, the present study suggests that species diversity has been overestimated in the species-rich genus Xanthoparmelia.

  12. Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

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    Gottscho, Andrew D.; Wood, Dustin A.; Vandergast, Amy; Lemos Espinal, Julio A.; Gatesy, John; Reeder, Tod

    2017-01-01

    Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of theUma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.

  13. Quantifying the Impact of Different Ways to Delimit Study Areas on the Assessment of Species Diversity of an Urban Forest

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    Rongxiao He

    2016-02-01

    Full Text Available Assessing the species diversity of an urban forest is important for understanding its structure and functions, but the result can be affected by sampling methods, times, and delimitations of the study area. In this study, we examined the influence of different ways to delimit boundaries of urban areas on the assessment of species diversity of urban forests through a case study conducted in Haikou, China. We surveyed the species diversity of the urban forest in Haikou twice using the same sampling protocol but two commonly used delimitations of the urban area. The two surveys produced significantly different estimates of species richness of the urban forest. Recorded species richness was 228 (144 woody and 84 herbaceous species and 303 (164 woody and 139 herbaceous species for the first and the second survey, respectively. The rarefaction analysis indicated that species richness of woody plants recorded in the two surveys could converge by doubling the sample size, but species richness of herbaceous plants was significantly different between the two surveys at the 95% confidence interval even at three times the original sample size. The value of the Simpson dissimilarity index between the two surveys was 0.417 and 0.357 for woody and herbaceous plants respectively, which implied noticeable dissimilarity of species compositions of plant assemblages in the two areas. We concluded that the assessment of biodiversity of an urban forest can be affected significantly by how the boundary of an urban area is defined. Caution should be taken when comparing species diversities of urban forests reported in different studies, especially when richness measures are used.

  14. Species delimitation in frogs from South American temperate forests: The case of Eupsophus, a taxonomically complex genus with high phenotypic variation.

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    Claudio Correa

    Full Text Available One of the most characteristic and abundant amphibian taxa of South American temperate forests is Eupsophus. The ten currently recognized species of the genus have been divided in two species groups, roseus and vertebralis, but most of them, eight, belong to the roseus group. Recent phylogeographic and phylogenetic studies have suggested that species diversity of the roseus group could be underestimated. An examination of the literature shows that species of the roseus group exhibit high levels of variation in their external characteristics, particularly those used as diagnostic characters, which compromises their taxonomy and hinders their field recognition. High levels of variation were also observed in several new populations of the roseus group discovered in southern Chile (36°-40°S, which could not be identified to the species level by their external characteristics. On the other hand, the literature reveals a scarse karyotype differentiation and a high bioacoustic uniformity among the species of the roseus group. We performed a Bayesian phylogenetic analysis using mitochondrial and nuclear genes to reevaluate the species diversity of the roseus group, including all the nominal species of Eupsophus and new populations. This analysis was complemented with three species delimitation approaches, General Mixed Yule Coalescent, multi-rate Poisson Tree Process and Automatic Barcode Gap Discovery. We favored a conservative delimitation of only four species for the roseus group, a result more consistent with the distribution of pairwise genetic distances, and the available chromosome and bioacoustic evidence. The four recognized lineages, which have nearly completely allopatric distributions, are named after the earliest nominal species that they include, but because high levels of phenotypic variation, they are not diagnosable by consistent differences in external morphology. We discuss the implications of this new proposal for the taxonomy and

  15. Species-delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis, including a new species from Brazil.

    Science.gov (United States)

    de Jesus, Priscila Barreto; Nauer, Fabio; Lyra, Goia de Mattos; Cassano, Valéria; Oliveira, Mariana Cabral; Nunes, José Marcos de Castro; Schnadelbach, Alessandra Selbach

    2016-10-01

    Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI-5P and rbcL) and performed several DNA-based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods. © 2016 Phycological Society of America.

  16. Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment for use in routine bioassessment

    Science.gov (United States)

    Species delimitation (grouping individuals into distinct taxonomic groups) is an essential part of evolutionary, conservation, and molecular ecology. Deoxyribonucleic acid (DNA) barcodes, short fragments of the cytochrome c oxidase subunit I (COI) gene, are being used in environm...

  17. Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae grouping: species delimitations, karyotypic evolution and intraspecific diversification

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    Ricardo Utsunomia

    Full Text Available The fish species Synbranchus marmoratushas been reported to exist as a species complex due to high intraspecific karyotypic variability in spite of the difficulty or impossibility to distinguish them using morphological traits alone. The goal of this work was to use cytogenetic and molecular methods to determine the species delimitations and understand the karyoevolution ofS. marmoratususing samples collected from distinct Brazilian localities. Among the analyzed specimens, a large degree of cytogenetic variation related to diploid numbers and karyotype structure was observed, with karyotypes showing 2n=42, 44 and 46 chromosomes. In addition, using sequences of three mitochondrial genes, the phylogenetic relationships between every sample with a known karyotype were determined, which revealed significant nucleotide divergence among the karyomorphs. Also, the analyses indicate that chromosomal rearrangements occurred independently within the distinct lineages of S. marmoratuscomplex, which resulted in the appearance of distinct karyotypic variants in a non-linear fashion related to diploid numbers and in the appearance of similar non-homologous chromosomes. Finally, the integration of both molecular cytogenetic and phylogenetic approaches allowed the determination of specific chromosomes possibly involved in rearrangements and a better understanding about the evolutionary processes involved in the differentiation ofSynbranchusgenus.

  18. Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species.

    Science.gov (United States)

    Doughty, Paul; Bourke, Gayleen; Tedeschi, Leonardo G; Pratt, Renae C; Oliver, Paul M; Palmer, Russell A; Moritz, Craig

    2018-04-04

    Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis revealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to explore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA introgressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the relatively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species limits among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.

  19. Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences.

    Science.gov (United States)

    Song, Shuli; Zhao, Jinliang; Li, Chenhong

    2017-06-01

    The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs. C. liui. Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data, 16,943 loci of single-copy coding sequence data from nine sinipercid species, eight putative sister taxa and two outgroups. Targeted sequences were collected using gene enrichment and Illumina sequencing, yielding thousands of protein coding sequences and single nucleotide polymorphisms (SNPs) data. Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees. We confirmed that the centrarchids are sister to the sinipercids. A monophyletic Sinipercidae with two genera, Siniperca and Coreoperca was also supported. Different from most previous studies, S. scherzeri was found as the most basal taxon to other species of Siniperca, which consists of two clades: a clade having S. roulei sister to S. chuatsi and S. kneri, and a clade consisting S. loona sister to S. obscura and S. undulata. We found that both S. loona and C. liui are valid species using Bayes factor delimitation (BFD ∗ ) based on SNPs data. Species delimitation also provided decisive support for S. chuatsi and S. kneri being two distinct species. We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST, and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis (DEC model) and Statistical Dispersal-Vicariance Analysis (S-DIVA) implemented in RASP. Divergence time

  20. Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae.

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    Marcus K Drotz

    Full Text Available Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation.

  1. Delimiting the species Neosiphonia yendoi (Rhodomelaceae, Rhodophyta) based on COI and rbcL genetic variation in Korea and Japan

    Science.gov (United States)

    Kim, Byeongseok; Yang, Mi Yeon; Kim, Myung Sook

    2016-09-01

    Although the marine red algal genus Neosiphonia is well characterized, many species of Neosiphonia are poorly understood. To correctly define the species delimitation of Neosiphonia yendoi using genetic variation, owing to the confusion over identification with " N. sphaerocarpa" from Korea, we investigated intensively the haplotype network of the mitochondrial COI and the plastid rbcL genes of specimens collected from Korea and Japan. The molecular analyses indicated that specimens collected in different sites of Korea and Japan belong to the same species, Neosiphonia yendoi and " Neosiphonia sphaerocarpa" from Korea, which is distinguished from N. sphaerocarpa from Florida and is allied with N. yendoi collected from the type locality, Muroran of Japan. A total of 29 COI and 13 rbcL haplotypes were found and the COI haplotype network shows evidence of a clear break between specimens from Jeju Island and all other locations of Korea, suggesting the possibility of cryptic diversity within N. yendoi.

  2. Complex patterns of speciation in cosmopolitan "rock posy" lichens--discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota).

    Science.gov (United States)

    Leavitt, Steven D; Fankhauser, Johnathon D; Leavitt, Dean H; Porter, Lyndon D; Johnson, Leigh A; St Clair, Larry L

    2011-06-01

    A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan "rock posy" lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Delimiting diagrams

    NARCIS (Netherlands)

    Oostrom, V. van

    2004-01-01

    We introduce the unifying notion of delimiting diagram. Hitherto unrelated results such as: Minimality of the internal needed strategy for orthogonal first-order term rewriting systems, maximality of the limit strategy for orthogonal higher-order pattern rewrite systems (with maximality of the

  4. Species delimitation in asexual insects of economic importance: The case of black scale (Parasaissetia nigra, a cosmopolitan parthenogenetic pest scale insect.

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    Yen-Po Lin

    Full Text Available Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861 (Hemiptera: Coccidae is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families. Here, we implement multiple approaches to assess the species status of P. nigra, including coalescence-based analyses of mitochondrial and nuclear genes, and ecological niche modelling. Our results indicate that the sampled specimens of P. nigra should be considered to comprise at least two ecotypes (or "species" that are ecologically differentiated, particularly in relation to temperature and moisture. The presence of more than one ecotype under the current concept of P. nigra has implications for biosecurity because the geographic extent of each type is not fully known: some countries may currently have only one of the biotypes. Introduction of additional lineages could expand the geographic extent of damage by the pest in some countries.

  5. Monograph of Arctium L. (Asteraceae). Generic delimitation (including Cousinia Cass, p.p.), revision of the species, pollen morphology, and hybrids

    NARCIS (Netherlands)

    Duistermaat, Helena

    1996-01-01

    The subject of this thesis is a monograph of the genus Arctium, now including also five species formerly placed into Cousinia. Based on herbarium material and some field observations, this study presents new insights on three subjects: a) the generic delimitation of Arctium, b) the species

  6. Molecular systematics of pinniped hookworms (Nematoda: Uncinaria): species delimitation, host associations and host-induced morphometric variation.

    Science.gov (United States)

    Nadler, Steven A; Lyons, Eugene T; Pagan, Christopher; Hyman, Derek; Lewis, Edwin E; Beckmen, Kimberlee; Bell, Cameron M; Castinel, Aurelie; Delong, Robert L; Duignan, Padraig J; Farinpour, Cher; Huntington, Kathy Burek; Kuiken, Thijs; Morgades, Diana; Naem, Soraya; Norman, Richard; Parker, Corwin; Ramos, Paul; Spraker, Terry R; Berón-Vera, Bárbara

    2013-12-01

    host species representing the more recent host-parasite association. Intraspecific host-induced size differences are inconsistent with the exclusive use of morphometrics to delimit and diagnose species of Uncinaria from pinnipeds. Copyright © 2013 Australian Society for Parasitology Inc. All rights reserved.

  7. Biogeography and taxonomy of racket-tail hummingbirds (Aves: Trochilidae: Ocreatus): evidence for species delimitation from morphology and display behavior.

    Science.gov (United States)

    Schuchmann, Karl-L; Weller, André-A; Jürgens, Dietmar

    2016-11-27

    We analyzed geographic variation, biogeography, and intrageneric relationships of racket-tail hummingbirds Ocreatus (Aves, Trochilidae). Presently, the genus is usually considered monospecific, with O. underwoodii including eight subspecies (polystictus, discifer, underwoodii, incommodus, melanantherus, peruanus, annae, addae), although up to three species have been recognized by some authors. In order to evaluate the current taxonomy we studied geographic variation in coloration, mensural characters, and behavioral data of all Ocreatus taxa. We briefly review the taxonomic history of the genus. Applying the Biological Species Concept, species delimitation was based on a qualitative-quantitative criteria analysis including an evaluation of character states. Our results indicate that the genus should be considered a superspecies with four species, the monotypic Ocreatus addae, O. annae, and O. peruanus, and the polytypic O. underwoodii (including the subspecies underwoodii, discifer, incommodus, melanantherus, polystictus). In this taxonomic treatment, O. annae becomes an endemic species to Peru and O. addae is endemic to Bolivia. We recommend additional sampling of distributional, ethological, and molecular data for an improved resolution of the evolutionary history of Ocreatus.

  8. A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification

    NARCIS (Netherlands)

    Skrede, I.; Carlsen, T.; Schumacher, T.

    2017-01-01

    Helvella is a widespread, speciose genus of large apothecial ascomycetes (Pezizomycete: Pezizales) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on

  9. Exploring the utility of DNA barcoding in species delimitation of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae).

    Science.gov (United States)

    Song, Chao; Wang, Qian; Zhang, Ruilei; Sun, Bingjiao; Wang, Xinhua

    2016-02-16

    In this study, we tested the utility of the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) as the barcode region to deal with taxonomical problems of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae). The 114 DNA barcodes representing 27 morphospecies are divided into 33 well separated clusters based on both Neighbor Joining and Maximum Likelihood methods. DNA barcodes revealed an 82% success rate in matching with morphospecies. The selected DNA barcode data support 37-64 operational taxonomic units (OTUs) based on the methods of Automatic Barcode Gap Discovery (ABGD) and Poisson Tree Process (PTP). Furthermore, a priori species based on consistent phenotypic variations were attested by molecular analysis, and a taxonomical misidentification of barcode sequences from GenBank was found. We could not observe a distinct barcode gap but an overlap ranged from 9-12%. Our results supported DNA barcoding as an ideal method to detect cryptic species, delimit sibling species, and associate different life stages in non-biting midges.

  10. Species delimitation and conservation genetics of the Canarian endemic Bethencourtia (Asteraceae).

    Science.gov (United States)

    Rodríguez-Rodríguez, Priscila; Pérez de Paz, Pedro Luis; Sosa, Pedro A

    2018-04-01

    Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia. To achieve these objectives, we characterized 10 polymorphic SSR markers. Eleven natural populations (276 individuals) were analyzed (three for B. hermosae, five for B. rupicola and three for B. palmensis). The results obtained by AMOVA, PCoA and Bayesian analysis on STRUCTURE confirmed the evidence of well-structured groups corresponding to the three species. At the intra-specific level, B. hermosae and B. rupicola did not show a clear population structure, while B. palmensis was aggregated according to island of origin. This is consistent with self-incompatibility in the group and high gene flow within species. Overall, the genetic diversity of the three species was low, with expected heterozygosity values of 0.302 (B. hermosae), 0.382 (B. rupicola) and 0.454 (B. palmensis). Recent bottleneck events and a low number of individuals per population are probably the causes of the low genetic diversity. We consider that they are naturally rare species associated with specific habitats. The results given in this article will provide useful information to assist in conservation genetics programs for this endemic genus.

  11. Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

    Directory of Open Access Journals (Sweden)

    Waengsothorn Surachit

    2010-06-01

    Full Text Available Abstract Background Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. Results We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006 that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. Conclusions Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of

  12. Antitropical distributions and species delimitation in a group of ophiocomid brittle stars (Echinodermata: Ophiuroidea: Ophiocomidae).

    Science.gov (United States)

    Naughton, K M; O'Hara, T D; Appleton, B; Cisternas, P A

    2014-09-01

    In this paper we examine the phylogeny and biogeography of the temperate genera of the Ophiocomidae (Echinodermata: Ophiuroidea) which have an interesting asymmetrical anti-tropical distribution, with two genera (Ophiocomina and Ophiopteris) previously considered to have a separate species in both the North and South hemispheres, and the third (Clarkcoma) diversifying in the southern Australian/New Zealand region. Our phylogeny, generated from one mitochondrial and two nuclear markers, revealed that Ophiopteris is sister to a mixed Ophiocomina/Clarkcoma clade. Ophiocomina was polyphyletic, with O. nigra and an undescribed species from the South Atlantic Ocean sister to a clade including Clarkcoma species and O. australis. The phylogeny also revealed a number of recently diverged lineages occurring within Clarkcoma, some of which are considered to be cryptic species due to the similarity in morphology combined with the apparent absence of interbreeding in a sympatric distribution, while the status of others is less certain. The phylogeny provides support for two transequatorial events in the group under study. A molecular clock analysis places both events in the middle to late Miocene. The analysis excludes a tectonic vicariance hypothesis for the antitropical distribution associated with the breakup of Pangaea and also excludes the hypothesis of more recent gene flow associated with Plio/Pleistocene glacial cycling. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Skeletal muscle proteins: a new approach to delimitate the time since death.

    Science.gov (United States)

    Foditsch, Elena Esra; Saenger, Alexandra Maria; Monticelli, Fabio Carlo

    2016-03-01

    Skeletal muscle tissue is proposed as a forensic model tissue with strong potential, as it is easily accessible and its true-to-life state structure and function is well known. Despite this strong potential, skeletal muscle degradation studies are rare. The aim of this study was to test if a skeletal muscle-based protein analysis is applicable to delimitate the time since death. Under standard conditions, two pigs were stored either at 22 °C for 5 days or 4 °C for 21 days. Their Mm. biceps femori were sampled periodically for analyses of ten skeletal muscle proteins postmortem. All analyzed proteins can serve as markers for a delimitation of the time since death. Desmin, nebulin, titin, and SERCA 1 displayed distinct protein patterns at certain points of time. The other five proteins, α-actinin, calsequestrin-1, laminin, troponin T-C, and SERCA 2, showed no degradation patterns within the analyzed postmortem time frame. Referring to specific skeletal muscle proteins, results showed short-term stabilities for just a minority of analyzed proteins, while the majority of investigated proteins displayed characteristics as long-term markers. Due to specific patterns and the possibility to determine definite constraints of the presence, absence, or pattern alterations of single proteins, the feasibility of porcine skeletal muscle as forensic model tissue is outlined and the potential of skeletal muscle as forensic model tissue is underlined, especially with respect to later postmortem phases, which so far lack feasible methods to delimitate the time since death.

  14. Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats

    OpenAIRE

    Esselstyn, Jacob A.; Evans, Ben J.; Sedlock, Jodi L.; Anwarali Khan, Faisal Ali; Heaney, Lawrence R.

    2012-01-01

    Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule–coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries s...

  15. How much variation can one ant species hold? Species delimitation in the Crematogaster kelleri-group in Madagascar.

    Directory of Open Access Journals (Sweden)

    Bonnie B Blaimer

    Full Text Available We investigated the species-level taxonomy of the Malagasy Crematogaster (Crematogaster kelleri-group and an additional more distantly related species of the same subgenus. Morphological data from worker, queen and male ants, as well as genetic data from three nuclear genes (long wavelength rhodopsin, arginine kinase and carbomoylphosphate synthase and one mitochondrial marker (cytochrome oxidase I led to the recognition of six species. Within the C. kelleri-group, three new species are described: C. hazolava Blaimer sp. n., C. hafahafa Blaimer sp. n. and C. tavaratra Blaimer sp. n. The previously described taxa C. kelleri Forel and C. madagascariensis André are validated by our analysis. Conversely, our data suggests synonymy of C. adrepens Forel (with C. kelleri and C. gibba Emery (with C. madagascariensis. A more distantly related and phylogenetically isolated species, C. tsisitsilo Blaimer sp. n., is further described. We report high levels of morphological and molecular variation in C. kelleri and illustrate that this variation can be explained partly by geography. Species descriptions, images, distribution maps and identification keys based on worker ants, as well as on queen and male ants where available, are presented for all six species. Our work highlights the elevated species richness of Crematogaster ants throughout Madagascar's humid forests, especially in the far northern tip of the island, and the need to use multiple data sources to ensure clear demarcation of this diversity.

  16. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

  17. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species

    KAUST Repository

    Arrigoni, Roberto; Berumen, Michael L.; Chen, Chaolun Allen; Terraneo, Tullia Isotta; Baird, Andrew H.; Payri, Claude; Benzoni, Francesca

    2016-01-01

    Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach

  18. Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization?

    Directory of Open Access Journals (Sweden)

    Flot Jean-François

    2011-10-01

    Full Text Available Abstract Background Morphological data suggest that, unlike most other groups of marine organisms, scleractinian corals of the genus Stylophora are more diverse in the western Indian Ocean and in the Red Sea than in the central Indo-Pacific. However, the morphology of corals is often a poor predictor of their actual biodiversity: hence, we conducted a genetic survey of Stylophora corals collected in Madagascar, Okinawa, the Philippines and New Caledonia in an attempt to find out the true number of species in these various locations. Results A molecular phylogenetic analysis of the mitochondrial ORF and putative control region concurs with a haploweb analysis of nuclear ITS2 sequences in delimiting three species among our dataset: species A and B are found in Madagascar whereas species C occurs in Okinawa, the Philippines and New Caledonia. Comparison of ITS1 sequences from these three species with data available online suggests that species C is also found on the Great Barrier Reef, in Malaysia, in the South China Sea and in Taiwan, and that a distinct species D occurs in the Red Sea. Shallow-water morphs of species A correspond to the morphological description of Stylophora madagascarensis, species B presents the morphology of Stylophora mordax, whereas species C comprises various morphotypes including Stylophora pistillata and Stylophora mordax. Conclusions Genetic analysis of the coral genus Stylophora reveals species boundaries that are not congruent with morphological traits. Of the four hypotheses that may explain such discrepancy (phenotypic plasticity, morphological stasis, morphological convergence, and interspecific hybridization, the first two appear likely to play a role but the fourth one is rejected since mitochondrial and nuclear markers yield congruent species delimitations. The position of the root in our molecular phylogenies suggests that the center of origin of Stylophora is located in the western Indian Ocean, which probably

  19. Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats.

    Science.gov (United States)

    Esselstyn, Jacob A; Evans, Ben J; Sedlock, Jodi L; Anwarali Khan, Faisal Ali; Heaney, Lawrence R

    2012-09-22

    Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

  20. Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo-West Pacific

    KAUST Repository

    Titus, Benjamin M.

    2018-04-27

    Aim The “sexy shrimp” Thor amboinensis is currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis that T. amboinensis is a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic. Location Coral reefs in all tropical oceans. Methods Specimens of Thor amboinensis were obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals, 30 sample localities), while phylogeographical reconstruction in the TWA was based on COI only (n = 303 individuals, 10 sample localities). Results We found evidence for at least five cryptic lineages (9%–22% COI pairwise sequence divergence): four in the Indo‐West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co‐occurring lineage that is widespread throughout the Indo‐West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km. Main conclusions Thor amboinensis is a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo‐West Pacific. Nuclear‐ and mitochondrial‐ gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between

  1. Identification and systems methodologies for territorial delimitation

    Directory of Open Access Journals (Sweden)

    Iván Montoya R

    2010-12-01

    Full Text Available This document identifies the main issues affecting the delimitation of territories and explores the conceptual approaches for describing the relationship of the territories understood as organizations with their environment. Subsequently, we studied the systems methodologies known as soft systems methodology, SSM, and complex adaptive systems, CAS. Finally, the advantages of systemic approaches to territorial delimitation are shown

  2. Growing Degree Vegetation Production Index (GDVPI): A Novel and Data-Driven Approach to Delimit Season Cycles

    Science.gov (United States)

    Graham, W. D.; Spruce, J.; Ross, K. W.; Gasser, J.; Grulke, N.

    2014-12-01

    Growing Degree Vegetation Production Index (GDVPI) is a parametric approach to delimiting vegetation seasonal growth and decline cycles using incremental growing degree days (GDD), and NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) normalized difference vegetation index (NDVI) 8-day composite cumulative integral data. We obtain a specific location's daily minimum and maximum temperatures from the nearest National Oceanic and Atmospheric Administration (NOAA) weather stations posted on the National Climate Data Center (NCDC) Climate Data Online (CDO) archive and compute GDD. The date range for this study is January 1, 2000 through December 31, 2012. We employ a novel process, a repeating logistic product (RLP), to compensate for short-term weather variability and data drops from the recording stations and fit a curve to the median daily GDD values, adjusting for asymmetry, amplitude, and phase shift that minimize the sum of squared errors when comparing the observed and predicted GDD. The resulting curve, here referred to as the surrogate GDD, is the time-temperature phasing parameter used to convert Cartesian NDVI values into polar coordinate pairs, multiplying the NDVI values as the radial by the cosine and sine of the surrogate GDD as the angular. Depending on the vegetation type and the original NDVI curve, the polar NDVI curve may be nearly circular, kidney-shaped, or pear-shaped in the case of conifers, deciduous, or agriculture, respectively. We examine the points of tangency about the polar coordinate NDVI curve, identifying values of 1, 0, -1, or infinity, as each of these represent natural inflection points. Lines connecting the origin to each tangent point illustrate and quantify the parametrically segmentation of the growing season based on the GDD and NDVI ostensible dependency. Furthermore, the area contained by each segment represents the apparent vegetation production. A particular benefit is that the inflection points are determined

  3. Delimiting communities in the Pacific Northwest.

    Science.gov (United States)

    Ellen M. Donoghue

    2003-01-01

    The paper presents an approach for delimiting communities in the Northwest Forest Plan (NWFP) region of the Pacific Northwest that responds to the need to assess impacts and issues associated with broad-scale ecosystem management. Census block groups are aggregated to provide an alternative to more commonly used geographic delimitations of communities, specifically...

  4. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae occurring sympatrically in the Red River region of China

    Directory of Open Access Journals (Sweden)

    Liu eJian

    2015-09-01

    Full Text Available Delimitating species boundaries could be of critical importance when evaluating the species’ evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH and trnL-rps4 and two single copy nuclear (RPB1 and SmHP DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into Yuanjiang-Nanhun basin and Ejia-Jiepai basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the

  5. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Directory of Open Access Journals (Sweden)

    Pablo D Lavinia

    Full Text Available Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%, with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana. In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  6. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Science.gov (United States)

    Lavinia, Pablo D; Núñez Bustos, Ezequiel O; Kopuchian, Cecilia; Lijtmaer, Darío A; García, Natalia C; Hebert, Paul D N; Tubaro, Pablo L

    2017-01-01

    Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  7. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

  8. Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba.

    Science.gov (United States)

    Rodríguez, Ariel; Dugo-Cota, Álvaro; Montero-Mendieta, Santiago; Gonzalez-Voyer, Alejandro; Bosch, Roberto Alonso; Vences, Miguel; Vilà, Carles

    2017-01-20

    We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob genes identify two allopatric and strongly supported mitochondrial clades (phylogroups) which also showed no haplotype sharing in the nuclear Rag-1 gene. Bioacustic, and morphological comparisons concordantly identify these two phylogroups as independent evolutionary lineages. Therefore, we herein restrict the name Eleutherodactylus glamyrus Estrada and Hedges to populations represented in our analyses as the western phylogroup (Cordillera del Turquino to Pico La Bayamesa) and consider specimens from the eastern phylogroup (Sierra del Cobre) to represent a new species described and named as Eleutherodactylus cattus. Our results add to the growing list of Eleutherodactylus species endemic to Cuba and highlight the importance of combining different sources of evidence for obtaining robust assessments of species limits in amphibians.

  9. Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae).

    Science.gov (United States)

    Janssen, Toon; Karssen, Gerrit; Orlando, Valeria; Subbotin, Sergei A; Bert, Wim

    2017-12-01

    Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology.

    Science.gov (United States)

    Pinzón, Jorge H; LaJeunesse, Todd C

    2011-01-01

    Stony corals in the genus Pocillopora are among the most common and widely distributed of Indo-Pacific corals and, as such, are often the subject of physiological and ecological research. In the far Tropical Eastern Pacific (TEP), they are major constituents of shallow coral communities, exhibiting considerable variability in colony shape and branch morphology and marked differences in response to thermal stress. Numerous intermediates occur between morphospecies that may relate to extensive hybridization. The diversity of the Pocillopora genus in the TEP was analysed genetically using nuclear ribosomal (ITS2) and mitochondrial (ORF) sequences, and population genetic markers (seven microsatellite loci). The resident dinoflagellate endosymbiont (Symbiodinium sp.) in each sample was also characterized using sequences of the internal transcribed spacer 2 (ITS2) rDNA and the noncoding region of the chloroplast psbA minicircle. From these analyses, three symbiotically distinct, reproductively isolated, nonhybridizing, evolutionarily divergent animal lineages were identified. Designated types 1, 2 and 3, these groupings were incongruent with traditional morphospecies classification. Type 1 was abundant and widespread throughout the TEP; type 2 was restricted to the Clipperton Atoll; and type 3 was found only in Panama and the Galapagos Islands. Each type harboured a different Symbiodinium'species lineage' in Clade C, and only type 1 associated with the 'stress-tolerant'Symbiodinium glynni (D1). The accurate delineation of species and implementation of a proper taxonomy may profoundly improve our assessment of Pocillopora's reproductive biology, biogeographic distributions, and resilience to climate warming, information that must be considered when planning for the conservation of reef corals. © 2010 Blackwell Publishing Ltd.

  11. Methods for species delimitation in bumblebees (Hymenoptera, Apidae, Bombus): towards an integrative approach

    Czech Academy of Sciences Publication Activity Database

    Lecocq, T.; Dellicour, S.; Michez, D.; Dehon, M.; Dewulf, A.; De Meulemeester, T.; Brasero, N.; Valterová, Irena; Rasplus, J. Y.; Rasmont, P.

    2015-01-01

    Roč. 44, č. 3 (2015), s. 281-297 ISSN 0300-3256 Institutional support: RVO:61388963 Keywords : bumblebee taxonomy * genetic analysis * pheromone composition Subject RIV: CC - Organic Chemistry Impact factor: 2.733, year: 2015

  12. Delimiting Inclusive Design

    DEFF Research Database (Denmark)

    Herriott, Richard

    2014-01-01

    This paper was written as an answer to the question raised by my PhD dissertation on accessibility through user-centred and Inclusive Design (ID) methods: can Inclusive Design be delimited? The literature on Inclusive Design deals almost entrirely with consumer product design and assistive...

  13. Delimiting areas of endemism through kernel interpolation.

    Science.gov (United States)

    Oliveira, Ubirajara; Brescovit, Antonio D; Santos, Adalberto J

    2015-01-01

    We propose a new approach for identification of areas of endemism, the Geographical Interpolation of Endemism (GIE), based on kernel spatial interpolation. This method differs from others in being independent of grid cells. This new approach is based on estimating the overlap between the distribution of species through a kernel interpolation of centroids of species distribution and areas of influence defined from the distance between the centroid and the farthest point of occurrence of each species. We used this method to delimit areas of endemism of spiders from Brazil. To assess the effectiveness of GIE, we analyzed the same data using Parsimony Analysis of Endemism and NDM and compared the areas identified through each method. The analyses using GIE identified 101 areas of endemism of spiders in Brazil GIE demonstrated to be effective in identifying areas of endemism in multiple scales, with fuzzy edges and supported by more synendemic species than in the other methods. The areas of endemism identified with GIE were generally congruent with those identified for other taxonomic groups, suggesting that common processes can be responsible for the origin and maintenance of these biogeographic units.

  14. Delimiting areas of endemism through kernel interpolation.

    Directory of Open Access Journals (Sweden)

    Ubirajara Oliveira

    Full Text Available We propose a new approach for identification of areas of endemism, the Geographical Interpolation of Endemism (GIE, based on kernel spatial interpolation. This method differs from others in being independent of grid cells. This new approach is based on estimating the overlap between the distribution of species through a kernel interpolation of centroids of species distribution and areas of influence defined from the distance between the centroid and the farthest point of occurrence of each species. We used this method to delimit areas of endemism of spiders from Brazil. To assess the effectiveness of GIE, we analyzed the same data using Parsimony Analysis of Endemism and NDM and compared the areas identified through each method. The analyses using GIE identified 101 areas of endemism of spiders in Brazil GIE demonstrated to be effective in identifying areas of endemism in multiple scales, with fuzzy edges and supported by more synendemic species than in the other methods. The areas of endemism identified with GIE were generally congruent with those identified for other taxonomic groups, suggesting that common processes can be responsible for the origin and maintenance of these biogeographic units.

  15. CONCEPTUAL DELIMITATIONS OF CONTROLLING

    Directory of Open Access Journals (Sweden)

    Nedelcu Serban

    2011-12-01

    Full Text Available CONCEPTUAL DELIMITATIONS OF CONTROLLING Nedelcu Serban Universitatea ,,Babes-Bolyai`` Facultatea de Stiinte Economice si Gestiunea Afacerilor 'Controlling' represents a new concept in the Romanian economic environement, being implemented successfully in very few companies. Unlike the German space where controlling is very well represented both at a practical level and in the academia, in Romania controlling can only be found at a practical level, and the specialized literature is restraint, almost absent. Since the practicians of controlling in Romania only know the toolkit they use and not the theoretical elements as well, what is needed in this case is a conceptual delimitation so that controlling would be better implemented, and improved with various elements of the economic environment. In practice, inside various linguistic areas different problems of communication may occur very often in regards to the use of different concepts that may be missunderstood. Therefore in the Romanian research area it becomes imperative to try and clarify the existing issues and to intensify the reasearch in this field. Studying the evolution of the concept we observe that the need for its implementation is primarily experienced at the practical level of the companies, to be then followed by a debate in the specialized literature. The internationalization and the fierce competition that the Romanian companies are confronting on the ecenomic market represent the decissive factor in adopting the concept of controlling.This article is part of the research conducted for my doctoral thesis, 'Controlling in hetergenous economic envirnoments', under the coordination and supervision of Prof.Dr.Dumitru Matis. Keywords: Controlling, Management Accounting, Management Control, Accounting, Internal audit JEL Code: M49

  16. POSITIONINGS AND DELIMITATIONS CONCERNING THE PERFORMANCE AUDIT

    OpenAIRE

    Victoria FIRESCU

    2014-01-01

    The objectives of the present research are related to the approaches concerning the “performance audit” concept in the specialized literature and practice as well as the clear delimitation of this concept of financial audit and internal audit. For a clear emphasis of the objectives and principles of the performance audit, I highlighted the similarities and differences among the three types of audit by means of several criteria such as: audit standards, audited subjects, nature of the audit ev...

  17. DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation

    NARCIS (Netherlands)

    Vu, D; Groenewald, M; Szöke, S; Cardinali, G; Eberhardt, U; Stielow, B; de Vries, M; Verkleij, G J M; Crous, P W; Boekhout, T; Robert, V

    DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic

  18. The phylogenetic position of Lygodactylus angularis and the utility of using the 16S rDNA gene for delimiting species in Lygodactylus (Squamata, Gekkonidae

    Directory of Open Access Journals (Sweden)

    Riccardo Castiglia

    2011-06-01

    Full Text Available The African genus Lygodactylus Gray, is composed of roughly 60 species of diurnal geckos that inhabit tropical and temperate Africa, Madagascar, and South America. In this study, we assessed the phylogenetic position of L. angularis, for which molecular data were so far lacking, by means of sequence analysis of the mitochondrial 16S rDNA gene. We also compared intraspecific vs. interspecific genetic divergences using an extended data set (34 species, 153 sequences, to determine whether a fragment of this gene can be useful for species identification and to reveal the possible existence of new cryptic species in the genus. The analysis placed L. angularis in a monophyletic group together with members of “fischeri” and “picturatus” groups. Nevertheless, the independence of the “angularis” lineage is supported by the high genetic divergence. Comparison of intraspecific vs. interspecific genetic distances highlights that, assuming an equal molecular rate of evolution among the studied species for the used gene, the threshold value useful for recognising a candidate new species can be tentatively placed at 7%. We identified four species that showed an intraspecific divergence higher than, or close to, the 7% threshold: L. capensis (8.7%, L. gutturalis (9.3%, L. madagascariensis (6.5% and L. picturatus (8.1%. Moreover, two species, L. mombasicus and L. verticillatus, are paraphyletic in terms of gene genealogy. Thus, the study shows that a short fragment of the 16S rDNA gene can be an informative tool for species-level taxonomy in the genus Lygodactylus.

  19. CONCEPTUAL DELIMITATIONS ON SUSTAINABLE DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Ienciu Ionel-Alin

    2013-07-01

    Full Text Available Sustainable development is a model for resource use meant to satisfy human needs, without polluting the environment, so that these needs can be satisfied not only in the present, but in the future as well. It is a concept of nowadays with no generally accepted definition, placing environment first and foremost, aiming at implementing the environmental policies in all structures and at all economic levels. Within the present study we have aimed at creating a conceptual delimitation on sustainable development, sustainability and socialresponsibility, concepts of present interest, that tend to become a mystery for the academic community and practitioners by their variety and complexity of approaches. During our scientific endeavor we believe that social responsibility is the foundation of sustainable development. Sustainable development is a concept used especially at macro-economic level, while social responsibility is used at entity level and incorporates the economic, environmental and social dimension, which has a voluntary character and tries to respond to the information needs of the society and other stakeholders. Sustainability at the entity\\'s level is the goal or final objective of sustainable development – satisfaction of present needs without compromising the possibility for future generations to satisfy their own needs, while social responsibility is an intermediate phase of sustainability wherein entities try to balance the economic, social and environmental dimension. Thus, we can state we include ourselves within social corporatism, slightly close to social institutionalism, which is characteristic to developed countries, giving a particular importance to social contract and relations between entity and society. We believe that in Romania, a POSDRU funded project should be regarded as a legal person with social values, which must be based on sustainable development and to promote, besides legal liability of automatically deriving

  20. Intercultural communication: conceptual delimitations

    Directory of Open Access Journals (Sweden)

    Stela SPÎNU

    2018-06-01

    Full Text Available In an era of interference, intercultural communication is timely and advisable. The article analyzes the relation between communication/ language and culture. Starting from a description of different approaches and models of the concept of culture that have influenced and still influence the intercultural communication, and a description of the linguistic theories regarding the relation between language and culture.

  1. Gyrinops ledermannii (Thymelaeaceae), being an agarwood-producing species prompts call for further examination of taxonomic implications in the generic delimitation between Aquilaria and Gyrinops

    NARCIS (Netherlands)

    Compton, J.G.S.; Zich, F.A.

    2002-01-01

    Field research conducted in Papua New Guinea (PNG) has recorded Gyrinops ledermannii Domke (Thymelaeaceae) as an agarwood-producing species for the first time. Aquilaria malaccensis Lam. (incl. A. agallocha Roxb.; Thymelaeaceae) or agarwood (also known as aloeswood, eaglewood, gaharu, and

  2. The phylogenetic position of Lygodactylus angularis and the utility of the 16S rDNA gene for delimiting species in Lygodactylus (Squamata, Gekkonidae

    Directory of Open Access Journals (Sweden)

    Riccardo Castiglia

    2011-06-01

    Hidden="false" UnhideWhenUsed="false" QFormat="true" Name="Subtle Emphasis" />

    The African genus Lygodactylus Gray, is composed of about 60 species of diurnal geckos inhabiting tropical and temperate Africa, Madagascar and South America. In this paper we analysed, by means of the mitochondrial 16S rDNA gene

  3. Delimitation of cryptic species inside Claviceps purpurea

    Czech Academy of Sciences Publication Activity Database

    Pažoutová, Sylvie; Pešicová, Kamila; Chudíčková, Milada; Šrůtka, P.; Kolařík, Miroslav

    2015-01-01

    Roč. 119, č. 1 (2015), s. 7-26 ISSN 1878-6146 R&D Projects: GA ČR(CZ) GA13-00788S Institutional support: RVO:61388971 Keywords : C. arundinis * C. humidiphila * C. microcephala Subject RIV: EE - Microbiology, Virology Impact factor: 2.244, year: 2015

  4. POSITIONINGS AND DELIMITATIONS CONCERNING THE PERFORMANCE AUDIT

    Directory of Open Access Journals (Sweden)

    Victoria FIRESCU

    2014-12-01

    Full Text Available The objectives of the present research are related to the approaches concerning the “performance audit” concept in the specialized literature and practice as well as the clear delimitation of this concept of financial audit and internal audit. For a clear emphasis of the objectives and principles of the performance audit, I highlighted the similarities and differences among the three types of audit by means of several criteria such as: audit standards, audited subjects, nature of the audit evidence, manners of assessment. Within this basically predominant research, I used several research methods and techniques such as: the critical analysis of the bibliographic sources concerning the performance audit, the documentation related to the international audit standards, comparative studies.

  5. A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

    Directory of Open Access Journals (Sweden)

    Mickael Orgeur

    2018-01-01

    Full Text Available The sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads, and the gene annotation that defines gene features, must also be taken into account. A partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and a de novo transcriptome assembly. This dual approach enabled us to increase the assignment rate of RNA-seq data by nearly 20% as compared to when using only the chicken reference annotation, contributing therefore to a more accurate estimation of transcript abundance. More generally, this strategy could be applied to any organism with partial genome sequence and/or lacking a manually-curated reference annotation in order to improve the accuracy of gene expression studies.

  6. hydrographic network extraction and watersheds delimitation

    African Journals Online (AJOL)

    A. Ayache

    2018-01-01

    Jan 1, 2018 ... is a roughly flat highlands of an average altitude of 1000 m area delimited ... matter rate in the horizontal surface offering a favorable particle structure to water and wind .... French loamy soils at a given organizational level.

  7. Delimitation of kala-azar risk areas in the district of Vaishali in Bihar (India using a geo-environmental approach

    Directory of Open Access Journals (Sweden)

    Gouri Sankar Bhunia

    2012-08-01

    Full Text Available Remote sensing and geographical information technologies were used to discriminate areas of high and low risk for contracting kala-azar or visceral leishmaniasis. Satellite data were digitally processed to generate maps of land cover and spectral indices, such as the normalised difference vegetation index and wetness index. To map estimated vector abundance and indoor climate data, local polynomial interpolations were used based on the weightage values. Attribute layers were prepared based on illiteracy and the unemployed proportion of the population and associated with village boundaries. Pearson's correlation coefficient was used to estimate the relationship between environmental variables and disease incidence across the study area. The cell values for each input raster in the analysis were assigned values from the evaluation scale. Simple weighting/ratings based on the degree of favourable conditions for kala-azar transmission were used for all the variables, leading to geo-environmental risk model. Variables such as, land use/land cover, vegetation conditions, surface dampness, the indoor climate, illiteracy rates and the size of the unemployed population were considered for inclusion in the geo-environmental kala-azar risk model. The risk model was stratified into areas of "risk"and "non-risk"for the disease, based on calculation of risk indices. The described approach constitutes a promising tool for microlevel kala-azar surveillance and aids in directing control efforts.

  8. An Operational Foundation for Delimited Continuations

    DEFF Research Database (Denmark)

    Biernacka, Malgorzata; Biernacki, Dariusz; Danvy, Olivier

    2004-01-01

    We present an abstract machine and a reduction semantics for the lambda-calculus extended with control operators that give access to delimited continuations in the CPS hierarchy. The abstract machine is derived from an evaluator in continuation-passing style (CPS); the reduction semantics (i.......e., a small-step operational semantics with an explicit representation of evaluation contexts) is constructed from the abstract machine; and the control operators are the shift and reset family. We also present new applications of delimited continuations in the CPS hierarchy: finding list prefixes...

  9. Unpacking the species conundrum: philosophy, practice and a way forward.

    Science.gov (United States)

    Shanker, Kartik; Vijayakumar, S P; Ganeshaiah, K N

    2017-07-01

    The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as 'individuals' while the criteria for categorization treats them as 'classes'. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an 'inclusive' probabilistic approach for understanding and delimiting species. Finally, we provide aWallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and 'inclusive' probabilistic approaches may work best for delimitation.

  10. Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach.

    Science.gov (United States)

    Baumsteiger, Jason; Kinziger, Andrew P; Aguilar, Andres

    2012-12-01

    The west coast of North America contains a number of biogeographic freshwater provinces which reflect an ever-changing aquatic landscape. Clues to understanding this complex structure are often encapsulated genetically in the ichthyofauna, though frequently as unresolved evolutionary relationships and putative cryptic species. Advances in molecular phylogenetics through species tree analyses now allow for improved exploration of these relationships. Using a comprehensive approach, we analyzed two mitochondrial and nine nuclear loci for a group of endemic freshwater fish (sculpin-Cottus) known for a wide ranging distribution and complex species structure in this region. Species delimitation techniques identified three novel cryptic lineages, all well supported by phylogenetic analyses. Comparative phylogenetic analyses consistently found five distinct clades reflecting a number of unique biogeographic provinces. Some internal node relationships varied by species tree reconstruction method, and were associated with either Bayesian or maximum likelihood statistical approaches or between mitochondrial, nuclear, and combined datasets. Limited cases of mitochondrial capture were also evident, suggestive of putative ancestral hybridization between species. Biogeographic diversification was associated with four major regions and revealed historical faunal exchanges across regions. Mapping of an important life-history character (amphidromy) revealed two separate instances of trait evolution, a transition that has occurred repeatedly in Cottus. This study demonstrates the power of current phylogenetic methods, the need for a comprehensive phylogenetic approach, and the potential for sculpin to serve as an indicator of biogeographic history for native ichthyofauna in the region. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. A Landscape Approach to Invasive Species Management.

    Directory of Open Access Journals (Sweden)

    Miguel Lurgi

    distributed links. Our modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

  12. A Landscape Approach to Invasive Species Management.

    Science.gov (United States)

    Lurgi, Miguel; Wells, Konstans; Kennedy, Malcolm; Campbell, Susan; Fordham, Damien A

    2016-01-01

    modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

  13. Investigating Species Boundaries within the Hard Coral Genus Goniopora (Cnidaria, Scleractinia) from the Red Sea Using an Integrative Morphomolecular Approach

    KAUST Repository

    Terraneo, Tullia Isotta

    2015-12-01

    In the present study the species boundaries of the scleractinian coral genus Goniopora from the Saudi Arabian Red Sea were investigated. An integrated morpho-molecular approach was used to better clarify the complex scenario derived from traditional classification efforts based on skeletal morphology. Traditional taxonomy of this genus considers skeletal morphology first and polyp morphology as a secondary discriminating character. This leads to potential complication due to plasticity in skeletal features within a species. To address this issue, molecular analyses of evolutionary relationships between nine traditional morphospecies of Goniopora from the Red Sea were performed and were used to re-evaluate the informativeness of macromorphological and micromorphological features. Between four and six putative molecular lineages were identified within Goniopora samples from the Saudi Arabian Red Sea on the basis of four molecular markers: the mitochondrial intergenic spacer between Cytochrome b and the NADH dehydrogenase subunit 2, the entire nuclear ribosomal internal transcribed spacer region, the ATP synthase subunit β gene, and a portion of the Calmodulin gene. The results were strongly corroborated by three distinct analyses of species delimitation. Subsequent analyses of micromorphological and microstructural skeletal features identified the presence of distinctive characters in each of the molecular clades. Unique in vivo morphologies were associated with the genetic-delimited lineages, further supporting the molecular findings. The proposed re-organization of Goniopora will resolve several taxonomic problems in this genus while reconciling molecular and morphological evidence. Reliable species-level identification of Goniopora spp. can be achieved with polyp morphology under the proposed revision.

  14. Bisimulations for Delimited-Control Operators

    OpenAIRE

    Biernacki , Dariusz; Lenglet , Sergueï; Polesiuk , Piotr

    2017-01-01

    We propose a survey of the behavioral theory of an untyped lambda-calculus extended with the delimited-control operators shift and reset. We define a contextual equivalence for this calculus, that we then aim to characterize with coinductively defined relations, called bisimilarities. We study different styles of bisimilarities (namely applicative, normal form, and environmental), and we give several examples to illustrate their respective strengths and weaknesses. We also discuss how to exte...

  15. Maritime zones delimitation - Problems and solutions

    Science.gov (United States)

    Kastrisios, Christos; Tsoulos, Lysandros

    2018-05-01

    The delimitation of maritime zones and boundaries foreseen by the United Nations Convention on the Law of the Sea (UNCLOS) is a factor of economic growth, effective management of the coastal and ocean environment and the cornerstone for maritime spatial planning. Maritime zones and boundaries form the outermost limits of coastal states and their accurate delineation and cartographic portrayal is a matter of national priority. Although UNCLOS is a legal document, its implementation -at first place- is purely technical and requires -amongst others- theoretical and applied background on Geodesy, Cartography and Geographic Information Systems (GIS) for those involved. This paper provides a brief historical background of the evolution of the UNCLOS, presents the various concepts of the Convention and identifies the problems inherent in the maritime delimitation process. Furthermore, it presents solutions that will facilitate the cartographer's work in order to achieve unquestionable results. Through the paper it becomes evident that the role of the cartographer and the GIS expert is critical for the successful implementation of maritime delimitation.

  16. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.

    Science.gov (United States)

    Chakraborty, Mohua; Dhar, Bishal; Ghosh, Sankar Kumar

    2017-11-01

    The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification. © 2017 John Wiley & Sons Ltd.

  17. Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo-West Pacific Ocean.

    Science.gov (United States)

    Stern, N; Rinkevich, B; Goren, M

    2016-11-01

    To deal with the difficulties of species differentiation and delimitation among the commercially important sardines from the genus Sardinella, an integrative approach was adopted, incorporating traditional taxonomy with four DNA markers (coI, cytb, 16s and nuclear rag2). Combining these methodologies has enabled a thorough re-description of three of the most common species of Sardinella of the Indo-west Pacific Ocean: white sardinella Sardinella albella, fringescale sardinella Sardinella fimbriata and the goldstripe sardinella Sardinella gibbosa, as well as a description of a new species, Gon's sardinella Sardinella goni, from the island of Boracay, Philippines. In addition, extensive widespread sampling of S. gibbosa reveals a significant genetic separation between the populations from the western Indian Ocean and the west Pacific Ocean, despite no supporting morphological differentiation. An updated morphological key of the species of Sardinella of the Indo-west Pacific Ocean is also provided in order to minimize future misidentifications within these economically important taxa. Finally, the genetic and morphological variabilities within and between the investigated species are used to discuss their biogeographical distribution and possible processes of speciation. © 2016 The Fisheries Society of the British Isles.

  18. Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae with descriptions of three new species from Peru

    Directory of Open Access Journals (Sweden)

    Cesar Aguilar

    2013-12-01

    Full Text Available Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided.

  19. Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

    Science.gov (United States)

    Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

    2017-11-01

    Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

  20. A Dynamic Continuation-Passing Style for Dynamic Delimited Continuations

    DEFF Research Database (Denmark)

    Biernacki, Dariusz; Danvy, Olivier; Millikin, Kevin Scott

    2005-01-01

    We present a new abstract machine that accounts for dynamic delimited continuations. We prove the correctness of this new abstract machine with respect to a pre-existing, definitional abstract machine. Unlike this definitional abstract machine, the new abstract machine is in defunctionalized form......, which makes it possible to state the corresponding higher-order evaluator. This evaluator is in continuation+state passing style and threads a trail of delimited continuations and a meta-continuation. Since this style accounts for dynamic delimited continuations, we refer to it as `dynamic continuation......-passing style.' We show that the new machine operates more efficiently than the definitional one and that the notion of computation induced by the corresponding evaluator takes the form of a monad. We also present new examples and a new simulation of dynamic delimited continuations in terms of static ones....

  1. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis in the grasslands of Queensland, Australia.

    Directory of Open Access Journals (Sweden)

    Jane Melville

    Full Text Available Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora, which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1 revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  2. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

    Science.gov (United States)

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  3. Use of isotopic tools to delimit areas of harnessing for drinking water supply - Final report

    International Nuclear Information System (INIS)

    Gourcy, L.; Petelet-Giraud, E.

    2011-03-01

    Within the frame of an action of the ONEMA-BRGM convention (Methodological approaches and tools for the protection of drinking water harnessing against diffuse pollutions), this study aims at developing a synthesis of isotopic geochemical tools to obtain the information required for the delimitation of harnessing supply areas. The report first describes the conventional tools: water molecule steady isotopes, radioactive isotopes, water dating tools, tools developed for another use, and artificial tracers. It presents the possible uses of natural and artificial tracers to determine parameters like flow directions, water residence duration, exchanges between aquifers and water sheet-river interactions. It gives an overview of knowledge on the use of isotopic methods to determine the origin of contaminants. It proposes a brief overview of a previous study of water sheets-rivers relationships. It finally discusses the use of geochemical and isotopic tools when delimiting supply areas for harnessing aimed at drinking water supply

  4. Chorological classification approach for species and ecosystem conservation practice

    Science.gov (United States)

    Rogova, T. V.; Kozevnikova, M. V.; Prokhorov, V. E.; Timofeeva, N. O.

    2018-01-01

    The habitat type allocation approach based on the EUNIS Habitat Classification and the JUICE version 7 software is used for the conservation of species and ecosystem biodiversity. Using the vegetation plots of the Vegetation Database of Tatarstan, included in the EVA (European Vegetation Archive) and GIVD (Global Index of Vegetation-plots Databases) types of habitats of dry meadows and steppes are distinguished by differing compositions of the leading families composing their flora - Asteraceae, Fabaceae, Poaceae and Rosaceae. E12a - Semi-dry perennial calcareous grassland, and E12b - Perennial calcareous grassland and basic steppes were identified. The selected group of relevés that do not correspond to any of the EUNIS types can be considered specific for ecotone forest-steppe landscapes of the southeast of the Republic of Tatarstan. In all types of studied habitats, rare and protected plant species are noted, most of which are South-East-European-Asian species.

  5. An Operational Foundation for Delimited Continuations in the CPS Hierarchy

    DEFF Research Database (Denmark)

    Biernacka, Malgorzata; Biernacki, Dariusz; Danvy, Olivier

    2004-01-01

    We present an abstract machine and a reduction semantics for the lambda-calculus extended with control operators that give access to delimited continuations in the CPS hierarchy. The abstract machine is derived from an evaluator in continuation-passing style (CPS); the reduction semantics (i.......e., a small-step operational semantics with an explicit representation of evaluation contexts) is constructed from the abstract machine; and the control operators are the shift and reset family. We also present new applications of delimited continuations in the CPS hierarchy: finding list prefixes...

  6. An Operational Foundation for Delimited Continuations in the CPS Hierarchy

    DEFF Research Database (Denmark)

    Biernacka, Malgorzata; Biernacki, Dariusz; Danvy, Olivier

    2005-01-01

    We present an abstract machine and a reduction semantics for the lambda-calculus extended with control operators that give access to delimited continuations in the CPS hierarchy. The abstract machine is derived from an evaluator in continuation-passing style (CPS); the reduction semantics (i.......e., a small-step operational semantics with an explicit representation of evaluation contexts) is constructed from the abstract machine; and the control operators are the shift and reset family. We also present new applications of delimited continuations in the CPS hierarchy: finding list prefixes...

  7. Benchmarking novel approaches for modelling species range dynamics.

    Science.gov (United States)

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

    2016-08-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  8. Minimal barcode distance between two water mite species from Madeira Island: a cautionary tale.

    Science.gov (United States)

    García-Jiménez, Ricardo; Horreo, Jose Luis; Valdecasas, Antonio G

    2017-06-01

    In this work, we compare morphological and molecular data in their ability to distinguish between species of water mites (Acari, Prostigmata, Hydrachnidia). We have focused on the two species of the genus Lebertia inhabiting the island of Madeira. While traditional morphological traits were initially sufficient to distinguish between these two species, the molecular data were more dependable on the kind of analysis carried out. Single arbitrary genetic distance (e.g. a K2P distance below 2%) may lead to the conclusion that the specimens under study belong to the same species. Analysing the same specimens with the coalescent model has proved the evolutionary independence of both Lebertia clades in Madeira. Furthermore, multi-rate Poisson Tree Process analysis confirmed both lineages as independent species. Our results agree with previous studies warning of the dangers of rigid species delimitation based on arbitrary molecular distances. In addition, the importance of different molecular data approaches for correct species delimitation in water mites is highlighted.

  9. An approach to grouping species for ecological risk assessment

    International Nuclear Information System (INIS)

    Hampton, N.L.; VanHorn, R.L.; Morris, R.; Brewer, R.

    1994-01-01

    The ecological risk assessment (ERA) paradigm acknowledges all levels of ecological organization as having potential for defining assessment and measurement endpoints. However, assessment goals and endpoints are generally concentrated at individual species and population levels. As part of a sitewide, screening-level ERA process at the Idaho National Engineering Laboratory (INEL), a ''functional group'' approach was developed to incorporate assessment at a higher level of ecological organization into the risk analysis process. Functional groups demonstrating biological similarity and similar potential for contaminant exposure were developed using taxonomic, trophic and habitat parameters. As defined, all species are potential surrogates for the other members of the same functional group. Measurement endpoint data for several species may be integrated to address the risk to the group as a whole. The functional group concept was applied throughout the problem formulation, analysis, and risk characterization phases of the assessment process. This approach allows the ERA to be focused on risk to the integrity of individual functional groups, which can subsequently be related to guild and community integrity

  10. Cryptic species as a window into the paradigm shift of the species concept.

    Science.gov (United States)

    Fišer, Cene; Robinson, Christopher T; Malard, Florian

    2018-02-01

    The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty. © 2018 John Wiley & Sons Ltd.

  11. Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

    Science.gov (United States)

    Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

    2008-06-01

    Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

  12. Delimiting tropical mountain ecoregions for conservation

    DEFF Research Database (Denmark)

    Platts, Philip J.; Burgess, Neil David; Gereau, Roy E.

    2011-01-01

    Ecological regions aggregate habitats with similar biophysical characteristics within well-defined boundaries, providing spatially consistent platforms for monitoring, managing and forecasting the health of interrelated ecosystems. A major obstacle to the implementation of this approach is imprec......Ecological regions aggregate habitats with similar biophysical characteristics within well-defined boundaries, providing spatially consistent platforms for monitoring, managing and forecasting the health of interrelated ecosystems. A major obstacle to the implementation of this approach...... boundaries. LandScan and census data show population density inside the ecoregion to be higher than in rural lowlands, and lowland settlement to be most probable within 30 km. This definition should help to align landscape scale conservation strategies in the Eastern Arc and promote new research in areas...

  13. A good compromise: rapid and robust species proxies for inventorying biodiversity hotspots using the Terebridae (Gastropoda: Conoidea).

    Science.gov (United States)

    Modica, Maria Vittoria; Puillandre, Nicolas; Castelin, Magalie; Zhang, Yu; Holford, Mandë

    2014-01-01

    Devising a reproducible approach for species delimitation of hyperdiverse groups is an ongoing challenge in evolutionary biology. Speciation processes combine modes of passive and adaptive trait divergence requiring an integrative taxonomy approach to accurately generate robust species hypotheses. However, in light of the rapid decline of diversity on Earth, complete integrative approaches may not be practical in certain species-rich environments. As an alternative, we applied a two-step strategy combining ABGD (Automated Barcode Gap Discovery) and Klee diagrams, to balance speed and accuracy in producing primary species hypotheses (PSHs). Specifically, an ABGD/Klee approach was used for species delimitation in the Terebridae, a neurotoxin-producing marine snail family included in the Conoidea. Delimitation of species boundaries is problematic in the Conoidea, as traditional taxonomic approaches are hampered by the high levels of variation, convergence and morphological plasticity of shell characters. We used ABGD to analyze gaps in the distribution of pairwise distances of 454 COI sequences attributed to 87 morphospecies and obtained 98 to 125 Primary Species Hypotheses (PSHs). The PSH partitions were subsequently visualized as a Klee diagram color map, allowing easy detection of the incongruences that were further evaluated individually with two other species delimitation models, General Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP). GMYC and PTP results confirmed the presence of 17 putative cryptic terebrid species in our dataset. The consensus of GMYC, PTP, and ABGD/Klee findings suggest the combination of ABGD and Klee diagrams is an effective approach for rapidly proposing primary species proxies in hyperdiverse groups and a reliable first step for macroscopic biodiversity assessment.

  14. Automatic delimitation of microwatershed using SRTM data of the NASA

    Directory of Open Access Journals (Sweden)

    Freddy Aníbal Jumbo Castillo

    2015-12-01

    Full Text Available The watershed as the basic territorial unit of planning and management of water resources, requires its proper delimitation of the catchment or drainage area, faced with this situation, the lack of geographic information of Casacay river micro watersheds, hydrographic unit should be resolved, for this purpose the research was aimed at automatic delimitation of micro watersheds using of Geographic Information Systems (GIS techniques and the project Shuttle Radar Topographic Mission (SRTM 30 meters spatial resolution data. The selected methodology was the Pfafstetter one, with which nine micro watersheds were obtained with their respective codification allowing to continue with watersheds standardization adopted by Ecuador Water's Secretariat. With the investigation results watersheds will be updated with more detail information, promoting the execution of tasks or activities related to the integrated management of the hydrographic unit studied

  15. Phylogenetic Reconstruction, Morphological Diversification and Generic Delimitation of Disepalum (Annonaceae).

    Science.gov (United States)

    Li, Pui-Sze; Thomas, Daniel C; Saunders, Richard M K

    2015-01-01

    Taxonomic delimitation of Disepalum (Annonaceae) is contentious, with some researchers favoring a narrow circumscription following segregation of the genus Enicosanthellum. We reconstruct the phylogeny of Disepalum and related taxa based on four chloroplast and two nuclear DNA regions as a framework for clarifying taxonomic delimitation and assessing evolutionary transitions in key morphological characters. Maximum parsimony, maximum likelihood and Bayesian methods resulted in a consistent, well-resolved and strongly supported topology. Disepalum s.l. is monophyletic and strongly supported, with Disepalum s.str. and Enicosanthellum retrieved as sister groups. Although this topology is consistent with both taxonomic delimitations, the distribution of morphological synapomorphies provides greater support for the inclusion of Enicosanthellum within Disepalum s.l. We propose a novel infrageneric classification with two subgenera. Subgen. Disepalum (= Disepalum s.str.) is supported by numerous synapomorphies, including the reduction of the calyx to two sepals and connation of petals. Subgen. Enicosanthellum lacks obvious morphological synapomorphies, but possesses several diagnostic characters (symplesiomorphies), including a trimerous calyx and free petals in two whorls. We evaluate changes in petal morphology in relation to hypotheses of the genetic control of floral development and suggest that the compression of two petal whorls into one and the associated fusion of contiguous petals may be associated with the loss of the pollination chamber, which in turn may be associated with a shift in primary pollinator. We also suggest that the formation of pollen octads may be selectively advantageous when pollinator visits are infrequent, although this would only be applicable if multiple ovules could be fertilized by each octad; since the flowers are apocarpous, this would require an extragynoecial compitum to enable intercarpellary growth of pollen tubes. We furthermore

  16. Phylogenetic Reconstruction, Morphological Diversification and Generic Delimitation of Disepalum (Annonaceae.

    Directory of Open Access Journals (Sweden)

    Pui-Sze Li

    Full Text Available Taxonomic delimitation of Disepalum (Annonaceae is contentious, with some researchers favoring a narrow circumscription following segregation of the genus Enicosanthellum. We reconstruct the phylogeny of Disepalum and related taxa based on four chloroplast and two nuclear DNA regions as a framework for clarifying taxonomic delimitation and assessing evolutionary transitions in key morphological characters. Maximum parsimony, maximum likelihood and Bayesian methods resulted in a consistent, well-resolved and strongly supported topology. Disepalum s.l. is monophyletic and strongly supported, with Disepalum s.str. and Enicosanthellum retrieved as sister groups. Although this topology is consistent with both taxonomic delimitations, the distribution of morphological synapomorphies provides greater support for the inclusion of Enicosanthellum within Disepalum s.l. We propose a novel infrageneric classification with two subgenera. Subgen. Disepalum (= Disepalum s.str. is supported by numerous synapomorphies, including the reduction of the calyx to two sepals and connation of petals. Subgen. Enicosanthellum lacks obvious morphological synapomorphies, but possesses several diagnostic characters (symplesiomorphies, including a trimerous calyx and free petals in two whorls. We evaluate changes in petal morphology in relation to hypotheses of the genetic control of floral development and suggest that the compression of two petal whorls into one and the associated fusion of contiguous petals may be associated with the loss of the pollination chamber, which in turn may be associated with a shift in primary pollinator. We also suggest that the formation of pollen octads may be selectively advantageous when pollinator visits are infrequent, although this would only be applicable if multiple ovules could be fertilized by each octad; since the flowers are apocarpous, this would require an extragynoecial compitum to enable intercarpellary growth of pollen tubes

  17. Montane and coastal species diversification in the economically important Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).

    Science.gov (United States)

    Pedraza-Lara, Carlos; Barrientos-Lozano, Ludivina; Rocha-Sánchez, Aurora Y; Zaldívar-Riverón, Alejandro

    2015-03-01

    The genus Sphenarium (Pyrgomorphidae) is a small group of grasshoppers endemic to México and Guatemala that are economically and culturally important both as a food source and as agricultural pests. However, its taxonomy has been largely neglected mainly due to its conserved interspecific external morphology and the considerable intraspecific variation in colour pattern of some taxa. Here we examined morphological as well as mitochondrial and nuclear DNA sequence data to assess the species boundaries and evolutionary history in Sphenarium. Our morphological identification and DNA sequence-based species delimitation, carried out with three different approaches (DNA barcoding, general mixed Yule-coalescent model, Bayesian species delimitation), all recovered a higher number of putative species of Sphenarium than previously recognised. We unambiguously delimit seven species, and between five and ten additional species depending on the data/method analysed. Phylogenetic relationships within the genus strongly support two main clades, one exclusively montane, the other coastal. Divergence time estimates suggest late Miocene to Pliocene ages for the origin and most of the early diversification events in the genus, which were probably influenced by the formation of the Trans-Mexican Volcanic Belt. A series of Pleistocene events could have led to the current species diversification in both montane and coastal regions. This study not only reveals an overlooked species richness for the most popular edible insect in Mexico, but also highlights the influence of the dynamic geological and climatic history of the region in shaping its current diversity. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. COMPLEMENTARY APPROACHES TO THE DETERMINATION OF ARSENIC SPECIES RELEVANT TO CONCENTRATED ANIMAL FEEDING OPERATIONS

    Science.gov (United States)

    Ion-exchange chromatography is the most often used analytical approach for arsenicspeciation, due to the weak-acid nature of several of its species. However, no singletechnique can determine all potentially occurring arsenic species, especially in complexe...

  19. A MULTIVARIATE APPROACH TO ANALYSE NATIVE FOREST TREE SPECIE SEEDS

    Directory of Open Access Journals (Sweden)

    Alessandro Dal Col Lúcio

    2006-03-01

    Full Text Available This work grouped, by species, the most similar seed tree, using the variables observed in exotic forest species of theBrazilian flora of seeds collected in the Forest Research and Soil Conservation Center of Santa Maria, Rio Grande do Sul, analyzedfrom January, 1997, to march, 2003. For the cluster analysis, all the species that possessed four or more analyses per lot wereanalyzed by the hierarchical Clustering method, of the standardized Euclidian medium distance, being also a principal componentanalysis technique for reducing the number of variables. The species Callistemon speciosus, Cassia fistula, Eucalyptus grandis,Eucalyptus robusta, Eucalyptus saligna, Eucalyptus tereticornis, Delonix regia, Jacaranda mimosaefolia e Pinus elliottii presentedmore than four analyses per lot, in which the third and fourth main components explained 80% of the total variation. The clusteranalysis was efficient in the separation of the groups of all tested species, as well as the method of the main components.

  20. Use of geographical information systems for delimiting health service areas in China

    Directory of Open Access Journals (Sweden)

    Xuechen Xiong

    2017-05-01

    Full Text Available With the objective of choosing a practical and valid method to delimit health service areas of regional health service centres to build a regional basic health service network, we first drew lessons from traditional geographic methods of delimiting trade areas and then applied two methods to delimit health service areas, i.e. the proximal method and the gravity method. We verified the effectiveness of these methods by an index of similarity with the aid of real in-patient data. Calculation of the similarity indices shows that health service areas delimited by the proximal method has an 87.3% similarity to the real health service area, while the gravity method gives 88.6%. Our conclusion is that both methods are suitable for delimiting health service areas at regional health service centres, but find that the proximal method is more practicable in operational terms for delimiting health service areas in region health planning.

  1. Theoretical and Practical Significance of the Issue of Maritime Delimitation in the Law of the Sea

    OpenAIRE

    Lakićević-Đuranović, Bojana

    2017-01-01

    This paper aims to show the significance of maritime delimitation in the Law of the Sea, as well as the contribution of international jurisprudence to the creation of the rules of maritime delimitation. The decisions of the International Court of Justice (ICJ) and the awards of arbitration tribunals are especially significant in the part of the Law of the Sea dealing with maritime delimitation. Based on the analysis of the principle of equity and the method of equidistance, the jurisprudence ...

  2. Evaluation of a multiple-species approach to monitoring species at the ecoregional scale

    Science.gov (United States)

    Patricia N. Manley; William J. Zielinski; Matthew D. Schlesinger; Sylvia R. Mori

    2004-01-01

    Monitoring is required of land managers and conservation practitioners to assess the success of management actions. "Shortcuts" are sought to reduce monitoring costs, most often consisting of the selection of a small number of species that are closely monitored to represent the status of many associated species and environmental correlates. Assumptions...

  3. Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae).

    Science.gov (United States)

    Maguilla, Enrique; Escudero, Marcial

    2016-01-01

    Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation.

  4. A step towards a new delimitation of functional somatic syndromes

    DEFF Research Database (Denmark)

    Eliasen, Marie; Schröder, Andreas; Fink, Per

    2018-01-01

    (17%), gastrointestinal symptoms (6%), and general symptoms (13%). Three profiles had multiple symptoms in specific combinations: musculoskeletal and general symptoms (7%); fatigue, musculoskeletal and gastrointestinal symptoms (3%); and cardiopulmonary, gastrointestinal and general symptoms (3......%). Lastly, one profile (2%) had high probability of all symptoms. The last four profiles (15%) were strongly associated with BDS case-status, poor self-perceived health and high impact of symptoms. Analyses excluding persons with multi-symptomatic chronic disease showed similar results. CONCLUSIONS: We...... identified eight symptom profiles characterized by specific combinations of symptoms. Four of these had multiple symptoms from several bodily systems showing large overlap with BDS, possibly indicating subtypes of FSS. The profiles contribute to a new delimitation of FSS by illustrating the importance...

  5. multivariate approach to the study of aquatic species diversity

    African Journals Online (AJOL)

    User

    2016-12-02

    Dec 2, 2016 ... Eigen value of the three variables namely; Temperature, pH and Electrical Conductivity ... affect the stream macroinvertebrates (Fornaroli et al., 2016). ... relation to stream land use activities (Tinotenda et al., ... to rotate the multivariate data cloud and extract the ..... community modeling of species distribution.

  6. Predicting animal production on sourveld: a species-based approach

    African Journals Online (AJOL)

    The model was based upon measured ingestive and digestive characteristics of different grass species and incorporates an explicit digestive constraint based upon rumen mass and turnover rate. Illustrates with graphs, diagrams and tables. Keywords: ADG; Andropogon appendiculatus; Average daily gain; Cattle; Cynodon ...

  7. Trophic position of coexisting krill species: a stable isotope approach

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Bode, Antonio; Nielsen, Torkel Gissel

    2014-01-01

    Four krill species with overlapping functional biology coexist in Greenland waters. Here, we used stable isotopes to investigate and discuss their trophic role and mode of coexistence. Bulk carbon (δ13C) and nitrogen (δ15N) stable isotope analyses of Thysanoessa longicaudata, T. inermis, T. raschii...

  8. Do DNA barcoding delimitation methods affect our view of stream biodiversity?

    Science.gov (United States)

    How we delimit molecular operational taxonomic units (MOTUs) is an important aspect in the use of DNA barcoding for bioassessment. Four delimitation methods were examined to gain an understanding of their relative strengths at organizing data from 5300 specimens collected during ...

  9. Sharing the space: distribution, habitat segregation and delimitation of a new sympatric area of subterranean rodents.

    Directory of Open Access Journals (Sweden)

    Bruno Busnello Kubiak

    Full Text Available Subterranean rodents of the genus Ctenomys usually present an allopatric or parapatric distribution. Currently, two cases of sympatry have been recognized for the genus in the coastal dunes of southern Argentina and southern Brazil. In this context, they are ideal models to test hypotheses about the factors that delimit the patterns of space use and to understand interspecific interactions in small mammals. We investigated the vegetation structure, plant biomass and soil hardness selected by two species of subterranean rodents (Ctenomys flamarioni and C. minutus when distributed in sympatry and allopatry from nine different areas along the line of coastal dunes in southern Brazil. In addition, our work presents a new record of a third area of sympatry for the genus Ctenomys. Ctenomys flamarioni and C. minutus show habitat segregation in the area where they occur in sympatry. These species show segregation in their selection of microhabitats, differing in relation to soil hardness, plant biomass, and plant cover. Ctenomys flamarioni showed a distinction in habitat selection when occurring in allopatry and sympatry, whereas C. minutus selected the same habitat characteristics under both conditions. A possible explanation to the observed pattern is that these species have acquired different adaptations over time which allows them the ability to exploit different resources and thus avoid competitive interactions all together.

  10. Development of Geospatial Map Based Portal for Delimitation of Mcd Wards

    Science.gov (United States)

    Gupta, A. Kumar Chandra; Kumar, P.; Sharma, P. Kumar

    2017-09-01

    The Geospatial Delhi Limited (GSDL), a Govt. of NCT of Delhi Company formed in order to provide the geospatial information of National Capital Territory of Delhi (NCTD) to the Government of National Capital Territory of Delhi (GNCTD) and its organs such as DDA, MCD, DJB, State Election Department, DMRC etc., for the benefit of all citizens of Government of National Capital Territory of Delhi (GNCTD). This paper describes the development of Geospatial Map based Portal for Delimitation of MCD Wards (GMPDW) and election of 3 Municipal Corporations of NCT of Delhi. The portal has been developed as a map based spatial decision support system (SDSS) for delimitation of MCD Wards and draw of peripheral wards boundaries to planning and management of MCD Election process of State Election Commission, and as an MCD election related information searching tools (Polling Station, MCD Wards and Assembly constituency etc.,) for the citizens of NCTD. The GMPDW is based on Client-Server architecture model. It has been developed using Arc GIS Server 10.0 with .NET (pronounced dot net) technology. The GMPDW is scalable to enterprise SDSS with enterprise Geo Database & Virtual Private Network (VPN) connectivity. Spatial data to GMPDW includes Enumeration Block (EB) and Enumeration Blocks Group (EBG) boundaries of Citizens of Delhi, Assembly Constituency, Parliamentary Constituency, Election District, Landmark locations of Polling Stations & basic amenities (Police Stations, Hospitals, Schools and Fire Stations etc.). GMPDW could help achieve not only the desired transparency and easiness in planning process but also facilitates through efficient & effective tools for management of MCD election. It enables a faster response to the changing ground realities in the development planning, owing to its in-built scientific approach and open-ended design.

  11. DEVELOPMENT OF GEOSPATIAL MAP BASED PORTAL FOR DELIMITATION OF MCD WARDS

    Directory of Open Access Journals (Sweden)

    A. Kumar Chandra Gupta

    2017-09-01

    Full Text Available The Geospatial Delhi Limited (GSDL, a Govt. of NCT of Delhi Company formed in order to provide the geospatial information of National Capital Territory of Delhi (NCTD to the Government of National Capital Territory of Delhi (GNCTD and its organs such as DDA, MCD, DJB, State Election Department, DMRC etc., for the benefit of all citizens of Government of National Capital Territory of Delhi (GNCTD. This paper describes the development of Geospatial Map based Portal for Delimitation of MCD Wards (GMPDW and election of 3 Municipal Corporations of NCT of Delhi. The portal has been developed as a map based spatial decision support system (SDSS for delimitation of MCD Wards and draw of peripheral wards boundaries to planning and management of MCD Election process of State Election Commission, and as an MCD election related information searching tools (Polling Station, MCD Wards and Assembly constituency etc., for the citizens of NCTD. The GMPDW is based on Client-Server architecture model. It has been developed using Arc GIS Server 10.0 with .NET (pronounced dot net technology. The GMPDW is scalable to enterprise SDSS with enterprise Geo Database & Virtual Private Network (VPN connectivity. Spatial data to GMPDW includes Enumeration Block (EB and Enumeration Blocks Group (EBG boundaries of Citizens of Delhi, Assembly Constituency, Parliamentary Constituency, Election District, Landmark locations of Polling Stations & basic amenities (Police Stations, Hospitals, Schools and Fire Stations etc.. GMPDW could help achieve not only the desired transparency and easiness in planning process but also facilitates through efficient & effective tools for management of MCD election. It enables a faster response to the changing ground realities in the development planning, owing to its in-built scientific approach and open-ended design.

  12. Setting water quality criteria in China: approaches for developing species sensitivity distributions for metals and metalloids.

    Science.gov (United States)

    Liu, Yuedan; Wu, Fengchang; Mu, Yunsong; Feng, Chenglian; Fang, Yixiang; Chen, Lulu; Giesy, John P

    2014-01-01

    Both nonparametric and parametric approaches were used to construct SSDs for use in ecological risk assessments. Based on toxicity to representative aquatic species and typical water contaminants of metals and metalloids in China, nonparametric methods based on the bootstrap were statistically superior to the parametric curve-fitting approaches. Knowing what the SSDs for each targeted species are might help in selecting efficient indicator species to use for water quality monitoring. The species evaluated herein showed sensitivity variations to different chemical treatments that were used in constructing the SSDs. For example, D. magna was more sensitive than most species to most chemical treatments, whereas D. rerio was sensitive to Hg and Pb but was tolerant to Zn. HC5 values, derived for the pollutants in this study for protecting Chinese species, differed from those published by the USEPA. Such differences may result from differences in geographical conditions and biota between China and the United States. Thus, the degree of protection desired for aquatic organisms should be formulated to fit local conditions. For approach selection, we recommend all approaches be considered and the most suitable approaches chosen. The selection should be based on the practical information needs of the researcher (viz., species composition, species sensitivity, and geological characteristics of aquatic habitats), since risk assessments usually are focused on certain substances, species, or monitoring sites. We used Tai Lake as a typical freshwater lake in China to assess the risk of metals and metalloids to the aquatic species. We calculated hazard quotients for the metals and metalloids that were found in the water of this lake. Results indicated the decreasing ecological risk of these contaminants in the following order: Hg metalloids to aquatic species. Based on the MEC and HC5 derived from SSDs by nonparametric and parametric approaches together, the risk levels of metals

  13. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2008-09-01

    Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

  14. Delimitation of some neotropical laccate Ganoderma (Ganodermataceae): molecular phylogeny and morphology.

    Science.gov (United States)

    De Lima Júnior, Nelson Correia; Baptista Gibertone, Tatiana; Malosso, Elaine

    2014-09-01

    Ganoderma includes species of great economic and ecological importance, but taxonomists judge the current nomenclatural situation as chaotic and poorly studied in the neotropics. From this perspective, phylogenetic analyses inferred from ribosomal DNA sequences have aided the clarification of the genus status. In this study, 14 specimens of Ganoderma and two of Tomophagus collected in Brazil were used for DNA extraction, amplification and sequencing of the ITS and LSU regions (rDNA). The phylogenetic delimitation of six neotropical taxa (G. chalceum, G. multiplicatum, G. orbiforme, G. parvulum, G. aff. oerstedtii and Tomophagus colossus) was determined based on these Brazilian specimens and found to be distinct from the laccate Ganoderma from Asia, Europe, North America and from some specimens from Argentina. Phylogenetic reconstructions confirmed that the laccate Ganoderna is distinct from Tomophagus, although they belong to the same group. The use of taxonomic synonyms Ganoderma subamboinense for G. multiplicatumnz, G. boninense for G. orbiforme and G. chalceum for G. cupreum was not confirmed. However, Ganoderma parvulum was confirmed as the correct name for specimens called G. stipitatu. Furthermore, the name G. hucidumn should be used only for European species. The use of valid published names is proposed according to the specimen geographical distribution, their morphological characteristics and rDNA analysis. 1208. Epub 2014 September 01.

  15. Molecular phylogeny of tribe Theeae (Theaceae s.s. and its implications for generic delimitation.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    Full Text Available Tribe Theeae, which includes some economically important and widely grown plants, such as beverage tea and a number of woody ornamentals, is the largest member of the Theaceae family. Using five genomic regions (chloroplast: atpI-H, matK, psbA5'R-ALS-11F, rbcL; nuclear: LEAFY and 30 species representing four of the five genera in this tribe (Apterosperma, Camellia, Polyspora, and Pyrenaria s.l., we investigated the phylogeny of Theeae and assessed the delimitation of genera in the tribe. Our results showed that Polyspora was monophyletic and the sister of the three other genera of Theeae investigated, Camellia was paraphyletic and Pyrenaria was polyphyletic. The inconsistent phylogenetic placement of some species of Theeae between the nuclear and chloroplast trees suggested widespread hybridization between Camellia and Pyrenaria, Polyspora and Parapyrenaria. These results indicate that hybridization, rather than morphological homoplasy, has confused the current classification of Theeae. In addition, the phylogenetic placement and possible allies of Laplacea are also discussed.

  16. Calcific Uremic Arteriolopathy: Pathophysiology, Reactive Oxygen Species and Therapeutic Approaches

    Directory of Open Access Journals (Sweden)

    Kurt M. Sowers

    2010-01-01

    Full Text Available Calcific uremic arteriolopathy (CUA/calciphylaxis is an important cause of morbidity and mortality in patients with chronic kidney disease requiring renal replacement. Once thought to be rare, it is being increasingly recognized and reported on a global scale. The uremic milieu predisposes to multiple metabolic toxicities including increased levels of reactive oxygen species and inflammation. Increased oxidative stress and inflammation promote this arteriolopathy by adversely affecting endothelial function resulting in a prothrombotic milieu and significant remodeling effects on vascular smooth muscle cells. These arteriolar pathological effects include intimal hyperplasia, inflammation, endovascular fibrosis and vascular smooth muscle cell apoptosis and differentiation into bone forming osteoblast-like cells resulting in medial calcification. Systemic factors promoting this vascular condition include elevated calcium, parathyroid hormone and hyperphosphatemia with consequent increases in the calcium × phosphate product. The uremic milieu contributes to a marked increased in upstream reactive oxygen species—oxidative stress and subsequent downstream increased inflammation, in part, via activation of the nuclear transcription factor NFκB and associated downstream cytokine pathways. Consitutive anti-calcification proteins such as Fetuin-A and matrix GLA proteins and their signaling pathways may be decreased, which further contributes to medial vascular calcification. The resulting clinical entity is painful, debilitating and contributes to the excess morbidity and mortality associated with chronic kidney disease and end stage renal disease. These same histopathologic conditions also occur in patients without uremia and therefore, the term calcific obliterative arteriolopathy could be utilized in these conditions.

  17. Predicting the consequences of species loss using size-structured biodiversity approaches

    DEFF Research Database (Denmark)

    Brose, Ulrich; Blanchard, Julia L.; Eklöf, Anna

    2017-01-01

    Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic...... stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments...... trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss....

  18. Towards an integrated approach to modelling the risks and impacts of invasive forest species

    Science.gov (United States)

    Denys Yemshanov; Daniel McKenney; John Pedlar; Frank Koch; David Cook

    2009-01-01

    In this paper we provide an overview of an integrated approach to modelling the risks and impacts associated with non-indigenous forest pest species. This is a broad and important topic given the scale of ecological and economic consequences associated with non-indigenous species in north america and elsewhere. Assessments of risk and impacts remain difficult due to...

  19. Systematic Approach to Calculate the Concentration of Chemical Species in Multi-Equilibrium Problems

    Science.gov (United States)

    Baeza-Baeza, Juan Jose; Garcia-Alvarez-Coque, Maria Celia

    2011-01-01

    A general systematic approach is proposed for the numerical calculation of multi-equilibrium problems. The approach involves several steps: (i) the establishment of balances involving the chemical species in solution (e.g., mass balances, charge balance, and stoichiometric balance for the reaction products), (ii) the selection of the unknowns (the…

  20. Focal species and landscape "naturalness" corridor models offer complementary approaches for connectivity conservation planning

    Science.gov (United States)

    Meade Krosby; Ian Breckheimer; D. John Pierce; Peter H. Singleton; Sonia A. Hall; Karl C. Halupka; William L. Gaines; Robert A. Long; Brad H. McRae; Brian L. Cosentino; Joanne P. Schuett-Hames

    2015-01-01

    Context   The dual threats of habitat fragmentation and climate change have led to a proliferation of approaches for connectivity conservation planning. Corridor analyses have traditionally taken a focal species approach, but the landscape ‘‘naturalness’’ approach of modeling connectivity among areas of low human modification has gained popularity...

  1. Using a systematic approach to select flagship species for bird conservation.

    Science.gov (United States)

    Veríssimo, Diogo; Pongiluppi, Tatiana; Santos, Maria Cintia M; Develey, Pedro F; Fraser, Iain; Smith, Robert J; MacMilan, Douglas C

    2014-02-01

    Conservation marketing campaigns that focus on flagship species play a vital role in biological diversity conservation because they raise funds and change people's behavior. However, most flagship species are selected without considering the target audience of the campaign, which can hamper the campaign's effectiveness. To address this problem, we used a systematic and stakeholder-driven approach to select flagship species for a conservation campaign in the Serra do Urubu in northeastern Brazil. We based our techniques on environmental economic and marketing methods. We used choice experiments to examine the species attributes that drive preference and latent-class models to segment respondents into groups by preferences and socioeconomic characteristics. We used respondent preferences and information on bird species inhabiting the Serra do Urubu to calculate a flagship species suitability score. We also asked respondents to indicate their favorite species from a set list to enable comparison between methods. The species' traits that drove audience preference were geographic distribution, population size, visibility, attractiveness, and survival in captivity. However, the importance of these factors differed among groups and groups differed in their views on whether species with small populations and the ability to survive in captivity should be prioritized. The popularity rankings of species differed between approaches, a result that was probably related to the different ways in which the 2 methods measured preference. Our new approach is a transparent and evidence-based method that can be used to refine the way stakeholders are engaged in the design of conservation marketing campaigns. © 2013 Society for Conservation Biology.

  2. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

    Directory of Open Access Journals (Sweden)

    Edwards Scott V

    2010-10-01

    Full Text Available Abstract Background Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE of the species tree (topology, branch lengths, and population sizes from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE of species trees, with branch lengths of the species tree in coalescent units. Results We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1. The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals. Conclusions MP-EST can consistently estimate the topology and branch lengths (in coalescent units of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT, the MP-EST method is robust to a small amount of HGT in the

  3. Estimation of the species richness of fish parasite fauna: an ecological approach

    Directory of Open Access Journals (Sweden)

    Ieshko Evgeny Pavlovich

    2012-12-01

    Full Text Available We studied the biological diversity of the parasite fauna in pike from four habitats found in northern lakes of Karelia. The curves of the expected species richness versus sampling effort (the number of examined specimens dependency were plotted. A universal approach to the description of the new species replenishment dynamics is proposed – including finding (through combinatorial analysis the median value between the fastest and the slowest paths of the species richness growth followed by approximation using logistic function . Our analysis showed that the leading ecological factors controlling the formation of the parasite species richness in a specific waterbody are the richness of infracommunities and the age composition of the host sample. The sample of 15 host specimens contains at least 80% of all species in the parasite community.

  4. Postmortem muscle protein degradation in humans as a tool for PMI delimitation.

    Science.gov (United States)

    Pittner, Stefan; Ehrenfellner, Bianca; Monticelli, Fabio C; Zissler, Angela; Sänger, Alexandra M; Stoiber, Walter; Steinbacher, Peter

    2016-11-01

    Forensic estimation of time since death relies on diverse approaches, including measurement and comparison of environmental and body core temperature and analysis of insect colonization on a dead body. However, most of the applied methods have practical limitations or provide insufficient results under certain circumstances. Thus, new methods that can easily be implemented into forensic routine work are required to deliver more and discrete information about the postmortem interval (PMI). Following a previous work on skeletal muscle degradation in the porcine model, we analyzed human postmortem skeletal muscle samples of 40 forensic cases by Western blotting and casein zymography. Our results demonstrate predictable protein degradation processes in human muscle that are distinctly associated with temperature and the PMI. We provide information on promising degradation markers for certain periods of time postmortem, which can be useful tools for time since death delimitation. In addition, we discuss external influencing factors such as age, body mass index, sex, and cause of death that need to be considered in future routine application of the method in humans.

  5. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

  6. Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species.

    Science.gov (United States)

    Irizarry, Kristopher J L; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L; Barrett, Gini; Barr, Margaret C

    2016-01-01

    Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

  7. A phylogenetic delimitation of the "Sphagnum subsecundum complex" (Sphagnaceae, Bryophyta).

    Science.gov (United States)

    Shaw, A Jonathan; Boles, Sandra; Shaw, Blanka

    2008-06-01

    A seemingly obvious but sometimes overlooked premise of any evolutionary analysis is delineating the group of taxa under study. This is especially problematic in some bryophyte groups because of morphological simplicity and convergence. This research applies information from nucleotide sequences for eight plastid and nuclear loci to delineate a group of northern hemisphere peat moss species, the so-called Sphagnum subsecundum complex, which includes species known to be gametophytically haploid or diploid (i.e., sporophytically diploid-tetraploid). Despite the fact that S. subsecundum and several species in the complex have been attributed disjunct ranges that include all major continents, phylogenetic analyses suggest that the group is actually restricted to Europe and eastern North America. Plants from western North America, from California to Alaska, which are morphologically similar to species of the S. subsecundum complex in eastern N. America and Europe, actually belong to a different deep clade within Sphagnum section Subsecunda. One species often considered part of the S. subsecundum complex, S. contortum, likely has a reticulate history involving species in the two deepest clades within section Subsecunda. Nucleotide sequences have a strong geographic structure across the section Subsecunda, but shallow tip clades suggest repeated long-distance dispersal in the section as well.

  8. Approaches to evaluating climate change impacts on species: A guide to initiating the adaptation planning process

    Science.gov (United States)

    Erika L. Rowland; Jennifer E. Davison; Lisa J. Graumlich

    2011-01-01

    Assessing the impact of climate change on species and associated management objectives is a critical initial step for engaging in the adaptation planning process. Multiple approaches are available. While all possess limitations to their application associated with the uncertainties inherent in the data and models that inform their results, conducting and incorporating...

  9. 32 species validation of a new Illumina paired-end approach for the development of microsatellites.

    Directory of Open Access Journals (Sweden)

    Stacey L Lance

    Full Text Available Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485, with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.

  10. Identification and characterization of a novel tospovirus species using a new RT-PCR approach

    NARCIS (Netherlands)

    Cortez, I.; Saaijer, J.; Wonjkaew, K.S.; Pereira, A.M.; Goldbach, R.W.; Peters, D.; Kormelink, R.

    2001-01-01

    Summary. A novel tospovirus serologically distinct from all established tospo- virus species was found in Thailand in Physalis minima L. The S RNA of this virus was cloned by a new RT-PCR approach revealing a nucleotide sequence of 3257 nucleotides. The ambisense RNA segment encoded a nonstructural

  11. Dynamic species classification of microorganisms across time, abiotic and biotic environments-A sliding window approach.

    Directory of Open Access Journals (Sweden)

    Frank Pennekamp

    Full Text Available The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learning (ML algorithms into meaningful ecological information. ML uses user defined classes (e.g. species, derived from a subset (i.e. training data of video-observed quantitative features (e.g. phenotypic variation, to infer classes in subsequent observations. However, phenotypic variation often changes due to environmental conditions, which may lead to poor classification, if environmentally induced variation in phenotypes is not accounted for. Here we describe a framework for classifying species under changing environmental conditions based on the random forest classification. A sliding window approach was developed that restricts temporal and environmentally conditions to improve the classification. We tested our approach by applying the classification framework to experimental data. The experiment used a set of six ciliate species to monitor changes in community structure and behavior over hundreds of generations, in dozens of species combinations and across a temperature gradient. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, as phenotypic differences driven by environmental change, could be captured by the classifier. Importantly, classification using the random forest algorithm showed comparable success when validated against traditional, slower, manual identification. Our framework allows for reliable classification in dynamic environments, and may help to improve strategies for long-term monitoring of species in changing environments. Our

  12. Multi-scale approach for predicting fish species distributions across coral reef seascapes.

    Directory of Open Access Journals (Sweden)

    Simon J Pittman

    Full Text Available Two of the major limitations to effective management of coral reef ecosystems are a lack of information on the spatial distribution of marine species and a paucity of data on the interacting environmental variables that drive distributional patterns. Advances in marine remote sensing, together with the novel integration of landscape ecology and advanced niche modelling techniques provide an unprecedented opportunity to reliably model and map marine species distributions across many kilometres of coral reef ecosystems. We developed a multi-scale approach using three-dimensional seafloor morphology and across-shelf location to predict spatial distributions for five common Caribbean fish species. Seascape topography was quantified from high resolution bathymetry at five spatial scales (5-300 m radii surrounding fish survey sites. Model performance and map accuracy was assessed for two high performing machine-learning algorithms: Boosted Regression Trees (BRT and Maximum Entropy Species Distribution Modelling (MaxEnt. The three most important predictors were geographical location across the shelf, followed by a measure of topographic complexity. Predictor contribution differed among species, yet rarely changed across spatial scales. BRT provided 'outstanding' model predictions (AUC = >0.9 for three of five fish species. MaxEnt provided 'outstanding' model predictions for two of five species, with the remaining three models considered 'excellent' (AUC = 0.8-0.9. In contrast, MaxEnt spatial predictions were markedly more accurate (92% map accuracy than BRT (68% map accuracy. We demonstrate that reliable spatial predictions for a range of key fish species can be achieved by modelling the interaction between the geographical location across the shelf and the topographic heterogeneity of seafloor structure. This multi-scale, analytic approach is an important new cost-effective tool to accurately delineate essential fish habitat and support

  13. High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States.

    Science.gov (United States)

    Holguin, Claudia M; Baeza, Juan A; Mueller, John D; Agudelo, Paula

    2015-07-01

    Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.

  14. Evaluation of Two Approaches to Defining Extinction Risk under the U.S. Endangered Species Act.

    Science.gov (United States)

    Thompson, Grant G; Maguire, Lynn A; Regan, Tracey J

    2018-05-01

    The predominant definition of extinction risk in conservation biology involves evaluating the cumulative distribution function (CDF) of extinction time at a particular point (the "time horizon"). Using the principles of decision theory, this article develops an alternative definition of extinction risk as the expected loss (EL) to society resulting from eventual extinction of a species. Distinct roles are identified for time preference and risk aversion. Ranges of tentative values for the parameters of the two approaches are proposed, and the performances of the two approaches are compared and contrasted for a small set of real-world species with published extinction time distributions and a large set of hypothetical extinction time distributions. Potential issues with each approach are evaluated, and the EL approach is recommended as the better of the two. The CDF approach suffers from the fact that extinctions that occur at any time before the specified time horizon are weighted equally, while extinctions that occur beyond the specified time horizon receive no weight at all. It also suffers from the fact that the time horizon does not correspond to any natural phenomenon, and so is impossible to specify nonarbitrarily; yet the results can depend critically on the specified value. In contrast, the EL approach has the advantage of weighting extinction time continuously, with no artificial time horizon, and the parameters of the approach (the rates of time preference and risk aversion) do correspond to natural phenomena, and so can be specified nonarbitrarily. © 2017 Society for Risk Analysis.

  15. Advances in conservation endocrinology: the application of molecular approaches to the conservation of endangered species.

    Science.gov (United States)

    Tubbs, Christopher; McDonough, Caitlin E; Felton, Rachel; Milnes, Matthew R

    2014-07-01

    Among the numerous societal benefits of comparative endocrinology is the application of our collective knowledge of hormone signaling towards the conservation of threatened and endangered species - conservation endocrinology. For several decades endocrinologists have used longitudinal hormone profiles to monitor reproductive status in a multitude of species. Knowledge of reproductive status among individuals has been used to assist in the management of captive and free-ranging populations. More recently, researchers have begun utilizing molecular and cell-based techniques to gain a more complete understanding of hormone signaling in wildlife species, and to identify potential causes of disrupted hormone signaling. In this review we examine various in vitro approaches we have used to compare estrogen receptor binding and activation by endogenous hormones and phytoestrogens in two species of rhinoceros; southern white and greater one-horned. We have found many of these techniques valuable and practical in species where access to research subjects and/or tissues is limited due to their conservation status. From cell-free, competitive binding assays to full-length receptor activation assays; each technique has strengths and weaknesses related to cost, sensitivity, complexity of the protocols, and relevance to in vivo signaling. We then present a novel approach, in which receptor activation assays are performed in primary cell lines derived from the species of interest, to minimize the artifacts of traditional heterologous expression systems. Finally, we speculate on the promise of next generation sequencing and transcriptome profiling as tools for characterizing hormone signaling in threatened and endangered species. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Nonlinear flowering responses to climate: are species approaching their limits of phenological change?

    Science.gov (United States)

    Iler, Amy M.; Høye, Toke T.; Inouye, David W.; Schmidt, Niels M.

    2013-01-01

    Many alpine and subalpine plant species exhibit phenological advancements in association with earlier snowmelt. While the phenology of some plant species does not advance beyond a threshold snowmelt date, the prevalence of such threshold phenological responses within plant communities is largely unknown. We therefore examined the shape of flowering phenology responses (linear versus nonlinear) to climate using two long-term datasets from plant communities in snow-dominated environments: Gothic, CO, USA (1974–2011) and Zackenberg, Greenland (1996–2011). For a total of 64 species, we determined whether a linear or nonlinear regression model best explained interannual variation in flowering phenology in response to increasing temperatures and advancing snowmelt dates. The most common nonlinear trend was for species to flower earlier as snowmelt advanced, with either no change or a slower rate of change when snowmelt was early (average 20% of cases). By contrast, some species advanced their flowering at a faster rate over the warmest temperatures relative to cooler temperatures (average 5% of cases). Thus, some species seem to be approaching their limits of phenological change in response to snowmelt but not temperature. Such phenological thresholds could either be a result of minimum springtime photoperiod cues for flowering or a slower rate of adaptive change in flowering time relative to changing climatic conditions. PMID:23836793

  17. Drought resilience across ecologically dominant species: An experiment-model integration approach

    Science.gov (United States)

    Felton, A. J.; Warren, J.; Ricciuto, D. M.; Smith, M. D.

    2017-12-01

    Poorly understood are the mechanisms contributing to variability in ecosystem recovery following drought. Grasslands of the central U.S. are ecologically and economically important ecosystems, yet are also highly sensitive to drought. Although characteristics of these ecosystems change across gradients of temperature and precipitation, a consistent feature among these systems is the presence of highly abundant, dominant grass species that control biomass production. As a result, the incorporation of these species' traits into terrestrial biosphere models may constrain predictions amid increases in climatic variability. Here we report the results of a modeling-experiment (MODEX) research approach. We investigated the physiological, morphological and growth responses of the dominant grass species from each of the four major grasslands of the central U.S. (ranging from tallgrass prairie to desert grassland) following severe drought. Despite significant differences in baseline values, full recovery in leaf physiological function was evident across species, of which was consistently driven by the production of new leaves. Further, recovery in whole-plant carbon uptake tended to be driven by shifts in allocation from belowground to aboveground structures. However, there was clear variability among species in the magnitude of this dynamic as well as the relative allocation to stem versus leaf production. As a result, all species harbored the physiological capacity to recover from drought, yet we posit that variability in the recovery of whole-plant carbon uptake to be more strongly driven by variability in the sensitivity of species' morphology to soil moisture increases. The next step of this project will be to incorporate these and other existing data on these species and ecosystems into the community land model in an effort to test the sensitivity of this model to these data.

  18. Species diversity of the genus Osmundea (Ceramiales, Rhodophyta) in the Macaronesian region.

    Science.gov (United States)

    Machín-Sánchez, María; Rousseau, Florence; Le Gall, Line; Cassano, Valéria; Neto, Ana I; Sentíes, Abel; T Fujii, Mutue; Gil-Rodríguez, María Candelaria

    2016-08-01

    Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first-order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI-5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra- and interspecific relationships. Subsequently, one or several sequences of plastid-encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as "Osmundea sp.1," which is a sister taxon of O. hybrida. © 2016 Phycological Society of America.

  19. Approach to non-human species radiation dose assessment in the republic of Korea

    International Nuclear Information System (INIS)

    Keum, D. K.; Jun, I.; Lim, K. M.; Choi, Y. H.

    2011-01-01

    This paper describes the approach to non-human species radiation dose assessment in Korea. As the tentative reference organisms, one plant and seven animals were selected based on the new International Commission on Radiological Protection recommendation issued in 2007, and the size of the selected organisms was determined from the corresponding Korean endemic species. A set of 25 radionuclides was considered as a potential source term of causing radiological damage to organisms. External and internal dose conversion coefficients for the selected organisms and radionuclides were calculated by the uniform isotropic model or Monte Carlo simulation. Concentration ratios of some endemic species are being measured in laboratory experiments, in parallel with the review of existing data. (authors)

  20. PCR amplification of repetitive sequences as a possible approach in relative species quantification

    DEFF Research Database (Denmark)

    Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

    2012-01-01

    Abstract Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification...... of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species...... to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control....

  1. Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

    Science.gov (United States)

    Springer, Mark S; Gatesy, John

    2018-02-26

    coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

  2. Automated classification of tropical shrub species: a hybrid of leaf shape and machine learning approach.

    Science.gov (United States)

    Murat, Miraemiliana; Chang, Siow-Wee; Abu, Arpah; Yap, Hwa Jen; Yong, Kien-Thai

    2017-01-01

    Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities. However, it is a difficult task to identify plant species because it requires specialized knowledge. Developing an automated classification system for plant species is necessary and valuable since it can help specialists as well as the public in identifying plant species easily. Shape descriptors were applied on the myDAUN dataset that contains 45 tropical shrub species collected from the University of Malaya (UM), Malaysia. Based on literature review, this is the first study in the development of tropical shrub species image dataset and classification using a hybrid of leaf shape and machine learning approach. Four types of shape descriptors were used in this study namely morphological shape descriptors (MSD), Histogram of Oriented Gradients (HOG), Hu invariant moments (Hu) and Zernike moments (ZM). Single descriptor, as well as the combination of hybrid descriptors were tested and compared. The tropical shrub species are classified using six different classifiers, which are artificial neural network (ANN), random forest (RF), support vector machine (SVM), k-nearest neighbour (k-NN), linear discriminant analysis (LDA) and directed acyclic graph multiclass least squares twin support vector machine (DAG MLSTSVM). In addition, three types of feature selection methods were tested in the myDAUN dataset, Relief, Correlation-based feature selection (CFS) and Pearson's coefficient correlation (PCC). The well-known Flavia dataset and Swedish Leaf dataset were used as the validation dataset on the proposed methods. The results showed that the hybrid of all descriptors of ANN outperformed the other classifiers with an average classification accuracy of 98.23% for the myDAUN dataset, 95.25% for the Flavia dataset and 99

  3. A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

    Directory of Open Access Journals (Sweden)

    Robert J Elshire

    Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

  4. Emissions of gaseous nitrogen species from manure management: A new approach

    Energy Technology Data Exchange (ETDEWEB)

    Daemmgen, Ulrich [Federal Agricultural Research Centre, Institute of Agroecology, Bundesallee 50, 38116 Braunschweig (Germany)], E-mail: ulrich.daemmgen@fal.de; Hutchings, Nicholas J. [Danish Institute of Agricultural Sciences, Department of Agroecology, Tjele (Denmark)], E-mail: nick.hutchings@agrsci.dk

    2008-08-15

    A procedure for the assessment of emissions of nitrogen (N) species (ammonia, nitrous oxide, nitric oxide, di-nitrogen) from the manure management system is developed, which treats N pools and flows including emissions strictly according to conservation of mass criteria. As all relevant flows in the husbandry of mammals are depicted, the methodology is considered a Tier 3 approach in IPCC terminology or a detailed methodology in UN ECE terminology. The importance of accounting for all N species is illustrated by comparing emission estimates obtained using this approach with those obtained from the application the present detailed/Tier 2 methodology. - A cow is a cow. There is no distinction between an IPCC and a UN ECE cow{exclamation_point}.

  5. Emissions of gaseous nitrogen species from manure management: A new approach

    International Nuclear Information System (INIS)

    Daemmgen, Ulrich; Hutchings, Nicholas J.

    2008-01-01

    A procedure for the assessment of emissions of nitrogen (N) species (ammonia, nitrous oxide, nitric oxide, di-nitrogen) from the manure management system is developed, which treats N pools and flows including emissions strictly according to conservation of mass criteria. As all relevant flows in the husbandry of mammals are depicted, the methodology is considered a Tier 3 approach in IPCC terminology or a detailed methodology in UN ECE terminology. The importance of accounting for all N species is illustrated by comparing emission estimates obtained using this approach with those obtained from the application the present detailed/Tier 2 methodology. - A cow is a cow. There is no distinction between an IPCC and a UN ECE cow!

  6. An approach to consider behavioral plasticity as a source of uncertainty when forecasting species' response to climate change.

    Science.gov (United States)

    Muñoz, Antonio-Román; Márquez, Ana Luz; Real, Raimundo

    2015-06-01

    The rapid ecological shifts that are occurring due to climate change present major challenges for managers and policymakers and, therefore, are one of the main concerns for environmental modelers and evolutionary biologists. Species distribution models (SDM) are appropriate tools for assessing the relationship between species distribution and environmental conditions, so being customarily used to forecast the biogeographical response of species to climate change. A serious limitation of species distribution models when forecasting the effects of climate change is that they normally assume that species behavior and climatic tolerances will remain constant through time. In this study, we propose a new methodology, based on fuzzy logic, useful for incorporating the potential capacity of species to adapt to new conditions into species distribution models. Our results demonstrate that it is possible to include different behavioral responses of species when predicting the effects of climate change on species distribution. Favorability models offered in this study show two extremes: one considering that the species will not modify its present behavior, and another assuming that the species will take full advantage of the possibilities offered by an increase in environmental favorability. This methodology may mean a more realistic approach to the assessment of the consequences of global change on species' distribution and conservation. Overlooking the potential of species' phenotypical plasticity may under- or overestimate the predicted response of species to changes in environmental drivers and its effects on species distribution. Using this approach, we could reinforce the science behind conservation planning in the current situation of rapid climate change.

  7. A comparative approach using ecotoxicological methods from single-species bioassays to model ecosystems.

    Science.gov (United States)

    Haegerbaeumer, Arne; Höss, Sebastian; Ristau, Kai; Claus, Evelyn; Möhlenkamp, Christel; Heininger, Peter; Traunspurger, Walter

    2016-12-01

    Soft sediments are often hotspots of chemical contamination, and a thorough ecotoxicological assessment of this habitat can help to identify the causes of stress and to improve the health of the respective ecosystems. As an important component of the ecologically relevant meiobenthic fauna, nematodes can be used for sediment assessments, with various assay tools ranging from single-species toxicity tests to field studies. In the present study, microcosms containing sediment were used to investigate direct and indirect effects of zinc on natural nematode assemblages, and acute community toxicity tests considering only direct toxicity were conducted. The responses of the various freshwater nematode species in both approaches were compared with those of Caenorhabditis elegans, determined in standardized tests (ISO 10872). At a median lethal concentration (LC50) of 20 mg Zn/L, C. elegans represented the median susceptibility of 15 examined nematode species examined in the acute community toxicity tests. In the microcosms, Zn affected the nematodes dose-dependently, with changes in species composition first detected at 13 mg Zn/kg to 19 mg Zn/kg sediment dry weight. The observed species sensitivities in the microcosms corresponded better to field observations than to the results of the acute community toxicity tests. Environ Toxicol Chem 2016;35:2987-2997. © 2016 SETAC. © 2016 SETAC.

  8. A High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures

    Science.gov (United States)

    Musah, Rabi A.; Espinoza, Edgard O.; Cody, Robert B.; Lesiak, Ashton D.; Christensen, Earl D.; Moore, Hannah E.; Maleknia, Simin; Drijfhout, Falko P.

    2015-01-01

    A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. A range of both polar and non-polar chemotypes are instantaneously detected. The result is identification and species level classification based on the entire DART-MS spectrum. Here, we illustrate how the method can be used to: (1) distinguish between endangered woods regulated by the Convention for the International Trade of Endangered Flora and Fauna (CITES) treaty; (2) assess the origin and by extension the properties of biodiesel feedstocks; (3) determine insect species from analysis of puparial casings; (4) distinguish between psychoactive plants products; and (5) differentiate between Eucalyptus species. An advantage of the hierarchical clustering approach to processing of the DART-MS derived fingerprint is that it shows both similarities and differences between species based on their chemotypes. Furthermore, full knowledge of the identities of the constituents contained within the small molecule profile of analyzed samples is not required. PMID:26156000

  9. An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change.

    Directory of Open Access Journals (Sweden)

    Nicolas Casajus

    Full Text Available An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one.

  10. An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change.

    Science.gov (United States)

    Casajus, Nicolas; Périé, Catherine; Logan, Travis; Lambert, Marie-Claude; de Blois, Sylvie; Berteaux, Dominique

    2016-01-01

    An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one.

  11. A pilot study to delimit tsetse target populations in Zimbabwe.

    Directory of Open Access Journals (Sweden)

    Gerald Chikowore

    2017-05-01

    Full Text Available Tsetse (Glossina sensu stricto are cyclical vectors of human and animal trypanosomoses, that are presently targeted by the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC coordinated by the African Union. In order to achieve effective control of tsetse, there is need to produce elaborate plans to guide intervention programmes. A model intended to aid in the planning of intervention programmes and assist a fuller understanding of tsetse distribution was applied, in a pilot study in the Masoka area, Mid-Zambezi valley in Zimbabwe, and targeting two savannah species, Glossina morsitans morsitans and Glossina pallidipes.The field study was conducted between March and December 2015 in 105 sites following a standardized grid sampling frame. Presence data were used to study habitat suitability of both species based on climatic and environmental data derived from MODIS and SPOT 5 satellite images. Factors influencing distribution were studied using an Ecological Niche Factor Analysis (ENFA whilst habitat suitability was predicted using a Maximum Entropy (MaxEnt model at a spatial resolution of 250 m. Area Under the Curve (AUC, an indicator of model performance, was 0.89 for G. m. morsitans and 0.96 for G. pallidipes. We then used the predicted suitable areas to calculate the probability that flies were really absent from the grid cells where they were not captured during the study based on a probability model using a risk threshold of 0.05. Apart from grid cells where G. m. morsitans and G. pallidipes were captured, there was a high probability of presence in an additional 128 km2 and 144 km2 respectively.The modelling process promised to be useful in optimizing the outputs of presence/absence surveys, allowing the definition of tsetse infested areas with improved accuracy. The methodology proposed here can be extended to all the tsetse infested parts of Zimbabwe and may also be useful for other PATTEC national initiatives in other

  12. Selection bias in species distribution models: An econometric approach on forest trees based on structural modeling

    Science.gov (United States)

    Martin-StPaul, N. K.; Ay, J. S.; Guillemot, J.; Doyen, L.; Leadley, P.

    2014-12-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global changes on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of applications on forest trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8km). We also compared the outputs of the SSDM with outputs of a classical SDM (i.e. Biomod ensemble modelling) in terms of bioclimatic response curves and potential distributions under current climate and climate change scenarios. The shapes of the bioclimatic response curves and the modelled species distribution maps differed markedly between SSDM and classical SDMs, with contrasted patterns according to species and spatial resolutions. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents

  13. Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach.

    Science.gov (United States)

    Santos, Guilherme Brzoskowski; Espínola, Sergio Martín; Ferreira, Henrique Bunselmeyer; Margis, Rogerio; Zaha, Arnaldo

    2013-11-14

    High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family.

  14. Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera

    NARCIS (Netherlands)

    Mutanen, M.; Kivelä, S.M.; Vos, R.A.; Doorenweerd, C.; Ratnasingham, S.; Hausmann, A.; Huemer, P.; Dinca, V.; Nieukerken, van E.J.; Lopez-Vaamonde, C.; Vila, R.; Aarvik, L.; Decaëns, T.; Efetov, K.A.; Hebert, P.D.N.; Johnsen, A.; Karsholt, O.; Pentinsaari, M.; Rougerie, R.; Segerer, A.; Tarmann, G.; Zahiri, R.; Godfray, H.C.J.

    2016-01-01

    The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between

  15. Technical Note: "Mitochondrial and nuclear DNA approaches for reliable identification of Lucilia (Diptera, Calliphoridae) species of forensic interest from Southern Europe".

    Science.gov (United States)

    GilArriortua, Maite; Saloña-Bordas, Marta I; Cainé, Laura M; Pinheiro, Fátima; M de Pancorbo, Marian

    2015-12-01

    In forensic entomology, rapid and unambiguous identification of blowfly species is a critical prerequisite for accurately estimating the post-mortem interval (PMI). The conventional diagnosis of cadaveric entomofauna based on external characters is hampered by the morphological similarities between species, especially in immature stages. Genetic analysis has been shown to allow precise and reliable diagnosis and delimitation of insect species. Nevertheless, the taxonomy of some species remains unresolved. This study was focused on improving the effectiveness and accuracy of analysis based on the widely used cytochrome c oxidase subunit I barcode region (COI barcode, 658 bp), complemented by other mitochondrial and nuclear regions, such as cytochrome b (Cyt-b, 307 bp) and the second internal transcribed spacer (ITS2, 310-331 bp), for the identification of Southern European blowflies. We analyzed a total of 209 specimens, collected from 38 human corpses, belonging to three Calliphoridae genera and seven species: Chrysomya (Ch. albiceps), Calliphora (C. vicina and C. vomitoria), and Lucilia (L. sericata, L. ampullacea, L. caesar and L. illustris). These species are the most common PMI indicators in Portugal. The results revealed that unambiguous separation of species of the Lucilia genus requires different loci from the barcode region. Furthermore, we conclude that the ITS2 (310-331 bp) molecular marker is a promising diagnostic tool because its inter-specific discriminatory power enables unequivocal and consistent distinctions to be made, even between closely related species (L. caesar-L. illustris). This work also contributes new genetic data that may be of interest in performing species diagnosis for Southern European blowflies. Notably, to the best of our knowledge, we provide the first records of the Cyt-b (307 bp) locus for L. illustris and the ITS2 (310-331 bp) region for Iberian Peninsula Lucilia species. Copyright © 2015 Elsevier Ireland Ltd. All rights

  16. A Robust Approach to Risk Assessment Based on Species Sensitivity Distributions.

    Science.gov (United States)

    Monti, Gianna S; Filzmoser, Peter; Deutsch, Roland C

    2018-05-03

    The guidelines for setting environmental quality standards are increasingly based on probabilistic risk assessment due to a growing general awareness of the need for probabilistic procedures. One of the commonly used tools in probabilistic risk assessment is the species sensitivity distribution (SSD), which represents the proportion of species affected belonging to a biological assemblage as a function of exposure to a specific toxicant. Our focus is on the inverse use of the SSD curve with the aim of estimating the concentration, HCp, of a toxic compound that is hazardous to p% of the biological community under study. Toward this end, we propose the use of robust statistical methods in order to take into account the presence of outliers or apparent skew in the data, which may occur without any ecological basis. A robust approach exploits the full neighborhood of a parametric model, enabling the analyst to account for the typical real-world deviations from ideal models. We examine two classic HCp estimation approaches and consider robust versions of these estimators. In addition, we also use data transformations in conjunction with robust estimation methods in case of heteroscedasticity. Different scenarios using real data sets as well as simulated data are presented in order to illustrate and compare the proposed approaches. These scenarios illustrate that the use of robust estimation methods enhances HCp estimation. © 2018 Society for Risk Analysis.

  17. Assumption-versus data-based approaches to summarizing species' ranges.

    Science.gov (United States)

    Peterson, A Townsend; Navarro-Sigüenza, Adolfo G; Gordillo, Alejandro

    2018-06-01

    For conservation decision making, species' geographic distributions are mapped using various approaches. Some such efforts have downscaled versions of coarse-resolution extent-of-occurrence maps to fine resolutions for conservation planning. We examined the quality of the extent-of-occurrence maps as range summaries and the utility of refining those maps into fine-resolution distributional hypotheses. Extent-of-occurrence maps tend to be overly simple, omit many known and well-documented populations, and likely frequently include many areas not holding populations. Refinement steps involve typological assumptions about habitat preferences and elevational ranges of species, which can introduce substantial error in estimates of species' true areas of distribution. However, no model-evaluation steps are taken to assess the predictive ability of these models, so model inaccuracies are not noticed. Whereas range summaries derived by these methods may be useful in coarse-grained, global-extent studies, their continued use in on-the-ground conservation applications at fine spatial resolutions is not advisable in light of reliance on assumptions, lack of real spatial resolution, and lack of testing. In contrast, data-driven techniques that integrate primary data on biodiversity occurrence with remotely sensed data that summarize environmental dimensions (i.e., ecological niche modeling or species distribution modeling) offer data-driven solutions based on a minimum of assumptions that can be evaluated and validated quantitatively to offer a well-founded, widely accepted method for summarizing species' distributional patterns for conservation applications. © 2016 Society for Conservation Biology.

  18. A study on the development of automatic economic profit and loss calculation system for maritime boundary delimitation

    Science.gov (United States)

    Kwak, G.; Kim, K.; Park, Y.

    2014-02-01

    As the maritime boundary delimitation is important for the purpose of securing marine resources, in addition to the aspect of maritime security, interest in maritime boundary delimitation to help national benefits are increasing over the world. In Korea, the importance of maritime boundary delimitation with the neighbouring countries is also increasing in practice. The quantity of obtainable marine resources depending on maritime boundary acts as an important factor for maritime boundary delimitation. Accordingly, a study is required to calculate quantity of our obtainable marine resources depending on maritime boundary delimitation. This study intends to calculate obtainable marine resources depending on various maritime boundary scenarios insisted by several countries. It mainly aims at developing a GIS-based automation system to be utilized for decision making of the maritime boundary delimitation. For this target, it has designed a module using spatial analysis technique to automatically calculate profit and loss waters area of each country upon maritime boundary and another module to estimate economic profits and losses obtained by each country using the calculated waters area and pricing information of the marine resources. By linking both the designed modules, it has implemented an automatic economic profit and loss calculation system for the GIS-based maritime boundary delimitation. The system developed from this study automatically calculate quantity of the obtainable marine resources of a country for the maritime boundary to be added and created in the future. Thus, it is expected to support decision making for the maritime boundary negotiators.

  19. A study on the development of automatic economic profit and loss calculation system for maritime boundary delimitation

    International Nuclear Information System (INIS)

    Kwak, G; Kim, K; Park, Y

    2014-01-01

    As the maritime boundary delimitation is important for the purpose of securing marine resources, in addition to the aspect of maritime security, interest in maritime boundary delimitation to help national benefits are increasing over the world. In Korea, the importance of maritime boundary delimitation with the neighbouring countries is also increasing in practice. The quantity of obtainable marine resources depending on maritime boundary acts as an important factor for maritime boundary delimitation. Accordingly, a study is required to calculate quantity of our obtainable marine resources depending on maritime boundary delimitation. This study intends to calculate obtainable marine resources depending on various maritime boundary scenarios insisted by several countries. It mainly aims at developing a GIS-based automation system to be utilized for decision making of the maritime boundary delimitation. For this target, it has designed a module using spatial analysis technique to automatically calculate profit and loss waters area of each country upon maritime boundary and another module to estimate economic profits and losses obtained by each country using the calculated waters area and pricing information of the marine resources. By linking both the designed modules, it has implemented an automatic economic profit and loss calculation system for the GIS-based maritime boundary delimitation. The system developed from this study automatically calculate quantity of the obtainable marine resources of a country for the maritime boundary to be added and created in the future. Thus, it is expected to support decision making for the maritime boundary negotiators

  20. Papadakis methodology for agroclimatic delimitation, applied to Sinaloa State, Mexico

    Directory of Open Access Journals (Sweden)

    Israel Velasco

    2011-02-01

    Full Text Available Relief influences on climate, lead to a wide environmental conditions, even more than latitude. The Köppen Method, one of the most used, is of physical type, and leads to excellent approaches to real climate conditions, but it doesn't consider in a full dimension the water-soil-cultivated-plant-atmosphere interaction, being that these factors decide so much the natural vegetation as crops. The periods with freezing temperatures or with high frost risk, and the duration of dry months, all of them are decisive for agriculture. These risk factors are considered in the Papadakis Method, which allows evaluating the potentiality and limitations of the climatic areas, related to crops. In this work an application is made of this method on a wide region in Northwest Mexico, where agriculture is very important, and the obtained results converge to define that existent climatic groups are the following, according to Papadakis Method: 1.4: continental savanna 1.5: tropical semi-arid 1.9: tropical with fresh winter 2.3: medium-cold highland 4.2: continental subtropical 4.3: continental semitropical

  1. Automated classification of tropical shrub species: a hybrid of leaf shape and machine learning approach

    Directory of Open Access Journals (Sweden)

    Miraemiliana Murat

    2017-09-01

    Full Text Available Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities. However, it is a difficult task to identify plant species because it requires specialized knowledge. Developing an automated classification system for plant species is necessary and valuable since it can help specialists as well as the public in identifying plant species easily. Shape descriptors were applied on the myDAUN dataset that contains 45 tropical shrub species collected from the University of Malaya (UM, Malaysia. Based on literature review, this is the first study in the development of tropical shrub species image dataset and classification using a hybrid of leaf shape and machine learning approach. Four types of shape descriptors were used in this study namely morphological shape descriptors (MSD, Histogram of Oriented Gradients (HOG, Hu invariant moments (Hu and Zernike moments (ZM. Single descriptor, as well as the combination of hybrid descriptors were tested and compared. The tropical shrub species are classified using six different classifiers, which are artificial neural network (ANN, random forest (RF, support vector machine (SVM, k-nearest neighbour (k-NN, linear discriminant analysis (LDA and directed acyclic graph multiclass least squares twin support vector machine (DAG MLSTSVM. In addition, three types of feature selection methods were tested in the myDAUN dataset, Relief, Correlation-based feature selection (CFS and Pearson’s coefficient correlation (PCC. The well-known Flavia dataset and Swedish Leaf dataset were used as the validation dataset on the proposed methods. The results showed that the hybrid of all descriptors of ANN outperformed the other classifiers with an average classification accuracy of 98.23% for the myDAUN dataset, 95.25% for the Flavia

  2. Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes.

    Directory of Open Access Journals (Sweden)

    Jesse M Meik

    Full Text Available Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"; the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA, phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable traits (nDNA, mtDNA, phenotype, and discordance is explained by biological processes (e.g., ontogeny, hybridization. In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.

  3. Pauses in theatrical interpretation: delimitation of prosodic constituents

    Directory of Open Access Journals (Sweden)

    Lourenço Chacon

    2014-07-01

    Full Text Available We intend to observe the function of a linguistic resource – the pause – in theatrical interpretation. Connected to the field of speech therapy, we search for theoretical support in the Linguistics field, mainly in prosodic phonology – specifically, we highlight intonational phrase and phonological utterance, prosodic constituents –, proposing a dialogue between these fields, regarding the work with actors. In speech therapy literature, the work with actors focuses, centrally, in organic issues involved in the vocal process, such as “misuse” or “voice abuse”. To a smaller extent, we find, in this literature, researches that emphasize issues regarding interpretation and expressive resources, besides a few emphasizing the importance of linguistic resources in interpretation. Differently, in linguistics literature, the pause is approached, to a larger extent, from the phonetic perspective, related to several language levels. In this research, we analyzed audio recordings of four actors from a same theatrical group, acting the theatrical text Brutas flores, focused on these aims: (1 detect the place where pauses happen in the interpretation of a single text by four actors; (2 survey physical characteristics of length of these pauses; (3 check to what extent the length of a pause is related to the place where it happens, regarding the prosodic limits of intonational phrases (I and phonological utterance (U. We could observe that, although the interpretation is characterized by the subjectivity of the actor, the interpretation is constructed based in the possibilities offered by the prosodic organization of the text itself, being more or less flexible.We were also able to confirm, by considering the length of VVs units containing pauses, the prosodic hierarchy proposed by Nespor & Vogel, once the length of these units in U's limits was significantly higher than the length in I's limits. Thus, our results reinforce the premise that a

  4. Delimiting family in syntheses of research on childhood chronic conditions and family life.

    Science.gov (United States)

    Knafl, Kathleen; Leeman, Jennifer; Havill, Nancy; Crandell, Jamie; Sandelowski, Margarete

    2015-03-01

    Synthesis of family research presents unique challenges to investigators who must delimit what will be included as a family study in the proposed review. In this paper, the authors discuss the conceptual and pragmatic challenges of conducting systematic reviews of the literature on the intersection between family life and childhood chronic conditions. A proposed framework for delimiting the family domain of interest is presented. The framework addresses both topical salience and level of relevance and provides direction to future researchers, with the goal of supporting the overall quality of family research synthesis efforts. For users of synthesis studies, knowledge of how investigators conceptualize the boundaries of family research is important contextual information for understanding the limits and applicability of the results. © 2014 Family Process Institute.

  5. SUBSTANTIAL EXCEPTIONS AND (DELIMITATIONS OF THE POWERS OF THE JUDGES ON CIVIL PROCEDURAL LAW

    Directory of Open Access Journals (Sweden)

    Igor Raatz

    2017-08-01

    Full Text Available This essay aims to unveil the role of the substantial exceptions on delimiting the powers of the judges on civil procedural law, especially regarding the ex officio judicial activity. This way, under a phenomenological method and based on a vision of guarantee of rights on procedural law, the article offers a brief explanation of the question concerning the content of the object under litigation and its role of (delimiting the powers of the judges. The work hypothesis is the addition of the substantial exceptions among the content of the object under litigation, along with the claim itself and the cause of action. The results lie on the premise that, by the substantial exceptions, the defendant extends the object under litigation – which is formed dynamically on civil procedure. The conclusion points towards the idea that the substantial exceptions act in a way of limiting the ex officio judicial activity on civil procedural law

  6. Determination of the soil hazardous concentrations of bisphenol A using the species sensitivity approach.

    Science.gov (United States)

    Kwak, Jin Il; Moon, Jongmin; Kim, Dokyung; Cui, Rongxue; An, Youn-Joo

    2018-02-15

    This study describes the determination of the species sensitivity distribution (SSD)-based soil hazardous contamination of bisphenol A for environmental risk assessment. We conducted a battery of bioassays, including acute assays using eight species from six different taxonomic groups and chronic assays using five species from four different taxonomic groups. We determined that our dataset satisfied Australia & New Zealand's guidelines for applying the SSD methodology. Finally, the chronic soil HC 5 and HC 50 values for bisphenol A were estimated to be 13.7 and 74.7mg/kg soil, respectively, for soil ecosystem protection against chronic exposure using the data generated from this and previous studies. Because the soil standard values of bisphenol A for protection of the soil ecosystem are not currently available, the HC values of bisphenol A that we suggested based on the SSD approach would be applied as fundamental data to establish soil standards of bisphenol A for soil ecosystem protection. To our knowledge, this is the first study reporting the soil hazardous concentration of bisphenol A for environmental risk assessment. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Transferability of species distribution models: a functional habitat approach for two regionally threatened butterflies.

    Science.gov (United States)

    Vanreusel, Wouter; Maes, Dirk; Van Dyck, Hans

    2007-02-01

    Numerous models for predicting species distribution have been developed for conservation purposes. Most of them make use of environmental data (e.g., climate, topography, land use) at a coarse grid resolution (often kilometres). Such approaches are useful for conservation policy issues including reserve-network selection. The efficiency of predictive models for species distribution is usually tested on the area for which they were developed. Although highly interesting from the point of view of conservation efficiency, transferability of such models to independent areas is still under debate. We tested the transferability of habitat-based predictive distribution models for two regionally threatened butterflies, the green hairstreak (Callophrys rubi) and the grayling (Hipparchia semele), within and among three nature reserves in northeastern Belgium. We built predictive models based on spatially detailed maps of area-wide distribution and density of ecological resources. We used resources directly related to ecological functions (host plants, nectar sources, shelter, microclimate) rather than environmental surrogate variables. We obtained models that performed well with few resource variables. All models were transferable--although to different degrees--among the independent areas within the same broad geographical region. We argue that habitat models based on essential functional resources could transfer better in space than models that use indirect environmental variables. Because functional variables can easily be interpreted and even be directly affected by terrain managers, these models can be useful tools to guide species-adapted reserve management.

  8. Wireless-Delimited Secure Zones with Encrypted Attribute-Based Broadcast for Safe Firearms

    OpenAIRE

    Portnoi, Marcos; Shen, Chien-Chung

    2014-01-01

    This work presents an application of the highly expressive Attribute-Based Encryption to implement wireless-delimited Secure Zones for firearms. Within these zones, radio-transmitted local policies based on attributes of the consumer and the firearm are received by embedded hardware in the firearms, which then advises the consumer about safe operations. The Secure Zones utilize Attribute-Based Encryption to encode the policies and consumer or user attributes, and providing privacy and securit...

  9. The occurrence of Toxocara species in naturally infected broiler chickens revealed by molecular approaches.

    Science.gov (United States)

    Zibaei, M; Sadjjadi, S M; Maraghi, S

    2017-09-01

    Consuming raw and undercooked meat is known to enhance the risk of human toxocariasis because Toxocara species have a wide range of paratenic hosts, including chickens. The aim of this study was to identify species of Toxocara in naturally infected broiler chickens using molecular approaches. A polymerase chain reaction (PCR) method was used for the differentiation of Toxocara canis and Toxocara cati larvae recovered from tissues and organs, and identified by microscopic observations. Thirty-three 35- to 47-day-old broiler chickens were used for examination of Toxocara larvae. The duodenum, liver, lungs, heart, kidneys, skeletal muscles and brain of each chicken were examined using the pepsin method, and DNA from each tissue was extracted as the template for PCR assay. The findings revealed that 5 of 33 (15.2%) broiler chickens were infected with Toxocara larvae. Larvae were recovered from the liver (n = 19), duodenum (n = 8), skeletal muscles (n = 8) and brain (n = 2) of broiler chickens naturally infected with Toxocara spp. The results showed that the frequencies of the species in the chickens were T. canis larvae (n = 5, 83.3%) and T. cati larvae (n = 1, 16.7%). Our data from the present study demonstrated the importance of broiler chickens as a paratenic host for the parasite's life cycle in the environment. The implementation of DNA amplification as a routine diagnostic technique is a specific and alternative method for identification of Toxocara larvae, and allowed the observation of specific species under field conditions within the locations where broiler chickens are typically raised and exposed to Toxocara spp. eggs or larvae.

  10. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

    Science.gov (United States)

    DeBiasse, Melissa B; Hellberg, Michael E

    2015-02-01

    Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.

  11. Taxonomic value of stem anatomical characters in classification of some Adonis (Ranunculaceae species in Iran

    Directory of Open Access Journals (Sweden)

    Majid Ghorbani Nohooji

    2011-06-01

    (A. aestivalis, A. flammea and A. dentata were evaluated using numerical taxonomic methods. Obtained results demonstrated that simultaneous application of both qualitative and relative characters offers a better chance in species delimitation in future researches.

  12. Primary subacute epiphyseal osteomyelitis caused by Mycobacterium species in young children: a modern diagnostic approach.

    Science.gov (United States)

    El Houmami, N; Minodier, P; Bouvier, C; Seligmann, H; Jouve, J-L; Raoult, D; Fournier, P-E

    2017-05-01

    Primary epiphyseal subacute osteomyelitis (PESAO) caused by Mycobacterium species in young children is poorly recognized. We aimed to define the spectrum of this uncommon condition and to propose a novel diagnostic approach. We performed a systematic review of the literature on the PubMed website by selecting all reports of isolated infantile PESAO caused by Mycobacterium species since 1975. We identified 350 citations, of which 174 were assessed for eligibility based on title and abstract. The full text of 81 eligible citations was screened, and relevant data of 15 children under 4 years of age with mycobacterial PESAO were extracted. These data were pooled with those from our Institution. Data from 16 children were reviewed. The median age was 16 ± 7 months and the male:female ratio 1.7. The knee was the most common infection site (94%). The diagnosis of mycobacterial disease was delayed in all cases (range, 2 weeks to 6 months), and initially presumed by histology in 15 children (94%). Microbiologically proven diagnosis was confirmed by bone cultures in 8 of the 15 children (53%), and by specific PCR in 2 of the 3 culture-negative bone specimens (67%). Three children experienced long-term orthopedic complications despite surgical drainage and prolonged antimycobacterial regimens. All recently reported cases came from high-burden tuberculosis areas. Mycobacterium species contribute to the burden of infantile PESAO in endemic tuberculosis areas and may cause growth disturbances. We argue in favor of the early recognition of mycobacterial disease by specific molecular assays in children with infantile PESAO living in high-burden areas.

  13. A volatolomic approach for studying plant variability: the case of selected Helichrysum species (Asteraceae).

    Science.gov (United States)

    Giuliani, Claudia; Lazzaro, Lorenzo; Calamassi, Roberto; Calamai, Luca; Romoli, Riccardo; Fico, Gelsomina; Foggi, Bruno; Mariotti Lippi, Marta

    2016-10-01

    The species of Helichrysum sect. Stoechadina (Asteraceae) are well-known for their secondary metabolite content and the characteristic aromatic bouquets. In the wild, populations exhibit a wide phenotypic plasticity which makes critical the circumscription of species and infraspecific ranks. Previous investigations on Helichrysum italicum complex focused on a possible phytochemical typification based on hydrodistilled essential oils. Aims of this paper are three-fold: (i) characterizing the volatile profiles of different populations, testing (ii) how these profiles vary across populations and (iii) how the phytochemical diversity may contribute in solving taxonomic problems. Nine selected Helichrysum populations, included within the H. italicum complex, Helichrysum litoreum and Helichrysum stoechas, were investigated. H. stoechas was chosen as outgroup for validating the method. After collection in the wild, plants were cultivated in standard growing conditions for over one year. Annual leafy shoots were screened in the post-blooming period for the emissions of volatile organic compounds (VOCs) by means of headspace solid phase microextraction coupled with gas-chromatography and mass spectrometry (HS-SPME-GC/MS). The VOC composition analysis revealed the production of overall 386 different compounds, with terpenes being the most represented compound class. Statistical data processing allowed the identification of the indicator compounds that differentiate the single populations, revealing the influence of the geographical provenance area in determining the volatile profiles. These results suggested the potential use of VOCs as valuable diacritical characters in discriminating the Helichrysum populations. In addition, the cross-validation analysis hinted the potentiality of this volatolomic study in the discrimination of the Helichrysum species and subspecies, highlighting a general congruence with the current taxonomic treatment of the genus. The consistency

  14. Employing Measures of Heterogeneity and an Object-Based Approach to Extrapolate Tree Species Distribution Data

    Directory of Open Access Journals (Sweden)

    Trevor G. Jones

    2014-07-01

    Full Text Available Information derived from high spatial resolution remotely sensed data is critical for the effective management of forested ecosystems. However, high spatial resolution data-sets are typically costly to acquire and process and usually provide limited geographic coverage. In contrast, moderate spatial resolution remotely sensed data, while not able to provide the spectral or spatial detail required for certain types of products and applications, offer inexpensive, comprehensive landscape-level coverage. This study assessed using an object-based approach to extrapolate detailed tree species heterogeneity beyond the extent of hyperspectral/LiDAR flightlines to the broader area covered by a Landsat scene. Using image segments, regression trees established ecologically decipherable relationships between tree species heterogeneity and the spectral properties of Landsat segments. The spectral properties of Landsat bands 4 (i.e., NIR: 0.76–0.90 µm, 5 (i.e., SWIR: 1.55–1.75 µm and 7 (SWIR: 2.08–2.35 µm were consistently selected as predictor variables, explaining approximately 50% of variance in richness and diversity. Results have important ramifications for ongoing management initiatives in the study area and are applicable to wide range of applications.

  15. Delimiting the Prospect of Openness: An Examination of Initial Student Approaches to E-Learning

    Directory of Open Access Journals (Sweden)

    Christopher Naughton

    2011-02-01

    Full Text Available When converting from a paper-based distance mode to an online mode of teaching, certain expectations arise that students may engage not only in the development of extended research activity but that the quality of discussion and thinking will change. With access to open-ended discussion within the online forum the opportunity is afforded to students to share ideas and in turn develop their shared knowledge, a facility denied to them when in the paper distance mode. However, in a recent study conducted in New Zealand, it was shown that despite having access to online forums students moving to an online platform refrained from participation in this social exchange. A possible explanation for this indifference was thought to be the students realising that the online exchange made no impact on their assessment. Hence, the collaborative rhetoric of Web 2.0 made little impact when the summative evaluation remained unchanged from previous paper-based assessment. This paper reports on the introduction of online learning at a private tertiary college in New Zealand and describes the response of students who found difficulty in reconciling a community of learners and openness within what was perceived as an evaluation that remained individualistic and competitive in nature.

  16. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches

    OpenAIRE

    Rodrigues, Paula; Venâncio, Armando; Lima, Nelson

    2011-01-01

    Section Flavi is one of the most significant Sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by MALDI-TOF ICMS, and to evaluate the discriminatory power of the various approaches in species identification. Methods and ...

  17. A Case of Equitable Maritime Delimitation: Nicaragua and Colombia in the Western Caribbean Sea

    Directory of Open Access Journals (Sweden)

    Paul S. Reichler

    2013-06-01

    Full Text Available The unanimous judgment the International Court of Justice in November 2012 which resolved the boundary dispute between Nicaragua and Colombia in the western Caribbean Sea has generated considerable attention and commentary. Almost all of it has been highly favorable, with the sole exception of the reaction by Colombia, which purported to “reject” the Court’s Judgment and commenced procedures to withdraw its acceptance of ICJ jurisdiction in regard to future cases. This article demonstrates that the Court’s Judgment reflects the application of well-established legal principles of maritime boundary delimitation, and results in an equitable solution that is balanced and fair to both Parties. By analyzing the unique geographical circumstances of this case and discussing the methodologies and reasoning the Court employed in these circumstances to delimit the disputed maritime area, the article demonstrates that the delimitation line established by the Court was a creative solution to a difficult and complex geographic situation, which at the same time is firmly rooted in and consistent with well-established jurisprudence. As a result, the maritime boundary that the Court fixed between Nicaragua and Colombia allows the coasts of both States to generate maritime entitlements in a reasonable and mutually balanced way. Not only is the Court’s Judgment equitable to both Parties; it is also legally binding on them. There is no basis for either State to “reject” it, and no justification for refusing to entrust future cases to the Court, which remains an indispensable forum for the peaceful resolution of disputes between States according to the rule of law.

  18. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

    Science.gov (United States)

    Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

    2010-12-01

    Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect

  19. Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach.

    Science.gov (United States)

    Shaar-Moshe, Lidor; Hübner, Sariel; Peleg, Zvi

    2015-05-03

    Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary conservation. Empirically defined filtering criteria were used to facilitate a robust integration of 17 deposited microarray experiments (148 arrays) of Arabidopsis, rice, wheat and barley. By prioritizing consistency over intensity, our approach was able to identify 225 differentially expressed genes shared across studies and taxa. Gene ontology enrichment and pathway analyses classified the shared genes into functional categories involved predominantly in metabolic processes (e.g. amino acid and carbohydrate metabolism), regulatory function (e.g. protein degradation and transcription) and response to stimulus. We further investigated drought related cis-acting elements in the shared gene promoters, and the evolutionary conservation of shared genes. The universal nature of the identified drought-adaptive genes was further validated in a fifth species, Brachypodium distachyon that was not included in the meta-analysis. qPCR analysis of 27, randomly selected, shared orthologs showed similar expression pattern as was found by the CSA:Drought.In accordance, morpho-physiological characterization of progressive drought stress, in B. distachyon, highlighted the key role of osmotic adjustment as evolutionary conserved drought-adaptive mechanism. Our CSA:Drought strategy highlights major drought-adaptive genes and metabolic pathways that were only partially, if at all, reported in the original studies included in the meta-analysis. These genes include a group of unclassified genes that could be involved

  20. SSR markers: a tool for species identification in Psidium (Myrtaceae).

    Science.gov (United States)

    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

  1. An Ecosystem-Service Approach to Evaluate the Role of Non-Native Species in Urbanized Wetlands

    Directory of Open Access Journals (Sweden)

    Rita S. W. Yam

    2015-04-01

    Full Text Available Natural wetlands have been increasingly transformed into urbanized ecosystems commonly colonized by stress-tolerant non-native species. Although non-native species present numerous threats to natural ecosystems, some could provide important benefits to urbanized ecosystems. This study investigated the extent of colonization by non-native fish and bird species of three urbanized wetlands in subtropical Taiwan. Using literature data the role of each non-native species in the urbanized wetland was evaluated by their effect (benefits/damages on ecosystem services (ES based on their ecological traits. Our sites were seriously colonized by non-native fishes (39%–100%, but <3% by non-native birds. Although most non-native species could damage ES regulation (disease control and wastewater purification, some could be beneficial to the urbanized wetland ES. Our results indicated the importance of non-native fishes in supporting ES by serving as food source to fish-eating waterbirds (native, and migratory species due to their high abundance, particularly for Oreochromis spp. However, all non-native birds are regarded as “harmful” species causing important ecosystem disservices, and thus eradication of these bird-invaders from urban wetlands would be needed. This simple framework for role evaluation of non-native species represents a holistic and transferable approach to facilitate decision making on management priority of non-native species in urbanized wetlands.

  2. Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches

    OpenAIRE

    Andre, Thiago; Specht, Chelsea; Salzman, Shayla; Palma-Silva, Clarisse [UNESP; Wendt, Tania

    2015-01-01

    While most species within the genus Chamaecostus (Costaceae) are well defined, the broad geographic range and long list of synonyms associated with Chamaecostus subsessilis led us to believe there may be some cryptic species within the complex. We thus investigate the phylogenetic relationships of species in the Chamaecostus lineage and specifically test the monophyly and diversity of the Chamaecostus subsessilis species complex from a population perspective by analyzing molecular sequence da...

  3. Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices.

    Science.gov (United States)

    Bellier, Edwige; Grøtan, Vidar; Engen, Steinar; Schartau, Ann Kristin; Diserud, Ola H; Finstad, Anders G

    2012-10-01

    Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.

  4. Nest survival modelling using a multi-species approach in forests managed for timber and biofuel feedstock

    Science.gov (United States)

    Loman, Zachary G.; Monroe, Adrian; Riffell, Samuel K.; Miller, Darren A.; Vilella, Francisco; Wheat, Bradley R.; Rush, Scott A.; Martin, James A.

    2018-01-01

    Switchgrass (Panicum virgatum) intercropping is a novel forest management practice for biomass production intended to generate cellulosic feedstocks within intensively managed loblolly pine‐dominated landscapes. These pine plantations are important for early‐successional bird species, as short rotation times continually maintain early‐successional habitat. We tested the efficacy of using community models compared to individual surrogate species models in understanding influences on nest survival. We analysed nest data to test for differences in habitat use for 14 bird species in plots managed for switchgrass intercropping and controls within loblolly pine (Pinus taeda) plantations in Mississippi, USA.We adapted hierarchical models using hyper‐parameters to incorporate information from both common and rare species to understand community‐level nest survival. This approach incorporates rare species that are often discarded due to low sample sizes, but can inform community‐level demographic parameter estimates. We illustrate use of this approach in generating both species‐level and community‐wide estimates of daily survival rates for songbird nests. We were able to include rare species with low sample size (minimum n = 5) to inform a hyper‐prior, allowing us to estimate effects of covariates on daily survival at the community level, then compare this with a single‐species approach using surrogate species. Using single‐species models, we were unable to generate estimates below a sample size of 21 nests per species.Community model species‐level survival and parameter estimates were similar to those generated by five single‐species models, with improved precision in community model parameters.Covariates of nest placement indicated that switchgrass at the nest site (<4 m) reduced daily nest survival, although intercropping at the forest stand level increased daily nest survival.Synthesis and applications. Community models represent a viable

  5. Stuttering-Psycholinguistic Approach

    Science.gov (United States)

    Hategan, Carolina Bodea; Anca, Maria; Prihoi, Lacramioara

    2012-01-01

    This research promotes psycholinguistic paradigm, it focusing in delimitating several specific particularities in stuttering pathology. Structural approach, on language sides proves both the recurrent aspects found within specialized national and international literature and the psycholinguistic approaches dependence on the features of the…

  6. Two thrush species as dispersers of Miconia prasina (Sw. DC. (Melastomataceae: an experimental approach

    Directory of Open Access Journals (Sweden)

    MAS. Alves

    Full Text Available We carried out a seed germination experiment using two thrush species in captivity. We compared the number of germinated seeds and germination time of control seeds (manually removed from fruits and ingested seeds of Miconia prasina by two bird species, Turdus albicollis and T. amaurochalinus, and also compared retention times of seeds by both thrush species. Control seeds germinated more frequently than those ingested for one species, T. albicollis. The germination time of ingested seeds by T. amaurochalinus was similar to the control seeds but seeds ingested by T. albicollis took longer to germinate than the controls. Both thrush species had a similar seed defecation pattern. The cumulative number of defecated seeds increased by 2 hours after fruit ingestion. At the end of the first 30 minutes both species had already defecated approximately 50% of the seeds ingested Our results suggest that both species could act as disperser agents of M. prasina.

  7. Crown-level tree species classification from AISA hyperspectral imagery using an innovative pixel-weighting approach

    Science.gov (United States)

    Liu, Haijian; Wu, Changshan

    2018-06-01

    Crown-level tree species classification is a challenging task due to the spectral similarity among different tree species. Shadow, underlying objects, and other materials within a crown may decrease the purity of extracted crown spectra and further reduce classification accuracy. To address this problem, an innovative pixel-weighting approach was developed for tree species classification at the crown level. The method utilized high density discrete LiDAR data for individual tree delineation and Airborne Imaging Spectrometer for Applications (AISA) hyperspectral imagery for pure crown-scale spectra extraction. Specifically, three steps were included: 1) individual tree identification using LiDAR data, 2) pixel-weighted representative crown spectra calculation using hyperspectral imagery, with which pixel-based illuminated-leaf fractions estimated using a linear spectral mixture analysis (LSMA) were employed as weighted factors, and 3) representative spectra based tree species classification was performed through applying a support vector machine (SVM) approach. Analysis of results suggests that the developed pixel-weighting approach (OA = 82.12%, Kc = 0.74) performed better than treetop-based (OA = 70.86%, Kc = 0.58) and pixel-majority methods (OA = 72.26, Kc = 0.62) in terms of classification accuracy. McNemar tests indicated the differences in accuracy between pixel-weighting and treetop-based approaches as well as that between pixel-weighting and pixel-majority approaches were statistically significant.

  8. An Ecosystem-Service Approach to Evaluate the Role of Non-Native Species in Urbanized Wetlands

    Science.gov (United States)

    Yam, Rita S. W.; Huang, Ko-Pu; Hsieh, Hwey-Lian; Lin, Hsing-Juh; Huang, Shou-Chung

    2015-01-01

    Natural wetlands have been increasingly transformed into urbanized ecosystems commonly colonized by stress-tolerant non-native species. Although non-native species present numerous threats to natural ecosystems, some could provide important benefits to urbanized ecosystems. This study investigated the extent of colonization by non-native fish and bird species of three urbanized wetlands in subtropical Taiwan. Using literature data the role of each non-native species in the urbanized wetland was evaluated by their effect (benefits/damages) on ecosystem services (ES) based on their ecological traits. Our sites were seriously colonized by non-native fishes (39%–100%), but wetland ES. Our results indicated the importance of non-native fishes in supporting ES by serving as food source to fish-eating waterbirds (native, and migratory species) due to their high abundance, particularly for Oreochromis spp. However, all non-native birds are regarded as “harmful” species causing important ecosystem disservices, and thus eradication of these bird-invaders from urban wetlands would be needed. This simple framework for role evaluation of non-native species represents a holistic and transferable approach to facilitate decision making on management priority of non-native species in urbanized wetlands. PMID:25860870

  9. The hidden Heuchera: How science Twitter uncovered a globally imperiled species in Pennsylvania, USA

    Directory of Open Access Journals (Sweden)

    Scott Schuette

    2018-04-01

    Full Text Available The genus Heuchera is recognized as one of the most diverse endemic radiations of Saxifragaceae in North America, yet species delimitation and geographic distribution within the group remain controversial. Many species remain difficult to identify, including Heuchera alba, a narrow Appalachian endemic and globally imperiled (G2 taxon recorded only from West Virginia and Virginia that occurs in sympatry with H. pubescens and H. americana. A recent survey of the cliffside flora of the Shikellamy Bluffs, PA recorded dozens of Heuchera individuals that, through the use of social media, were positively identified as H. alba. Aided by examination of historical herbarium records, subsequent searches of similar habitats in Pennsylvania led to the discovery of seven more populations and established a significant range expansion for this rare species. The uncovering of H. alba in Pennsylvania is an exciting conservation outcome and an example of what can happen when botanists embrace a combination of modern and classical approaches to discovery and collaboration.

  10. An overview to the investigative approach to species testing in wildlife forensic science

    Science.gov (United States)

    2011-01-01

    The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results. PMID:21232099

  11. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures.

    Directory of Open Access Journals (Sweden)

    Francesca Bertolini

    Full Text Available The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43% in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97 and lower for avian species (0.70. PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.

  12. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L. Moench and related model species.

    Directory of Open Access Journals (Sweden)

    Adugna Abdi Woldesemayat

    Full Text Available Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO, Trait Ontology (TO, Plant Ontology (PO, Growth Ontology (GRO and Environment Ontology (EO were used to semantically integrate drought related information.Target genes linked to Quantitative Trait Loci (QTLs controlling yield and stress tolerance in sorghum (Sorghum bicolor (L. Moench and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%, salt (32%, cold (20%, heat (8% and oxidative stress (25% were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs

  13. Development of anthers and pollen in Brazilian heterostylic species of Erythroxylum (Erythroxylaceae): an ecological approach

    International Nuclear Information System (INIS)

    Silva, L.D.; Fernandes, C. L.

    2016-01-01

    This study describes the development of anthers and pollen in heterostylic flowers of two species of Erythroxylum. The features of anthers and their developmental pattern, which is of the dicotyledonous type, do not vary according to morphs or species. The pollen grains of both morphs show differences in their morphology, development, and content stored as a reserve source. In both species, thrum (short-styled) flowers presented bicellular pollen grains, while pin (long-styled) ones yielded bi- and tricellular pollen grains. The presence of inviable pollen grains in the two flower morphs of both species and the malformation of one of the four microsporanges in the thrum flowers of E. campestre are noteworthy. We verified that features found both in the anther wall and in the pollen grains could be related to the reproductive success and adaptation of the species to the Brazilian savanna biome. (author)

  14. Delimitation of the continental shelf and exclusive economic Zone the Sea Border between Romania and Ukraine

    Directory of Open Access Journals (Sweden)

    Mihai Mereuţă

    2011-07-01

    Full Text Available Decision I.C.J. from The Hague, since 3rd February 2009, in the case of “Romania vs. Ukraine - the maritime delimitation in the Black Sea”, has an important role in bilateral relations and regional plans of the riparian states and thus also eliminating a potential factor of instability at the sea border between the two countries and in the Black Sea. Drawing a line of demarcation equitable maritime economic zone and continental shelf between the two countries was an example of dispute settlement in the wider Black Sea area. Snake Island was not considered relevant in substantiating the court decision, because the I.C.J. has not declared it a rock, giving it a length of 12 nautical miles territorial sea and has not ruled on the nature of this formation, in accordance with the provisions of art. 121 of the Montego Bay Convention of 1982.

  15. Hyperspectral Data for Mangrove Species Mapping: A Comparison of Pixel-Based and Object-Based Approach

    Directory of Open Access Journals (Sweden)

    Muhammad Kamal

    2011-10-01

    Full Text Available Visual image interpretation and digital image classification have been used to map and monitor mangrove extent and composition for decades. The presence of a high-spatial resolution hyperspectral sensor can potentially improve our ability to differentiate mangrove species. However, little research has explored the use of pixel-based and object-based approaches on high-spatial hyperspectral datasets for this purpose. This study assessed the ability of CASI-2 data for mangrove species mapping using pixel-based and object-based approaches at the mouth of the Brisbane River area, southeast Queensland, Australia. Three mapping techniques used in this study: spectral angle mapper (SAM and linear spectral unmixing (LSU for the pixel-based approaches, and multi-scale segmentation for the object-based image analysis (OBIA. The endmembers for the pixel-based approach were collected based on existing vegetation community map. Nine targeted classes were mapped in the study area from each approach, including three mangrove species: Avicennia marina, Rhizophora stylosa, and Ceriops australis. The mapping results showed that SAM produced accurate class polygons with only few unclassified pixels (overall accuracy 69%, Kappa 0.57, the LSU resulted in a patchy polygon pattern with many unclassified pixels (overall accuracy 56%, Kappa 0.41, and the object-based mapping produced the most accurate results (overall accuracy 76%, Kappa 0.67. Our results demonstrated that the object-based approach, which combined a rule-based and nearest-neighbor classification method, was the best classifier to map mangrove species and its adjacent environments.

  16. Conservation of food tree species in Niger: towards a participatory approach in rural communities

    International Nuclear Information System (INIS)

    Agúndez Leal, D.; Douma, S.; Madrigal, J.; Gómez-Ramos, A.; Vicenti, B.; Alía, R.; Mahamane, A.

    2016-01-01

    Aim of the study: Indigenous woody species play an important role as a complement on the diet of rural populations in Niger, especially in periods of food scarcity. However, these species are nowadays overexploited and management programmes are necessary to conserve them. In order to design a conservation programme for edible woody species, this paper presents a sociological analysis about the use of edible woody species and their products during shortage periods in Niger. Area of study: Four villages in two distinct agro-ecological regions were selected to conduct structured enquiries based on focus group discussions and surveys with key informants. Material and Methods: Perceptions of the conservation status of these species were identified; as well the factors affecting food values, perceptions, management and collection practices. Main results: Results show that B. senegalensis was a staple food in the driest areas, and M. crassifolia was used for fodder and human consumption in the most critical situations. The local communities related the drivers of species conservation status specific to the agro-ecological regions, and gender and ethnic differences were also identified. Research highlights: Understanding these factors constitutes a first step towards adaptive management strategies for the conservation of woody food species in rural communities of Niger. (Author)

  17. A Source Area Approach Demonstrates Moderate Predictive Ability but Pronounced Variability of Invasive Species Traits.

    Directory of Open Access Journals (Sweden)

    Günther Klonner

    Full Text Available The search for traits that make alien species invasive has mostly concentrated on comparing successful invaders and different comparison groups with respect to average trait values. By contrast, little attention has been paid to trait variability among invaders. Here, we combine an analysis of trait differences between invasive and non-invasive species with a comparison of multidimensional trait variability within these two species groups. We collected data on biological and distributional traits for 1402 species of the native, non-woody vascular plant flora of Austria. We then compared the subsets of species recorded and not recorded as invasive aliens anywhere in the world, respectively, first, with respect to the sampled traits using univariate and multiple regression models; and, second, with respect to their multidimensional trait diversity by calculating functional richness and dispersion metrics. Attributes related to competitiveness (strategy type, nitrogen indicator value, habitat use (agricultural and ruderal habitats, occurrence under the montane belt, and propagule pressure (frequency were most closely associated with invasiveness. However, even the best multiple model, including interactions, only explained a moderate fraction of the differences in invasive success. In addition, multidimensional variability in trait space was even larger among invasive than among non-invasive species. This pronounced variability suggests that invasive success has a considerable idiosyncratic component and is probably highly context specific. We conclude that basing risk assessment protocols on species trait profiles will probably face hardly reducible uncertainties.

  18. Conservation of food tree species in Niger: towards a participatory approach in rural communities

    Energy Technology Data Exchange (ETDEWEB)

    Agúndez Leal, D.; Douma, S.; Madrigal, J.; Gómez-Ramos, A.; Vicenti, B.; Alía, R.; Mahamane, A.

    2016-07-01

    Aim of the study: Indigenous woody species play an important role as a complement on the diet of rural populations in Niger, especially in periods of food scarcity. However, these species are nowadays overexploited and management programmes are necessary to conserve them. In order to design a conservation programme for edible woody species, this paper presents a sociological analysis about the use of edible woody species and their products during shortage periods in Niger. Area of study: Four villages in two distinct agro-ecological regions were selected to conduct structured enquiries based on focus group discussions and surveys with key informants. Material and Methods: Perceptions of the conservation status of these species were identified; as well the factors affecting food values, perceptions, management and collection practices. Main results: Results show that B. senegalensis was a staple food in the driest areas, and M. crassifolia was used for fodder and human consumption in the most critical situations. The local communities related the drivers of species conservation status specific to the agro-ecological regions, and gender and ethnic differences were also identified. Research highlights: Understanding these factors constitutes a first step towards adaptive management strategies for the conservation of woody food species in rural communities of Niger. (Author)

  19. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    Science.gov (United States)

    Buckley, Ralf C; Castley, J Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

  20. A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

    Science.gov (United States)

    Buckley, Ralf C.; Castley, J. Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C.; Steven, Rochelle

    2012-01-01

    Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species. PMID:22984467

  1. A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

    Directory of Open Access Journals (Sweden)

    Ralf C Buckley

    Full Text Available Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

  2. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

  3. Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach

    DEFF Research Database (Denmark)

    Lombard, Fabien; Labeyrie, L.; Michel, E.

    2011-01-01

    We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa...... in the marine carbon cycle....... ocean (PISCES) instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%). Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data...

  4. Reconstruction of molecular phylogeny of closely related Amorphophallus species of India using plastid DNA marker and fingerprinting approaches.

    Science.gov (United States)

    Gholave, Avinash R; Pawar, Kiran D; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

    2017-01-01

    Plastid DNA markers sequencing and DNA fingerprinting approaches were used and compared for resolving molecular phylogeny of closely related, previously unexplored Amorphophallus species of India. The utility of individual plastid markers namely rbcL , matK , trnH - psbA , trnLC - trnLD , their combined dataset and two fingerprinting techniques viz. RAPD and ISSR were tested for their efficacy to resolves Amorphophallus species into three sections specific clades namely Rhaphiophallus , Conophallus and Amorphophallus . In the present study, sequences of these four plastid DNA regions as well as RAPD and ISSR profiles of 16 Amorphophallus species together with six varieties of two species were generated and analyzed. Maximum likelihood and Bayesian Inference based construction of phylogenetic trees indicated that among the four plastid DNA regions tested individually and their combined dataset, rbcL was found best suited for resolving closely related Amorphophallus species into section specific clades. When analyzed individually, rbcL exhibited better discrimination ability than matK , trnH - psbA , trnLC - trnLD and combination of all four tested plastid markers. Among two fingerprinting techniques used, the resolution of Amorphophallus species using RAPD was better than ISSR and combination of RAPD +ISSR and in congruence with resolution based on rbcL .

  5. Approaches for quantifying antimicrobial consumption per animal species based on national sales data: a Swiss example, 2006 to 2013.

    Science.gov (United States)

    Carmo, Luís P; Schüpbach-Regula, Gertraud; Müntener, Cedric; Chevance, Anne; Moulin, Gérard; Magouras, Ioannis

    2017-02-09

    Antimicrobial use in animals is known to contribute to the global burden of antimicrobial resistance. Therefore, it is critical to monitor antimicrobial sales for livestock and pets. Despite the availability of veterinary antimicrobial sales data in most European countries, surveillance currently lacks consumption monitoring at the animal species level. In this study, alternative methods were investigated for stratifying antimicrobial sales per species using Swiss data (2006-2013). Three approaches were considered: (i) Equal Distribution (ED) allocated antimicrobial sales evenly across all species each product was licensed for; (ii) Biomass Distribution (BMD) stratified antimicrobial consumption, weighting the representativeness of each species' total biomass; and (iii) Longitudinal Study Extrapolation (LSE) assigned antimicrobial sales per species based on a field study describing prescription patterns in Switzerland. LSE is expected to provide the best estimates because it relies on field data. Given the Swiss example, BMD appears to be a reliable method when prescription data are not available, whereas ED seems to underestimate consumption in species with larger populations and higher treatment intensity. These methods represent a valuable tool for improving the monitoring systems of veterinary antimicrobial consumption across Europe. This article is copyright of The Authors, 2017.

  6. Hierarchical faunal filters: An approach to assessing effects of habitat and nonnative species on native fishes

    Science.gov (United States)

    Quist, M.C.; Rahel, F.J.; Hubert, W.A.

    2005-01-01

    Understanding factors related to the occurrence of species across multiple spatial and temporal scales is critical to the conservation and management of native fishes, especially for those species at the edge of their natural distribution. We used the concept of hierarchical faunal filters to provide a framework for investigating the influence of habitat characteristics and normative piscivores on the occurrence of 10 native fishes in streams of the North Platte River watershed in Wyoming. Three faunal filters were developed for each species: (i) large-scale biogeographic, (ii) local abiotic, and (iii) biotic. The large-scale biogeographic filter, composed of elevation and stream-size thresholds, was used to determine the boundaries within which each species might be expected to occur. Then, a local abiotic filter (i.e., habitat associations), developed using binary logistic-regression analysis, estimated the probability of occurrence of each species from features such as maximum depth, substrate composition, submergent aquatic vegetation, woody debris, and channel morphology (e.g., amount of pool habitat). Lastly, a biotic faunal filter was developed using binary logistic regression to estimate the probability of occurrence of each species relative to the abundance of nonnative piscivores in a reach. Conceptualising fish assemblages within a framework of hierarchical faunal filters is simple and logical, helps direct conservation and management activities, and provides important information on the ecology of fishes in the western Great Plains of North America. ?? Blackwell Munksgaard, 2004.

  7. Taking a comparative approach: analysing personality as a multivariate behavioural response across species.

    Directory of Open Access Journals (Sweden)

    Alecia J Carter

    Full Text Available Animal personality, repeatable behaviour through time and across contexts, is ecologically and evolutionarily important as it can account for the exhibition of sub-optimal behaviours. Interspecific comparisons have been suggested as important for understanding the evolution of animal personality; however, these are seldom accomplished due, in part, to the lack of statistical tools for quantifying differences and similarities in behaviour between groups of individuals. We used nine species of closely-related coral reef fishes to investigate the usefulness of ecological community analyses for the analysis of between-species behavioural differences and behavioural heterogeneity. We first documented behavioural carryover across species by observing the fishes' behaviour and measuring their response to a threatening stimulus to quantify boldness. Bold fish spent more time away from the reef and fed more than shy fish. We then used ecological community analysis tools (canonical variate analysis, multi-response permutation procedure, and permutational analysis of multivariate dispersion and identified four 'clusters' of behaviourally similar fishes, and found that the species differ in the behavioural variation expressed; some species are more behaviourally heterogeneous than others. We found that ecological community analysis tools are easily and fruitfully applied to comparative studies of personality and encourage their use by future studies.

  8. Assessment of harmful algal species using different approaches: the case study of the Sardinian coasts

    Directory of Open Access Journals (Sweden)

    C.T. Satta

    2014-04-01

    Full Text Available The presence and distribution of harmful algal species were investigated along the coasts of Sardinia in the summer of 2012. Fourteen potentially noxious taxa were identified at 74 beaches. The majority of the recovered taxa were potentially toxic and/or high biomass producers. Alexandrium taylorii, Gymnodinium instriatum, and Ostreopsis cf. ovata were the most frequent and abundant taxa, although Barrufeta bravensis reached the highest density (4.4 × 106 cells L−1. Barrufeta bravensis, A. taylorii, and G. instriatum were responsible for intense water discoloration at two of the beaches sampled. Polymerase chain reaction (PCR analyses supported the identification of several taxa and decisively identified B. bravensis. PCR assays increased the information available on the species distributions. The locations studied were heterogeneous in their prevailing environmental conditions and their morphodynamic profiles. Statistical analyses indicated that the distributions of harmful algal species correlated with gravel and medium-fine sand substrata. These data provide substantial knowledge on the distributions of harmful algal species on beaches, which have been poorly studied on a global scale. The apparent relationship between noxious species and grain size suggests that vegetative cells may be recruited from cyst beds in beach sediments.

  9. Natural Constraints to Species Diversification.

    Directory of Open Access Journals (Sweden)

    Eric Lewitus

    2016-08-01

    Full Text Available Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the

  10. Natural Constraints to Species Diversification.

    Science.gov (United States)

    Lewitus, Eric; Morlon, Hélène

    2016-08-01

    Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of

  11. Natural Constraints to Species Diversification

    Science.gov (United States)

    Lewitus, Eric; Morlon, Hélène

    2016-01-01

    Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of

  12. An integrated approach shows different use of water resources from Mediterranean maquis species in a coastal dune ecosystem

    Science.gov (United States)

    Mereu, S.; Salvatori, E.; Fusaro, L.; Gerosa, G.; Muys, B.; Manes, F.

    2009-11-01

    An integrated approach has been used to analyse the dependence of three Mediterranean species, A. unedo L., Q. ilex L., and P. latifolia L. co-occurring in a coastal dune ecosystem on two different water resources: groundwater and rainfed upper soil layers. The approach included leaf level gas exchanges, sap flow measurements and structural adaptations between 15 May and 31 July 2007. During this period it was possible to capture different species-specific response patterns to an environment characterized by a sandy soil, with a low water retention capacity, and the presence of a water table. The latter did not completely prevent the development of a drought response and, combined with previous studies in the same area, response differences between species have been partially attributed to different root distributions. Sap flow of A. unedo decreased rapidly with the decline of soil water content, while that of Q. ilex decreased only moderately. Midday leaf water potential of P. latifolia and A. unedo ranged between -2.2 and -2.7 MPa throughout the measuring period, while in Q. ilex it decreased down to -3.4 MPa at the end of the season. A. unedo was the only species that responded to drought with a decrease of its leaf area to sapwood area ratio from 23.9±1.2 (May) to 15.2±1.5 (July). While A. unedo also underwent an almost stepwise loss on hydraulic conductivity, such a loss did not occur for Q. ilex, whereas P. latifolia was able to slightly increase its hydraulic conducitivity. These differences show how different plant compartments coordinate differently between species in their responses to drought. The different responses appear to be mediated by different root distributions of the species and their relative resistances to drought are likely to depend on the duration of the periods in which water remains extractable in the upper soil layers.

  13. Levels of specificity of Xylaria species associated with fungus-growing termites: a phylogenetic approach

    DEFF Research Database (Denmark)

    Visser, Andre; Ros, V I D; De Beer, Z. W.

    2009-01-01

    of the ascomycete genus Xylaria appear and rapidly cover the fungus garden. This raises the question whether certain Xylaria species are specialised in occupying termite nests or whether they are just occasional visitors. We tested Xylaria specificity at four levels: (1) fungus-growing termites, (2) termite genera...... of the ITS region revealed 16 operational taxonomic units of Xylaria, indicating high levels of Xylaria species richness. Not much of this variation was explained by termite genus, species, or colony; thus, at level 2-4 the specificity is low. Analysis of the large subunit rDNA region, showed that all...... termite-associated Xylaria belong to a single clade, together with only three of the 26 non-termite-associated strains. Termite-associated Xylaria thus show specificity for fungus-growing termites (level 1). We did not find evidence for geographic or temporal structuring in these Xylaria phylogenies...

  14. Collision density approach of radiation damage in a multi-species medium

    International Nuclear Information System (INIS)

    Lux, I.; Pazsit, I.

    1981-05-01

    Space-energy dependent foward type equations for the collision densities of energetic atoms in multi-species semi-infinite homogeneous medium are formulated. The introduction of the one-dimensional isotropic forward-backward model of Fermi for the scattering and application of the Laplace transformation with respect to the lethargy variable leads to a linear differential equation system with constant coefficients. This equation system is solved for an arbitrary number of species and relations between the collision densities and defect distributions of the different species are given in the Kinchin Pease model. The case of an alien particle incident on a two-component target is examined in some detail and the sputtering spectra are given numerically. (author)

  15. Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.).

    Science.gov (United States)

    Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

    2015-06-01

    The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.

  16. Using species sensitivity distribution approach to assess the risks of commonly detected agricultural pesticides to Australia's tropical freshwater ecosystems.

    Science.gov (United States)

    Pathiratne, Asoka; Kroon, Frederieke J

    2016-02-01

    To assess the potential impacts of agricultural pesticides on tropical freshwater ecosystems, the present study developed temperature-specific, freshwater species protection concentrations (i.e., ecotoxicity threshold values) for 8 pesticides commonly detected in Australia's tropical freshwaters. Because relevant toxicity data for native tropical freshwater species to assess the ecological risks were mostly absent, scientifically robust toxicity data obtained at ≥20 °C were used for ecologically relevant taxonomic groups representing primary producers and consumers. Species sensitivity distribution (SSD) curves were subsequently generated for predicted chronic exposure using Burrlioz 2.0 software with mixed chronic and converted acute data relevant to exposure conditions at ≥20 °C. Ecotoxicity threshold values for tropical freshwater ecosystem protection were generated for ametryn, atrazine, diuron, metolachlor, and imidacloprid (all moderate reliability), as well as simazine, hexazinone, and tebuthiuron (all low reliability). Using these SSD curves, the retrospective risk assessments for recently reported pesticide concentrations highlight that the herbicides ametryn, atrazine, and diuron are of major concern for ecological health in Australia's tropical freshwater ecosystems. The insecticide imidacloprid also appears to pose an emerging threat to the most sensitive species in tropical freshwater ecosystems. The exposed temperature-specific approach may be applied to develop water quality guideline values for other environmental contaminants detected in tropical freshwater ecosystems until reliable and relevant toxicity data are generated using representative native species. © 2015 SETAC.

  17. Enhancing the effectiveness of biological control programs of invasive species through a more comprehensive pest management approach.

    Science.gov (United States)

    DiTomaso, Joseph M; Van Steenwyk, Robert A; Nowierski, Robert M; Vollmer, Jennifer L; Lane, Eric; Chilton, Earl; Burch, Patrick L; Cowan, Phil E; Zimmerman, Kenneth; Dionigi, Christopher P

    2017-01-01

    Invasive species are one of the greatest economic and ecological threats to agriculture and natural areas in the US and the world. Among the available management tools, biological control provides one of the most economical and long-term effective strategies for managing widespread and damaging invasive species populations of nearly all taxa. However, integrating biological control programs in a more complete integrated pest management approach that utilizes increased information and communication, post-release monitoring, adaptive management practices, long-term stewardship strategies, and new and innovative ecological and genetic technologies can greatly improve the effectiveness of biological control. In addition, expanding partnerships among relevant national, regional, and local agencies, as well as academic scientists and land managers, offers far greater opportunities for long-term success in the suppression of established invasive species. In this paper we direct our recommendations to federal agencies that oversee, fund, conduct research, and develop classical biological control programs for invasive species. By incorporating these recommendations into adaptive management strategies, private and public land managers will have far greater opportunities for long-term success in suppression of established invasive species. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches.

    Science.gov (United States)

    Schmieder, Daniela A; Benítez, Hugo A; Borissov, Ivailo M; Fruciano, Carmelo

    2015-01-01

    External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species--in this case European horseshoe bats (Rhinolophidae, Chiroptera)--based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.

  19. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches.

    Directory of Open Access Journals (Sweden)

    Daniela A Schmieder

    Full Text Available External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species--in this case European horseshoe bats (Rhinolophidae, Chiroptera--based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.

  20. A distribution-oriented approach to support landscape connectivity for ecologically distinct bird species.

    Science.gov (United States)

    Herrera, José M; Alagador, Diogo; Salgueiro, Pedro; Mira, António

    2018-01-01

    Managing landscape connectivity is a widely recognized overarching strategy for conserving biodiversity in human-impacted landscapes. However, planning the conservation and management of landscape connectivity of multiple and ecologically distinct species is still challenging. Here we provide a spatially-explicit framework which identifies and prioritizes connectivity conservation and restoration actions for species with distinct habitat affinities. Specifically, our study system comprised three groups of common bird species, forest-specialists, farmland-specialists, and generalists, populating a highly heterogeneous agricultural countryside in the southwestern Iberian Peninsula. We first performed a comprehensive analysis of the environmental variables underlying the distributional patterns of each bird species to reveal generalities in their guild-specific responses to landscape structure. Then, we identified sites which could be considered pivotal in maintaining current levels of landscape connectivity for the three bird guilds simultaneously, as well as the number and location of sites that need to be restored to maximize connectivity levels. Interestingly, we found that a small number of sites defined the shortest connectivity paths for the three bird guilds simultaneously, and were therefore considered key for conservation. Moreover, an even smaller number of sites were identified as critical to expand the landscape connectivity at maximum for the regional bird assemblage as a whole. Our spatially-explicit framework can provide valuable decision-making support to conservation practitioners aiming to identify key connectivity and restoration sites, a particularly urgent task in rapidly changing landscapes such as agroecosystems.

  1. A polyphasic approach to the taxonomy of the Alternaria infectoria species-group

    DEFF Research Database (Denmark)

    Andersen, Birgitte; Sørensen, Jens Laurids; Nielsen, Kristian Fog

    2009-01-01

    Different taxa in the species-group of Alternaria infectoria (teleomorph Lewia spp.) are often isolated from various cereals including barley, maize and wheat grain, ornamental plants and skin lesions from animals and humans. In the present study we made a polyphasic characterization of 39 strains...

  2. A novel approach to internal crown characterization for coniferous tree species classification

    Science.gov (United States)

    Harikumar, A.; Bovolo, F.; Bruzzone, L.

    2016-10-01

    The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

  3. A new approach to horizon-scanning: identifying potentially invasive alien species and their introduction pathways

    NARCIS (Netherlands)

    Matthews, Jonathan; Beringen, Ruud; Creemers, Raymond; Hollander, Hans; van Kessel, Nils; van Kleef, Hein; de Koppel, Sander van; Lemaire, Adrienne J. J.; Ode, Baudewijn; Verbrugge, Laura N. H.; Hendriks, A. Jan; Schipper, Aafke M.; van der Velde, Gerard; Leuven, Rob S. E. W.

    Invasive alien species (IAS) are considered an important threat to global biodiversity due to major ecological impacts. In 2014, the European Union (EU) introduced a regulation (EU) No 1143/2014 on the prevention and management of the introduction and spread of IAS. The first risk prioritized list

  4. Passerine extrapair mating dynamics: a bayesian modeling approach comparing four species

    NARCIS (Netherlands)

    Brommer, J.E.; Alho, J.S.; Biard, C.; Chapman, J.R.; Charmantier, A.; Dreiss, A.; Hartley, I.R.; Hjernquist, M.B.; Kempenaers, B.; Komdeur, J.; Laaksonen, T.; Lehtonen, P.K.; Lubjuhn, T.; Patrick, S.C.; Rosivall, B.; Tinbergen, J.M.; Van der Velde, M.; Van Oers, K.; Wilk, T.; Winkel, W.

    2010-01-01

    In many socially monogamous animals, females engage in extrapair copulation (EPC), causing some broods to contain both within‐pair and extrapair young (EPY). The proportion of all young that are EPY varies across populations and species. Because an EPC that does not result in EPY leaves no forensic

  5. Passerine Extrapair Mating Dynamics : A Bayesian Modeling Approach Comparing Four Species

    NARCIS (Netherlands)

    Brommer, Jon E.; Alho, Jussi S.; Biard, Clotilde; Chapman, Joanne R.; Charmantier, Anne; Dreiss, Amelie; Hartley, Ian R.; Hjernquist, Marten B.; Kempenaers, Bart; Komdeur, Jan; Laaksonen, Toni; Lehtonen, Paula K.; Lubjuhn, Thomas; Patrick, Samantha C.; Rosivall, Balazs; Tinbergen, Joost M.; van der Velde, Marco; van Oers, Kees; Wilk, Tomasz; Winkel, Wolfgang; Hjernquist, Mårten B.; Boughman, Janette; DeAngelis, Donald L.

    In many socially monogamous animals, females engage in extrapair copulation (EPC), causing some broods to contain both within-pair and extrapair young (EPY). The proportion of all young that are EPY varies across populations and species. Because an EPC that does not result in EPY leaves no forensic

  6. Water use patterns of three species in subalpine forest, Southwest China: the deuterium isotope approach

    Science.gov (United States)

    Qing Xu; Harbin Li; Jiquan Chen; Jiquan Cheng; Xiaoli Cheng; Shirong Liu; Shuqing An

    2011-01-01

    Determination of water sources of plant species in a community is critical for understanding the hydrological processes and their importance in ecosystem functions. Such partitioning of plant xylem water into specific sources (i.e. precipitation, groundwater) can be achieved by analyzing deuterium isotopic composition (δD) values for source waters. A subalpine dark...

  7. Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.

    Science.gov (United States)

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Beduschi, Giovanni

    2009-09-01

    Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

  8. Using combined morphological, allometric and molecular approaches to identify species of the genus Raillietiella (Pentastomida.

    Directory of Open Access Journals (Sweden)

    Crystal Kelehear

    Full Text Available Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina, the invasive Asian house gecko (Hemidactylus frenatus, and a native tree frog (Litoria caerulea in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica and another from lizards (Raillietiella frenatus. However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness and

  9. Spatially explicit multi-threat assessment of food tree species in Burkina Faso: A fine-scale approach.

    Directory of Open Access Journals (Sweden)

    Hannes Gaisberger

    Full Text Available Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change. We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs, climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as 'highly threatened' due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted

  10. Identification and mapping the high nature value farmland by the comparison of a combined and species approaches in Tuscany, Italy

    Directory of Open Access Journals (Sweden)

    Giulio Lazzerini

    2015-09-01

    Full Text Available Low-intensity farming systems play a crucial role in nature conservation by preserving 50% of habitats, flora and fauna occurring in Europe. For this reason the identification, classification and mapping of high nature value farmlands (HNVfs is becoming an overriding concern. In this study, two different approaches, namely combined approach and species-based approach, were used to spatially identify HNVfs (type 1, 2 and 3 across Tuscany region (Italy. The first approach calculated different indicators (extensive practices indicator, crop diversity indicator, landscape element indicator at 1×1 km grid cell spatial resolution using pre-existent spatial datasets integrated within a global information system environment. Whilst, the speciesbased approach relied on a pre-existent regional naturalistic inventory. All indicators and the resulting HNVfs derived from the two approaches were aggregated at municipality level. Despite some difference, the two adopted approaches intercepted spatially the same HNVfs areas, accounting for 35% of the total utilised agricultural area of the region. Just 16% of HNVfs resulted located inside protected areas, thus under current conservation and protection management actions. Finally, HNVfs of the Tuscany region were spatially aggregated in four relevant agro-ecosystems by taking into consideration the cropping systems and the landscape elements’ characteristics peculiar in the region.

  11. A whole plant approach to evaluate the water use of mediterranean maquis species in a coastal dune ecosystem

    Science.gov (United States)

    Mereu, S.; Salvatori, E.; Fusaro, L.; Gerosa, G.; Muys, B.; Manes, F.

    2009-02-01

    An integrated approach has been used to analyse the water relations of three Mediterranean species, A. unedo L., Q. ilex L. and P. latifolia L. co-occurring in a coastal dune ecosystem. The approach considered leaf level gas exchange, sap flow measurements and structural adaptations between 15 May and 31 July 2007, and was necessary to capture the different response of the three species to the same environment. The complexity of the response was proportional to the complexity of the system, characterized by a sandy soil with a low water retention capacity and the presence of a water table. The latter did not completely prevent the development of a drought response, and species differences in this responses have been partially attributed to a different root distribution. Sap flow of A. unedo decreased rapidly in response to the decline of Soil Water Content, while that of Q. ilex decreased only moderately. Midday leaf water potential of P. latifolia and A. unedo was between 2.2 and 2.7 MPa through the measuring period, while in Q. ilex it reached a value of 3.4 MPa at the end of the season. A. unedo was the only species to decrease the leaf area to sapwood area ratio from 23.9±1.2 (May) to 15.2±1.5 (July), as a response to drought. A. unedo also underwent an almost stepwise loss on hydraulic conductivity, such a loss didn't occur for Q. ilex, while P. latifolia was able to slightly increase hydraulic conductivity, showing how different plant compartments coordinate differently between species as a response to drought. Such different coordination affects the gas exchange between vegetation and the atmosphere, and has implications for the response of the Mediterranean coastal dune ecosystems to climate change.

  12. Using various lines of evidence to identify Chironomus species (Diptera: Chironomidae) in eastern Canadian lakes.

    Science.gov (United States)

    Proulx, Isabelle; Martin, Jon; Carew, Melissa; Hare, Landis

    2013-11-29

    Chironomus Meigen (Diptera, Chironomidae) larvae are usually the largest sediment-burrowing chironomids, and as such often constitute a major part of the freshwater infaunal biomass. However, use of this genus in ecological, environmental and paleoecological studies is hampered by the fact that Chironomus larvae are difficult to identify to species because the larvae of many species are morphologically similar. We used a combination of morphological, cytological and genetic techniques to distinguish Chironomus larvae collected from 31 water bodies located in eastern Canada, producing 17 distinguishable groupings. These groups of larvae were ultimately identified as belonging to 14 known species (C. anthracinus, C. bifurcatus, C. cucini, C. decorus-group sp. 2, C. dilutus, C. entis, C. frommeri, C. harpi, C. maturus, C. nr. atroviridis (sp. 2i), C. ochreatus, C. plumosus, C. staegeri and C. 'tigris') and three other species that remain unidentified (C. sp. NAI-III). No single approach served to delimit and identify larvae of all 17 Chironomus species that we collected. Although we expected that morphological criteria alone would be insufficient, our results suggest that DNA barcoding, using either the mitochondrial cox1 or the nuclear gb2β gene, was also inadequate for separating some Chironomus species. Thus we suggest that multiple approaches will often be needed to correctly identify Chironomus larvae to species.

  13. Modelling planktic foraminifer growth and distribution using an ecophysiological multi-species approach

    Directory of Open Access Journals (Sweden)

    F. Lombard

    2011-04-01

    Full Text Available We present an eco-physiological model reproducing the growth of eight foraminifer species (Neogloboquadrina pachyderma, Neogloboquadrina incompta, Neogloboquadrina dutertrei, Globigerina bulloides, Globigerinoides ruber, Globigerinoides sacculifer, Globigerinella siphonifera and Orbulina universa. By using the main physiological rates of foraminifers (nutrition, respiration, symbiotic photosynthesis, this model estimates their growth as a function of temperature, light availability, and food concentration. Model parameters are directly derived or calibrated from experimental observations and only the influence of food concentration (estimated via Chlorophyll-a concentration was calibrated against field observations. Growth rates estimated from the model show positive correlation with observed abundance from plankton net data suggesting close coupling between individual growth and population abundance. This observation was used to directly estimate potential abundance from the model-derived growth. Using satellite data, the model simulate the dominant foraminifer species with a 70.5% efficiency when compared to a data set of 576 field observations worldwide. Using outputs of a biogeochemical model of the global ocean (PISCES instead of satellite images as forcing variables gives also good results, but with lower efficiency (58.9%. Compared to core tops observations, the model also correctly reproduces the relative worldwide abundance and the diversity of the eight species when using either satellite data either PISCES results. This model allows prediction of the season and water depth at which each species has its maximum abundance potential. This offers promising perspectives for both an improved quantification of paleoceanographic reconstructions and for a better understanding of the foraminiferal role in the marine carbon cycle.

  14. Polyphasic approach including maldi-tof mass spectrometry to characterise aflatoxigenic species of aspergillus section flavi

    OpenAIRE

    Rodrigues, Paula; Santos, Cledir; Kozakiewicz, Zofia; Venâncio, Armando; Lima, Nelson

    2009-01-01

    Aflatoxins are toxic compounds which are produced as secondary metabolites by the fungi Aspergillus flavus, A. parasiticus and A. nomius growing on a variety of food products and are known to be carcinogenic, mutagenic, teratogenic and immunosuppressive1,2. Aspergillus is a large genus, with a complex taxonomy. The genus is easily identified by its characteristic conidiophore, but species identification and differentiation is complex, mainly because it is traditionally based on a range of mor...

  15. A High Throughput Ambient Mass Spectrometric Approach to Species Identification and Classification from Chemical Fingerprint Signatures

    OpenAIRE

    Musah, Rabi A.; Espinoza, Edgard O.; Cody, Robert B.; Lesiak, Ashton D.; Christensen, Earl D.; Moore, Hannah E.; Maleknia, Simin; Drijfhout, Falko P.

    2015-01-01

    A high throughput method for species identification and classification through chemometric processing of direct analysis in real time (DART) mass spectrometry-derived fingerprint signatures has been developed. The method entails introduction of samples to the open air space between the DART ion source and the mass spectrometer inlet, with the entire observed mass spectral fingerprint subjected to unsupervised hierarchical clustering processing. A range of both polar and non-polar chemotypes a...

  16. Approach to determine the diversity of Legionella species by nested PCR-DGGE in aquatic environments

    Science.gov (United States)

    Huang, Wen-Chien; Tsai, Hsin-Chi; Tao, Chi-Wei; Chen, Jung-Sheng; Shih, Yi-Jia; Kao, Po-Min; Huang, Tung-Yi; Hsu, Bing-Mu

    2017-01-01

    In this study, we describe a nested PCR-DGGE strategy to detect Legionella communities from river water samples. The nearly full-length 16S rRNA gene was amplified using bacterial primer in the first step. After, the amplicons were employed as DNA templates in the second PCR using Legionella specific primer. The third round of gene amplification was conducted to gain PCR fragments apposite for DGGE analysis. Then the total numbers of amplified genes were observed in DGGE bands of products gained with primers specific for the diversity of Legionella species. The DGGE patterns are thus potential for a high-throughput preliminary determination of aquatic environmental Legionella species before sequencing. Comparative DNA sequence analysis of excised DGGE unique band patterns showed the identity of the Legionella community members, including a reference profile with two pathogenic species of Legionella strains. In addition, only members of Legionella pneumophila and uncultured Legionella sp. were detected. Development of three step nested PCR-DGGE tactic is seen as a useful method for studying the diversity of Legionella community. The method is rapid and provided sequence information for phylogenetic analysis. PMID:28166249

  17. Accounting for selection bias in species distribution models: An econometric approach on forested trees based on structural modeling

    Science.gov (United States)

    Ay, Jean-Sauveur; Guillemot, Joannès; Martin-StPaul, Nicolas K.; Doyen, Luc; Leadley, Paul

    2015-04-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global change on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of application on forested trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8 km). We also compared the output of the SSDM with outputs of a classical SDM in term of bioclimatic response curves and potential distribution under current climate. According to the species and the spatial resolution of the calibration dataset, shapes of bioclimatic response curves the modelled species distribution maps differed markedly between the SSDM and classical SDMs. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents a crucial step to account for economic constraints on tree

  18. Hierarchical demographic approaches for assessing invasion dynamics of non-indigenous species: An example using northern snakehead (Channa argus)

    Science.gov (United States)

    Jiao, Y.; Lapointe, N.W.R.; Angermeier, P.L.; Murphy, B.R.

    2009-01-01

    Models of species' demographic features are commonly used to understand population dynamics and inform management tactics. Hierarchical demographic models are ideal for the assessment of non-indigenous species because our knowledge of non-indigenous populations is usually limited, data on demographic traits often come from a species' native range, these traits vary among populations, and traits are likely to vary considerably over time as species adapt to new environments. Hierarchical models readily incorporate this spatiotemporal variation in species' demographic traits by representing demographic parameters as multi-level hierarchies. As is done for traditional non-hierarchical matrix models, sensitivity and elasticity analyses are used to evaluate the contributions of different life stages and parameters to estimates of population growth rate. We applied a hierarchical model to northern snakehead (Channa argus), a fish currently invading the eastern United States. We used a Monte Carlo approach to simulate uncertainties in the sensitivity and elasticity analyses and to project future population persistence under selected management tactics. We gathered key biological information on northern snakehead natural mortality, maturity and recruitment in its native Asian environment. We compared the model performance with and without hierarchy of parameters. Our results suggest that ignoring the hierarchy of parameters in demographic models may result in poor estimates of population size and growth and may lead to erroneous management advice. In our case, the hierarchy used multi-level distributions to simulate the heterogeneity of demographic parameters across different locations or situations. The probability that the northern snakehead population will increase and harm the native fauna is considerable. Our elasticity and prognostic analyses showed that intensive control efforts immediately prior to spawning and/or juvenile-dispersal periods would be more effective

  19. Pleistocene climate, phylogeny, and climate envelope models: an integrative approach to better understand species' response to climate change.

    Directory of Open Access Journals (Sweden)

    A Michelle Lawing

    Full Text Available Mean annual temperature reported by the Intergovernmental Panel on Climate Change increases at least 1.1°C to 6.4°C over the next 90 years. In context, a change in climate of 6°C is approximately the difference between the mean annual temperature of the Last Glacial Maximum (LGM and our current warm interglacial. Species have been responding to changing climate throughout Earth's history and their previous biological responses can inform our expectations for future climate change. Here we synthesize geological evidence in the form of stable oxygen isotopes, general circulation paleoclimate models, species' evolutionary relatedness, and species' geographic distributions. We use the stable oxygen isotope record to develop a series of temporally high-resolution paleoclimate reconstructions spanning the Middle Pleistocene to Recent, which we use to map ancestral climatic envelope reconstructions for North American rattlesnakes. A simple linear interpolation between current climate and a general circulation paleoclimate model of the LGM using stable oxygen isotope ratios provides good estimates of paleoclimate at other time periods. We use geologically informed rates of change derived from these reconstructions to predict magnitudes and rates of change in species' suitable habitat over the next century. Our approach to modeling the past suitable habitat of species is general and can be adopted by others. We use multiple lines of evidence of past climate (isotopes and climate models, phylogenetic topology (to correct the models for long-term changes in the suitable habitat of a species, and the fossil record, however sparse, to cross check the models. Our models indicate the annual rate of displacement in a clade of rattlesnakes over the next century will be 2 to 3 orders of magnitude greater (430-2,420 m/yr than it has been on average for the past 320 ky (2.3 m/yr.

  20. Health economic value of an innovation: delimiting the scope and framework of future market entry agreements.

    Science.gov (United States)

    Launois, Robert; Navarrete, Lucia Fiestas; Ethgen, Olivier; Le Moine, Jean-Gabriel; Gatsinga, René

    2014-01-01

    The objective of our paper is to offer a new, payer-friendly taxonomy of market entry agreements (MEAs) that aims to twin contracts with their methodological designs in an effort to clarify the distinction between contracts that are based on performance and those that are based on demonstrated effect. Our analysis proceeds in two stages: First, we delimit the scope and framework of pay for performance (P4P) and pay for demonstrated effect (P4E) agreements. Second, we distinguish the methodological designs supporting the implementation of each of these contracts. We elucidate why P4P contracts prevent the payer from funding the true effectiveness of an innovation by expanding on their limitations. These include: 1) the normative nature of comparisons, 2) the impossibility of true effect imputability for each individual, and 3) the use of intermediary outcome measures. We then explore three main criticisms that payers must take into account when reasoning in terms of performance rather than in terms of the product effectiveness. The potential effect that performance-based reimbursements may have on dissociating the components of the cost-effectiveness ratio constitutes an obstacle to a true health economic reasoning.

  1. Utility of surface pollen assemblages to delimit Eastern Eurasian steppe types.

    Directory of Open Access Journals (Sweden)

    Feng Qin

    Full Text Available Modern pollen records have been used to successfully distinguish between specific prairie types in North America. Whether the pollen records can be used to detect the occurrence of Eurasian steppe, or even to further delimit various steppe types was until now unclear. Here we characterized modern pollen assemblages of meadow steppe, typical steppe and desert steppe from eastern Eurasia along an ecological humidity gradient. The multivariate ordination of the pollen data indicated that Eurasian steppe types could be clearly differentiated. The different steppe types could be distinguished primarily by xerophilous elements in the pollen assemblages. Redundancy analysis indicated that the relative abundances of Ephedra, Tamarix, Nitraria and Zygophyllaceae were positively correlated with aridity. The relative abundances of Ephedra increased from meadow steppe to typical steppe and desert steppe. Tamarix and Zygophyllaceae were found in both typical steppe and desert steppe, but not in meadow steppe. Nitraria was only found in desert steppe. The relative abundances of xerophilous elements were greater in desert steppe than in typical steppe. These findings indicate that Eurasian steppe types can be differentiated based on recent pollen rain.

  2. Engagement and well-being university teacher. Towards the delimitation of evaluative indicators

    Directory of Open Access Journals (Sweden)

    Antonio Bernal Guerrero

    2017-02-01

    Full Text Available Building a professional teacher identity is affected by the framework of the social changes of our time. These are associated with complex mechanisms of deinstitutionalization and reorganization which produce considerable emotional burnout. We have carried out an investigation of teaching well-being linked to the phenomenon called engagement. This is presented as a way to combat teachers’ malaise and foster well-being. There is a paucity of studies on the delimiting of substantive descriptors for the evaluation of engagement in university teaching. We have therefore done an exploratory qualitative study in theUniversityofSeville. In doing this, we have used the biographic-narrative method and the interview technique in order to progress in this educational line. The results of the study appear to reflect that there are certain factors which influence well-being: institutional stability, labor conditions, social recognition and the improvement of the teachers’ training. Likewise, a series of evaluation indicators connected with the personal level are outlined: an active willingness toward enhancement, a capacity to set up optimal relations, perseverance, an enthusiastic link with the profession and an emotional balance expressed in reconciling different areas of life.

  3. Penumbra characteristics of square photon beams delimited by a GEMS multi-leaf collimator

    Energy Technology Data Exchange (ETDEWEB)

    Briot, E; Julia, F [Centre de Lutte Contre le Cancer Gustave-Roussy, 94 - Villejuif (France)

    1995-12-01

    A multi-leaf collimator (MLC) has been designed to replace directly the standard collimator of a SATURNE IV Series linac. It consists of 2 x 32 tungsten leaves and one set of upper block jaws. Isodose curves and dose profiles were measured for symmetric fields at the depth of the maximum and the reference depths for 6 MV, 10 MV, 18 MV photon beams. The penumbra (80%-20%) corresponding to the face and the side of the leaves have been compared with the standard collimators. Along with the X direction, the field delimitation is performed primarily with the leaves which are continuously variable in position. Along the Y direction, the field is initially approximated by the closure of opposite leaf pairs; then the Y upper jaws produce the exact size of the required field. As the leaves move linearly the penumbra (80%-20%) corresponding to the leaf ends is minimized and held constant at all positions by curvature of their faces. Penumbra obtained with the superposition of leaves and Y jaws depend on their relative position. The penumbra is minimum when the leaf side and the Y jaw edge coincide and the comparison of the measurement values with the conventional collimator shows that the differences are within 1 mm. When the leaves delineating the field are not entirely covered by the Y block upper jaws, the penumbra increases, and the junction of the opposing leaves, a width increase up to 3.5 mm has been measured.

  4. Approach for discrimination and quantification of electroactive species: kinetics difference revealed by higher harmonics of Fourier transformed sinusoidal voltammetry.

    Science.gov (United States)

    Fang, Yishan; Huang, Xinjian; Wang, Lishi

    2015-01-06

    Discrimination and quantification of electroactive species are traditionally realized by a potential difference which is mainly determined by thermodynamics. However, the resolution of this approach is limited to tens of millivolts. In this paper, we described an application of Fourier transformed sinusoidal voltammetry (FT-SV) that provides a new approach for discrimination and quantitative evaluation of electroactive species, especially thermodynamic similar ones. Numerical simulation indicates that electron transfer kinetics difference between electroactive species can be revealed by the phase angle of higher order harmonics of FT-SV, and the difference can be amplified order by order. Thus, even a very subtle kinetics difference can be amplified to be distinguishable at a certain order of harmonics. This method was verified with structurally similar ferrocene derivatives which were chosen as the model systems. Although these molecules have very close redox potential (harmonics. The results demonstrated the feasibility and reliability of the method. It was also implied that the combination of the traditional thermodynamic method and this kinetics method can form a two-dimension resolved detection method, and it has the potential to extend the resolution of voltammetric techniques to a new level.

  5. An approach for identification and determination of arsenic species in the extract of kelp.

    Science.gov (United States)

    Yu, Lee L; Wei, Chao; Zeisler, Rolf; Tong, Junting; Oflaz, Rabia; Bao, Haixia; Wang, Jun

    2015-05-01

    The National Institute of Standards and Technology is developing a kelp powder standard reference material (SRM) in support of dietary supplement measurements. Edible seaweeds such as kelp and laver consumed as diet or dietary supplement contain tens of mg/kg arsenic. The speciation information of arsenic in the seaweed should be provided because the total arsenic alone does not fully address the safety issue of the dietary supplement as the value assignment is originally intended. The inability to avail all arsenic species for value assignment measurements prevented the certification of arsenic species in the candidate SRM; however, approximately 70 % of total arsenic extracted with a 1:1 volume fraction of methanol:water mixture allowed arsenic speciation values to be assigned to a procedure-defined extract, which may be used for method validation in research to improve upon current extraction and measurement practices. Arsenic species in kelp and laver were identified using electrospray ionization ion trap time of flight mass spectrometry (ESI-IT-TOF). Arsenosugars As(328), As(482), and As(392) were found in the kelp candidate SRM while As(328) and As(482) were found in GBW 08521, a certified reference material (CRM) of laver produced by the National Institute of Metrology of China (NIM). A discovery that the digests of kelp and laver contained only dimethylarsinic acid led to the conclusion that the seaweeds did not contain detectible levels of arsenobetaine, arsenocholine or trimethylarsine oxide that could overlap with the peaks of arsenosugars in the separation. The mean ± s of (5.68 ± 0.28) mg/kg and (13.43 ± 0.31) mg/kg found for As(482) and As(392) in kelp, respectively, using instrumental neutron activation analysis (INAA) demonstrated that value assignment measurement of arsenosugars was possible without arsenosugar calibration standards.

  6. Cross-species transcriptomic approach reveals genes in hamster implantation sites.

    Science.gov (United States)

    Lei, Wei; Herington, Jennifer; Galindo, Cristi L; Ding, Tianbing; Brown, Naoko; Reese, Jeff; Paria, Bibhash C

    2014-12-01

    The mouse model has greatly contributed to understanding molecular mechanisms involved in the regulation of progesterone (P4) plus estrogen (E)-dependent blastocyst implantation process. However, little is known about contributory molecular mechanisms of the P4-only-dependent blastocyst implantation process that occurs in species such as hamsters, guineapigs, rabbits, pigs, rhesus monkeys, and perhaps humans. We used the hamster as a model of P4-only-dependent blastocyst implantation and carried out cross-species microarray (CSM) analyses to reveal differentially expressed genes at the blastocyst implantation site (BIS), in order to advance the understanding of molecular mechanisms of implantation. Upregulation of 112 genes and downregulation of 77 genes at the BIS were identified using a mouse microarray platform, while use of the human microarray revealed 62 up- and 38 down-regulated genes at the BIS. Excitingly, a sizable number of genes (30 up- and 11 down-regulated genes) were identified as a shared pool by both CSMs. Real-time RT-PCR and in situ hybridization validated the expression patterns of several up- and down-regulated genes identified by both CSMs at the hamster and mouse BIS to demonstrate the merit of CSM findings across species, in addition to revealing genes specific to hamsters. Functional annotation analysis found that genes involved in the spliceosome, proteasome, and ubiquination pathways are enriched at the hamster BIS, while genes associated with tight junction, SAPK/JNK signaling, and PPARα/RXRα signalings are repressed at the BIS. Overall, this study provides a pool of genes and evidence of their participation in up- and down-regulated cellular functions/pathways at the hamster BIS. © 2014 Society for Reproduction and Fertility.

  7. Trust Species and Habitat Branch: using the innovative approaches of today to conserve biodiversity for tomorrow

    Science.gov (United States)

    Stevens, Patricia; Walters, Katie D.

    2015-01-01

    Some of the biggest challenges facing wildlife today are changes to their environment from both natural and anthropogenic causes. Natural resource managers, planners, policy makers, industry and private landowners must make informed decisions and policies regarding management, conservation, and restoration of species, habitats, and ecosystem function in response to these changes. Specific needs include (1) a better understanding of population status and trends; (2) understanding of species’ habitat needs and roles in supporting ecosystem functions; (3) the ability to assess species’ responses to environmental changes and predict future responses; and (4) the development of innovative techniques and tools to better understand, minimize or prevent any unintended consequences of environmental change.

  8. Combined molecular and biochemical approach identifies Aspergillus japonicus and Aspergillus aculeatus as two species

    DEFF Research Database (Denmark)

    Parenicova, L.; Skouboe, P.; Frisvad, Jens Christian

    2001-01-01

    of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene could not be used to distinguish between A. japonicus and A. aculeatus but did show that these two taxa are more closely related to each other than to other species of black aspergilli. Aspergillus niger pyruvate kinase (pkiA) and pectin...... variation when they were probed with the pelA gene. The secondary-metabolite profiles supported division of the isolates into the two species and differed from those of other black aspergilli. The strains classified as A. japonicus produced indole alkaloids and a polar metabolite, while the A. aculeatus...... lyase A (pelA) and Agaricus bisporus 28S rRNA genes, which were used as probes in the RFLP analysis, revealed clear polymorphism between these two taxa. The A. niger pkiA and pelA probes placed six strains in an A. japonicus group and 12 isolates in an A. aculeatus group, which exhibited intraspecific...

  9. Proteomics approach to identify unique xylem sap proteins in Pierce's disease-tolerant Vitis species.

    Science.gov (United States)

    Basha, Sheikh M; Mazhar, Hifza; Vasanthaiah, Hemanth K N

    2010-03-01

    Pierce's disease (PD) is a destructive bacterial disease of grapes caused by Xylella fastidiosa which is xylem-confined. The tolerance level to this disease varies among Vitis species. Our research was aimed at identifying unique xylem sap proteins present in PD-tolerant Vitis species. The results showed wide variation in the xylem sap protein composition, where a set of polypeptides with pI between 4.5 and 4.7 and M(r) of 31 kDa were present in abundant amount in muscadine (Vitis rotundifolia, PD-tolerant), in reduced levels in Florida hybrid bunch (Vitis spp., PD-tolerant) and absent in bunch grapes (Vitis vinifera, PD-susceptible). Liquid chromatography/mass spectrometry/mass spectrometry analysis of these proteins revealed their similarity to beta-1, 3-glucanase, peroxidase, and a subunit of oxygen-evolving enhancer protein 1, which are known to play role in defense and oxygen generation. In addition, the amount of free amino acids and soluble sugars was found to be significantly lower in xylem sap of muscadine genotypes compared to V. vinifera genotypes, indicating that the higher nutritional value of bunch grape sap may be more suitable for Xylella growth. These data suggest that the presence of these unique proteins in xylem sap is vital for PD tolerance in muscadine and Florida hybrid bunch grapes.

  10. SNP markers retrieval for a non-model species: a practical approach

    Directory of Open Access Journals (Sweden)

    Shahin Arwa

    2012-01-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC on 454 data from four lily genotypes and compared results with respect to SNP retrieval. Results CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs. Conclusion In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.

  11. Delimitation and Classified Planning Management of Functional Renovation Zone: Experience of and Discussion on Shenzhen's Practice of Urban Renewal

    Institute of Scientific and Technical Information of China (English)

    Hao Wenxuan; Tong De; Liu Qing; Feng Changchun; Liu Jinxin

    2016-01-01

    Urban renewal is one of the important issues of urban development in China.Along with its development in the contemporary time,China has seen considerable achievements and problems as well in urban renewal.Taking into account that Shenzhen has carried out plenty of explorations on urban planning renewal,this paper takes it as an example to firstly analyze the plights of its urban renewal planning,the shortcomings of its urban renewal projects,and the advantages of functional renovation zones to manifest the necessity of the delimitation and classified planning management of functional renovation zone in urban renewal.It then summarizes the experience of its urban renewal unit planning in terms of the methods of zoning and implementation,and finally discusses the conceptual connotations of functional renovation zone,as well as the logic and characteristics of renovations of its delimitation and classified planning management,in hope of providing other Chinese cities with some references.

  12. An integrated approach shows different use of water resources from Mediterranean maquis species in a coastal dune ecosystem

    Directory of Open Access Journals (Sweden)

    F. Manes

    2009-11-01

    Full Text Available An integrated approach has been used to analyse the dependence of three Mediterranean species, A. unedo L., Q. ilex L., and P. latifolia L. co-occurring in a coastal dune ecosystem on two different water resources: groundwater and rainfed upper soil layers. The approach included leaf level gas exchanges, sap flow measurements and structural adaptations between 15 May and 31 July 2007. During this period it was possible to capture different species-specific response patterns to an environment characterized by a sandy soil, with a low water retention capacity, and the presence of a water table. The latter did not completely prevent the development of a drought response and, combined with previous studies in the same area, response differences between species have been partially attributed to different root distributions. Sap flow of A. unedo decreased rapidly with the decline of soil water content, while that of Q. ilex decreased only moderately. Midday leaf water potential of P. latifolia and A. unedo ranged between −2.2 and −2.7 MPa throughout the measuring period, while in Q. ilex it decreased down to −3.4 MPa at the end of the season. A. unedo was the only species that responded to drought with a decrease of its leaf area to sapwood area ratio from 23.9±1.2 (May to 15.2±1.5 (July. While A. unedo also underwent an almost stepwise loss on hydraulic conductivity, such a loss did not occur for Q. ilex, whereas P. latifolia was able to slightly increase its hydraulic conducitivity. These differences show how different plant compartments coordinate differently between species in their responses to drought. The different responses appear to be mediated by different root distributions of the species and their relative resistances to drought are likely to depend on the duration of the periods in which water remains extractable in the upper soil layers.

  13. Phylogenetic relationships and generic delimitation of Eurasian Aster (Asteraceae: Astereae) inferred from ITS, ETS and trnL-F sequence data

    Science.gov (United States)

    Li, Wei-Ping; Yang, Fu-Sheng; Jivkova, Todorka; Yin, Gen-Shen

    2012-01-01

    Background and Aims The classification and phylogeny of Eurasian (EA) Aster (Asterinae, Astereae, Asteraceae) remain poorly resolved. Some taxonomists adopt a broad definition of EA Aster, whereas others favour a narrow generic concept. The present study aims to delimit EA Aster sensu stricto (s.s.), elucidate the phylogenetic relationships of EA Aster s.s. and segregate genera. Methods The internal and external transcribed spacers of nuclear ribosomal DNA and the plastid DNA trnL-F region were used to reconstruct the phylogeny of EA Aster through maximum parsimony and Bayesian analyses. Key Results The analyses strongly support an Aster clade including the genera Sheareria, Rhynchospermum, Kalimeris (excluding Kalimeris longipetiolata), Heteropappus, Miyamayomena, Turczaninowia, Rhinactinidia, eastern Asian Doellingeria, Asterothamnus and Arctogeron. Many well-recognized species of Chinese Aster s.s. lie outside of the Aster clade. Conclusions The results reveal that EA Aster s.s. is both paraphyletic and polyphyletic. Sheareria, Rhynchospermum, Kalimeris (excluding K. longipetiolata), Heteropappus, Miyamayomena, Turczaninowia, Rhinactinidia, eastern Asian Doellingeria, Asterothamnus and Arctogeron should be included in Aster, whereas many species of Chinese Aster s.s. should be excluded. The recircumscribed Aster should be divided into two subgenera and nine sections. Kalimeris longipetiolata, Aster batangensis, A. ser. Albescentes, A. series Hersileoides, a two-species group composed of A. senecioides and A. fuscescens, and a six-species group including A. asteroides, should be elevated to generic level. With the Aster clade, they belong to the Australasian lineages. The generic status of Callistephus should be maintained. Whether Galatella (including Crinitina) and Tripolium should remain as genera or be merged into a single genus remains to be determined. In addition, the taxonomic status of A. auriculatus and the A. pycnophyllus–A. panduratus clade remains

  14. Assessment of genetic diversity within the Merodon ruficornis species group (Diptera: Syrphidae by RAPD analysis

    Directory of Open Access Journals (Sweden)

    Andrić Andrijana

    2017-01-01

    Full Text Available As one of the most distinct groups in the hoverfly genus Merodon, the monophyletic ruficornis species group has been the focus of several studies using different approaches. Molecular methods have shown incongruences between morphological and molecular data. In the present study, we investigated four species of the Merodon ruficornis group (i.e. M. loewi, M. armipes, M. papillus and M. hoplitis with the aim of detecting intra- and interspecific genetic diversity, and we examined the usefulness of random amplified polymorphic DNA (RAPD in an integrative taxonomic approach to species delimitation. Analysis of Nei’s genetic variation over all loci showed that genetic diversity for the analyzed Merodon species was h=0.24. Based on UPGMA, PCoA and Bayesian clustering analyses, our results clearly differentiated four groups that correspond to the four morphologically-defined Merodon species. Among the analyzed species, M. armipes and M. hoplitis showed the lowest level of genetic divergence; M. loewi was clearly separated from both M. armipes and M. papillus. Based on our data, we propose the use of RAPD-PCR as an additional tool for resolving taxonomic problems within Merodon. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no.173002

  15. In-gel and OFFGEL-based proteomic approach for authentication of meat species from minced meat and meat products.

    Science.gov (United States)

    Naveena, Basappa M; Jagadeesh, Deepak S; Kamuni, Veeranna; Muthukumar, Muthupalani; Kulkarni, Vinayak V; Kiran, Mohan; Rapole, Srikanth

    2018-02-01

    Fraudulent mislabelling of processed meat products on a global scale that cannot be detected using conventional techniques necessitates sensitive, robust and accurate methods of meat authentication to ensure food safety and public health. In the present study, we developed an in-gel (two-dimensional gel electrophoresis, 2DE) and OFFGEL-based proteomic method for authenticating raw and cooked water buffalo (Bubalus bubalis), sheep (Ovis aries) and goat (Caprus hircus) meat and their mixes. The matrix-assisted liquid desorption/ionization time-of-flight mass spectrometric analysis of proteins separated using 2DE or OFFGEL electrophoresis delineated species-specific peptide biomarkers derived from myosin light chain 1 and 2 (MLC1 and MLC2) of buffalo-sheep-goat meat mix in definite proportions at 98:1:1, 99:0.5:0.5 and 99.8:0.1:0.1 that were found stable to resist thermal processing. In-gel and OFFGEL-based proteomic approaches are efficient in authenticating meat mixes spiked at minimum 1.0% and 0.1% levels, respectively, in triple meat mix for both raw and cooked samples. The study demonstrated that authentication of meat from a complex mix of three closely related species requires identification of more than one species-specific peptide due to close similarity between their amino acid sequences. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  16. An object-based approach for tree species extraction from digital orthophoto maps

    Science.gov (United States)

    Jamil, Akhtar; Bayram, Bulent

    2018-05-01

    Tree segmentation is an active and ongoing research area in the field of photogrammetry and remote sensing. It is more challenging due to both intra-class and inter-class similarities among various tree species. In this study, we exploited various statistical features for extraction of hazelnut trees from 1 : 5000 scaled digital orthophoto maps. Initially, the non-vegetation areas were eliminated using traditional normalized difference vegetation index (NDVI) followed by application of mean shift segmentation for transforming the pixels into meaningful homogeneous objects. In order to eliminate false positives, morphological opening and closing was employed on candidate objects. A number of heuristics were also derived to eliminate unwanted effects such as shadow and bounding box aspect ratios, before passing them into the classification stage. Finally, a knowledge based decision tree was constructed to distinguish the hazelnut trees from rest of objects which include manmade objects and other type of vegetation. We evaluated the proposed methodology on 10 sample orthophoto maps obtained from Giresun province in Turkey. The manually digitized hazelnut tree boundaries were taken as reference data for accuracy assessment. Both manually digitized and segmented tree borders were converted into binary images and the differences were calculated. According to the obtained results, the proposed methodology obtained an overall accuracy of more than 85 % for all sample images.

  17. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    Directory of Open Access Journals (Sweden)

    Li Hai-Long

    2011-06-01

    Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  18. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

    Science.gov (United States)

    Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

    2011-06-10

    Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  19. Molecular Fingerprinting Approach in Plant Species Evaluation for a Nuclear Power Programme

    International Nuclear Information System (INIS)

    Azhar Mohamed

    2011-01-01

    Deoxyribonucleic acid (DNA) as a tool for marker technology is found to be remarkable, advanced and exciting in recent years. DNA markers are valuable tools and important in various plant breeding analyses for identification, gene mapping, marker systems and mutagenesis response. As gene expression is related to concurrent cellular activities and is mobilised in the adaptation of plants to adverse environmental conditions, changes at the DNA levels can be detected simultaneously. The changes also reflect response onto plant traits in which selection for better quality plant materials can be made and/or used as bio-indicator response in tracking any environmental change. The objective of the present study is to show Inter Simple Sequence Repeat (ISSR) markers as an important technique in differentiating plant DNA genomic in various species for the evaluation of their diversity and radiation effects in population. The technique has been found to be rapid, simple, reliable and robust in generating molecular fingerprinting database in bio surveillance for a nuclear power programme. (author)

  20. A new species of Indo-Pacific Modulidae (Mollusca: Caenogastropoda).

    Science.gov (United States)

    Lozouet, Pierre; Krygelmans, Anouchka

    2016-04-12

    Modulidae is a littoral cerithioid family exclusively encountered in tropical and subtropical regions. It contains 12 to 15 living species (some species are not clearly delimited). Only one species is known to occur in the vast Indo-Pacific region (Bouchet 2015) and two species in the eastern Atlantic. By comparison, the tropical American regions are relatively rich with at least eleven living species (two or three species in the eastern Pacific and nine or more in the western Atlantic), and an equivalent number or more of fossil species (Landau et al. 2014).

  1. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

    Directory of Open Access Journals (Sweden)

    Deborah Galpert

    2015-01-01

    Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

  2. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches.

    Science.gov (United States)

    Rodrigues, P; Santos, C; Venâncio, A; Lima, N

    2011-10-01

    Section Flavi is one of the most significant sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF ICMS) and to evaluate the discriminatory power of the various approaches in species identification.   Aspergillus section Flavi isolates obtained from Portuguese almonds were characterized in terms of macro- and micromorphology, mycotoxin pattern, calmodulin gene sequence and MALDI-TOF protein fingerprint spectra. For each approach, dendrograms were created and results were compared. All data sets divided the isolates into three groups, corresponding to taxa closely related to Aspergillus flavus, Aspergillus parasiticus and Aspergillus tamarii. In the A. flavus clade, molecular and spectral analyses were not able to resolve between aflatoxigenic and nonaflatoxigenic isolates. In the A. parasiticus cluster, two well-resolved clades corresponded to unidentified taxa, corresponding to those isolates with mycotoxin profile different from that expected for A. parasiticus. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

  3. Direct Detection and Differentiation of Pathogenic Leptospira Species Using a Multi-Gene Targeted Real Time PCR Approach

    Science.gov (United States)

    Ferreira, Ana Sofia; Costa, Pedro; Rocha, Teresa; Amaro, Ana; Vieira, Maria Luísa; Ahmed, Ahmed; Thompson, Gertrude; Hartskeerl, Rudy A.; Inácio, João

    2014-01-01

    Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE) in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis. PMID:25398140

  4. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    International Nuclear Information System (INIS)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-01-01

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries

  5. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  6. STUTTERING-PSYCHOLINGUISTIC APPROACH

    OpenAIRE

    Maria Anca; Carolina Bodea Haţegan; Lăcrămioara Prihoi

    2012-01-01

    This research promotes psycholinguistic paradigm, it focusing in delimitating several specific particularities in stuttering pathology. Structural approach, on language sides proves both the recurrent aspects found within specialized national and international literature and the psycholinguistic approaches dependence on the features of the linguistic material. Thus, the conclusions of this research study offer the possibility of promoting cross-cultural and cross-linguistic researches, with t...

  7. Species limits and relationships within Otidea inferred from multiple gene phylogenies

    NARCIS (Netherlands)

    Hansen, K.; Olariaga, I.

    2015-01-01

    The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high species diversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multi-gene analyses it formed a highly supported monophyletic group. Species delimitation

  8. A review of the genus Bulbothrix Hale: the species with medullary norstictic or protocetraric acids

    Directory of Open Access Journals (Sweden)

    Michel Benatti

    2012-03-01

    Full Text Available This study presents data of eight Bulbothrix (Parmeliaceae, Lichenized Fungi species containing norstictic or protocetraric acid in the medulla. The current species delimitations were confirmed. New synonyms are proposed, new characteriscts are detailed and range extensions are added.

  9. Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

    Science.gov (United States)

    Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina. Capelari

    2014-01-01

    In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

  10. Combining non-invasive techniques for delimitation and monitoring of chlorinated solvents in groundwater

    Science.gov (United States)

    Sparrenbom, Charlotte; Åkesson, Sofia; Hagerberg, David; Dahlin, Torleif; Holmstrand, Henry; Johansson, Sara

    2016-04-01

    groundwater sampling provide reference data within the project and for calibrating interpretations. In our studies, we show the results from DCIP measurements from two different areasin sothern Sweden with chlorinated solvent contamination. From one of the areas, a pilot test on stimulation reductive dechlorination has been carried out and the treated area reveals sharp anomalies in the DCIP response. Time lapse measurements show changes within the stimulated area and this could be used to follow remediation changes and i.e. groundwater quality changes. Tests with DCIP time lapse are also carried out in the second area together with multiple CSIA analyses of groundwater samples and ongoing is the planning for the gas samples. Evaluation of the possible uses, benefits and limitations of the technique for monitoring changes and delimit polluted areas to be able to monitor and follow groundwater quality changes is ongoing.

  11. Genome-wide SNP data and morphology support the distinction of two new species of Kovarikia Soleglad, Fet & Graham, 2014 endemic to California (Scorpiones, Vaejovidae

    Directory of Open Access Journals (Sweden)

    Robert W. Bryson Jr.

    2018-02-01

    Full Text Available Morphologically conserved taxa such as scorpions represent a challenge to delimit. We recently discovered populations of scorpions in the genus Kovarikia Soleglad, Fet & Graham, 2014 on two isolated mountain ranges in southern California. We generated genome-wide single nucleotide polymorphism data and used Bayes factors species delimitation to compare alternative species delimitation scenarios which variously placed scorpions from the two localities with geographically adjacent species or into separate lineages. We also estimated a time-calibrated phylogeny of Kovarikia and examined and compared the morphology of preserved specimens from across its distribution. Genetic results strongly support the distinction of two new lineages, which we describe and name here. Morphology among the species of Kovarikia was relatively conserved, despite deep genetic divergences, consistent with recent studies of stenotopic scorpions with limited vagility. Phylogeographic structure discovered in several previously described species also suggests additional cryptic species are probably present in the genus.

  12. Genome-wide SNP data and morphology support the distinction of two new species of Kovarikia Soleglad, Fet & Graham, 2014 endemic to California (Scorpiones, Vaejovidae)

    Science.gov (United States)

    Bryson, Robert W.; Wood, Dustin A.; Graham, Matthew R.; Soleglad, Michael E.; McCormack, John E.

    2018-01-01

    Morphologically conserved taxa such as scorpions represent a challenge to delimit. We recently discovered populations of scorpions in the genus Kovarikia Soleglad, Fet & Graham, 2014 on two isolated mountain ranges in southern California. We generated genome-wide single nucleotide polymorphism data and used Bayes factors species delimitation to compare alternative species delimitation scenarios which variously placed scorpions from the two localities with geographically adjacent species or into separate lineages. We also estimated a time-calibrated phylogeny of Kovarikia and examined and compared the morphology of preserved specimens from across its distribution. Genetic results strongly support the distinction of two new lineages, which we describe and name here. Morphology among the species of Kovarikia was relatively conserved, despite deep genetic divergences, consistent with recent studies of stenotopic scorpions with limited vagility. Phylogeographic structure discovered in several previously described species also suggests additional cryptic species are probably present in the genus.

  13. Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

    Directory of Open Access Journals (Sweden)

    Stephen R. Lindemann

    2017-06-01

    Full Text Available The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

  14. A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

    Directory of Open Access Journals (Sweden)

    Michael Hiller

    2012-10-01

    Full Text Available Genotype-phenotype mapping is hampered by countless genomic changes between species. We introduce a computational “forward genomics” strategy that—given only an independently lost phenotype and whole genomes—matches genomic and phenotypic loss patterns to associate specific genomic regions with this phenotype. We conducted genome-wide screens for two metabolic phenotypes. First, our approach correctly matches the inactivated Gulo gene exactly with the species that lost the ability to synthesize vitamin C. Second, we attribute naturally low biliary phospholipid levels in guinea pigs and horses to the inactivated phospholipid transporter Abcb4. Human ABCB4 mutations also result in low phospholipid levels but lead to severe liver disease, suggesting compensatory mechanisms in guinea pig and horse. Our simulation studies, counts of independent changes in existing phenotype surveys, and the forthcoming availability of many new genomes all suggest that forward genomics can be applied to many phenotypes, including those relevant for human evolution and disease.

  15. A nature-based approach for managing the invasive weed species Gutenbergia cordifolia for sustainable rangeland management.

    Science.gov (United States)

    Ngondya, Issakwisa B; Munishi, Linus K; Treydte, Anna C; Ndakidemi, Patrick A

    2016-01-01

    The invasive weed species Gutenbergia cordifolia has been observed to suppress native plants and to dominate more than half of the entire crater floor (250 km 2 ) in the Ngorongoro Conservation Area (NCA). As this species has been found to be toxic to ruminants it might strongly impact animal populations in this ecologically diverse ecosystem. Hence, a nature-based approach is urgently needed to manage its spread. We tested two Desmodium spp extracts applied to G. cordifolia and assessed the latter's germination rate, height, fresh weight and leaf total chlorophyll content after 30 days in both laboratory and screen house experiments. Seedling germination rate was halved by Desmodium uncinatum leaf extract (DuL), particularly under higher concentrations (≥75 %) rather than lower concentrations (≤62.5 %). Likewise, in both laboratory and screen house experiments, germination rate under DuL treatments declined with increasing concentrations. Seedling height, fresh weight and leaf total chlorophyll content (Chl) were also most strongly affected by DuL treatments rather than D. uncinatum root extract, Desmodium intortum leaf extract or D. intortum root extract treatments. Generally, seedlings treated with higher DuL concentrations were half as tall, had one-third the weight and half the leaf Chl content compared to those treated with lower concentrations. Our study shows a novel technique that can be applied where G. cordifolia may be driving native flora and fauna to local extinction. Our data further suggest that this innovative approach is both ecologically safe and effective and that D. uncinatum can be sustainably used to manage invasive plants, and thus, to improve rangeland productivity.

  16. Multi–criteria evaluation and simulated annealing for delimiting high priority habitats of Alectoris chukar and Phasianus colchicus in Iran

    Directory of Open Access Journals (Sweden)

    Momeni Dehaghi, I.

    2018-01-01

    Full Text Available Habitat degradation and hunting are among the most important causes of population decline for Alectoris chukar and Phasianus colchicus, two of the most threatened game species in the Golestan Province of Iran. Limited data on distribution and location of high–quality habitats for the two species make conservation efforts more difficult in the province. We used multi–criteria evaluation (MCE as a coarse–filter approach to refine the general distribution areas into habitat suitability maps for the species. We then used these maps as input to simulated annealing as a heuristic algorithm through Marxan in order to prioritize areas for conservation of the two species. To find the optimal solution, we tested various boundary length modifier (BLM values in the simulated annealing process. Our results showed that the MCE approach was useful to refine general habitat maps. Assessment of the selected reserves confirmed the suitability of the selected areas (mainly neighboring the current reserves making their management easier and more feasible. The total area of the selected reserves was about 476 km2. As current reserves of the Golestan Province represent only 23 % of the optimal area, further protected areas should be considered to efficiently conserve these two species.

  17. Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae using integrative taxonomy, with the description of a new species

    Directory of Open Access Journals (Sweden)

    Jelena Ačanski

    2016-10-01

    Full Text Available Several recent studies have detected and described complexes of cryptic and sibling species in the genus Merodon (Diptera, Syrphidae. One representative of these complexes is the Merodon avidus complex that contains four sibling species, which have proven difficult to distinguish using traditional morphological characters. In the present study, we use two geometric morphometric approaches, as well as molecular characters of the 5’-end of the mtDNA COI gene, to delimit sibling taxa. Analyses based on these data were used to strengthen species boundaries within the complex, and to validate the status of a previously-recognized cryptic taxon from Lesvos Island (Greece, here described as Merodon megavidus Vujić & Radenković sp. nov. Geometric morphometric results of both wing and surstylus shape confirm the present classification for three sibling species-M. avidus (Rossi, 1790, M. moenium Wiedemann in Meigen, 1822 and M. ibericus Vujić, 2015-and, importantly, clearly discriminate the newly-described taxon Merodon megavidus sp. nov. In addition to our geometric morphometric results, supporting characters were obtained from molecular analyses of mtDNA COI sequences, which clearly differentiated M. megavidus sp. nov. from the other members of the M. avidus complex. Molecular analyses revealed that the earliest divergence of M. ibericus occurred around 800 ky BP, while the most recent separation happened between M. avidus and M. moenium around 87 ky BP.

  18. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

    Science.gov (United States)

    Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

    2017-01-01

    Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID

  19. Generic delimitation between Fragariocoptes and Sierraphytoptus (Acari: Eriophyoidea: Phytoptidae) and a supplementary description of Fragariocoptes gansuensis with remarks on searching for mummified eriophyoid mites in herbaria under UV light.

    Science.gov (United States)

    Chetverikov, Philipp E

    2016-01-15

    Generic concepts of Fragariocoptes Roivainen, 1951 and Sierraphytoptus Keifer, 1939 are discussed and the correct delimitation between these two genera is given. A supplementary description of Fragariocoptes gansuensis Wei, Chen & Luo, 2005 is included based on fresh specimens from Astrakhan, Russia and dried mummies found in old herbaria collected in 1919 from southern European Russia of the cinquefoil, Potentilla bifurca L. (Rosaceae) with pathological stem proliferation. The male of this species is described for the first time. The cuticle of eriophyoid mummies emitted a faint glow under UV light wavelength equal to 365 nm of a common UV Light-Emitting diode (LED) lamp showing that this characteristic could be useful for quickly detecting eriophyoids in old herbaria which would otherwise be almost indistinguishable against the background under the regular white light source of a stereomicroscope. This was only possible for plant material stored in appropriate conditions enabling the autofluorescent signal of the dried mite cuticle to remain strong enough for observation.

  20. Malesian and Australian Tournefortia transferred to Heliotropium and notes on delimitation of Boraginaceae

    NARCIS (Netherlands)

    Craven, L.A.

    2005-01-01

    Boraginaceae is expanded to comprise seven subfamilies, two of which are based on Hydrophyllaceae and Lennoaceae, respectively. The type species of Tournefortia sect. Tournefortia is transferred to Heliotropium, as are its Malesian–Australian representatives.

  1. Using Remote Sensing Technology on the Delimitation of the Conservation Area for the Jianan Irrigation System Cultural Landsccape

    Directory of Open Access Journals (Sweden)

    C. H. Wang

    2015-08-01

    Full Text Available In recent years the cultural landscape has become an important issue for cultural heritages throughout the world. It represents the "combined works of nature and of man" designated in Article 1 of the World Heritage Convention. When a landscape has a cultural heritage value, important features should be marked and mapped through the delimitation of a conservation area, which may be essential for further conservation work. However, a cultural landscape’s spatial area is usually wider than the ordinary architectural type of cultural heritage, since various elements and impact factors, forming the cultural landscape’s character, lie within a wide geographic area. It is argued that the conservation of a cultural landscape may be influenced by the delimitation of the conservation area, the corresponding land management measures, the limits and encouragements. The Jianan Irrigation System, an historical cultural landscape in southern Taiwan, was registered as a living cultural heritage site in 2009. However, the system’s conservation should not be limited to just only the reservoir or canals, but expanded to irrigated areas where farmland may be the most relevant. Through the analysis process, only approximately 42,000 hectares was defined as a conservation area, but closely related to agricultural plantations and irrigated by the system. This is only half of the 1977 irrigated area due to urban sprawl and continuous industrial expansion.

  2. Delimitation of Areas of Environmental Conflicts on the Background of Geological Conditions, Exemplified by Stary Sącz Commune

    Directory of Open Access Journals (Sweden)

    Gałaś Slávka

    2014-12-01

    Full Text Available Delimitation and characterization of areas of conflict are essential to assess suitability of land for different activities carried out in the field of rational land use. In the paper, delimitation of the conflict areas and conflicts categorization in terms of possibility of their overcoming, the scale of the range and the period of their occurrence exemplified by urban - rural commune Stary Sącz have been presented. The software ArcGIS 10.1, the method of maps superimposing and analysis of interactions between different geoenvironmental factors have been applied to obtain the goal of the investigation. Specific geological structure together with morphological and climatic conditions in Stary Sącz commune create ideal conditions for occurrence of con-flict areas on the background of the geological conditions. Accurate and early recognition of these conflicts - existing and potential ones, is a prerequisite for the environmental risk prevention and elimination of its effects through the proper preparation of planning documents and development plans and programs.

  3. Using Remote Sensing Technology on the Delimitation of the Conservation Area for the Jianan Irrigation System Cultural Landsccape

    Science.gov (United States)

    Wang, C. H.

    2015-08-01

    In recent years the cultural landscape has become an important issue for cultural heritages throughout the world. It represents the "combined works of nature and of man" designated in Article 1 of the World Heritage Convention. When a landscape has a cultural heritage value, important features should be marked and mapped through the delimitation of a conservation area, which may be essential for further conservation work. However, a cultural landscape's spatial area is usually wider than the ordinary architectural type of cultural heritage, since various elements and impact factors, forming the cultural landscape's character, lie within a wide geographic area. It is argued that the conservation of a cultural landscape may be influenced by the delimitation of the conservation area, the corresponding land management measures, the limits and encouragements. The Jianan Irrigation System, an historical cultural landscape in southern Taiwan, was registered as a living cultural heritage site in 2009. However, the system's conservation should not be limited to just only the reservoir or canals, but expanded to irrigated areas where farmland may be the most relevant. Through the analysis process, only approximately 42,000 hectares was defined as a conservation area, but closely related to agricultural plantations and irrigated by the system. This is only half of the 1977 irrigated area due to urban sprawl and continuous industrial expansion.

  4. Two Distinct Approaches for CRISPR-Cas9-Mediated Gene Editing in Cryptococcus neoformans and Related Species.

    Science.gov (United States)

    Wang, Ping

    2018-06-27

    Cryptococcus neoformans and related species are encapsulated basidiomycetous fungi that cause meningoencephalitis in individuals with immune deficiency. This pathogen has a tractable genetic system; however, gene disruption via electroporation remains difficult, while biolistic transformation is often limited by lack of multiple genetic markers and the high initial cost of equipment. The approach using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has become the technology of choice for gene editing in many organisms due to its simplicity, efficiency, and versatility. The technique has been successfully demonstrated in C. neoformans and Cryptococcus deneoformans in which two DNA plasmids expressing either the Streptococcus pyogenes CAS9 gene or the guide RNA (gRNA) were employed. However, potential adverse effects due to constitutive expression and the time-consuming process of constructing vectors to express each gRNA remain as a primary barrier for wide adaptation. This report describes the delivery of preassembled CRISPR-Cas9-gRNA ribonucleoproteins (RNPs) via electroporation that is able to generate edited mutant alleles. RNP-mediated CRISPR-Cas9 was used to replace the wild-type GIB2 gene encoding a Gβ-like/RACK1 Gib2 protein with a gib2 :: NAT allele via homologous recombination in both C. neoformans and C. deneoformans In addition, a DNA plasmid (pCnCas9:U6-gRNA) that expresses both Cas9 and gRNA, allowing for convenient yet low-cost DNA-mediated gene editing, is described. pCnCas9:U6-gRNA contains an endogenous U6 promoter for gRNA expression and restriction sites for one-step insertion of a gRNA. These approaches and resources provide new opportunities to accelerate genetic studies of Cryptococcus species. IMPORTANCE For genetic studies of the Cryptococcus genus, generation of mutant strains is often hampered by a limited number of selectable genetic markers, the tedious process of vector

  5. Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species.

    Science.gov (United States)

    Chen, Hsi-Nien; Høeg, Jens T; Chan, Benny K K

    2013-01-01

    The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.

  6. A novel dendrochronological approach reveals drivers of carbon sequestration in tree species of riparian forests across spatiotemporal scales.

    Science.gov (United States)

    Rieger, Isaak; Kowarik, Ingo; Cherubini, Paolo; Cierjacks, Arne

    2017-01-01

    Aboveground carbon (C) sequestration in trees is important in global C dynamics, but reliable techniques for its modeling in highly productive and heterogeneous ecosystems are limited. We applied an extended dendrochronological approach to disentangle the functioning of drivers from the atmosphere (temperature, precipitation), the lithosphere (sedimentation rate), the hydrosphere (groundwater table, river water level fluctuation), the biosphere (tree characteristics), and the anthroposphere (dike construction). Carbon sequestration in aboveground biomass of riparian Quercus robur L. and Fraxinus excelsior L. was modeled (1) over time using boosted regression tree analysis (BRT) on cross-datable trees characterized by equal annual growth ring patterns and (2) across space using a subsequent classification and regression tree analysis (CART) on cross-datable and not cross-datable trees. While C sequestration of cross-datable Q. robur responded to precipitation and temperature, cross-datable F. excelsior also responded to a low Danube river water level. However, CART revealed that C sequestration over time is governed by tree height and parameters that vary over space (magnitude of fluctuation in the groundwater table, vertical distance to mean river water level, and longitudinal distance to upstream end of the study area). Thus, a uniform response to climatic drivers of aboveground C sequestration in Q. robur was only detectable in trees of an intermediate height class and in taller trees (>21.8m) on sites where the groundwater table fluctuated little (≤0.9m). The detection of climatic drivers and the river water level in F. excelsior depended on sites at lower altitudes above the mean river water level (≤2.7m) and along a less dynamic downstream section of the study area. Our approach indicates unexploited opportunities of understanding the interplay of different environmental drivers in aboveground C sequestration. Results may support species-specific and

  7. Classification of Suncus murinus species complex (Soricidae: Crocidurinae) in Peninsular Malaysia using image analysis and machine learning approaches.

    Science.gov (United States)

    Abu, Arpah; Leow, Lee Kien; Ramli, Rosli; Omar, Hasmahzaiti

    2016-12-22

    Taxonomists frequently identify specimen from various populations based on the morphological characteristics and molecular data. This study looks into another invasive process in identification of house shrew (Suncus murinus) using image analysis and machine learning approaches. Thus, an automated identification system is developed to assist and simplify this task. In this study, seven descriptors namely area, convex area, major axis length, minor axis length, perimeter, equivalent diameter and extent which are based on the shape are used as features to represent digital image of skull that consists of dorsal, lateral and jaw views for each specimen. An Artificial Neural Network (ANN) is used as classifier to classify the skulls of S. murinus based on region (northern and southern populations of Peninsular Malaysia) and sex (adult male and female). Thus, specimen classification using Training data set and identification using Testing data set were performed through two stages of ANNs. At present, the classifier used has achieved an accuracy of 100% based on skulls' views. Classification and identification to regions and sexes have also attained 72.5%, 87.5% and 80.0% of accuracy for dorsal, lateral, and jaw views, respectively. This results show that the shape characteristic features used are substantial because they can differentiate the specimens based on regions and sexes up to the accuracy of 80% and above. Finally, an application was developed and can be used for the scientific community. This automated system demonstrates the practicability of using computer-assisted systems in providing interesting alternative approach for quick and easy identification of unknown species.

  8. Combining Human Epigenetics and Sleep Studies in Caenorhabditis elegans: A Cross-Species Approach for Finding Conserved Genes Regulating Sleep.

    Science.gov (United States)

    Huang, Huiyan; Zhu, Yong; Eliot, Melissa N; Knopik, Valerie S; McGeary, John E; Carskadon, Mary A; Hart, Anne C

    2017-06-01

    We aimed to test a combined approach to identify conserved genes regulating sleep and to explore the association between DNA methylation and sleep length. We identified candidate genes associated with shorter versus longer sleep duration in college students based on DNA methylation using Illumina Infinium HumanMethylation450 BeadChip arrays. Orthologous genes in Caenorhabditis elegans were identified, and we examined whether their loss of function affected C. elegans sleep. For genes whose perturbation affected C. elegans sleep, we subsequently undertook a small pilot study to re-examine DNA methylation in an independent set of human participants with shorter versus longer sleep durations. Eighty-seven out of 485,577 CpG sites had significant differential methylation in young adults with shorter versus longer sleep duration, corresponding to 52 candidate genes. We identified 34 C. elegans orthologs, including NPY/flp-18 and flp-21, which are known to affect sleep. Loss of five additional genes alters developmentally timed C. elegans sleep (B4GALT6/bre-4, DOCK180/ced-5, GNB2L1/rack-1, PTPRN2/ida-1, ZFYVE28/lst-2). For one of these genes, ZFYVE28 (also known as hLst2), the pilot replication study again found decreased DNA methylation associated with shorter sleep duration at the same two CpG sites in the first intron of ZFYVE28. Using an approach that combines human epigenetics and C. elegans sleep studies, we identified five genes that play previously unidentified roles in C. elegans sleep. We suggest sleep duration in humans may be associated with differential DNA methylation at specific sites and that the conserved genes identified here likely play roles in C. elegans sleep and in other species. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  9. A Mixed-Method Approach for Quantifying Illegal Fishing and Its Impact on an Endangered Fish Species.

    Science.gov (United States)

    Free, Christopher M; Jensen, Olaf P; Mendsaikhan, Bud

    2015-01-01

    Illegal harvest is recognized as a widespread problem in natural resource management. The use of multiple methods for quantifying illegal harvest has been widely recommended yet infrequently applied. We used a mixed-method approach to evaluate the extent, character, and motivations of illegal gillnet fishing in Lake Hovsgol National Park, Mongolia and its impact on the lake's fish populations, especially that of the endangered endemic Hovsgol grayling (Thymallus nigrescens). Surveys for derelict fishing gear indicate that gillnet fishing is widespread and increasing and that fishers generally use 3-4 cm mesh gillnet. Interviews with resident herders and park rangers suggest that many residents fish for subsistence during the spring grayling spawning migration and that some residents fish commercially year-round. Interviewed herders and rangers generally agree that fish population sizes are decreasing but are divided on the causes and solutions. Biological monitoring indicates that the gillnet mesh sizes used by fishers efficiently target Hovsgol grayling. Of the five species sampled in the monitoring program, only burbot (Lota lota) showed a significant decrease in population abundance from 2009-2013. However, grayling, burbot, and roach (Rutilus rutilus) all showed significant declines in average body size, suggesting a negative fishing impact. Data-poor stock assessment methods suggest that the fishing effort equivalent to each resident family fishing 50-m of gillnet 11-15 nights per year would be sufficient to overexploit the grayling population. Results from the derelict fishing gear survey and interviews suggest that this level of effort is not implausible. Overall, we demonstrate the ability for a mixed-method approach to effectively describe an illegal fishery and suggest that these methods be used to assess illegal fishing and its impacts in other protected areas.

  10. COMPARISON OF WETLANDS DESIGNATED IN PROJECT ISOK AND BY DELIMITATION OF SOILS METHOD IN ŚRODA ŚLĄSKA DISTRICT

    Directory of Open Access Journals (Sweden)

    Adam Górecki

    2014-11-01

    Full Text Available This paper presents the results of a comparison floodareas made by two methods in Środa Śląska district. Using the tools of GIS did spatial analysis of maximum ranges of the floodaccording to the Preliminary Flood Risk Assessment method in Global Monitoring for Enviroment and Security Project (ISOK and the method base on delimitation of soils. The difference between wetlands designated in project ISOK compared to areas designated by the delimitation of soil method in the north-eastern part of the district is result of imprecision of the spatial and historical data about floods.Presented in the paper method designation of areas potentially floodingrisk by the delimitation of the soil, increase the spatial data about the phenomenon of flooding,and after considering borders of the parcels, can be used with ISOK resource by the local government in planning land cover.

  11. Using a distribution and conservation status weighted hotspot approach to identify areas in need of conservation action to benefit Idaho bird species

    Science.gov (United States)

    Haines, Aaron M.; Leu, Matthias; Svancara, Leona K.; Wilson, Gina; Scott, J. Michael

    2010-01-01

    Identification of biodiversity hotspots (hereafter, hotspots) has become a common strategy to delineate important areas for wildlife conservation. However, the use of hotspots has not often incorporated important habitat types, ecosystem services, anthropogenic activity, or consistency in identifying important conservation areas. The purpose of this study was to identify hotspots to improve avian conservation efforts for Species of Greatest Conservation Need (SGCN) in the state of Idaho, United States. We evaluated multiple approaches to define hotspots and used a unique approach based on weighting species by their distribution size and conservation status to identify hotspot areas. All hotspot approaches identified bodies of water (Bear Lake, Grays Lake, and American Falls Reservoir) as important hotspots for Idaho avian SGCN, but we found that the weighted approach produced more congruent hotspot areas when compared to other hotspot approaches. To incorporate anthropogenic activity into hotspot analysis, we grouped species based on their sensitivity to specific human threats (i.e., urban development, agriculture, fire suppression, grazing, roads, and logging) and identified ecological sections within Idaho that may require specific conservation actions to address these human threats using the weighted approach. The Snake River Basalts and Overthrust Mountains ecological sections were important areas for potential implementation of conservation actions to conserve biodiversity. Our approach to identifying hotspots may be useful as part of a larger conservation strategy to aid land managers or local governments in applying conservation actions on the ground.

  12. Revision of the West Palaearctic Polistes Latreille, with the descriptions of two species – an integrative approach using morphology and DNA barcodes (Hymenoptera, Vespidae

    Directory of Open Access Journals (Sweden)

    Christian Schmid-Egger

    2017-11-01

    Full Text Available The genus Polistes is revised for the West Palaearctic region based on morphology and DNA barcodes. The revision includes all known West Palaearctic species, raising the number of species in Europe to 14 and to 17 for the West Palaearctic realm. DNA barcodes were recovered from 15 species, 14 of which belong to the subgenus Polistes, and one, P. wattii, to the subgenus Gyrostoma. An integrative taxonomic approach combining morphology and molecular data (DNA barcoding was employed to resolve longstanding taxonomic problems in this group. Two species, P. austroccidentalis van Achterberg & Neumeyer, sp. n. (= P. semenowi auctt. from W and SW Europe and P. maroccanus Schmid-Egger, sp. n. from Morocco are described as new. Polistes bucharensis Erichson, 1849, and P. foederatus Kohl, 1898, were restored from synonymy. The following new synonyms are proposed: P. sulcifer Zimmermann, 1930, and Pseudopolistes sulcifer var. similator Zirngiebl, 1955, under P. semenowi Morawitz, 1889, syn. n.; Polistes iranus Guiglia, 1976, Polistes gallica var. ornata Weyrauch, 1938 and Polistes gallicus muchei Gusenleitner, 1976, under P. bucharensis Erichson, 1849, syn. n.; Polistes omissus var. ordubadensis Zirngiebl, 1955, and P. hellenicus Arens, 2011, under Polistes mongolicus du Buysson, 1911, syn. n. An illustrated key includes all species and additionally three species from the subgenera Aphanilopterus Meunier, 1888 and Gyrostoma Kirby, 1828 (including a Nearctic species recently introduced to Spain and two species occurring in Egypt, the Arabian Peninsula, and SW Asia. A phylogenetic analysis using Bayesian inference provides insights into phylogenetic relationships within the genus Polistes.

  13. Spatial pattern of nitrogen deposition flux over Czech forests: a novel approach accounting for unmeasured nitrogen species

    Science.gov (United States)

    Hůnová, Iva; Stoklasová, Petra; Kurfürst, Pavel; Vlček, Ondřej; Schovánková, Jana; Stráník, Vojtěch

    2015-04-01

    atmospheric nitrogen deposition flux over the Czech forests collating all available data and model results. The aim of the presented study is to provide an improved, more reliable and more realistic estimate of spatial pattern of nitrogen deposition flux over one country. This has so far been based standardly on measurements of ambient N/NOx concentrations as dry deposition proxy, and N/NH4+ and N/NO3- as wet deposition proxy. For estimate of unmeasured species contributing to dry deposition, we used an Eulerian photochemical dispersion model CAMx, the Comprehensive Air Quality Model with extensions (ESSS, 2011), coupled with a high resolution regional numeric weather prediction model Aladin (Vlček, Corbet, 2011). Contribution of fog was estimated using a geostatistical data driven model. Final maps accounting for unmeasured species clearly indicate, that so far used approach results in substantial underestimation of nitrogen deposition flux. Substitution of unmeasured nitrogen species by modeled values seems to be a plausible way for approximation of total nitrogen deposition, and getting more realistic spatial pattern as input for further studies of likely nitrogen impacts on ecosystems. Acknowledgements: We would like to acknowledge the grants GA14-12262S - Effects of changing growth conditions on tree increment, stand production and vitality - danger or opportunity for the Central-European forestry?, and NAZV QI112A168 (ForSoil) of the Czech Ministry for Agriculture for support of this contribution. The input data used for the analysis were provided by the Czech Hydrometeorological Institute. References: Bobbink, R., Hicks, K., Galloway, J., Spranger, T., Alkemade, R. et al. (2010): Global Assessment of Nitrogen Deposition Effects on Terrestrial Plant Diversity: a Synthesis. Ecological Applications 20 (1), 30-59. Fowler D., O'Donoghue M., Muller J.B.A, et al. (2005): A chronology of nitrogen deposition in the UK between 1900 and 2000. Watter, Air & Soil Pollution: Focus

  14. A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach.

    Science.gov (United States)

    Faurby, Søren; Svenning, Jens-Christian

    2015-03-01

    Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions.

    Science.gov (United States)

    Powers, T O; Bernard, E C; Harris, T; Higgins, R; Olson, M; Olson, S; Lodema, M; Matczyszyn, J; Mullin, P; Sutton, L; Powers, K S

    2016-03-03

    There are many nematode species that, following formal description, are seldom mentioned again in the scientific literature. Lobocriconema thornei and L. incrassatum are two such species, described from North American forests, respectively 37 and 49 years ago. In the course of a 3-year nematode biodiversity survey of North American ecoregions, specimens resembling Lobocriconema species appeared in soil samples from both grassland and forested sites. Using a combination of molecular and morphological analyses, together with a set of species delimitation approaches, we have expanded the known range of these species, added to the species descriptions, and discovered a related group of species that form a monophyletic group with the two described species. In this study, 148 specimens potentially belonging to the genus Lobocriconema were isolated from soil, individually measured, digitally imaged, and DNA barcoded using a 721 bp region of cytochrome oxidase subunit 1 (COI). One-third of the specimens were also analyzed using amplified DNA from the 3' region of the small subunit ribosomal RNA gene (18SrDNA) and the adjacent first internal transcribed spacer (ITS1). Eighteen mitochondrial haplotype groups, falling into four major clades, were identified by well-supported nodes in Bayesian and maximum likelihood trees and recognized as distinct lineages by species delimitation metrics. Discriminant function analysis of a set of morphological characters indicated that the major clades in the dataset possessed a strong morphological signal that decreased in comparisons of haplotype groups within clades. Evidence of biogeographic and phylogeographic patterns was apparent in the dataset. COI haplotype diversity was high in the southern Appalachian Mountains and Gulf Coast states and lessened in northern temperate forests. Lobocriconema distribution suggests the existence of phylogeographic patterns associated with recolonization of formerly glaciated regions by eastern

  16. Plant species diversity as a driver of early succession in abandoned fields: a multi-site approach.

    Science.gov (United States)

    Van der Putten, W H; Mortimer, S R; Hedlund, K; Van Dijk, C; Brown, V K; Lepä, J; Rodriguez-Barrueco, C; Roy, J; Diaz Len, T A; Gormsen, D; Korthals, G W; Lavorel, S; Regina, I Santa; Smilauer, P

    2000-07-01

    Succession is one of the most studied processes in ecology and succession theory provides strong predictability. However, few attempts have been made to influence the course of succession thereby testing the hypothesis that passing through one stage is essential before entering the next one. At each stage of succession ecosystem processes may be affected by the diversity of species present, but there is little empirical evidence showing that plant species diversity may affect succession. On ex-arable land, a major constraint of vegetation succession is the dominance of perennial early-successional (arable weed) species. Our aim was to change the initial vegetation succession by the direct sowing of later-successional plant species. The hypothesis was tested that a diverse plant species mixture would be more successful in weed suppression than species-poor mixtures. In order to provide a robust test including a wide range of environmental conditions and plant species, experiments were carried out at five sites across Europe. At each site, an identical experiment was set up, albeit that the plant species composition of the sown mixtures differed from site to site. Results of the 2-year study showed that diverse plant species mixtures were more effective at reducing the number of natural colonisers (mainly weeds from the seed bank) than the average low-diversity treatment. However, the effect of the low-diversity treatment depended on the composition of the species mixture. Thus, the effect of enhanced species diversity strongly depended on the species composition of the low-diversity treatments used for comparison. The effects of high-diversity plant species mixtures on weed suppression differed between sites. Low-productivity sites gave the weakest response to the diversity treatments. These differences among sites did not change the general pattern. The present results have implications for understanding biological invasions. It has been hypothesised that alien

  17. Delimitation of Umbelopsis (Mucorales, Umbelopsidaceae fam. nov.) based on ITS sequence and RFLP data.

    Science.gov (United States)

    Meyer, Wieland; Gams, Walter

    2003-03-01

    In a continuation of studies started by de Ruiter et al. (1993), all known species of the Mortierella isabellina-group (Micromucor/Umbelopsis clade of O'Donnell et al. 2001) and a few other Mucorales and species of Mortierella were investigated by RFLP (including ITS1, 5.8S, ITS2 and the 5' end of the large subunit rDNA gene) and ITS1 sequence analyses. This monophyletic group is unrelated to Mortierella and is only distantly related to the core group of the Mucoraceae. M. longicollis falls outside the Umbelopsis clade. Molecular data resolved two subclades within the M. isabellina-group; however, they are not correlated with any differences in sporangial wall and shape, spore pigmentation and shape, or sporangiophore branching. Therefore we subsume all taxa in one genus, Umbelopsis. The new family Umbelopsidaceae and the new combinations U. isabellina, U. ramanniana, and U. autotrophica are proposed.

  18. DELIMITATION OF THE DISCRETIONARY POWER FROM THE POWER EXCESS IN THE ACTIVITY OF THE STATE’S AUTHORITIES

    Directory of Open Access Journals (Sweden)

    MARIUS ANDREESCU

    2012-05-01

    Full Text Available A problem of essence of the lawful state is to delimitate the discretionary power and respectively, the abuse ofright in the state’s institutions activities. The legal behavior of the state institutions is being materialized by their right of appreciation, and the power excess yields in the violation of a subjective right or a legitimate interest of the citizen. The application and observance of the lawfulness principle in the activity of the state authorities is a complex problem because the exercise of the state’s functions assumes the discretionary power with which the state’s organs are invested with, or otherwise said the ‘right of appreciation” of the state’s authorities regarding the moment of adopting and the contents of the disposed measures. The discretionary power cannot be opposed to the lawfulness principle, as a dimension of the lawful state. In this study we propose ourselves to analyze the discretionary power concepts and respectively, the excess of power, having as landmark the legislation, jurisprudence and the doctrine in the matter. At the same time, we wish to identify the most important criterions that will allow the practitioner, no matter whether he / she is an administrator, a public clerk or a judge, to delimit the legal behavior of the state’s institutions from the power excess. In this regard, we appreciate that the principle of proportionality represents such a criterion. We consider that the law courts, by applying the principle of Constitution’s supremacy, can censor some juridical acts contrary to the constitutional norms, if the Lawmaker does not foresee the competence of the Constitutional Court in this matter. In our opinion, all law courts, within the limits of the competence granted by law, can control and censor the juridical acts of some public authorities issued by power excess. In order to demonstrate these assertions some theoretical and juridical practice arguments are being brought.

  19. The species sensivity distribution approach compared to a micrososm study: A case study with the fungicide fluazinam

    NARCIS (Netherlands)

    Wijngaarden, van R.P.A.; Arts, G.H.P.; Belgers, J.D.M.; Boonstra, H.; Roessink, I.; Schroer, A.F.W.; Brock, T.C.M.

    2010-01-01

    We assessed the sensitivity of freshwater organisms (invertebrates and algae) to the fungicide Shirlan® (active ingredient fluazinam) in single-species laboratory tests and in microcosms. Species sensitivity distribution (SSD) curves were constructed by means of acute toxicity data for 14

  20. A multi-criteria decisionmaking approach to management indicator species selection for the Monongahela National Forest, West Virginia.

    Science.gov (United States)

    Kurtis R. Moseley; W.Mark Ford; John W. Edwards; Michael P. Strager

    2010-01-01

    The management indicator species concept is useful for land managers charged with monitoring and conserving complex biological diversity over large landscapes with limited available resources. We used the analytical hierarchy process (AHP) to determine the best management indicator species (MIS) for three...

  1. Biodiversity and biogeography of Fusarium species from northeastern North American asparagus fields based on microbiological and molecular approaches

    NARCIS (Netherlands)

    Vujanovic, V.; Hamel, C.; Yergeau, E.; St-Arnaud, M.

    2006-01-01

    Sixteen Fusarium species were recovered from 52 asparagus commercial fields, representing all major ecological (edaphic and climatic) area of asparagus production in the province of Québec, eastern Canada. This study extends our understanding of the geographic range of these species. It also

  2. High Species Richness of Scinax Treefrogs (Hylidae in a Threatened Amazonian Landscape Revealed by an Integrative Approach.

    Directory of Open Access Journals (Sweden)

    Miquéias Ferrão

    Full Text Available Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus Scinax over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of Scinax is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus Scinax, in addition to the already-known S. rostratus species Group. Quantifying and characterizing the number of undescribed Scinax taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian Scinax treefrogs.

  3. A mechanistic approach to link biological effects of radioactive substances from molecules to populations in wildlife species - A mechanistic approach to link biological effects of radionuclides from molecules to populations in wildlife species

    Energy Technology Data Exchange (ETDEWEB)

    Alonzo, Frederic; Parisot, Florian; Plaire, Delphine; Adam-Guillermin, Christelle; Garnier- Laplace, Jacqueline [Institut de Radioprotection et de Surete Nucleaire (IRSN), PRP-ENV, SERIS, LECO, Cadarache, Saint-Paul- Lez-Durance, 13115 (France)

    2014-07-01

    Understanding how toxic contaminants affect wildlife species at various levels of biological organisation (sub-cellular, histological, physiological, organism, population levels) is a major research goal in both ecotoxicology and radioecology. A mechanistic understanding of the links between the different observed perturbations is necessary to predict consequences for survival, growth and reproduction which are critical for population dynamics. However, time scales at which such links are established in the laboratory are rarely relevant for natural populations. With a small size and short life cycle, the cladoceran micro-crustacean Daphnia magna is a particularly suitable biological model for studying effects of radioactive contaminants over several generations. Multi-generational exposures are much more representative of the environmental context of field populations for which contaminations can last for durations which largely exceed individual longevity and involve exposure of many successive generations. Over the last decade, multi-generational investigations of toxic effects were conducted under controlled conditions in D. magna exposed to various radionuclides including depleted uranium, americium-241 and cesium-137, representing respectively a dominantly chemo-toxic metal, an alpha internal contamination and a gamma external radiation. Results showed in all cases that toxic effects on physiology and life history (survival, body size, fecundity) increased in severity across generations. These observations demonstrated that measured effects in one generation might not be representative of toxicity in the following offspring generations, and ultimately of the population response. Reduction in somatic growth and reproduction induced by uranium were analysed using the mechanistic modelling approach known as DEBtox (model of dynamic energy budget applied to toxicology). Modelling results suggested that uranium primarily affects assimilation. This metabolic mode

  4. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.

    Science.gov (United States)

    Chambers, E Anne; Hebert, Paul D N

    2016-01-01

    High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.

  5. Similarities and differences in adult tortoises: a morphological approach and its implication for reproduction and mobility between species

    Directory of Open Access Journals (Sweden)

    Marco A. L. Zuffi

    2007-11-01

    Full Text Available Sexes in Chelonia display marked differences. Sexual size dimorphism (SSD is important in evolutionary biology. Different sexual strategies result in species specific selection. Biometric variation in male and female tortoises of two species is studied. Eighteen biometrics were measured in 75 museum specimens (20 Testudo graeca; 55 T. hermanni. Nine of 18 parameters in T. hermanni and two of 18 in T. graeca were sexually dimorphic. Multivariate analyses (principal component analysis highlighted two components, with bridge length the first and anal divergence the second component. The bridge length can be used to separate sexes and species. Males of both species were most different, whereas females of two species overlapped in body shape measurements. We hypothesise that female similarity could be a by-product of reproductive biology and sexual selection that optimise individual fitness.

  6. Geographic variation in species richness, rarity, and the selection of areas for conservation: An integrative approach with Brazilian estuarine fishes

    Science.gov (United States)

    Vilar, Ciro C.; Joyeux, Jean-Christophe; Spach, Henry L.

    2017-09-01

    While the number of species is a key indicator of ecological assemblages, spatial conservation priorities solely identified from species richness are not necessarily efficient to protect other important biological assets. Hence, the results of spatial prioritization analysis would be greatly enhanced if richness were used in association to complementary biodiversity measures. In this study, geographic patterns in estuarine fish species rarity (i.e. the average range size in the study area), endemism and richness, were mapped and integrated to identify regions important for biodiversity conservation along the Brazilian coast. Furthermore, we analyzed the effectiveness of the national system of protected areas to represent these regions. Analyses were performed on presence/absence data of 412 fish species in 0.25° latitudinal bands covering the entire Brazilian biogeographical province. Species richness, rarity and endemism patterns differed and strongly reflected biogeographical limits and regions. However, among the existing 154 latitudinal bands, 48 were recognized as conservation priorities by concomitantly harboring high estuarine fish species richness and assemblages of geographically rare species. Priority areas identified for all estuarine fish species largely differed from those identified for Brazilian endemics. Moreover, there was no significant correlation between the different aspects of the fish assemblages considered (i.e. species richness, endemism or rarity), suggesting that designating reserves based on a single variable may lead to large gaps in the overall protection of biodiversity. Our results further revealed that the existing system of protected areas is insufficient for representing the priority bands we identified. This highlights the urgent need for expanding the national network of protected areas to maintain estuarine ecosystems with high conservation value.

  7. Peristome as a potential tool for delimiting Bryum Hedw. (Bryaceae) from India.

    Science.gov (United States)

    Bansal, Pooja; Nath, Virendra

    2018-02-26

    The peristome, an interesting and important taxonomic structure used in the systematics of mosses, is for the first time studied in detail for 21 taxa of Bryum, which constitute a fraction of Indian representatives. Macro- and micro-morphological characters including color, size and length of two components of peristome, tapering pattern, median line, and papillosity at upper part under light microscope; width of exostome border, number and inner surface of ventral trabeculae, presence or absence of longitudinal/oblique septae between ventral trabeculae, pattern of exostome surface and height of endostomial basal membrane, adherence, perforations, and surface of cilia under scanning electron microscope were examined to bring out submicroscopic differences. Detail surface structure of eight taxa, viz., B. apalodictyoides, B. evanidinerve, B. pachytheca, B. pseudotriquetrum var. subrotundum, B. reflexifolium, B. thomsonii, B. tuberosum, and B. turbinatum, under LM and nine species, namely, B. apalodictyoides, B. apiculatum, B. argenteum, B. billarderi, B. dichotomum, B. evanidinerve, B. recurvulum, B. turbinatum, and B. uliginosum, under SEM is being provided for the first time. Description of peristome surface and a key based on SEM and other taxonomical features is also being provided. The data obtained from the present study suggest that the species of this genus can easily be distinguished on the basis of peristomial surface pattern.

  8. Quantitative comparisons of three modeling approaches for characterizing drought response of a highly variable, widely grown crop species

    Science.gov (United States)

    Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B. E.; Wienig, C.

    2013-12-01

    Quantifying the drought tolerance of crop species and genotypes is essential in order to predict how water stress may impact agricultural productivity. As climate models predict an increase in both frequency and severity of drought corresponding plant hydraulic and biochemical models are needed to accurately predict crop drought tolerance. Drought can result in cavitation of xylem conduits and related loss of plant hydraulic conductivity. This study tested the hypothesis that a model incorporating a plants vulnerability to cavitation would best assess drought tolerance in Brassica rapa. Four Brassica genotypes were subjected to drought conditions at a field site in Laramie, WY. Concurrent leaf gas exchange, volumetric soil moisture content and xylem pressure measurements were made during the drought period. Three models were used to access genotype specific drought tolerance. All 3 models rely on the Farquhar biochemical/biophysical model of leaf level photosynthesis, which is integrated into the Terrestrial Regional Ecosystem Exchange Simulator (TREES). The models differ in how TREES applies the environmental driving data and plant physiological mechanisms; specifically how water availability at the site of photosynthesis is derived. Model 1 established leaf water availability from a modeled soil moisture content; Model 2 input soil moisture measurements directly to establish leaf water availability; Model 3 incorporated the Sperry soil-plant transport model, which calculates flows and pressure along the soil-plant water transport pathway to establish leaf water availability. This third model incorporated measured xylem pressures thus constraining leaf water availability via genotype specific vulnerability curves. A multi-model intercomparison was made using a Bayesian approach, which assessed the interaction between uncertainty in model results and data. The three models were further evaluated by assessing model accuracy and complexity via deviance information

  9. SNPs in Multi-Species Conserved Sequences (MCS as useful markers in association studies: a practical approach

    Directory of Open Access Journals (Sweden)

    Pericak-Vance Margaret A

    2007-08-01

    Full Text Available Abstract Background Although genes play a key role in many complex diseases, the specific genes involved in most complex diseases remain largely unidentified. Their discovery will hinge on the identification of key sequence variants that are conclusively associated with disease. While much attention has been focused on variants in protein-coding DNA, variants in noncoding regions may also play many important roles in complex disease by altering gene regulation. Since the vast majority of noncoding genomic sequence is of unknown function, this increases the challenge of identifying "functional" variants that cause disease. However, evolutionary conservation can be used as a guide to indicate regions of noncoding or coding DNA that are likely to have biological function, and thus may be more likely to harbor SNP variants with functional consequences. To help bias marker selection in favor of such variants, we devised a process that prioritizes annotated SNPs for genotyping studies based on their location within Multi-species Conserved Sequences (MCSs and used this process to select SNPs in a region of linkage to a complex disease. This allowed us to evaluate the utility of the chosen SNPs for further association studies. Previously, a region of chromosome 1q43 was linked to Multiple Sclerosis (MS in a genome-wide screen. We chose annotated SNPs in the region based on location within MCSs (termed MCS-SNPs. We then obtained genotypes for 478 MCS-SNPs in 989 individuals from MS families. Results Analysis of our MCS-SNP genotypes from the 1q43 region and comparison to HapMap data confirmed that annotated SNPs in MCS regions are frequently polymorphic and show subtle signatures of selective pressure, consistent with previous reports of genome-wide variation in conserved regions. We also present an online tool that allows MCS data to be directly exported to the UCSC genome browser so that MCS-SNPs can be easily identified within genomic regions of

  10. A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

    Science.gov (United States)

    Clerc-Blain, Jessica L E; Starr, Julian R; Bull, Roger D; Saarela, Jeffery M

    2010-01-01

    Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies. © 2009 Blackwell Publishing Ltd.

  11. A spatially and temporally explicit, individual-based, life-history and productivity modeling approach for aquatic species

    Science.gov (United States)

    Realized life history expression and productivity in aquatic species, and salmonid fishes in particular, is the result of multiple interacting factors including genetics, habitat, growth potential and condition, and the thermal regime individuals experience, both at critical stag...

  12. Salvinia molesta D. S. Mitchell (Giant Salvinia) in the United States: A Review of Species Ecology and Approaches to Management

    National Research Council Canada - National Science Library

    McFarland, D

    2004-01-01

    .... Though innocuous within its native range, elsewhere this species is an aggressive menace that has had devastating ecological and socioeconomic impacts on aquatic systems in parts of Africa, Sri Lanka...

  13. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

    2011-12-01

    Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

  14. Biodiversity of Fusarium species in Mexico associated with ear rot in maize, and their identification using a phylogenetic approach.

    Science.gov (United States)

    Morales-Rodríguez, Irma; Yañez-Morales, María de J; Silva-Rojas, Hilda V; García-de-Los-Santos, Gabino; Guzmán-de-Peña, Doralinda A

    2007-01-01

    Fusarium proliferatum, F. subglutinans, and F. verticillioides are known causes of ear and kernel rot in maize worldwide. In Mexico, only F. verticillioides and F. subglutinans, have been reported previously as causal agents of this disease. However, Fusarium isolates with different morphological characteristics to the species that are known to cause this disease were obtained in the Highland-Valley region of this country from symptomatic and symptomless ears of native and commercial maize genotypes. Moreover, while the morphological studies were not sufficient to identify the correct taxonomic position at the species level, analyses based in the Internal Transcribed Spacer region and the Nuclear Large Subunit Ribosomal partial sequences allowed for the identification of F. subglutinans, F. solani, and F. verticillioides, as well as four species (F. chlamydosporum, F. napiforme, F. poae, and F. pseudonygamai) that had not previously been reported to be associated with ear rot. In addition, F. napiforme and F. solani were absent from symptomless kernels. Phylogenetic analysis showed genetic changes in F. napiforme, and F. pseudonygamai isolates because they were not true clones, and probably constitute separate sibling species. The results of this study suggest that the biodiversity of Fusarium species involved in ear rot in Mexico is greater than that reported previously in other places in the world. This new knowledge will permit a better understanding of the relationship between all the species involved in ear rot disease and their relationship with maize.

  15. Characterization of the salt stress vulnerability of three invasive freshwater plant species using a metabolic profiling approach.

    Science.gov (United States)

    Thouvenot, Lise; Deleu, Carole; Berardocco, Solenne; Haury, Jacques; Thiébaut, Gabrielle

    2015-03-01

    The effects of salt stress on freshwater plants has been little studied up to now, despite the fact that they are expected to present different levels of salt sensitivity or salt resistance depending on the species. The aim of this work was to assess the effect of NaCl at two concentrations on three invasive freshwater species, Elodea canadensis, Myriophyllum aquaticum and Ludwigia grandiflora, by examining morphological and physiological parameters and using metabolic profiling. The growth rate (biomass and stem length) was reduced for all species, whatever the salt treatment, but the response to salt differed between the three species, depending on the NaCl concentration. For E. canadensis, the physiological traits and metabolic profiles were only slightly modified in response to salt, whereas M. aquaticum and L. grandiflora showed great changes. In both of these species, root number, photosynthetic pigment content, amino acids and carbohydrate metabolism were affected by the salt treatments. Moreover, we are the first to report the salt-induced accumulation of compatible solutes in both species. Indeed, in response to NaCl, L. grandiflora mainly accumulated sucrose. The response of M. aquaticum was more complex, because it accumulated not only sucrose and myo-inositol whatever the level of salt stress, but also amino acids such as proline and GABA, but only at high NaCl concentrations. These responses are the metabolic responses typically found in terrestrial plants. Copyright © 2014 Elsevier GmbH. All rights reserved.

  16. Otolith shape analysis and mitochondrial DNA markers distinguish three sand smelt species in the Atherina boyeri species complex in western Mediterranean

    Science.gov (United States)

    Boudinar, A. S.; Chaoui, L.; Quignard, J. P.; Aurelle, D.; Kara, M. H.

    2016-12-01

    Atherina boyeri is a common euryhaline teleost fish in the Mediterranean and adjacent areas, which inhabits coastal and estuarine waters, including coastal lagoons and more rarely inland waters. Several recent studies have pointed the possible existence of three distinct groups or species, one lagoon/freshwater group and two 'punctuated and unpunctuated on the flanks' marine groups, within an A. boyeri species complex. This study is a combined approach using otolith shape and molecular markers to better define the structure of the species in the western Mediterranean. Genetic differentiation and species delimitation among nine Atherina boyeri populations from several marine and lagoon/brakish habitat sites in Algeria, Tunisia and France were investigated using three mitochondrial (control region, Cyt b and 16S) and one nuclear markers (2nd intron of S7). For further phylogenetic and phylogeographic study, we added sequences from Genbank covering more areas (Ionian Sea, Adriatic Sea, Tyrrhenian Sea, Black Sea, Atlantic). Five groups were found. Two of them perfectly corresponded to two species already recognized Atherina presbyter and Atherina hepsetus, both living in marine waters; and three additional, including Atherina boyeri (brackish and freshwater environments) and two independent groups of marine punctated and unpunctated individuals. Those findings are corroborated by the study of the otolith contour shape of 362 individuals of seven populations from different habitats using Fourier analysis. Individuals could be discriminated into five groups based on the first two functions (Wilk's lambda = 0.07, p < 0.001). Samples from Ziama inlet, marine punctuated individuals and unpunctuated marine specimens from Annaba's Gulf formed three well separated groups. Specimens from Mellah and Mauguio lagoons formed another group. The last one includes individuals from Bizerte and Thau lagoons. The divergences between them strongly support the potential species within the

  17. Genetic differentiation among species of the genus Thermophis Malnate (Serpentes, Colubridae) and comments on T. shangrila.

    Science.gov (United States)

    Hofmann, Sylvia; Tillack, Frank; Miehe, Georg

    2015-10-07

    The genus Thermophis includes the two species, T. baileyi and T. zhaoermii, which differ morphologically, geographically and molecularly. Recently, a third Thermophis species was described from Shangri-La, northern Yunnan Province, China, and named T. shangrila. The new species was based on morphological and genetic data derived from three specimens. However, the morphological features used to delimit this species seem vague, because they may fall within the range of intraspecific variation of T. zhaoermii. Furthermore, the reported genetic differences in nuclear data are questionable. They likely resulted from a misinterpretation probably due to alignment/analytical flaws or sample/sequence mix-up. Here, we used partial sequences of three mitochondrial (CO1, ND4, cytb) genes and one nuclear (c-mos) gene to analyse the genetic variation between and within species of Thermophis. We inferred the phylogeny using Bayesian Inference and Maximum Likelihood approaches and present additional morphological data that contribute to the knowledge on intraspecific variation in the genus. Our results indicate lacking robustness in the distinguishing morphological features and in the genetic differentiation of T. shangrila and highlight the need for more detailed morphological and molecular studies from a substantially larger sample.

  18. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta.

    Directory of Open Access Journals (Sweden)

    Shanmei Zou

    Full Text Available Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.

  19. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)

    Science.gov (United States)

    Zou, Shanmei; Fei, Cong; Song, Jiameng; Bao, Yachao; He, Meilin; Wang, Changhai

    2016-01-01

    Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella–like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential “specific barcode” for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes. PMID:27092945

  20. Chemical modeling of groundwater in the Banat Plain, southwestern Romania, with elevated As content and co-occurring species by combining diagrams and unsupervised multivariate statistical approaches.

    Science.gov (United States)

    Butaciu, Sinziana; Senila, Marin; Sarbu, Costel; Ponta, Michaela; Tanaselia, Claudiu; Cadar, Oana; Roman, Marius; Radu, Emil; Sima, Mihaela; Frentiu, Tiberiu

    2017-04-01

    The study proposes a combined model based on diagrams (Gibbs, Piper, Stuyfzand Hydrogeochemical Classification System) and unsupervised statistical approaches (Cluster Analysis, Principal Component Analysis, Fuzzy Principal Component Analysis, Fuzzy Hierarchical Cross-Clustering) to describe natural enrichment of inorganic arsenic and co-occurring species in groundwater in the Banat Plain, southwestern Romania. Speciation of inorganic As (arsenite, arsenate), ion concentrations (Na + , K + , Ca 2+ , Mg 2+ , HCO 3 - , Cl - , F - , SO 4 2- , PO 4 3- , NO 3 - ), pH, redox potential, conductivity and total dissolved substances were performed. Classical diagrams provided the hydrochemical characterization, while statistical approaches were helpful to establish (i) the mechanism of naturally occurring of As and F - species and the anthropogenic one for NO 3 - , SO 4 2- , PO 4 3- and K + and (ii) classification of groundwater based on content of arsenic species. The HCO 3 - type of local groundwater and alkaline pH (8.31-8.49) were found to be responsible for the enrichment of arsenic species and occurrence of F - but by different paths. The PO 4 3- -AsO 4 3- ion exchange, water-rock interaction (silicates hydrolysis and desorption from clay) were associated to arsenate enrichment in the oxidizing aquifer. Fuzzy Hierarchical Cross-Clustering was the strongest tool for the rapid simultaneous classification of groundwaters as a function of arsenic content and hydrogeochemical characteristics. The approach indicated the Na + -F - -pH cluster as marker for groundwater with naturally elevated As and highlighted which parameters need to be monitored. A chemical conceptual model illustrating the natural and anthropogenic paths and enrichment of As and co-occurring species in the local groundwater supported by mineralogical analysis of rocks was established. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour.

    Science.gov (United States)

    Kaiser-Bunbury, Christopher N; Muff, Stefanie; Memmott, Jane; Müller, Christine B; Caflisch, Amedeo

    2010-04-01

    Species extinctions pose serious threats to the functioning of ecological communities worldwide. We used two qualitative and quantitative pollination networks to simulate extinction patterns following three removal scenarios: random removal and systematic removal of the strongest and weakest interactors. We accounted for pollinator behaviour by including potential links into temporal snapshots (12 consecutive 2-week networks) to reflect mutualists' ability to 'switch' interaction partners (re-wiring). Qualitative data suggested a linear or slower than linear secondary extinction while quantitative data showed sigmoidal decline of plant interaction strength upon removal of the strongest interactor. Temporal snapshots indicated greater stability of re-wired networks over static systems. Tolerance of generalized networks to species extinctions was high in the random removal scenario, with an increase in network stability if species formed new interactions. Anthropogenic disturbance, however, that promote the extinction of the strongest interactors might induce a sudden collapse of pollination networks.

  2. Rapid approach to identify the presence of Arabica and Robusta species in coffee using 1H NMR spectroscopy.

    Science.gov (United States)

    Monakhova, Yulia B; Ruge, Winfried; Kuballa, Thomas; Ilse, Maren; Winkelmann, Ole; Diehl, Bernd; Thomas, Freddy; Lachenmeier, Dirk W

    2015-09-01

    NMR spectroscopy was used to verify the presence of Arabica and Robusta species in coffee. Lipophilic extracts of authentic roasted and green coffees showed the presence of established markers for Robusta (16-O-methylcafestol (16-OMC)) and for Arabica (kahweol). The integration of the 16-OMC signal (δ 3.165 ppm) was used to estimate the amount of Robusta in coffee blends with an approximate limit of detection of 1-3%. The method was successfully applied for the analysis of 77 commercial coffee samples (coffee pods, coffee capsules, and coffee beans). Furthermore, principal component analysis (PCA) was applied to the spectra of lipophilic and aqueous extracts of 20 monovarietal authentic samples. Clusters of the two species were observed. NMR spectroscopy can be used as a rapid prescreening tool to discriminate Arabica and Robusta coffee species before the confirmation applying the official method. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. A spatially-explicit data driven approach to assess the effect of agricultural land occupation on species groups

    Science.gov (United States)

    Elshout, P.; van Zelm, R.; Karuppiah, R.; Laurenzi, I.; Huijbregts, M.

    2013-12-01

    Change of vegetation cover and increased land use intensity can directly affect the natural habitat and the wildlife it houses. The actual impact of agricultural land use is region specific as crops are grown under various climatic conditions and ways of cultivation and refining. Furthermore, growing a specific crop in a tropical region may require clearance of rainforest while the same crop may replace natural grasslands in temperate regions. Within life cycle impact assessment (LCIA), methods to address impacts of land use on a global scale are still in need of development. We aim to extend existing methods to improve the robustness of LCIA by allowing spatial differentiation of agricultural land use impacts. The goal of this study is to develop characterization factors for the direct impact of land use on biodiversity, which results from the replacement of natural habitat with farmland. The characterization factor expresses the change in species richness under crop cultivation compared to the species richness in the natural situation over a certain area. A second goal was to identify the differences in impacts caused by cultivation of different crop types, sensitivity of different taxonomic groups, and differences in natural land cover. Empirical data on species richness were collected from literature for both natural reference situations and agricultural land use situations. Reference situations were selected on an ecoregion or biome basis. We calculated characterization factors for four crop groups (oil palm, low crops, cereals, and perennial grasses), four species groups (arthropods, birds, mammals, vascular plants), and six biomes.

  4. Understanding the extreme species richness of semi-dry grasslands in east-central Europe: a comparative approach

    Czech Academy of Sciences Publication Activity Database

    Roleček, Jan; Čornej, I. I.; Tokarjuk, A. I.

    2014-01-01

    Roč. 86, č. 1 (2014), s. 13-34 ISSN 0032-7786 R&D Projects: GA ČR(CZ) GAP504/12/0649 Institutional support: RVO:67985939 Keywords : species richness * environmental history * disjunct distribution Subject RIV: EF - Botanics Impact factor: 4.104, year: 2014

  5. Neutralization and attenuation of metal species in acid mine drainage and mine leachates using magnesite: a batch experimental approach

    CSIR Research Space (South Africa)

    Masindi, Vhahangwele

    2014-08-01

    Full Text Available International Mine Water Association Conference – An Interdisciplinary Response to Mine Water Challenges, China University of Mining and Technogy, China, China, 18-22 August 2014 Neutralization and Attenuation of Metal Species in Acid Mine Drainage and Mine...

  6. The use of network analysis in the process of delimitation as exemplifi ed by the administrative division of Poland

    Directory of Open Access Journals (Sweden)

    Borowska-Stefańska Marta

    2017-12-01

    Full Text Available The cognitive aim of this study is to point to the optimum number of local government units and the optimum boundaries of spatial units in Poland with the assumption of minimizing the cumulated theoretical travel time to all settlement units in the country. The methodological aim, in turn, is to present the use of the ArcGIS location-allocation tool for the purposes of delimitation processes as exemplifi ed by administrative boundaries in Poland. The rationale for the implementation of this study is that number and the boundaries of units of all levels of Poland’s current territorial division are far from optimum in the light of minimization of accumulated theoretical travel time to all settlement units in the country. It may be concluded that it would be justifi able to increase the number of voivodships from the current number of 16 to 18. Besides it would be necessary to introduce modifi cations in relation to units with regional functions. In contrast, the number of districts and communes should be reduced. A continuation of this research may go in the direction of including analysis of public transport network in the research, creating in this way a multimodal set of network data. This would illustrate, apart from the potential itself resulting from the infrastructure, also the actually existing connections.

  7. The use of network analysis in the process of delimitation as exemplifi ed by the administrative division of Poland

    Science.gov (United States)

    Borowska-Stefańska, Marta; Wiśniewski, Szymon

    2017-12-01

    The cognitive aim of this study is to point to the optimum number of local government units and the optimum boundaries of spatial units in Poland with the assumption of minimizing the cumulated theoretical travel time to all settlement units in the country. The methodological aim, in turn, is to present the use of the ArcGIS location-allocation tool for the purposes of delimitation processes as exemplifi ed by administrative boundaries in Poland. The rationale for the implementation of this study is that number and the boundaries of units of all levels of Poland's current territorial division are far from optimum in the light of minimization of accumulated theoretical travel time to all settlement units in the country. It may be concluded that it would be justifi able to increase the number of voivodships from the current number of 16 to 18. Besides it would be necessary to introduce modifi cations in relation to units with regional functions. In contrast, the number of districts and communes should be reduced. A continuation of this research may go in the direction of including analysis of public transport network in the research, creating in this way a multimodal set of network data. This would illustrate, apart from the potential itself resulting from the infrastructure, also the actually existing connections.

  8. Forensic Image Analyses of Skin and Underlying Muscles as a Tool for Postmortem Interval Delimitation: Histopathologic Examination.

    Science.gov (United States)

    El-Nahass, El-Shaymaa; Moselhy, Walaa A; Hassan, Nour El-Houda Y

    2017-06-01

    One of the biggest challenges for forensic pathologists is to diagnose the postmortem interval (PMI) delimitation; therefore, the aim of this study was to use a routine histopathologic examination and quantitative analysis to obtain an accurate diagnosis of PMI. The current study was done by using 24 adult male albino rats divided into 8 groups based on the scarification schedule (0, 8, 16, 24, 32, 40, 48, and 72 hours PMI). Skin specimens were collected and subjected to a routine histopathologic processing. Examination of hematoxylin-eosin-stained sections from the skin, its appendages and underlying muscles were carried out. Morphometric analysis of epidermal nuclear chromatin intensities and area percentages, reticular dermis integrated density, and sebaceous gland nuclei areas and chromatin condensation was done. Progressive histopathologic changes could be detected in epidermis, dermis, hypodermis, underlying muscles including nerve endings, and red blood cells in relation to hours PMI. Significant difference was found in epidermal nuclear chromatin intensities at different-hours PMI (at P PMI. Quantitative analysis of measurements of dermal collagen area percentages revealed a high significant difference between 0 hours PMI and 24 to 72 hours PMI (P PMI increases, sebaceous gland nuclei and nuclear chromatin condensation showed a dramatic decrease. Significant differences of sebaceous gland nuclei areas between 0 hours and different-hours PMI (P PMI.

  9. A probabilistic approach for estimating the spatial extent of pesticide agricultural use sites and potential co-occurrence with listed species for use in ecological risk assessments.

    Science.gov (United States)

    Budreski, Katherine; Winchell, Michael; Padilla, Lauren; Bang, JiSu; Brain, Richard A

    2016-04-01

    A crop footprint refers to the estimated spatial extent of growing areas for a specific crop, and is commonly used to represent the potential "use site" footprint for a pesticide labeled for use on that crop. A methodology for developing probabilistic crop footprints to estimate the likelihood of pesticide use and the potential co-occurrence of pesticide use and listed species locations was tested at the national scale and compared to alternative methods. The probabilistic aspect of the approach accounts for annual crop rotations and the uncertainty in remotely sensed crop and land cover data sets. The crop footprints used historically are derived exclusively from the National Land Cover Database (NLCD) Cultivated Crops and/or Pasture/Hay classes. This approach broadly aggregates agriculture into 2 classes, which grossly overestimates the spatial extent of individual crops that are labeled for pesticide use. The approach also does not use all the available crop data, represents a single point in time, and does not account for the uncertainty in land cover data set classifications. The probabilistic crop footprint approach described herein incorporates best available information at the time of analysis from the National Agricultural Statistics Service (NASS) Cropland Data Layer (CDL) for 5 y (2008-2012 at the time of analysis), the 2006 NLCD, the 2007 NASS Census of Agriculture, and 5 y of NASS Quick Stats (2008-2012). The approach accounts for misclassification of crop classes in the CDL by incorporating accuracy assessment information by state, year, and crop. The NLCD provides additional information to improve the CDL crop probability through an adjustment based on the NLCD accuracy assessment data using the principles of Bayes' Theorem. Finally, crop probabilities are scaled at the state level by comparing against NASS surveys (Census of Agriculture and Quick Stats) of reported planted acres by crop. In an example application of the new method, the probabilistic

  10. When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice.

    Science.gov (United States)

    Martynov, Alexander; Ishida, Yoshiaki; Irimura, Seiichi; Tajiri, Rie; O'Hara, Timothy; Fujita, Toshihiko

    2015-01-01

    Current taxonomy offers numerous approaches and methods for species delimitation and description. However, most of them are based on the adult characters and rarely suggest a dynamic representation of developmental transformations of taxonomically important features. Here we show how the underestimation of ontogenetic changes may result in long term lack of recognition of a new species of one of the most common ophiacanthid brittle stars (Echinodermata: Ophiuroidea) from the North Pacific. Based on vast material collected predominantly by various Japanese expeditions in the course of more than 50 years, and thorough study of appropriate type material, we revise the complex of three common species of the ophiuroid genus Ophiacantha which have been persistently confused with each other. The present study thus reveals the previously unrecognized new species Ophiacantha kokusai sp.nov. which is commonly distributed off the Pacific coast of Japan. The new species shows developmental differentiation from the closely related species Ophiacantha rhachophora H. L. Clark, 1911 and retains clearly expressed early juvenile features in the adult morphology. Another species, Ophiacantha clypeata Kyte, 1977, which had been separated from O. rhachophora, is in turn shown to be just a juvenile stage of another North Pacific species, Ophiacantha trachybactra H.L. Clark, 1911. For every species, detailed morphological data from both adult and juvenile specimens based on scanning electron microscopy are presented. A special grinding method showing complex internal features has been utilized for the first time. For all three species in this complex, a clear bathymetric differentiation is revealed: O. rhachophora predominantly inhabits shallow waters, 0-250 m, the new species O. kokusai lives deeper, at 250-600 m, and the third species, O. trachybactra, is found at 500-2,000 m. The present case clearly highlights the importance of considering developmental transformations, not only for

  11. A review of the genus Bulbothrix Hale: the species with medullary salazinic acid lacking vegetative propagules

    Directory of Open Access Journals (Sweden)

    Michel Benatti

    2012-10-01

    Full Text Available Descriptions are presented for the seven known Bulbothrix (Parmeliaceae, Lichenized Fungi species with salazinic acid in the medulla and without vegetative propagules. Bulbothrix continua, previously considered as a synonym of B. hypocraea, is recognized as independent species. The current delimitations are confirmed for B. enormis, B. hypocraea, B. meizospora, B. linteolocarpa, B. sensibilis, and B. setschwanensis. New characteriscs and range extensions are provided.

  12. Rubroboletus le-galiae (Boletales, Basidiomycota, a species new for Poland

    Directory of Open Access Journals (Sweden)

    Marek Halama

    2016-01-01

    Full Text Available Rubroboletus le-galiae is reported for the first time from Poland. Macro- and micromorphological characters of the species are described and illustrated based on the study of material collected at three microlocalities in Łężczok reserve (SW Poland. The delimitation of R. le-galiae from related species of the genus Rubroboletus (R. satans, R. rubrosanguineus, R. rhodoxanthus is shortly discussed and the knowledge of its ecology and distribution is briefly summarized.

  13. High-throughput biodiversity analysis: Rapid assessment of species richness and ecological interactions of Chrysomelidae (Coleoptera) in the tropics

    Science.gov (United States)

    Gómez-Zurita, Jesús; Cardoso, Anabela; Coronado, Indiana; De la Cadena, Gissela; Jurado-Rivera, José A.; Maes, Jean-Michel; Montelongo, Tinguaro; Nguyen, Dinh Thi; Papadopoulou, Anna

    2016-01-01

    Abstract Biodiversity assessment has been the focus of intense debate and conceptual and methodological advances in recent years. The cultural, academic and aesthetic impulses to recognise and catalogue the diversity in our surroundings, in this case of living objects, is furthermore propelled by the urgency of understanding that we may be responsible for a dramatic reduction of biodiversity, comparable in magnitude to geological mass extinctions. One of the most important advances in this attempt to characterise biodiversity has been incorporating DNA-based characters and molecular taxonomy tools to achieve faster and more efficient species delimitation and identification, even in hyperdiverse tropical biomes. In this assay we advocate for a broad understanding of Biodiversity as the inventory of species in a given environment, but also the diversity of their interactions, with both aspects being attainable using molecular markers and phylogenetic approaches. We exemplify the suitability and utility of this framework for large-scale biodiversity assessment with the results of our ongoing projects trying to characterise the communities of leaf beetles and their host plants in several tropical setups. Moreover, we propose that approaches similar to ours, establishing the inventories of two ecologically inter-related and species-rich groups of organisms, such as insect herbivores and their angiosperm host-plants, can serve as the foundational stone to anchor a comprehensive assessment of diversity, also in tropical environments, by subsequent addition of trophic levels. PMID:27408583

  14. High-throughput biodiversity analysis: Rapid assessment of species richness and ecological interactions of Chrysomelidae (Coleoptera) in the tropics.

    Science.gov (United States)

    Gómez-Zurita, Jesús; Cardoso, Anabela; Coronado, Indiana; De la Cadena, Gissela; Jurado-Rivera, José A; Maes, Jean-Michel; Montelongo, Tinguaro; Nguyen, Dinh Thi; Papadopoulou, Anna

    2016-01-01

    Biodiversity assessment has been the focus of intense debate and conceptual and methodological advances in recent years. The cultural, academic and aesthetic impulses to recognise and catalogue the diversity in our surroundings, in this case of living objects, is furthermore propelled by the urgency of understanding that we may be responsible for a dramatic reduction of biodiversity, comparable in magnitude to geological mass extinctions. One of the most important advances in this attempt to characterise biodiversity has been incorporating DNA-based characters and molecular taxonomy tools to achieve faster and more efficient species delimitation and identification, even in hyperdiverse tropical biomes. In this assay we advocate for a broad understanding of Biodiversity as the inventory of species in a given environment, but also the diversity of their interactions, with both aspects being attainable using molecular markers and phylogenetic approaches. We exemplify the suitability and utility of this framework for large-scale biodiversity assessment with the results of our ongoing projects trying to characterise the communities of leaf beetles and their host plants in several tropical setups. Moreover, we propose that approaches similar to ours, establishing the inventories of two ecologically inter-related and species-rich groups of organisms, such as insect herbivores and their angiosperm host-plants, can serve as the foundational stone to anchor a comprehensive assessment of diversity, also in tropical environments, by subsequent addition of trophic levels.

  15. Spatial variability in intertidal macroalgal assemblages on the North Portuguese coast: consistence between species and functional group approaches

    Science.gov (United States)

    Veiga, P.; Rubal, M.; Vieira, R.; Arenas, F.; Sousa-Pinto, I.

    2013-03-01

    Natural assemblages are variable in space and time; therefore, quantification of their variability is imperative to identify relevant scales for investigating natural or anthropogenic processes shaping these assemblages. We studied the variability of intertidal macroalgal assemblages on the North Portuguese coast, considering three spatial scales (from metres to 10 s of kilometres) following a hierarchical design. We tested the hypotheses that (1) spatial pattern will be invariant at all the studied scales and (2) spatial variability of macroalgal assemblages obtained by using species will be consistent with that obtained using functional groups. This was done considering as univariate variables: total biomass and number of taxa as well as biomass of the most important species and functional groups and as multivariate variables the structure of macroalgal assemblages, both considering species and functional groups. Most of the univariate results confirmed the first hypothesis except for the total number of taxa and foliose macroalgae that showed significant variability at the scale of site and area, respectively. In contrast, when multivariate patterns were examined, the first hypothesis was rejected except at the scale of 10 s of kilometres. Both uni- and multivariate results indicated that variation was larger at the smallest scale, and thus, small-scale processes seem to have more effect on spatial variability patterns. Macroalgal assemblages, both considering species and functional groups as surrogate, showed consistent spatial patterns, and therefore, the second hypothesis was confirmed. Consequently, functional groups may be considered a reliable biological surrogate to study changes on macroalgal assemblages at least along the investigated Portuguese coastline.

  16. Improving discrimination of savanna tree species through a multiple endmember spectral-angle-mapper (SAM) approach: canopy level analysis

    CSIR Research Space (South Africa)

    Cho, Moses A

    2010-11-01

    Full Text Available sensing. The objectives of this paper were to (i) evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach (conventionally known as the nearest neighbour) in discriminating ten common African...

  17. DNA barcoding approaches for fishing authentication of exploited grouper species including the endangered and legally protected goliath grouper Epinephelus itajara

    Directory of Open Access Journals (Sweden)

    Rodrigo A. Torres

    2013-09-01

    Full Text Available Fishing strategies are constantly changing to meet the needs for new or alternative food sources. Consequently, management of fishing activities regarding rates of exploitation is essential, as a number of resources have reached situations of overexploitation. The aim of the present study was to use DNA barcoding from the goliath grouper and other exploited epinephelids in order to provide procedures for DNA authentication to be used as evidence for combating putative illegal fishing. The species studied were Epinephelus adscensionis, Mycteroperca bonaci, Mycteroperca interstitialis, Epinephelus itajara, Mycteroperca venenosa, Epinephelus mystacinus, Dermatolepis inermis, Alphestes afer, Cephalopholis fulva, Mycteroperca acutirostris, Rypticus saponaceus, Mycteroperca marginata and Epinephelus morio. Four of these species are the main epinephelids fished in the Atlantic Ocean. Differential patterns of polymerase chain reaction–restriction fragment length polymorphism were obtained from the species and additional single nucleotide polymorphisms were also detected among the four main epinephelids studied. The procedures proved very efficient and we suggest their applicability to the other fish groups as a way to control illegal capture and retail around the world, especially in cases in which filleting and other forms of de-characterization cause a lack of morpho-anatomical key characters.

  18. Delineating ecological boundaries of Hanuman langur species complex in peninsular India using MaxEnt modeling approach.

    Science.gov (United States)

    Nag, Chetan; Chetan, Nag; Karanth, K Praveen; Praveen, Karanth K; Gururaja, Kotambylu Vasudeva; Vasudeva, Gururaja Kotambylu

    2014-01-01

    Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

  19. Delimitation and Classified Planning Management of Functional Renovation Zone: Experience of and Discussion on Shenzhen’s Practice of Urban Renewal

    Institute of Scientific and Technical Information of China (English)

    Hao; Wenxuan; Tong; De; Liu; Qing; Feng; Changchun

    2016-01-01

    Urban renewal is one of the important issues of urban development in China.Along with its development in the contemporary time,China has seen considerable achievements and problems as well in urban renewal.Taking into account that Shenzhen has carried out plenty of explorations on urban planning renewal,this paper takes it as an example to firstly analyze the plights of its urban renewal planning,the shortcomings of its urban renewal projects,and the advantages of functional renovation zones to manifest the necessity of the delimitation and classified planning management of functional renovation zone in urban renewal.It then summarizes the experience of its urban renewal unit planning in terms of the methods of zoning and implementation,and finally discusses the conceptual connotations of functional renovation zone,as well as the logic and characteristics of renovations of its delimitation and classified planning management,in hope of providing other Chinese cities with some references.

  20. Do pseudo-absence selection strategies influence species distribution models and their predictions? An information-theoretic approach based on simulated data

    Directory of Open Access Journals (Sweden)

    Guisan Antoine

    2009-04-01

    Full Text Available Abstract Background Multiple logistic regression is precluded from many practical applications in ecology that aim to predict the geographic distributions of species because it requires absence data, which are rarely available or are unreliable. In order to use multiple logistic regression, many studies have simulated "pseudo-absences" through a number of strategies, but it is unknown how the choice of strategy influences models and their geographic predictions of species. In this paper we evaluate the effect of several prevailing pseudo-absence strategies on the predictions of the geographic distribution of a virtual species whose "true" distribution and relationship to three environmental predictors was predefined. We evaluated the effect of using a real absences b pseudo-absences selected randomly from the background and c two-step approaches: pseudo-absences selected from low suitability areas predicted by either Ecological Niche Factor Analysis: (ENFA or BIOCLIM. We compared how the choice of pseudo-absence strategy affected model fit, predictive power, and information-theoretic model selection results. Results Models built with true absences had the best predictive power, best discriminatory power, and the "true" model (the one that contained the correct predictors was supported by the data according to AIC, as expected. Models based on random pseudo-absences had among the lowest fit, but yielded the second highest AUC value (0.97, and the "true" model was also supported by the data. Models based on two-step approaches had intermediate fit, the lowest predictive power, and the "true" model was not supported by the data. Conclusion If ecologists wish to build parsimonious GLM models that will allow them to make robust predictions, a reasonable approach is to use a large number of randomly selected pseudo-absences, and perform model selection based on an information theoretic approach. However, the resulting models can be expected to have

  1. Multi-locus analyses of an Antarctic fish species flock (Teleostei, Notothenioidei, Trematominae): Phylogenetic approach and test of the early-radiation event

    International Nuclear Information System (INIS)

    Janko, K.; Musilova, Z.; Marshall, C.; Van Houdt, J.; Couloux, A.; Cruaud, C.; Lecointre, G.

    2011-01-01

    Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multi-locus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish. (authors)

  2. Species-Level Discrimination of Psychrotrophic Pathogenic and Spoilage Gram-Negative Raw Milk Isolates Using a Combined MALDI-TOF MS Proteomics-Bioinformatics-based Approach.

    Science.gov (United States)

    Vithanage, Nuwan R; Bhongir, Jeevana; Jadhav, Snehal R; Ranadheera, Chaminda S; Palombo, Enzo A; Yeager, Thomas R; Datta, Nivedita

    2017-06-02

    Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as postprocessing contaminants in pasteurized milk. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however, may require optimization for identification of pathogenic and spoilage bacteria in milk and dairy products. The current study evaluated the effects of various culture conditions and sample preparation methods on assigning of raw milk isolates to the species level by MALDI-TOF MS. The results indicated that culture media, incubation conditions (temperature and time), and sample preparation significantly affected the identification rates of bacteria to the species level. Nevertheless, the development of spectral libraries of isolates grown on different media using a web tool for hierarchical clustering of peptide mass spectra (SPECLUST) followed by a ribosomal protein based bioinformatics approach significantly enhanced the assigning of bacteria, with at least one unique candidate biomarker peak identified for each species. Phyloproteomic relationships based on spectral profiles were compared to phylogenetic analysis using 16S rRNA gene sequences and demonstrated similar clustering patterns with significant discriminatory power. Thus, with appropriate optimization, MALDI-TOF MS is a valuable tool for species-level discrimination of pathogenic and milk spoilage bacteria.

  3. METHODOLOGY FOR AUTOMATICALLY DELIMITING PERMANENT PRESERVATION AREAS ALONG WATER COURSES - THE USE OF GIS IN THE HYDROLOGICAL BASIN OF THE SERGIPE RIVER, BRAZIL

    Directory of Open Access Journals (Sweden)

    Janisson Batista de Jesus

    2016-04-01

    Full Text Available ABSTRACT Permanent Preservation Areas (PPAs along watercourses have been the focus of numerous studies, not only because of the fragility and ecological relevance of riverine vegetation, but also because of the inefficiency demonstrated in conforming to the legislation protecting it. One of the major difficulties encountered in terms of guaranteeing the effective conservation of these riverside areas is the absence of methodologies that can be used to define them rapidly and accurately without manually determining the widths of the rivers or assigning only uniform linear values for the entire watercourse. The present work sought to develop a spatial analysis methodology capable of automatically defining permanent preservation areas along watercourses using geographic information system (GIS software. The present study was undertaken in the Sergipe River basin, "considering the river itself and its principal affluents. We used the database of the Digital Atlas of Hydrological Resources (SEMARH/SE, and the delimitations of the PPAs were performed using ArcGIS 10.1 and the XToolPro 9.0 extension. A total of 5,003.82 hectares of Permanent Preservation Areas were delimited along the margins of the rivers analyzed, with a margin of error of <1% in delimiting the widths of the rivers within the entire area considered. The methodology described here can be used to define PPAs efficiently, relatively rapidly, and with very small margins of error, thus representing a technological advance in terms of using GIS for land management.

  4. Species Richness Responses to Structural or Compositional Habitat Diversity between and within Grassland Patches: A Multi-Taxon Approach

    Science.gov (United States)

    Lengyel, Szabolcs; Déri, Eszter; Magura, Tibor

    2016-01-01

    Habitat diversity (spatial heterogeneity within and between habitat patches in a landscape, HD) is often invoked as a driver of species diversity at small spatial scales. However, the effect of HD on species richness (SR) of multiple taxa is not well understood. We quantified HD and SR in a wet-dry gradient of open grassland habitats in Hortobágy National Park (E-Hungary) and tested the effect of compositional and structural factors of HD on SR of flowering plants, orthopterans, true bugs, spiders, ground beetles and birds. Our dataset on 434 grassland species (170 plants, 264 animals) showed that the wet-dry gradient (compositional HD at the between-patch scale) was primarily related to SR in orthopterans, ground-dwelling arthropods, and all animals combined. The patchiness, or plant association richness, of the vegetation (compositional HD at the within-patch scale) was related to SR of vegetation-dwelling arthropods, whereas vegetation height (structural HD at the within-patch scale) was related to SR of ground-dwelling arthropods and birds. Patch area was related to SR only in birds, whereas management (grazing, mowing, none) was related to SR of plants and true bugs. All relationships between HD and SR were positive, indicating increasing SR with increasing HD. However, total SR was not related to HD because different taxa showed similar positive responses to different HD variables. Our findings, therefore, show that even though HD positively influences SR in a wide range of grassland taxa, each taxon responds to different compositional or structural measures of HD, resulting in the lack of a consistent relationship between HD and SR when taxon responses are pooled. The idiosyncratic responses shown here exemplify the difficulties in detecting general HD-SR relationships over multiple taxa. Our results also suggest that management and restoration aimed specifically to sustain or increase the diversity of habitats are required to conserve biodiversity in

  5. Species Richness Responses to Structural or Compositional Habitat Diversity between and within Grassland Patches: A Multi-Taxon Approach.

    Directory of Open Access Journals (Sweden)

    Szabolcs Lengyel

    Full Text Available Habitat diversity (spatial heterogeneity within and between habitat patches in a landscape, HD is often invoked as a driver of species diversity at small spatial scales. However, the effect of HD on species richness (SR of multiple taxa is not well understood. We quantified HD and SR in a wet-dry gradient of open grassland habitats in Hortobágy National Park (E-Hungary and tested the effect of compositional and structural factors of HD on SR of flowering plants, orthopterans, true bugs, spiders, ground beetles and birds. Our dataset on 434 grassland species (170 plants, 264 animals showed that the wet-dry gradient (compositional HD at the between-patch scale was primarily related to SR in orthopterans, ground-dwelling arthropods, and all animals combined. The patchiness, or plant association richness, of the vegetation (compositional HD at the within-patch scale was related to SR of vegetation-dwelling arthropods, whereas vegetation height (structural HD at the within-patch scale was related to SR of ground-dwelling arthropods and birds. Patch area was related to SR only in birds, whereas management (grazing, mowing, none was related to SR of plants and true bugs. All relationships between HD and SR were positive, indicating increasing SR with increasing HD. However, total SR was not related to HD because different taxa showed similar positive responses to different HD variables. Our findings, therefore, show that even though HD positively influences SR in a wide range of grassland taxa, each taxon responds to different compositional or structural measures of HD, resulting in the lack of a consistent relationship between HD and SR when taxon responses are pooled. The idiosyncratic responses shown here exemplify the difficulties in detecting general HD-SR relationships over multiple taxa. Our results also suggest that management and restoration aimed specifically to sustain or increase the diversity of habitats are required to conserve

  6. New approaches for morphological diagnosis of bovine Eimeria species: a study on a subtropical organic dairy farm in Brazil.

    Science.gov (United States)

    Florião, Mônica Mateus; Lopes, Bruno do Bomfim; Berto, Bruno Pereira; Lopes, Carlos Wilson Gomes

    2016-03-01

    Bovine eimeriosis or coccidiosis is an intestinal disease caused by Eimeria spp. which is related to gastrointestinal disorders and, in some cases, death. The current work aimed to identify and provide detailed morphological characteristic features of the different Eimeria spp. parasites of crossbred cows of a subtropical organic dairy farm in Brazil, offering tools for the diagnosis of bovine eimeriosis. Eimeria auburnensis, Eimeria bovis, Eimeria bukidnonensis, Eimeria canadensis, Eimeria cylindrica, Eimeria ildefonsoi, and Eimeria zuernii were identified. The application of line regressions and ANOVA provided a means for the identification of these species. Finally, the current work proposes a dichotomous key to assist in the morphologic identification of bovine Eimeria spp. oocysts.

  7. Alien and invasive woody species in the dunes of the Wadden Sea Island of Vlieland: a remote sensing approach

    NARCIS (Netherlands)

    Hantson, W.; Kooistra, L.; Slim, P.A.

    2010-01-01

    In this study we mapped (alien) invasive shrubs for management and conservation purposes. On the study site, the Wadden Sea Island of Vlieland, they are a serious treat for the quality of the grey dune habitat. We developed a remote sensing approach that delivers detailed and standardized maps of

  8. Light Absorption in Coralline Algae (Rhodophyta: A Morphological and Functional Approach to Understanding Species Distribution in a Coral Reef Lagoon

    Directory of Open Access Journals (Sweden)

    Román M. Vásquez-Elizondo

    2017-09-01

    Full Text Available Red coralline algae are a cosmopolitan group with the ability to precipitate CaCO3 within the walls of their vegetative cells. The resultant carbonate structure is key for explaining their ecological success, as it provides protection against herbivores and resistance to water motion. However, its potential contribution to enhance thallus light absorption efficiency through multiple light scattering on algal skeleton, similar to the effect documented for scleractinian corals, has not been yet investigated. Here, we initiate this analysis, characterizing thallus optical properties of three coralline species, which differed in pigment content and thallus mass area (TMA, gDW m−2. The three species, the rhodolith Neogoniolithon sp., the crustose coralline alga (CCA, Lithothamnion sp., and the articulated alga Amphiroa tribulus, represent the more distinctive coralline growth-forms and are able to colonize contrasting light environments in Caribbean coral reefs. The thicker thalli of the rhodoliths were the most efficient light collectors, as evidenced by their higher pigment absorption efficiency (a*Chla; m2 mgChla−1 and photosynthetic rates per unit area. This could explain rhodolith success in oligotrophic, highly illuminated reef environments. In contrast, the thinner thalli of the CCA, a low-light specialist, showed the highest metabolic rates normalized to mass and the highest light absorption efficiencies per unit mass (a*M; m2 gdw−1. Therefore, the ecological success of the CCA in cryptic habitats within the reef cannot be explained only by its low-light physiology, but also by its capacity to reduce the structural costs of their thalli, and thus of its new growth. Lastly, the ecological success of Amphiroa tribulus, which displayed intermediate values for the efficiency of light absorption, metabolic rates and TMA, was explained by its ability to construct the largest light collectors (algal canopies thanks to the presence of flexible

  9. A proteomic approach provides new insights into the control of soil-borne plant pathogens by Bacillus species.

    Directory of Open Access Journals (Sweden)

    Omür Baysal

    Full Text Available Beneficial microorganisms (also known as biopesticides are considered to be one of the most promising methods for more rational and safe crop management practices. We used Bacillus strains EU07, QST713 and FZB24, and investigated their inhibitory effect on Fusarium. Bacterial cell cultures, cell-free supernatants and volatiles displayed varying degrees of suppressive effect. Proteomic analysis of secreted proteins from EU07 and FZB24 revealed the presence of lytic enzymes, cellulases, proteases, 1,4-β-glucanase and hydrolases, all of which contribute to degradation of the pathogen cell wall. Further proteomic investigations showed that proteins involved in metabolism, protein folding, protein degradation, translation, recognition and signal transduction cascade play an important role in the control of Fusarium oxysporum. Our findings provide new knowledge on the mechanism of action of Bacillus species and insight into biocontrol mechanisms.

  10. Kerteszia Theobald (Diptera: Culicidae) mosquitoes and bromeliads: A landscape ecology approach regarding two species in the Atlantic rainforest.

    Science.gov (United States)

    Chaves, Leonardo Suveges Moreira; Rodrigues de Sá, Ivy Luizi; Bergamaschi, Denise Pimentel; Sallum, Maria Anice Mureb

    2016-12-01

    On the ecological scale of an organism, a homogeneous geographical landscape can represent a mosaic of heterogeneous landscapes. The bionomy of Kerteszia mosquitoes can contribute to foundation landscape ecology by virtue of in the role of the configuration and composition of the habitat played in the distribution of mosquito species. Thus, this study aimed: to compare the abundance of Kerteszia in dense tropical rainforest, restinga and rural area, to assess the bioecological characteristics of the main bromeliads hosting Kerteszia, and to associate the bioecological arrangement of the bromeliads with Kerteszia distribution. Field collections were conducted in a monthly schedule from December of 2010 to November 2011. The vegetation of landscapes was characterized on the basis of a digital cartographic database, the manual of the Brazilian vegetation, environmental atlas information, satellite images and visits to the sites. Multivariate generalized linear models were employed using the R-project statistical program. The results were: Anopheles cruzii was the most frequent species in dense tropical rainforest (67.42%), with a positive association (deviance=25.8; P=0.002). Anopheles bellator was more abundant in the Restinga area (78.97%), with a positive association (deviance=10.4, P=0.018). There was a positive aggregation of Restinga with An. bellator (RR=2.42) but a lower level with An. cruzii (RR=0.31). Thus we can conclude that landscape characteristics influence the distribution of Kerteszia mosquitoes. An. bellator has a higher prevalence in Restinga areas, whereas An. cruzii was the most prevalent in the dense tropical rainforest. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Petroleum Hydrocarbon Mixture Toxicity and a Trait Based Approach to Soil Invertebrate Species for Site Specific Risk Assessments.

    Science.gov (United States)

    Gainer, Amy; Cousins, Mark; Hogan, Natacha; Siciliano, Steven D

    2018-05-05

    Although petroleum hydrocarbons (PHCs) released to the environment typically occur as mixtures, PHC remediation guidelines often reflect individual substance toxicity. It is well documented that groups of aliphatic PHCs act via the same mechanism of action, nonpolar narcosis and, theoretically, concentration addition mixture toxicity principles apply. To assess this theory, ten standardized acute and chronic soil invertebrate toxicity tests on a range of organisms (Eisenia fetida, Lumbricus terrestris, Enchytraeus crypticus, Folsomia candida, Oppia nitens and Hypoaspis aculeifer) were conducted with a refined PHC binary mixture. Reference models for concentration addition and independent action were applied to the mixture toxicity data with consideration of synergism, antagonism and dose level toxicity. Both concentration addition and independent action, without further interactions, provided the best fit with observed response to the mixture. Individual fraction effective concentration values were predicted from optimized, fitted reference models. Concentration addition provided a better estimate than independent action of individual fraction effective concentrations based on comparison with available literature and species trends observed in toxic responses to the mixture. Interspecies differences in standardized laboratory soil invertebrate species responses to PHC contaminated soil was reflected in unique traits. Diets that included soil, large body size, permeable cuticle, low lipid content, lack of ability to molt and no maternal transfer were traits linked to a sensitive survival response to PHC contaminated soil in laboratory tests. Traits linked to sensitive reproduction response in organisms tested were long life spans with small clutch sizes. By deriving single fraction toxicity endpoints considerate of mixtures, we reduce resources and time required in conducting site specific risk assessments for the protection of soil organism's exposure pathway. This

  12. ADMINISTRATIVE CONTRACTS. DELIMITATIONS

    Directory of Open Access Journals (Sweden)

    Liana Teodora PASCARIU

    2016-12-01

    Full Text Available Article examines whether all contracts of public persons are administrative contracts; in other words, if the administration may conclude contracts that, according to their legal nature, are not administrative. If we start from the definition of administrative contracts as it appears in Law no. 554/2004, these include contracts by public authorities which concern the enhancement of public property execution of works of public interest, public services, public procurement and other administrative contracts provided by special laws and subject to the jurisdiction of the administrative courts.

  13. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

    DEFF Research Database (Denmark)

    Bothwell, H.; Bisbing, S.; Therkildsen, Nina Overgaard

    2013-01-01

    It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental...... loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi...... variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major...

  14. The Megadiverse Australian Ant Genus Melophorus: Using CO1 Barcoding to Assess Species Richness

    Directory of Open Access Journals (Sweden)

    Alan N. Andersen

    2016-12-01

    Full Text Available Melophorus is an exceptionally diverse ant genus from arid Australia that has received little taxonomic attention, such that just a fraction of its remarkable number of species is described. The Commonwealth Scientific and Industrial Research Organization’s Tropical Ecosystems Research Centre (TERC in Darwin holds by far the most extensive collection of Melophorus, and as of September 2016 this comprised >850 sorted morphospecies. However, the reliability of such morphospecies is open to question because species delimitation is extremely challenging due to highly generalized morphology and worker polymorphism. Here we use CO1 barcoding of 401 Melophorus specimens from 188 morphospecies in the TERC collection to determine the reliability of morphologically-based species delimitations as a basis for assessing true diversity within the genus. Our CO1 data confirm the extremely challenging nature of morphologically-based species delimitation within Melophorus, and suggest substantially higher diversity than that indicated by morphospecies. We found many cases where combinations of high (>10% CO1 divergence, polyphyly, sympatric association, and morphological differentiation indicated that single morphospecies represented multiple lineages. Overall, our analysis indicates that the 188 morphospecies barcoded represent at least 225 independent CO1 lineages. We discuss these results in terms of both their limitations and implications for estimating the total number of species in this exceptionally diverse, arid-adapted ant genus.

  15. Combined field/modelling approaches to represent the air-vegetation distribution of benzo[a]pyrene using different vegetation species

    Science.gov (United States)

    Ratola, Nuno; Jiménez-Guerrero, Pedro

    2015-04-01

    A strategy designed to combine the features of field-based experiments and modelling approaches is presented in this work to assess air-vegetation distribution of benzo(a)pyrene (BaP) in the Iberian Peninsula (IP). Given the lack of simultaneous data in both environmental matrices, a methodology with two main steps was employed. First, evaluating the simulations with the chemistry transport model (CTM) WRF (Weather Research and Forecasting) + CHIMERE data against the European Monitoring and Evaluation Programme (EMEP) network, to test the aptitude of the CTM to replicate the respective atmospheric levels. Then, using modelled concentrations and a method to estimate air levels of BaP from biomonitoring data to compare the performance of different pine species (Pinus pinea, Pinus pinaster, Pinus nigra and Pinus halepensis) to describe the atmospheric evidences. The comparison of modelling vs. biomonitoring has a higher dependence on the location of the sampling points, rather than on the pine species, as some tend to overestimate and others to underestimate BaP concentrations, in most cases regardless of the season. The climatology of the canopy levels of BaP was successfully validated with the concentrations in pine needles (most biases below 26%), however, the model was unable to distinguish between species. This should be taken into consideration in future studies, as biases can rise up to 48%, especially in summer and autumn, the. The comparison with biomonitoring data showed a similar pattern, but with the best results in the warmer months.

  16. Distribution patterns of flavonoids from three Momordica species by ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry: a metabolomic profiling approach

    Directory of Open Access Journals (Sweden)

    Ntakadzeni Edwin Madala

    Full Text Available ABSTRACT Plants from the Momordica genus, Curcubitaceae, are used for several purposes, especially for their nutritional and medicinal properties. Commonly known as bitter gourds, melon and cucumber, these plants are characterized by a bitter taste owing to the large content of cucurbitacin compounds. However, several reports have shown an undisputed correlation between the therapeutic activities and polyphenolic flavonoid content. Using ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry in combination with multivariate data models such as principal component analysis and hierarchical cluster analysis, three Momordica species (M. foetida Schumach., M. charantia L. and M. balsamina L. were chemo-taxonomically grouped based on their flavonoid content. Using a conventional mass spectrometric-based approach, thirteen flavonoids were tentatively identified and the three species were found to contain different isomers of the quercetin-, kaempferol- and isorhamnetin-O-glycosides. Our results indicate that Momordica species are overall very rich sources of flavonoids but do contain different forms thereof. Furthermore, to the best of our knowledge, this is a first report on the flavonoid content of M. balsamina L.

  17. Ethnopharmacological Approaches for Therapy of Jaundice: Part II. Highly Used Plant Species from Acanthaceae, Euphorbiaceae, Asteraceae, Combretaceae, and Fabaceae Families

    Directory of Open Access Journals (Sweden)

    Devesh Tewari

    2017-08-01

    Full Text Available In many developing countries, jaundice is the common symptom of hepatic diseases which are a major cause of mortality. The use of natural product-based therapies is very popular for such hepatic disorders. A great number of medicinal plants have been utilized for this purpose and some facilitated the discovery of active compounds which helped the development of new synthetic drugs against jaundice. However, more epidemiological studies and clinical trials are required for the practical implementation of the plant pharmacotherapy of jaundice. The focus of this second part of our review is on several of the most prominent plants used against jaundice identified in the analysis performed in the first part of the review viz. Andrographis paniculata (Burm.f. Nees, Silybum marianum (L. Gaertn., Terminalia chebula Retz., Glycyrrhiza glabra L. and some species of genus Phyllanthus. Furthermore, we discuss their physiological effects, biologically active ingredients, and the potential mechanisms of action. Some of the most important active ingredients were silybin (also recommended by German commission, phyllanthin and andrographolide, whose action leads to bilirubin reduction and normalization of the levels of relevant serum enzymes indicative for the pathophysiological status of the liver.

  18. Approach to photocatalysis at the molecular level. Design of photocatalysts, detection of intermediate species, and reaction mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Anpo, Masakazu [Department of Applied Chemistry, University of Osaka Prefecture, Gakuen-cho, Sakai, Osaka (Japan)

    1995-08-01

    The characterization of the Cu{sup +}/ZSM-5 catalysts prepared via reduction of ion-exchanged Cu{sup 2+}/ZSM-5 samples and highly dispersed Ti-oxide catalysts anchored on Vycor glass has been undertaken by in-situ photoluminescence, EPR, XAFS (XANES and FT-EXAFS), and FT-IR spectroscopy. UV-irradiation of the Cu{sup +}/ZSM-5 catalyst in the presence of NO leads to the direct photocatalytic decomposition of NO into N{sub 2} and O{sub 2} at normal temperatures. UV-irradiation of the highly dispersed anchored Ti-oxide catalyst in the presence of CO{sub 2} and H{sub 2}O also leads to the evolution of CH{sub 4}, CO, and CH{sub 3}OH at normal temperatures. The clarification of the coordination structure of the active surface sites and the direct detection of the reaction precursors and intermediate species in these photocatalytic systems contributed significantly in characterizing the molecular scale reaction mechanisms. Based on these results, the design of highly concentrated and efficient photocatalysts has successfully been achieved by application of the sol-gel method

  19. Modeling of the removal of arsenic species from simulated groundwater containing As, Fe, and Mn: a neural network based approach

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, Prasenjit; Mohanty, Bikash; Balomajumder, Chandrajit [Department of Chemical Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttrakhand (India); Saraswati, Samir [Department of Mechanical Engineering, Motital Nehru National Institute of Technology, Allahabad, Uttar Pradesh (India)

    2012-03-15

    The present paper deals with the modeling of the removal of total arsenic As(T), trivalent arsenic As(III), and pentavalent arsenic As(V) from synthetic solutions containing total arsenic (0.167-2.0 mg/L), Fe (0.9-2.7 mg/L), and Mn (0.2-0.6 mg/L) in a batch reactor using Fe impregnated granular activated charcoal (GAC-Fe). Mass ratio of As(III) and As(V) in the solution was 1:1. Multi-layer neural network (MLNN) has been used and full factorial design technique has been applied for the selection of input data set. The developed models are able to predict the adsorption of arsenic species with an error limit of -0.3 to +1.7%. Combination of MLNN with design of experiment has been able to generalize the MLNN with less number of experimental points. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. A holistic approach to development of diets for Ballan wrasse (Labrus berggylta – a new species in aquaculture

    Directory of Open Access Journals (Sweden)

    Kristin Hamre

    2013-07-01

    Full Text Available Wild wrasses are used for delousing of farmed salmon but increasing demands have prompted the salmon industry to develop cultures of Ballan wrasse. One of the bottlenecks has been nutrition and feed intake in the juvenile phase, while broodstock nutrition is considered critical for production of viable offspring. The present study was aimed at developing functioning ongrowing and broodstock diets for Ballan wrasse. In juveniles the best lengthwise growth was identified at 65% dietary protein, 12% lipid and 16% carbohydrate. To investigate if the requirements for the other nutrients were covered by the diets developed for the species, the nutrient composition in juveniles (whole body and broodstock (female gonad were analyzed and compared to the composition in wild fish. We found that the levels of the lipid soluble Vitamins A, K and D were lower in cultured than in wild fish, however, the requirements for these nutrients in Ballan wrasse are not known. Other candidate nutrients for more in-depth investigation are the bone minerals, zinc, taurine and fatty acids.

  1. A Holistic Approach to Enhance the Use of Neglected and Underutilized Species: The Case of Andean Grains in Bolivia and Peru

    Directory of Open Access Journals (Sweden)

    Stefano Padulosi

    2014-03-01

    Full Text Available The IFAD-NUS project, implemented over the course of a decade in two phases, represents the first UN-supported global effort on neglected and underutilized species (NUS. This initiative, deployed and tested a holistic and innovative value chain framework using multi-stakeholder, participatory, inter-disciplinary, pro-poor gender- and nutrition-sensitive approaches. The project has been linking aspects often dealt with separately by R&D, such as genetic diversity, selection, cultivation, harvest, value addition, marketing, and final use, with the goal to contribute to conservation, better incomes, and improved nutrition and strengthened livelihood resilience. The project contributed to the greater conservation of Andean grains and their associated indigenous knowledge, through promoting wider use of their diversity by value chain actors, adoption of best cultivation practices, development of improved varieties, dissemination of high quality seed, and capacity development. Reduced drudgery in harvest and postharvest operations, and increased food safety were achieved through technological innovations. Development of innovative food products and inclusion of Andean grains in school meal programs is projected to have had a positive nutrition outcome for targeted communities. Increased income was recorded for all value chain actors, along with strengthened networking skills and self-reliance in marketing. The holistic approach taken in this study is advocated as an effective strategy to enhance the use of other neglected and underutilized species for conservation and livelihood benefits.

  2. Semi-mechanistic partial buffer approach to modeling pH, the buffer properties, and the distribution of ionic species in complex solutions.

    Science.gov (United States)

    Dougherty, Daniel P; Da Conceicao Neta, Edith Ramos; McFeeters, Roger F; Lubkin, Sharon R; Breidt, Frederick

    2006-08-09

    In many biological science and food processing applications, it is very important to control or modify pH. However, the complex, unknown composition of biological media and foods often limits the utility of purely theoretical approaches to modeling pH and calculating the distributions of ionizable species. This paper provides general formulas and efficient algorithms for predicting the pH, titration, ionic species concentrations, buffer capacity, and ionic strength of buffer solutions containing both defined and undefined components. A flexible, semi-mechanistic, partial buffering (SMPB) approach is presented that uses local polynomial regression to model the buffering influence of complex or undefined components in a solution, while identified components of known concentration are modeled using expressions based on extensions of the standard acid-base theory. The SMPB method is implemented in a freeware package, (pH)Tools, for use with Matlab. We validated the predictive accuracy of these methods by using strong acid titrations of cucumber slurries to predict the amount of a weak acid required to adjust pH to selected target values.

  3. A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

    Science.gov (United States)

    Drost, Derek R; Novaes, Evandro; Boaventura-Novaes, Carolina; Benedict, Catherine I; Brown, Ryan S; Yin, Tongming; Tuskan, Gerald A; Kirst, Matias

    2009-06-01

    Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.

  4. Scale Expansion of Community Investigations and Integration of the Effects of Abiotic and Biotic Processes on Maintenance of Species Diversity

    Directory of Open Access Journals (Sweden)

    Zhenhong Wang

    2011-01-01

    Full Text Available Information on the maintenance of diversity patterns from regional to local scales is dispersed among academic fields due to the local focus of community ecology. To better understand these patterns, the study of ecological communities needs to be expanded to larger scales and the various processes affecting them need to be integrated using a suitable quantitative method. We determined a range of communities on a flora-subregional scale in Yunnan province, China (383210.02 km2. A series of species pools were delimited from the regional to plot scales. Plant diversity was evaluated and abiotic and biotic processes identified at each pool level. The species pool effect was calculated using an innovative model, and the contribution of these processes to the maintenance of plant species diversity was determined and integrated: climate had the greatest effect at the flora-subregional scale, with historical and evolutionary processes contributing ∼11%; climate and human disturbance had the greatest effect at the local site pool scale; competition exclusion and stress limitation explained strong filtering at the successional stage pool scale; biotic processes contributed more on the local community scale than on the regional scale. Scale expansion combined with the filtering model approach solves the local problem in community ecology.

  5. Evaluating mating compatibility within fruit fly cryptic species complexes and the potential role of sex pheromones in pre-mating isolation

    Czech Academy of Sciences Publication Activity Database

    Juárez, M. L.; Devescovi, F.; Břízová, Radka; Bachmann, G.; Segura, D. F.; Kalinová, Blanka; Fernández, P.; Ruiz, M. J.; Yang, J.; Teal, P. E. A.; Cáceres, C.; Vreysen, M. J. B.; Hendrichs, J.; Vera, M. T.

    -, č. 540 (2015), s. 125-155 ISSN 1313-2989 R&D Projects: GA MŠk 7AMB13AR018 Institutional support: RVO:61388963 Keywords : species delimitation * field cages * Tephritidae * Anastrepha fraterculus * Bactrocera dorsalis Subject RIV: EG - Zoology Impact factor: 0.938, year: 2015 http://zookeys.pensoft.net/articles.php?id=6133

  6. Microscopy and image analysis based approaches for the species-specific identification of bovine and swine bone containing material

    Directory of Open Access Journals (Sweden)

    Matteo Ottoboni

    2014-05-01

    Full Text Available The aim of this study was to evaluate the potential of image analysis measurements in combination with the official analytical method for the detection of constituents of animal origin in feedstuffs, in distinguishing between bovine and swine (bone containing material. Authentic samples of controlled origin containing bovine or swine meat and bone meals were analysed by the microscopic method, in accordance with the official analytical method. Sediment fractions of each sample were observed with a compound microscope at X40. A total of 362 bone fragment lacunae images were recorded and processed through image analysis software, deriving 30 geometric variables for each lacuna. Results indicated that not only were most variables significantly (P<0.001 different between bovine and swine samples, but also that two thirds of the same variables were bigger in bovine than in swine. This information, however, does not seem to be so effective in practice since bovine and swine features and measurements overlapped. It can be concluded that the microscopic method even when combined with image analysis does not fit all the requirements for accurately identifying prohibited ingredients of animal origin. A combined approach with other methods is therefore recommended.

  7. Duox, Flotillin-2, and Src42A are required to activate or delimit the spread of the transcriptional response to epidermal wounds in Drosophila.

    Directory of Open Access Journals (Sweden)

    Michelle T Juarez

    2011-12-01

    Full Text Available The epidermis is the largest organ of the body for most animals, and the first line of defense against invading pathogens. A breach in the epidermal cell layer triggers a variety of localized responses that in favorable circumstances result in the repair of the wound. Many cellular and genetic responses must be limited to epidermal cells that are close to wounds, but how this is regulated is still poorly understood. The order and hierarchy of epidermal wound signaling factors are also still obscure. The Drosophila embryonic epidermis provides an excellent system to study genes that regulate wound healing processes. We have developed a variety of fluorescent reporters that provide a visible readout of wound-dependent transcriptional activation near epidermal wound sites. A large screen for mutants that alter the activity of these wound reporters has identified seven new genes required to activate or delimit wound-induced transcriptional responses to a narrow zone of cells surrounding wound sites. Among the genes required to delimit the spread of wound responses are Drosophila Flotillin-2 and Src42A, both of which are transcriptionally activated around wound sites. Flotillin-2 and constitutively active Src42A are also sufficient, when overexpressed at high levels, to inhibit wound-induced transcription in epidermal cells. One gene required to activate epidermal wound reporters encodes Dual oxidase, an enzyme that produces hydrogen peroxide. We also find that four biochemical treatments (a serine protease, a Src kinase inhibitor, methyl-ß-cyclodextrin, and hydrogen peroxide are sufficient to globally activate epidermal wound response genes in Drosophila embryos. We explore the epistatic relationships among the factors that induce or delimit the spread of epidermal wound signals. Our results define new genetic functions that interact to instruct only a limited number of cells around puncture wounds to mount a transcriptional response, mediating

  8. Systematic significance of anatomical characterization in some euphorbiaceous species

    International Nuclear Information System (INIS)

    Zahra, N.B.; Shinwari, Z.K.

    2014-01-01

    The study was aimed to explore the systematic potential of anatomical characters for identification and delimitation among Euphorbia species. Eight species of leafy spurges of genus Euphorbia L. (Euphorbiaceae) were evaluated for variations in micro morphological characters of foliar epidermal anatomy. While anatomical observations are of importance in the assessments and appraisals, use of these characters as an effective tool in interpreting phyletic evaluations and systematic delineations has its limitations too. The epidermal cell wall in majority of species was wavy to undulate on both adaxial and abaxial surfaces. The observations made in this study indicate that there is not a single type of stomata which appears as characteristic of the genus Euphorbia. Also their distribution whether epistomatic or hypostomatic is not a genus-characteristic. The trichomes found were simple, unicellular or multicellular, uniseriate. Present investigation revealed the utility of both qualitative and quantitative characters in systematic studies; also the potential influence in the delimitation of species cannot be ignored. Our results show that the micro-morphology of anatomical characters play an important role in definition of taxa at species and sectional levels. (author)

  9. Foliar phenolic compounds of ten wild species of Verbenacea as antioxidants and specific chemomarkers

    Directory of Open Access Journals (Sweden)

    J. A. Ávila-Reyes

    2017-06-01

    Full Text Available Abstract The family Verbenaceae hosts important species used in traditional medicine of many countries. The taxonomic controversies concerning the specific delimitation of several of its species make it difficult to guarantee the botanical origin of herbal preparations based on species of this family. To contribute to the development of both specific chemomarkers and a quality control tool to authenticate the botanical origin of herbal preparations of Verbenacea species, we determined the foliar HPLC-DAD phenolic profiles and the antioxidant properties of 10 wild species of this family occurring in Mexico. The contents of phenols and flavonoids varied significantly among species. Priva mexicana showed the highest levels of total phenolics (53.4 mg g-1 dry tissue and Verbena carolina had the highest levels of flavonoids (17.89 mg g-1 dry tissue. Relevant antioxidant properties revealed by antiradical and reducing power were found for the analyzed species. These properties varied significantly in a species-dependent manner. The phenolic compounds accumulated were flavones and phenolic acids. Flavones were the only type of flavonoids found. The results of a cluster analysis showed that the compounds were accumulated in species-specific profiles. The phenolic profiles are proposed as valuable chemomarkers that can become a useful tool for the quality control concerning the botanical origin of herbal medicinal preparations based on the species analyzed. In addition, phenolic profiles could contribute importantly to solve the taxonomic controversies concerning species delimitation in the family Verbenaceae.

  10. Grass species influence on plant N uptake - Determination of atmospheric N deposition to a semi-natural peat bog site using a 15N labelling approach

    Science.gov (United States)

    Hurkuck, Miriam; Brümmer, Christian; Spott, Oliver; Flessa, Heinz; Kutsch, Werner L.

    2014-05-01

    Large areas of natural peat bogs in Northwestern Germany have been converted to arable land and were subjected to draining and peat cutting in the past. The few protected peatland areas remaining are affected by high nitrogen (N) deposition. Our study site - a moderately drained raised bog - is surrounded by highly fertilized agricultural land and livestock production. In this study, we used a 15N pool dilution technique called 'Integrated Total Nitrogen Input' (ITNI) to quantify annual deposition of atmospheric N into biomonitoring pots over a two-year period. Since it considers direct N uptake by plants, it was expected to result in higher N input than conventional methods for determination of N deposition (e.g. micrometeorological approaches, bulk N samplers). Using Lolium multiflorum and Eriophorum vaginatum as monitor plants and low, medium and high levels of fertilization, we aimed to simulate increasing N deposition to planted pots and to allocate airborne N after its uptake by the soil-plant system in aboveground biomass, roots and soil. Increasing N fertilization was positively correlated with biomass production of Eriophorum vaginatum, whereas atmospheric plant N uptake decreased and highest airborne N input of 899.8 ± 67.4 µg N d-1 pot-1 was found for low N fertilization. In contrast, Lolium multiflorum showed a clear dependency of N supply on plant N uptake and was highest (688.7 ± 41.4 µg N d-1 pot-1) for highly fertilized vegetation pots. Our results suggest that grass species respond differently to increasing N input. While crop grasses such as Lolium multiflorum take up N according to N availability, species adopted to nutrient-limited conditions like Eriophorum vaginatum show N saturation effects with increasing N supply. Total airborne N input ranged from about 24 to 66 kg N ha-1 yr-1 dependent on the used indicator plant and the amount of added fertilizer. Parallel determination of atmospheric N deposition using a micrometeorological approach

  11. Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering

    Directory of Open Access Journals (Sweden)

    Sándor Csősz

    2016-03-01

    Full Text Available Background. Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hypothesis formation. In recent years a number of promising new algorithmic approaches have been developed to recognize morphological diversity among insects based on multivariate morphometric analyses. These algorithms objectively delimit components in the data by automatically assigning objects into clusters. Method. In this paper, hypotheses on the diversity of the Malagasy Nesomyrmex angulatus group are formulated via a highly automated protocol involving a fusion of two algorithms, (1 Nest Centroid clustering (NC clustering and (2 Partitioning Algorithm based on Recursive Thresholding (PART. Both algorithms assign samples into clusters, making the class assignment results of different algorithms readily inferable. The results were tested by confirmatory cross-validated Linear Discriminant Analysis (LOOCV-LDA. Results. Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using NC-PART-clustering on continuous morphological data, an approach that brings increased objectivity to taxonomy. We describe eight morphologically distinct species, including seven new species: Nesomyrmex angulatus (Mayr, 1862, N. bidentatus sp. n., N. clypeatus sp. n., N. devius sp. n., N. exiguus sp. n., N. fragilis sp. n., N. gracilis sp. n., and N. hirtellus sp. n.. An identification key for their worker castes using morphometric data is provided. Conclusions. Combining the dimensionality reduction feature of NC clustering with the assignment of samples into clusters by PART advances the automatization of morphometry-based alpha taxonomy.

  12. Profiling conserved biological pathways in Autosomal Dominant Polycystic Kidney Disorder (ADPKD) to elucidate key transcriptomic alterations regulating cystogenesis: A cross-species meta-analysis approach.

    Science.gov (United States)

    Chatterjee, Shatakshee; Verma, Srikant Prasad; Pandey, Priyanka

    2017-09-05

    Initiation and progression of fluid filled cysts mark Autosomal Dominant Polycystic Kidney Disease (ADPKD). Thus, improved therapeutics targeting cystogenesis remains a constant challenge. Microarray studies in single ADPKD animal models species with limited sample sizes tend to provide scattered views on underlying ADPKD pathogenesis. Thus we aim to perform a cross species meta-analysis to profile conserved biological pathways that might be key targets for therapy. Nine ADPKD microarray datasets on rat, mice and human fulfilled our study criteria and were chosen. Intra-species combined analysis was performed after considering removal of batch effect. Significantly enriched GO biological processes and KEGG pathways were computed and their overlap was observed. For the conserved pathways, biological modules and gene regulatory networks were observed. Additionally, Gene Set Enrichment Analysis (GSEA) using Molecular Signature Database (MSigDB) was performed for genes found in conserved pathways. We obtained 28 modules of significantly enriched GO processes and 5 major functional categories from significantly enriched KEGG pathways conserved in human, mice and rats that in turn suggest a global transcriptomic perturbation affecting cyst - formation, growth and progression. Significantly enriched pathways obtained from up-regulated genes such as Genomic instability, Protein localization in ER and Insulin Resistance were found to regulate cyst formation and growth whereas cyst progression due to increased cell adhesion and inflammation was suggested by perturbations in Angiogenesis, TGF-beta, CAMs, and Infection related pathways. Additionally, networks revealed shared genes among pathways e.g. SMAD2 and SMAD7 in Endocytosis and TGF-beta. Our study suggests cyst formation and progression to be an outcome of interplay between a set of several key deregulated pathways. Thus, further translational research is warranted focusing on developing a combinatorial therapeutic

  13. Operationalizing the telecoupling framework for migratory species using the spatial subsidies approach to examine ecosystem services provided by Mexican free-tailed bats

    Directory of Open Access Journals (Sweden)

    Laura López-Hoffman

    2017-12-01

    Full Text Available Drivers of environmental change in one location can have profound effects on ecosystem services and human well-being in distant locations, often across international borders. The telecoupling provides a conceptual framework for describing these interactions - for example, locations can be defined as sending areas (sources of flows of ecosystem services, energy, or information or receiving areas (recipients of flows. However, the ability to quantify feedbacks between ecosystem change in one area and societal benefits in other areas requires analytical approaches. We use spatial subsidies - an approach developed to measure the degree to which a migratory species' ability to provide services in one location depends on habitat in another location - as an example of how telecoupling can be operationalized. Using the cotton pest control and ecotourism services of Mexican free-tailed bats as an example, we determined that of the 16 states in the United States and Mexico where the species resides, three states (Texas, New Mexico, and Colorado are receiving areas, while the rest of the states are sending areas. In addition, the magnitude of spatial subsidy can be used as an indicator of the degree to which different locations are telecoupled to other locations. In this example, the Mexican free-tailed bat ecosystem services to cotton production and ecotourism in Texas and New Mexico are heavily dependent on winter habitat in four states in central and southern Mexico. In sum, spatial subsidies can be used to operationalize the telecoupling conceptual framework by identifying sending and receiving areas, and by indicating the degree to which locations are telecoupled to other locations.

  14. ENVIRONMENTAL IMPACTS AND DELIMITATION OF THE PRESERVATION AREA STANDING IN ESPINHARAS RIVER IN THE URBAN STRETCH OF THE CITY OF PATOS-PB

    Directory of Open Access Journals (Sweden)

    João Batista Alves

    2016-09-01

    Full Text Available This paper aimed to present and evaluate the proposal of the delimitation of the permanent preservation area (APP of the urban stretch of Espinharas River in the city of Patos-PB, carried out by the Superintendence and Management of the Environment - SUDEMA - Paraíba and to diagnose the main environmental impacts The demarcation was made from georeferenced points collected on the river, and the identification of the main environmental impacts. It identified a wide variation in the river rail between 10 and 50 meters, due to impacts and changes occurring in the anthropic process. The delimitation of PPA was 50 meters from the widest rail. The main impacts observed were: removal of riparian vegetation; pollution by the dumping of sewage and solid waste, siltation, invading of the banks with buildings and agricultural uses. It infers even though the lack of oversight occurs, failure of public authorities and of the local population in the search for solutions to the problems identified.

  15. Endangered Species

    Science.gov (United States)

    EPA's Endangered Species Protection Program helps promote recovery of listed species. The ESPP determines if pesticide use in a geographic area may affect any listed species. Find needed limits on pesticide use in Endangered Species Protection Bulletins.

  16. Approaching a Postcolonial Arctic

    DEFF Research Database (Denmark)

    Jensen, Lars

    2016-01-01

    This article explores different postcolonially configured approaches to the Arctic. It begins by considering the Arctic as a region, an entity, and how the customary political science informed approaches are delimited by their focus on understanding the Arctic as a region at the service...... of the contemporary neoliberal order. It moves on to explore how different parts of the Arctic are inscribed in a number of sub-Arctic nation-state binds, focusing mainly on Canada and Denmark. The article argues that the postcolonial can be understood as a prism or a methodology that asks pivotal questions to all...... approaches to the Arctic. Yet the postcolonial itself is characterised by limitations, not least in this context its lack of interest in the Arctic, and its bias towards conventional forms of representation in art. The article points to the need to develop a more integrated critique of colonial and neo...

  17. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

    Science.gov (United States)

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

  18. Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia

    Directory of Open Access Journals (Sweden)

    Natália Lima Boroni

    2017-10-01

    Full Text Available ABSTRACT The taxonomic identification of micromammals might be complicated when the study material is fragmented, as it is the case with pellets and fossil material. On the other hand, tooth morphology generally provides accurate information for species identification. Teeth preserve notably well, retaining their original morphology, unlike skulls and mandibles, which can get crushed or have missing parts. Here, we explored a geometric morphometrics approach (GM to identify fragmented specimens of two sympatric Calomys Waterhouse, 1837 species - Calomys tener (Winge, 1888 and Calomys expulsus (Lund, 1841 - using the morphology of intact molars as the basis for identification. Furthermore, we included some specimens of uncertain taxonomic identification to test their affinities and the utility of the shape of the molar to identify incomplete specimens. We evaluated the variations in the shape of the first upper molar (M1 among 46 owl pellets specimens of Calomys, including C. expulsus (n = 15, C. tener (n = 15, and unidentified specimens treated as Calomys sp. (n = 16 through GM analysis using 17 landmarks. The data was explored using PCA, PERMANOVA, and Discriminant analyses over the Procrustes residuals matrix were applied to evaluate inter- and intraspecific shape differences. Also, we evaluated whether allometric shape differences could impact the data, but found no evidence of a correlation between size and shape. Our results support that shape differences in the M1 are effective for discriminating between C. tener and C. expulsus. Moreover, the unidentified specimens do not represent a third shape but could be identified with confidence either as C. tener or C. expulsus. Our results show that even with fragmentary materials, GM is a feasible and useful tool for exploring inter-specific shape differences and assisting in taxonomic identification as a complement to traditional qualitative description of diagnostic features in poorly preserved

  19. An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert.

    Science.gov (United States)

    Larridon, Isabel; Walter, Helmut E; Guerrero, Pablo C; Duarte, Milén; Cisternas, Mauricio A; Hernández, Carol Peña; Bauters, Kenneth; Asselman, Pieter; Goetghebeur, Paul; Samain, Marie-Stéphanie

    2015-09-01

    Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively. Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas. Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity. © 2015 Botanical Society of America.

  20. Using Morphological, Molecular and Climatic Data to Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

    Science.gov (United States)

    Poudel, Ram C.; Möller, Michael; Gao, Lian-Ming; Ahrends, Antje; Baral, Sushim R.; Liu, Jie; Thomas, Philip; Li, De-Zhu

    2012-01-01

    Background Despite the availability of several studies to clarify taxonomic problems on the highly threatened yews of the Hindu Kush-Himalaya (HKH) and adjacent regions, the total number of species and their exact distribution ranges remains controversial. We explored the use of comprehensive sets of morphological, molecular and climatic data to clarify taxonomy and distributions of yews in this region. Methodology/Principal Findings A total of 743 samples from 46 populations of wild yew and 47 representative herbarium specimens were analyzed. Principle component analyses on 27 morphological characters and 15 bioclimatic variables plus altitude and maximum parsimony analysis on molecular ITS and trnL-F sequences indicated the existence of three distinct species occurring in different ecological (climatic) and altitudinal gradients along the HKH and adjacent regions Taxus contorta from eastern Afghanistan to the eastern end of Central Nepal, T. wallichiana from the western end of Central Nepal to Northwest China, and the first report of the South China low to mid-elevation species T. mairei in Nepal, Bhutan, Northeast India, Myanmar and South Vietnam. Conclusion/Significance The detailed sampling and combination of different data sets allowed us to identify three clearly delineated species and their precise distribution ranges in the HKH and adjacent regions, which showed no overlap or no distinct hybrid zone. This might be due to differences in the ecological (climatic) requirements of the species. The analyses further provided the selection of diagnostic morphological characters for the identification of yews occurring in the HKH and adjacent regions. Our work demonstrates that extensive sampling combined with the analysis of diverse data sets can reliably address the taxonomy of morphologically challenging plant taxa. PMID:23056501

  1. Horse species symposium: a novel approach to monitoring pathogen progression during uterine and placental infection in the mare using bioluminescence imaging technology and lux-modified bacteria.

    Science.gov (United States)

    Ryan, P L; Christiansen, D L; Hopper, R M; Walters, F K; Moulton, K; Curbelo, J; Greene, J M; Willard, S T

    2011-05-01

    Uterine and placental infections are the leading cause of abortion, stillbirth, and preterm delivery in the mare. Whereas uterine and placental infections in women have been studied extensively, a comprehensive examination of the pathogenic processes leading to this unsatisfactory pregnancy outcome in the mare has yet to be completed. Most information in the literature relating to late-term pregnancy loss in mares is based on retrospective studies of clinical cases submitted for necropsy. Here we report the development and application of a novel approach, whereby transgenically modified bacteria transformed with lux genes of Xenorhabdus luminescens or Photorhabdus luminescens origin and biophotonic imaging are utilized to better understand pathogen-induced preterm birth in late-term pregnant mares. This technology uses highly sensitive bioluminescence imaging camera systems to localize and monitor pathogen progression during tissue invasion by measuring the bioluminescent signatures emitted by the lux-modified pathogens. This method has an important advantage in that it allows for the potential tracking of pathogens in vivo in real time and over time, which was hitherto impossible. Although the application of this technology in domestic animals is in its infancy, investigators were successful in identifying the fetal lungs, sinuses, nares, urinary, and gastrointestinal systems as primary tissues for pathogen invasion after experimental infection of pregnant mares with lux-modified Escherichia coli. It is important that pathogens were not detected in other vital organs, such as the liver, brain, and cardiac system. Such precision in localizing sites of pathogen invasion provides potential application for this novel approach in the development of more targeted therapeutic interventions for pathogen-related diseases in the equine and other domestic species.

  2. BIOTECHNOLOGICAL APPROACHES FOR CONSERVATION OF THE ENDANGERED SPECIES Crambe koktebelica (JUNGE N. BUSCH AND EFFECT OF ASEPTIC IN VITRO CULTIVATION ON ITS BIOCHEMICAL PROPERTIES

    Directory of Open Access Journals (Sweden)

    Pushkarova

    2016-08-01

    Full Text Available The aim of the study was to establish efficient protocols of seed surface sterilization with further multiplication in vitro for threatened species Crambe koktebelica (Junge N. Busch and to show the effect of biotechnological approach (in vitro cultivation of biodiversity conservation on plants biochemical properties. Seed surface sterilization was carried out according to the original method with further microclonal multiplication of aseptic sprouts from lateral buds on the Murashige and Skoog (MS medium supplemented with different concentrations of growth regulators. Fatty acid content was determined using Gas chromatography-mass spectrophotometry of fatty acid ethers. Antioxidant activity was determined using 2.2-diphenyl-1-picrylhydrazyl radical scavenging method. Total soluble protein content was measured using Bradford method and polyfructan content determination was based upon ketosugars ability to color in the acidic environment with resorcinol. Plants that were grown under in vitro and in vivo conditions and seeds were used in this research. Efficient protocol of surface sterilization that resulted in 45% of aseptic seed material 50% of which has sprouted was elaborated for C. koktebelica as well as fast microclonal multiplication methods that provided with up to 5.25 ± 0.50 new formed plantlets from 1 lateral bud (on the MS medium that contained 1 mg/L of 6-benzylaminopurine. It was also shown that aseptic cultivation benefits to saturated fatty acid accumulation and increases protein content but on the other hand it reduces unsaturated fatty acid amount and polyfructan content as well as antioxidant activity of plant material. Obtained data confirms the prospect of biotechnology approach to biodiversity conservation and suggest the necessity of father in vitro cultivation effect on biochemical composition of plant study.

  3. Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

    Science.gov (United States)

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  4. Delineating landscape-scale processes of hydrology and plant dispersal for species-rich fen conservation : the Operational Landscape Unit approach

    NARCIS (Netherlands)

    Verhoeven, Jos T.A.; Beltman, Boudewijn; Janssen, Ron; Soons, Merel B.

    2017-01-01

    Restoration and conservation of species-rich nature reserves requires inclusion of landscape-scale connections and transport processes such as hydrologic flows and species dispersal. These are important because they provide suitable habitat conditions and an adequate species pool. This study aimed

  5. Primary processes of the electron-protic species coupling in pure aqueous phases: - femtosecond laser spectroscopy study; - quantum approach of the electron-water interaction

    International Nuclear Information System (INIS)

    Pommeret, Stanislas

    1991-01-01

    This thesis work deals with the coupling mechanisms between an electron, water molecules or protic species (hydronium ion, hydroxyl radical). Two complementary studies have been carry out in pure aqueous phases. The first one is concerned with the structural aspect of the hydrated electron which is studied via a semi-quantum approach Splitting Operator Method. The results indicates the importance of the second hydration shell in the localisation of an electron at 77 and 300 Kelvin. The second part of this work relates to the dynamic of the primary processes in light or heavy water at room temperature: the ion-molecule reaction, radical pair formation, geminate recombination of the hydrated electron with the hydronium ion and the hydroxyl radical. The dynamic of these reactions is studied by time resolved absorption spectroscopy from the near infrared to the near ultraviolet with a few tens femto-seconds temporal precision. The analysis of the primary processes takes into account the protic properties of water molecules. (author) [fr

  6. Study on the rules and practices in force abroad regarding the delimitation and access to regulated areas for radiation protection purposes. Final report - Appendices. Report no. 313

    International Nuclear Information System (INIS)

    Schieber, C.; Crouail, P.; Beltrami, L.A.; Reaud, C.

    2013-06-01

    Within the frame of a reviewing of European requirements in the field of radiation protection, this report presents a synthesis of rules which are applicable in seven countries (Belgium, Spain, United States, Finland, United-Kingdom, Sweden and Switzerland; a detailed report for each of these countries is provided in appendix) in the field of delimitation and access to regulated areas for radiation protection purposes. A synthesis is proposed for each country. Three countries are then selected (Finland, United Kingdom and Switzerland) and their rules and practices are applied to cases which correspond to representative exposure situations: a room with a glove box, a hall with hot spots, a parking of temporary warehousing (packages of used fuels), intermittent use of an X ray generator, use of an intense radiation beam, workshop being dismantled, laboratory in which radioactive iodine 131 is handled, and use of a mobile industrial radiography device

  7. Delimitação dos núcleos talâmicos pela eletrofisiologia estereotáxica Delimitation of the thalamic nuclei by stereotaxic electrophysiology

    Directory of Open Access Journals (Sweden)

    Nilton Luís Latuf

    1973-12-01

    Full Text Available Os limites da área destruída durante a cirurgia estereotáxica são descritos levando em consideração as complicações decorrentes de lesões determinadas erroneamente. São comentados os métodos empregados com a finalidade de controlar a delimitação do alvo, sendo descrita a técnica usada em 23 talamotomias com derivação da atividade elétrica celular dos núcleos talâmicos atravessados e a pesquisa de potenciais evocados, graças à somatotopia da representação táctil no núcleo ventral posterior. Com este método reduz-se de mais ou menos 1 mm o erro radiológico, prescisando-se o alvo terapêutico talâmico nos três planos de espaço.The limits of the area to be destroyed during the stereotaxic surgery for the treatment of tremors are described taking into account the complications due to lesions erroneously performed. The method applied is commented in order to control the accuracy of the target delimitation, describing the technique employed in 23 thalamotomies, recording the electrical activity of the thalamic nuclei acrossed and researching evoked potentials thanks to the somatotopic tactil representation in the ventral posterior nuclei. The method permits to reduce radiologic errors giving more accuracy for the delimitation of thalamic target in the three planes of space.

  8. The Delimitation of Urban Growth Boundaries Using the CLUE-S Land-Use Change Model: Study on Xinzhuang Town, Changshu City, China

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    Rui Zhou

    2016-11-01

    Full Text Available Over the past decades, urban growth boundaries (UGBs have been regarded as effective tools applied by planners and local governments to curb urban sprawl and guide urban smart growth. The UGBs help limit urban development to suitable areas and protect surrounding agricultural and ecological landscapes. At present, China’s Town and Country Planning Act officially requires the delimitation of UGBs in a city master planning outline and in central urban area planning. However, China’s practices in UGBs are usually determined by urban planners and local authorities, and lack a sound analytical basis. Consequently, Chinese UGBs are often proven to be inefficient for controlling urban expansion. In this paper, take the fast-growing Xinzhuang town of Changshu city, eastern China as an example, a new method towards establishing UGBs is proposed based on land-use change model (the Conversion of Land Use and its Effects at Small regional extent, CLUE-S. The results of our study show that the land-use change and urban growth simulation accuracy of CLUE-S model is high. The expansion of construction land and the decrease of paddy field would be the main changing trends of local land use, and a good deal of cultivated land and ecological land would be transformed into construction land in 2009–2027. There is remarkable discordance in the spatial distribution between the simulated UGBs based on the CLUE-S model and the planned UGBs based on the conventional method, where the simulated results may more closely reflect the reality of urban growth laws. Therefore, we believe that our method could be a useful planning tool for the delimitation of UGBs in Chinese cities.

  9. Using multi-date satellite imagery to monitor invasive grass species distribution in post-wildfire landscapes: An iterative, adaptable approach that employs open-source data and software

    Science.gov (United States)

    West, Amanda M.; Evangelista, Paul H.; Jarnevich, Catherine S.; Kumar, Sunil; Swallow, Aaron; Luizza, Matthew; Chignell, Steve

    2017-01-01

    Among the most pressing concerns of land managers in post-wildfire landscapes are the establishment and spread of invasive species. Land managers need accurate maps of invasive species cover for targeted management post-disturbance that are easily transferable across space and time. In this study, we sought to develop an iterative, replicable methodology based on limited invasive species occurrence data, freely available remotely sensed data, and open source software to predict the distribution of Bromus tectorum (cheatgrass) in a post-wildfire landscape. We developed four species distribution models using eight spectral indices derived from five months of Landsat 8 Operational Land Imager (OLI) data in 2014. These months corresponded to both cheatgrass growing period and time of field data collection in the study area. The four models were improved using an iterative approach in which a threshold for cover was established, and all models had high sensitivity values when tested on an independent dataset. We also quantified the area at highest risk for invasion in future seasons given 2014 distribution, topographic covariates, and seed dispersal limitations. These models demonstrate the effectiveness of using derived multi-date spectral indices as proxies for species occurrence on the landscape, the importance of selecting thresholds for invasive species cover to evaluate ecological risk in species distribution models, and the applicability of Landsat 8 OLI and the Software for Assisted Habitat Modeling for targeted invasive species management.

  10. Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae through DNA Barcoding.

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    Taeman Han

    Full Text Available The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4% was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5% were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%-3.67% suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having

  11. Echelon approach to areas of concern in synoptic regional monitoring

    Science.gov (United States)

    Myers, Wayne; Patil, Ganapati P.; Joly, Kyle

    1997-01-01

    Echelons provide an objective approach to prospecting for areas of potential concern in synoptic regional monitoring of a surface variable. Echelons can be regarded informally as stacked hill forms. The strategy is to identify regions of the surface which are elevated relative to surroundings (Relative ELEVATIONS or RELEVATIONS). These are areas which would continue to expand as islands with receding (virtual) floodwaters. Levels where islands would merge are critical elevations which delimit echelons in the vertical dimension. Families of echelons consist of surface sectors constituting separate islands for deeper waters that merge as water level declines. Pits which would hold water are disregarded in such a progression, but a complementary analysis of pits is obtained using the surface as a virtual mould to cast a counter-surface (bathymetric analysis). An echelon tree is a family tree of echelons with peaks as terminals and the lowest level as root. An echelon tree thus provides a dendrogram representation of surface topology which enables graph theoretic analysis and comparison of surface structures. Echelon top view maps show echelon cover sectors on the base plane. An echelon table summarizes characteristics of echelons as instances or cases of hill form surface structure. Determination of echelons requires only ordinal strength for the surface variable, and is thus appropriate for environmental indices as well as measurements. Since echelons are inherent in a surface rather than perceptual, they provide a basis for computer-intelligent understanding of surfaces. Echelons are given for broad-scale mammalian species richness in Pennsylvania.

  12. Molecular and morphometric evidence for separate species of Uncinaria (Nematoda: Ancylostomatidae) in California sea lions and northern fur seals: hypothesis testing supplants verification.

    Science.gov (United States)

    Nadler, S A; Adams, B J; Lyons, E T; DeLong, R L; Melin, S R

    2000-10-01

    California sea lions (Zalophus californianus) and northern fur seals (Callorhinus ursinus) are each believed to host distinct hookworm species (Uncinaria spp.). However, a recent morphometric analysis suggested that a single species parasitizes multiple pinniped hosts, and that the observed differences are host-induced. To explore the systematics of these hookworms and test these competing hypotheses, we obtained nucleotide sequences of nuclear ribosomal DNA (D2/D3 28S, D18/D19 28S, and internal transcribed spacer [ITS] regions) from 20 individual hookworms parasitizing California sea lion and northern fur seal pups where their breeding grounds are sympatric. Five individuals from an allopatric population of California sea lions were also sampled for ITS-1 and D18/D19 28S sequences. The 28S D2/D3 sequences showed no diagnostic differences among hookworms sampled from individual sea lions and fur seals, whereas the 28S D18/D19 sequences had one derived (apomorphic) character demarcating hookworms from northern fur seals. ITS sequences were variable for 7 characters, with 4 derived (apomorphic) states in ITS-1 demarcating hookworms from California sea lions. Multivariate analysis of morphometric data also revealed significant differences between nematodes representing these 2 host-associated lineages. These results indicate that these hookworms represent 2 species that are not distributed indiscriminately between these host species, but instead exhibit host fidelity, evolving independently with each respective host species. This evolutionary approach to analyzing sequence data for species delimitation is contrasted with similarity-based methods that have been applied to numerous diagnostic studies of nematode parasites.

  13. Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

    Science.gov (United States)

    Ishitani, Y.

    2017-12-01

    Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

  14. Mapping invasive woody species in coastal dunes in the Netherlands: a remote sensing approach using LIDAR and high-resolution aerial photographs

    NARCIS (Netherlands)

    Hantson, W.P.R.; Kooistra, L.; Slim, P.A.

    2012-01-01

    Questions Does remote sensing improve classification of invasive woody species in dunes, useful for shrub management? Does additional height information and an object-based classifier increase woody species classification accuracy? Location The dunes of Vlieland, one of the Wadden Sea Islands, the

  15. An overview of tropical pest species of bactrocera fruit flies (Diptera:Tephritidae) and the integration of biopesticides with other biological approaches for their management

    Science.gov (United States)

    Fruit flies (Diptera:Tephritidae) are among the most economically important pest species in the world, attacking a wide range of fruits and fleshy vegetables throughout tropical and sub-tropical areas of the world. These species are such devastating crop pests that major control and eradication prog...

  16. POPULATION STRUCTURES OF FOUR TREE SPECIES IN LOGGED-OVER TROPICAL FOREST IN SOUTH PAPUA, INDONESIA: AN INTEGRAL PROJECTION MODEL APPROACH

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    Relawan kuswandi

    2015-12-01

    Full Text Available Selective logging has been taking place in Papua for several decades. In contrast, very little is known about the stand structure in post-logged forest. Hence, this paper investigates stand structures in logged-over area of tropical forest in South Papua. Four species were selected in three one-hectare permanent sample plots (PSPs: Vatica rassak, Syzygium sp, Litsea timoriana and Canarium asperum. PSPs were located in the forest concession area of PT. Tunas Sawaerma in Assiki, Boven Digul, in South Papua. Data sets comprised measurements made in 2005 and 2012 consisting of species, diameter at breast height (DBH, mortality and number of tree of each species. Integral Projection Models (IPMs were developed, taking into account mortality, growth, recruitment and fecundity. Results show the pattern of stand structures of the four species were more or less similar, i.e. more individual trees were present in the small diameter classes than in the larger diameter classes. The general pattern of the individual distribution of the four species is the typical reverse-J shape. Syzygium sp. has a greater number of individuals in the small diameter classes than the other three species. Population growth rates (λ are above one, indicating that the stand structures of the population dynamics of the four species are recuperating. Conclusively, these results suggest that species composition and population structure in these logged-over forests are recovering increasingly.

  17. Application of PCR – RFLP markers for identification of genetically delimited groups of the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae

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    Buczkowska Katarzyna

    2015-06-01

    Full Text Available Currently, two subspecies are formally recognized within Calypogeia fissa: C. fissa subsp. fissa occurring in Europe and C. fissa subsp. neogea known from North America. Genetic studies have revealed a complex structure of this species. Within the European part of distribution, three genetically distinct groups PS, PB and G are distinguished. The combination of the SCAR marker Cal04 and PCR-RFLP markers with three restriction enzymes (SmaI, TaqI and TspGWI allowed the recognition of all groups within the C. fissa complex. The TaqI enzyme recognizing the restriction sites in the PCR product of SCAR marker Ca104 turned out to be the best marker

  18. BOREAS TGB-3 Plant Species Composition Data over the NSA Fen

    Science.gov (United States)

    Bubier, Jill L.; Hall, Forrest G. (Editor); Conrad, Sara K. (Editor)

    2000-01-01

    The BOReal Ecosystem-Atmosphere Study Trace Gas Biogeochemistry (BOREAS TGB-3) team collected several data sets that contributed to understanding the measured trace gas fluxes over sites in the Northern Study Area (NSA). This data set contains information about the composition of plant species that were within the collars used to measure Net Ecosystem Exchange of CO2 (NEE). The species composition was identified to understand the differences in NEE among the various plant communities in the NSA fen. The data were collected in July of 1994 and 1996. The data are contained in comma-delimited, ASCII files.

  19. Pollen morphology of some asiatic species of genus salsola (chenopodiaceae) and its taxonomic relationships

    International Nuclear Information System (INIS)

    Toderich, K.N.; Shuyskaya, E.V.; Ozturk, M

    2010-01-01

    Comparative studies on the pollen grain morphology of 27 Asiatic species of the genus Salsola were conducted by using scanning electron microscope (SEM analysis) in order to assess the taxonomic value of pollen traits. The pollen are radially symmetrical isopolar, pantopolyporate, spherical or subspheroid. The pollen characters like size, pore number, chord (C/D ratio), pore diameter, exine thickness, level of sinking of pore, convexness of mesoporial exine, spinule and minute-hole densities and number of spines on pore membrane appeared to be useful characters in distinguishing the species. Interesting intraspecific variations in pollen grain morphology were recorded for the C/D ratio. This parameter is highly specific, supporting the delimitation of Salsola species, and appears to be more conservative than some flower and fruit characters. The numerical value of form index comprising the ratio between the length of polar axis and diameter (P/E) also was an informative trait for delimitation of the species investigated here. Three pollen types were recognized. Euclidean distance was used to compute the dissimilarity matrix and a cladogram prepared. The quantitative characters of pollen morphology allowed clustering of groups and ordination analyses of species from different sections/subsections within genus Salsola. These features indicated that overall pollen traits reflect the current taxonomic boundaries, except for the Salsola species allocated to Climacoptera and Halothamnus, which should be accepted as separate genera. (author)

  20. SESAM – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

    DEFF Research Database (Denmark)

    Guisan, Antoine; Rahbek, Carsten

    2011-01-01

    Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts...

  1. Object-based semi-automatic approach for forest structure characterization using lidar data in heterogeneous Pinus sylvestris stands

    Science.gov (United States)

    C. Pascual; A. Garcia-Abril; L.G. Garcia-Montero; S. Martin-Fernandez; W.B. Cohen

    2008-01-01

    In this paper, we present a two-stage approach for characterizing the structure of Pinus sylvestris L. stands in forests of central Spain. The first stage was to delimit forest stands using eCognition and a digital canopy height model (DCHM) derived from lidar data. The polygons were then clustered into forest structure types based on the DCHM data...

  2. Revisiting plant conservation on wooded shrines by a transversal approach: "Core" vs. "satellite" species and anthropological knowledge in Bwaba land, Burkina Faso

    Directory of Open Access Journals (Sweden)

    Anne Fournier

    2013-03-01

    Full Text Available Studies on plant conservation in sacred groves provide mixed results, with some showing their effectiveness while others do not. We argue that beyond the variety of field cases, studies usually suffer from overrating rare species and insufficient consideration of societal data. The sacred sites of Bondoukuy department in Bwaba cultural area (Burkina Faso were geo-referenced and measured; the most abundant ligneous species were listed and their abundance recorded. Their conservation status and dynamics were assessed based on the core vs. satellite species model of Hanski. Data interpretations relied on the phytogeographical affinities of abundant species and on anthropological knowledge of the Bwaba society. The vast majority of shrines were less than 1 ha, located in or near villages in specific landscape features, and covered with trees. The most abundant species of shrines belonged mostly to local phytochories, but were subject to rather high anthropisation. The results support the concept that wooded shrines preserve local biodiversity, but indicate threats from an invasive alien species. The location and condition of shrines appeared to be constitutive features: the Bwaba system of thought involves a series of sacred sites (with and without trees located in remarkable features of the landscape, and their way of life has resulted in the proximity of these sites to the villages. The beliefs that promote plant cover conservation do so only to a certain extent and regardless of the species content, which raises the concern that alien species may upset the established communities. These beliefs have led the Bwaba to choose the most humid environments in which to set up their wooded shrines, which is interesting from a conservation perspective. The study advocates for a better consideration of social data to identify the key elements of the dynamics of the vegetation of sacred groves.

  3. Public service and politics in contemporary Ukraine: the stages of search for the model of interaction and delimitation

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    O. O. Ratsyk

    2014-02-01

    The author concludes that three main approaches were formed and fixed in the political and legal documents: de­politicization, political neutrality and political impartiality. For the first time the principle of de­politicization was mentioned in official documents from the beginning of the modern independent Ukrainian state. It means the prohibition for political parties to create its offices in government bodies and organizations. The principle of political neutrality was mentioned in «The Conception of Administrative Reform in Ukraine» (1996.  It means the need to restrict some political rights and freedoms for civil servants, that interfere perform their professional duties. The principle of political impartiality mentioned in official documents in 2000. It means the need to restrict, above all, the right to freedom of speech and information for civil servants.

  4. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  5. Detection of cryptic species

    International Nuclear Information System (INIS)

    Cockburn, A.F.; Jensen, T.; Seawright, J.A.

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author)

  6. Detection of cryptic species

    Energy Technology Data Exchange (ETDEWEB)

    Cockburn, A F; Jensen, T; Seawright, J A [United States Dept. of Agriculture, Agricultural Research Service, Medical and Veterinary Entomology Research Lab., Gainesville, FL (United States)

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author). 11 refs, 2 figs, 2 tabs.

  7. Study on the Delimitation of the Urban Development Boundary in a Special Economic Zone: A Case Study of the Central Urban Area of Doumen in Zhuhai, China

    Directory of Open Access Journals (Sweden)

    Biao Zheng

    2018-03-01

    Full Text Available Since it implemented open-door policies, China has become the fastest growing economy in the world, and its urbanization level has steadily improved. Taking a special economic zone as the object of study, this paper delineates the urban development boundary of the Central Urban Area of Doumen. Using multiple models and methods, the urban development rigid and elastic boundaries are delineated separately, with the rigid boundary serving as the premise and foundation for delineating the elastic boundary. The results are as follows. First, the scale of the urban development rigid boundary is 79.60 km². Moreover, the scales of the urban development elastic boundaries in 2020 and 2026 are 24.51 km² and 28.53 km², respectively. Second, by delimiting the urban development elastic boundary, the compactness of urban land will be improved. Third, the urban development boundary of this paper is reasonable in theory. This paper suggests that the urban development boundary can curb urban sprawl and guide rational urban development, which is conducive to optimizing an urban spatial layout.

  8. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes.

    Directory of Open Access Journals (Sweden)

    Duílio M Z de A Silva

    Full Text Available Supernumerary (B chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.

  9. Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives.

    Science.gov (United States)

    Gama, Renato; Aguirre-Gutiérrez, Jesús; Stech, Michael

    2017-10-01

    The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer , has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus . Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer . Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross-section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer , which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re-analysis of published and newly generated plastid atpB-rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus , C. pilifer (Old World clade), and the reinstated C. lame