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Sample records for delimit parapatric species

  1. 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.

  2. 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.

  3. Environmental niche divergence among three dune shrub sister species with parapatric distributions.

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    Chozas, Sergio; Chefaoui, Rosa M; Correia, Otília; Bonal, Raúl; Hortal, Joaquín

    2017-05-01

    The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula. The bioclimatic niche overlap between the three species was determined by using Schoener's index. The genetic differentiation of the Iberian and northern African populations of Stauracanthus species was characterized with GenalEx. The effects on genetic distances of the most important environmental drivers were assessed through Mantel tests and non-metric multidimensional scaling. The three Stauracanthus species show remarkably similar responses to climatic conditions. This supports the idea that all members of this recently diversified clade retain common adaptations to climate and consequently high levels of climatic niche overlap. This contrasts with the diverse edaphic requirements of Stauracanthus species. The populations of the S. genistoides-spectabilis clade grow on Miocene and Pliocene fine-textured sedimentary soils, whereas S. boivinii , the more genetically distant species, occurs on older and more coarse-textured sedimentary substrates. These patterns of diversification are largely consistent with a stochastic process of geographical range expansion and fragmentation coupled with niche evolution in the context of spatially complex environmental fluctuations. : The combined analysis of the distribution, realized environmental niche and phylogeographical relationships of parapatric species proposed in this work allows integration of the biogeographical

  4. Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S. dioica

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    Van Putten, W.F.; Biere, A.; Van Damme, J.M.M.

    2005-01-01

    We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus

  5. Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S-dioica

    NARCIS (Netherlands)

    Van Putten, WF; Biere, A; Van Damme, JMM

    We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

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    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.

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

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    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.

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

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    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. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

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

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    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.

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

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    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.

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

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    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.

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

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    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

  6. 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.

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

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    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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

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

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    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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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...

  3. 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.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

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

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    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.

  8. 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...

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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...

  2. Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs.

    Science.gov (United States)

    Hu, Junhua; Jiang, Jianping

    2018-02-02

    Identifying and understanding the mechanisms that shape barriers to dispersal and resulting biogeographic boundaries has been a longstanding, yet challenging, goal in ecology, evolution and biogeography. Characterized by stable, adjacent ranges, without any intervening physical barriers, and limited, if any, range overlap in a narrow contact zone, parapatric species are an interesting system for studying biogeographic boundaries. The geographic ranges of two parapatric frog species, Feirana quadranus and F. taihangnica, meet in a contact zone within the Qinling Mountains, an important watershed for East Asia. To identify possible ecological determinants of the parapatric range boundaries for two closely related frog species, we quantified the extent of their niche differentiation in both geographical and environmental space combining ecological niche models with an ordination technique. We tested two alternative null hypotheses (sharp environmental gradients versus a ribbon of unsuitable habitat dividing two highly suitable regions) for biogeographic boundaries, against the null expectation that environmental variation across a given boundary is no greater than expected by chance. We found that the niches of these two parapatric species are more similar than expected by chance, but not equivalent. No sharp environmental gradient was found, while a ribbon of unsuitable habitat did act as a barrier for F. quadranus, but not for F. taihangnica. Integrating our findings with historical biogeographic information, our results suggest that at a contact zone, environmental tolerance restricted F. quadranus from dispersing further north, while interspecific competition most likely prevented the southward expansion of F. taihangnica. This study highlights the importance of both climate and competition in exploring ecological explanations for parapatric range boundaries between ecologically similar frog species, in particular under the effects of changing climate.

  3. 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.

  4. 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

  5. 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.

  6. 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...

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

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    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

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    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.

  11. 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.

  12. 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

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

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    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

  14. 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.

  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. 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

  17. 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.

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

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    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.

  19. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient

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    Rossetto Maurizio

    2012-08-01

    Full Text Available Abstract Background Four of the five species of Telopea (Proteaceae are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation. Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Results Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR and six chloroplast microsatellites (cpSSR were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM. The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed

  20. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

    Science.gov (United States)

    Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

    2012-08-20

    Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters

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

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    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

  2. 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...

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

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    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus.

    Directory of Open Access Journals (Sweden)

    Anssi Karvonen

    Full Text Available Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

  9. Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus).

    Science.gov (United States)

    Karvonen, Anssi; Lucek, Kay; Marques, David A; Seehausen, Ole

    2015-01-01

    Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

  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. 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.

    Science.gov (United States)

    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

  12. 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

  13. 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...

  14. 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

  15. 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...

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones.

    Science.gov (United States)

    Engler, J O; Rödder, D; Elle, O; Hochkirch, A; Secondi, J

    2013-11-01

    Climate is a major factor delimiting species' distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species' interactions in hybrid zones and their responses to future climate change. We investigated the moving hybrid zone between the breeding ranges of two parapatric passerines in Europe. We conducted SDMs representing the climatic conditions during the breeding season. Our results show a large mismatch between the realized and potential distributions of the two species, suggesting that interspecific interactions, not climate, account for the present location of the contact zone. The SDM scenarios show that the southerly distributed species, Hippolais polyglotta, might lose large parts of its southern distribution under climate change, but a similar gain of novel habitat along the hybrid zone seems unlikely, because interactions with the other species (H. icterina) constrain its range expansion. Thus, whenever biotic interactions limit range expansion, species may become 'trapped' if range loss due to climate change is faster than the movement of the contact zone. An increasing number of moving hybrid zones are being reported, but the proximate causes of movement often remain unclear. In a global context of climate change, we call for more interest in their interactions with climate change. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  2. 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.

  3. 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.

  4. 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...

  5. 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

  6. 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

  7. 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.

  8. Natural selection on MHC IIβ in parapatric lake and stream stickleback: Balancing, divergent, both or neither?

    Science.gov (United States)

    Stutz, William E; Bolnick, Daniel I

    2017-09-01

    Major histocompatibility complex (MHC) genes encode proteins that play a central role in vertebrates' adaptive immunity to parasites. MHC loci are among the most polymorphic in vertebrates' genomes, inspiring many studies to identify evolutionary processes driving MHC polymorphism within populations and divergence between populations. Leading hypotheses include balancing selection favouring rare alleles within populations, and spatially divergent selection. These hypotheses do not always produce diagnosably distinct predictions, causing many studies of MHC to yield inconsistent or ambiguous results. We suggest a novel strategy to distinguish balancing vs. divergent selection on MHC, taking advantage of natural admixture between parapatric populations. With divergent selection, individuals with immigrant alleles will be more infected and less fit because they are susceptible to novel parasites in their new habitat. With balancing selection, individuals with locally rare immigrant alleles will be more fit (less infected). We tested these contrasting predictions using three-spine stickleback from three replicate pairs of parapatric lake and stream habitats. We found numerous positive and negative associations between particular MHC IIβ alleles and particular parasite taxa. A few allele-parasite comparisons supported balancing selection, and others supported divergent selection between habitats. But, there was no overall tendency for fish with immigrant MHC alleles to be more or less heavily infected. Instead, locally rare MHC alleles (not necessarily immigrants) were associated with heavier infections. Our results illustrate the complex relationship between MHC IIβ allelic variation and spatially varying multispecies parasite communities: different hypotheses may be concurrently true for different allele-parasite combinations. © 2017 John Wiley & Sons Ltd.

  9. 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...

  10. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.

    Science.gov (United States)

    Mutanen, Marko; Kivelä, Sami M; Vos, Rutger A; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A; Hebert, Paul D N; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H Charles J

    2016-11-01

    frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  11. 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...

  12. 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...

  13. 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.

  14. Increased genetic divergence between two closely related fir species in areas of range overlap

    Science.gov (United States)

    Wang, Jing; Abbott, Richard J; Ingvarsson, Pär K; Liu, Jianquan

    2014-01-01

    Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence. PMID:24772279

  15. 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.

  16. 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.

  17. Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

    Science.gov (United States)

    Wong, Mark K L; Woodman, James D; Rowell, David M

    2017-07-01

    Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

  18. Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean.

    Science.gov (United States)

    Deli, Temim; Kalkan, Evrim; Karhan, Selahattin Ünsal; Uzunova, Sonya; Keikhosravi, Alireza; Bilgin, Raşit; Schubart, Christoph D

    2018-04-11

    Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187). Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes

  19. 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....

  20. 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...

  1. 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...

  2. Chromosomal variation, macroevolution and possible parapatric speciation in Mepraia spinolai (Porter (Hemiptera: Reduviidae

    Directory of Open Access Journals (Sweden)

    Frias Daniel

    1998-01-01

    Full Text Available Mepraia spinolai is an endemic species in Chile that lives in wild and domestic habitats. It is the only species of the Reduviidae family that shows alate polymorphism; females are always wingless, but males can be found with and without wings. The M. spinolai karyotype consists of 10 pairs of autosomes and a complex sex determination system. Males from the northernmost regions I and II (latitude 18°-26° South are always winged (braquipterous and are X1X2Y, with a large Y chromosome. From region III to the metropolitan region (latitude 26°-33° South, males may be either winged or wingless but appear to be polymorphic for a small neo-Y chromosome, which may have originated by fracture of the large holocentric Y chromosome found in populations from farther north. Experimental crosses suggest that the genes for wings are linked in the Y chromosome and also that there are two cytologically indistinguishable types of neo-Y chromosomes. One form (Y1 bears a gene or genes for wings while the other (Y2 lacks such genes. Males that are X1X2Y1, X1X2Y1Y1 and X1X2Y1Y2 are winged, while the absence of Y1 (X1X2Y2 and X1X2Y2Y2 results in a wingless male. These chromosomes and morphological changes are correlated with a shift of the southern population into more arid habitats of the interior in the metropolitan region and region III.

  3. 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

  4. 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

  5. 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

  6. Postglacial species displacement in Triturus newts deduced from asymmetrically introgressed mitochondrial DNA and ecological niche models

    Directory of Open Access Journals (Sweden)

    Wielstra Ben

    2012-08-01

    Full Text Available Abstract Background If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large area. We explore this phenomenon using the two parapatric crested newt species, Triturus macedonicus and T. karelinii, distributed on the Balkan Peninsula in south-eastern Europe, as a model. Results We first delimit a ca. 54,000 km2 area in which T. macedonicus contains T. karelinii mitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T. karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes with those found in T. karelinii suggests a recent transfer across the species boundary. We then use ecological niche modeling to explore habitat suitability of the location of the present day introgression zone under current, mid-Holocene and Last Glacial Maximum conditions. This area was inhospitable during the Last Glacial Maximum for both species, but would have been habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generally increased for T. macedonicus, whereas it decreased for T. karelinii. Conclusion The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize the area where the present day introgression zone is positioned after the Last Glacial Maximum. Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which captured T. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecological niche modeling suggests that this replacement was likely facilitated by a shift in climate since the mid-Holocene. We suggest that the northwestern part of the current introgression zone was probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNA spread there through T. macedonicus exclusively. Considering the spatial distribution of the

  7. 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.

  8. 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 ...

  9. 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...

  10. 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 ...

  11. 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.

  12. 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.

  13. Revised species definitions and nomenclature of the rose colored Cithaerias butterflies (Lepidoptera, Nymphalidae, Satyrinae).

    Science.gov (United States)

    Penz, Carla M; Alexander, Laura G; Devries, Philip J

    2014-10-20

    This study provides updated species definitions for five rose-colored Cithaerias butterflies, starting with a historical overview of their taxonomy. Given their mostly transparent wings, genitalia morphology yielded the most reliable characters for species definition and identification. Genitalic divergence is more pronounced when multiple species occur in sympatry than between parapatric taxa. Cithaerias aurorina is granted full species status, C. cliftoni is reinstated as a full species, and one new combination is proposed, i.e. C. aurora tambopata. Two new synonyms are proposed, Callitaera phantoma and Callitaera aura = Cithaerias aurora. 

  14. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication.

    Directory of Open Access Journals (Sweden)

    Dustin A Wood

    Full Text Available Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

  15. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication.

    Science.gov (United States)

    Wood, Dustin A; Fisher, Robert N; Vandergast, Amy G

    2014-01-01

    Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

  16. Geographic morphological variation in parapatric Western Palearctic tree frogs, Hyla arborea and Hyla savignyi: are related species similarly affected by climatic conditions?

    Czech Academy of Sciences Publication Activity Database

    Gvoždík, Václav; Moravec, J.; Kratochvíl, L.

    2008-01-01

    Roč. 95, - (2008), s. 539-556 ISSN 0024-4066 R&D Projects: GA MŠk LC06073 Grant - others:GA ČR(CZ) GA206/05/2334 Institutional research plan: CEZ:AV0Z50450515 Keywords : amphibians * body shape * character displacement Subject RIV: EG - Zoology Impact factor: 2.019, year: 2008

  17. Isolation-by-distance and outbreeding depression are sufficient to drive parapatric speciation in the absence of environmental influences.

    Directory of Open Access Journals (Sweden)

    Guy A Hoelzer

    Full Text Available A commonly held view in evolutionary biology is that speciation (the emergence of genetically distinct and reproductively incompatible subpopulations is driven by external environmental constraints, such as localized barriers to dispersal or habitat-based variation in selection pressures. We have developed a spatially explicit model of a biological population to study the emergence of spatial and temporal patterns of genetic diversity in the absence of predetermined subpopulation boundaries. We propose a 2-D cellular automata model showing that an initially homogeneous population might spontaneously subdivide into reproductively incompatible species through sheer isolation-by-distance when the viability of offspring decreases as the genomes of parental gametes become increasingly different. This simple implementation of the Dobzhansky-Muller model provides the basis for assessing the process and completion of speciation, which is deemed to occur when there is complete postzygotic isolation between two subpopulations. The model shows an inherent tendency toward spatial self-organization, as has been the case with other spatially explicit models of evolution. A well-mixed version of the model exhibits a relatively stable and unimodal distribution of genetic differences as has been shown with previous models. A much more interesting pattern of temporal waves, however, emerges when the dispersal of individuals is limited to short distances. Each wave represents a subset of comparisons between members of emergent subpopulations diverging from one another, and a subset of these divergences proceeds to the point of speciation. The long-term persistence of diverging subpopulations is the essence of speciation in biological populations, so the rhythmic diversity waves that we have observed suggest an inherent disposition for a population experiencing isolation-by-distance to generate new species.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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...

  10. 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

  11. Chromosomal Speciation Revisited: Modes of Diversification in Australian Morabine Grasshoppers (Vandiemenella, viatica Species Group

    Directory of Open Access Journals (Sweden)

    Steven J. B. Cooper

    2011-03-01

    Full Text Available Chromosomal rearrangements can alter the rate and patterns of gene flow within or between species through a reduction in the fitness of chromosomal hybrids or by reducing recombination rates in rearranged areas of the genome. This concept, together with the observation that many species have structural variation in chromosomes, has led to the theory that the rearrangements may play a direct role in promoting speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group are an excellent model for studying the role of chromosomal rearrangement in speciation because they show extensive chromosomal variation, parapatric distribution patterns, and narrow hybrid zones at their boundaries. This species group stimulated development of one of the classic chromosomal speciation models, the stasipatric speciation model proposed by White in 1968. Our population genetic and phylogeographic analyses revealed extensive non-monophyly of chromosomal races along with historical and on-going gene introgression between them. These findings suggest that geographical isolation leading to the fixation of chromosomal variants in different geographic regions, followed by secondary contact, resulted in the present day parapatric distributions of chromosomal races. The significance of chromosomal rearrangements in the diversification of the viatica species group can be explored by comparing patterns of genetic differentiation between rearranged and co-linear parts of the genome.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Mammalian species - Neotoma magister

    Science.gov (United States)

    Steven B. Castleberry; Michael T. Mengak; W. Mark Ford

    2006-01-01

    External morphology of N. magister (Fig. 1) is similar to that of N. floridana, the only parapatric Neotoma. Although N. magister generally is larger in mass and with longer vibrissae, identification based on single measurements is unreliable because of morphometric overlap (Ray 2000)....

  20. Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species.

    Directory of Open Access Journals (Sweden)

    Cassandra N Trier

    2014-01-01

    Full Text Available Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP markers. After filtering for coverage, genotyping success (>97% and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse" at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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).

  11. 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

  12. 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.

  13. 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-...

  14. 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.

  15. 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.

  16. 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.

  17. CpDNA-based species identification and phylogeography: application to African tropical tree species.

    Science.gov (United States)

    Duminil, J; Heuertz, M; Doucet, J-L; Bourland, N; Cruaud, C; Gavory, F; Doumenge, C; Navascués, M; Hardy, O J

    2010-12-01

    Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations. © 2010 Blackwell Publishing Ltd.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Rubroboletus le-galiae (Boletales, Basidiomycota, a species new for Poland

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    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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Intercultural communication: conceptual delimitations

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    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. 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.

  2. The Megadiverse Australian Ant Genus Melophorus: Using CO1 Barcoding to Assess Species Richness

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    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.

  3. 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

  4. 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

  5. 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)

  6. Foliar phenolic compounds of ten wild species of Verbenacea as antioxidants and specific chemomarkers

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    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.

  7. Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra).

    Science.gov (United States)

    Moritz, Craig C; Pratt, Renae C; Bank, Sarah; Bourke, Gayleen; Bragg, Jason G; Doughty, Paul; Keogh, J Scott; Laver, Rebecca J; Potter, Sally; Teasdale, Luisa C; Tedeschi, Leonardo G; Oliver, Paul M

    2018-01-01

    Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  8. 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.

  9. 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.

  10. 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.

  11. New African species of Echinobothrium (Cestoda: Diphyllidea) and implications for the identities of their skate hosts.

    Science.gov (United States)

    Caira, J N; Rodriguez, N; Pickering, M

    2013-10-01

    Two new species of diphyllidean cestodes of the genus Echinobothrium, each hosted by a different skate species in the Raja miraletus complex, are described. Echinobothrium mercedesae n. sp. is described from R. cf. miraletus 2 off Senegal. Echinobothrium yiae n. sp. is described from R. cf. miraletus 1 off South Africa. Both species are small worms that differ from their 29 described congeners in the combination of number of cephalic peduncle spines per column, hook formula, number and arrangement of testes, and arrangement of vitelline follicles. They are easily distinguished from one another in that whereas the vitelline follicles of E. yiae n. sp. are circumcortical, they are lateral in E. mercedesae n. sp., and also in number of cephalic peduncle spines per column (14-17 vs. 10-12). Echinobothrium yiae n. sp. is also unusual in that the cephalic peduncle spines stop short of the anterior margin of the peduncle. In addition, although the paucity of available material precluded their formal description, evidence of 2 additional new species parasitizing R. miraletus also from Senegal is presented. In combination these worms provide support for the interpretation that what is currently recognized as Raja miraletus actually consists of a complex of geographically restricted species, rather than a polymorphic species of multiple parapatric or allopatrically distributed populations. This interpretation is not only supported by previously published molecular data, but also by newly collected morphological data involving differences in the color patterns of disc ocelli among host specimens of the 3 forms available as a result of digital efforts to ensure the accuracy of host identifications, which are also presented here.

  12. 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

  13. 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

  14. 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.

  15. The Delimitation of Urban Growth Boundaries Using the CLUE-S Land-Use Change Model: Study on Xinzhuang Town, Changshu City, China

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

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    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.

  1. Natural Constraints to Species Diversification.

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    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

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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)

  7. 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.

  8. On Gymnodactylus amarali Barbour, 1925, with the description of a new species (Sauria, Gekkonidae

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    Paulo Emilio Vanzolini

    2005-12-01

    Full Text Available Gymnodactylus amarali Barbour, 1925, was previously considered to be a subspecies of G. geckoides, with a wide distribution in the Brasilian cerrados. Examination of a specimen from Alto Parnaíba, Maranhão, near the type locality (Engenheiro Dodt, Piauí, indicates that it is a proper species, apparently limited to the upper Parnaíba basin. The form previously identified as G. geckoides amarali is described as a new species, G. carvalhoi, type locality Ipueiras, State of Tocantins, thus diagnosed: color pattern plain or, more often, with moderately contrasted ocelli; dorsal tubercles in 13 - 16 poorly organized longitudinal rows (mode 14, 72%; 31 - 49 tubercles in a paramedian row; 17 - 22 transverse rows of ventral scales; 13 - 18 infradigital lamellae on toe IV; tail longest in the genus. The new species is statistically compared to parapatric G. geckoides, widespread in the caatingas. Although only one meristic character (number of tubercle rows is by itself diagnostic, the species are easily told apart. It is thought on provisional evidence that they are better considered for the time being as full species, not subspecies. A brief consideration is made of the speciation model that seems suitable, to wit, parapatric.Gymnodactylus amarali vem sendo considerada uma subespécie de G. geckoides amplamente distribuida nos cerrados brasileiros. Exame de um exemplar de Alto Parnaíba, Maranhão, localidade próxima da localidade tipo, Engenheiro Dodt, Piauí, indica que se trata de uma espécie válida, aparentemente limitada ao Alto Parnaíba. A forma anteriormente identificada como Gymnodactylus geckoides amarali é aqui descrita como Gymnodactylus carvalhoi, sp. n., assim diagnosticada: padrão de colorido dorsal obsoleto ou, mais frequentemente, com ocelos de expressão moderada; 13 - 16 (moda 14, 72% fileiras longitudinais, pouco regulares, de tubérculos dorsais; 31 - 49 tubérculos em uma fileira para - mediana; 17 - 22 fileiras

  9. 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

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    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.

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

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    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.

  11. 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.

  12. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

    Science.gov (United States)

    Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

    2006-10-01

    Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

  13. Flood regime as a driver of the distribution of mangrove and salt marsh species in a subtropical estuary

    Science.gov (United States)

    Spier, Daphne; Gerum, Humberto L. N.; Noernberg, Maurício A.; Lana, Paulo C.

    2016-09-01

    Tidal patterns of the subtropical Paranaguá Estuarine Complex, in southern Brazil, are strongly affected by episodic cold fronts and by the coastal geometry and bottom topography, resulting in high temporal variability and marked gradients in flood regime. We delimit tolerance ranges of submersion and exposure for representative plant and animal species from local mangroves and salt marshes, through a quantitative analysis of flooding patterns in three estuarine sectors. Our results are consistent with flood regime being the leading factor on how species are distributed over the intertidal flats of the PEC. Subleading factors might be related to salinity, sediment composition and nutrient flow.

  14. Species or Genotypes? Reassessment of Four Recently Described Species of the Ceratocystis Wilt Pathogen, Ceratocystis fimbriata, on Mangifera indica.

    Science.gov (United States)

    Oliveira, Leonardo S S; Harrington, Thomas C; Ferreira, Maria A; Damacena, Michelle B; Al-Sadi, Abdullah M; Al-Mahmooli, Issa H S; Alfenas, Acelino C

    2015-09-01

    Ceratocystis wilt is among the most important diseases on mango (Mangifera indica) in Brazil, Oman, and Pakistan. The causal agent was originally identified in Brazil as Ceratocystis fimbriata, which is considered by some as a complex of many cryptic species, and four new species on mango trees were distinguished from C. fimbriata based on variation in internal transcribed spacer sequences. In the present study, phylogenetic analyses using DNA sequences of mating type genes, TEF-1α, and β-tubulin failed to identify lineages corresponding to the four new species names. Further, mating experiments found that the mango isolates representing the new species were interfertile with each other and a tester strain from sweet potato (Ipomoea batatas), on which the name C. fimbriata is based, and there was little morphological variation among the mango isolates. Microsatellite markers found substantial differentiation among mango isolates at the regional and population levels, but certain microsatellite genotypes were commonly found in multiple populations, suggesting that these genotypes had been disseminated in infected nursery stock. The most common microsatellite genotypes corresponded to the four recently named species (C. manginecans, C. acaciivora, C. mangicola, and C. mangivora), which are considered synonyms of C. fimbriata. This study points to the potential problems of naming new species based on introduced genotypes of a pathogen, the value of an understanding of natural variation within and among populations, and the importance of phenotype in delimiting species.

  15. Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?

    Science.gov (United States)

    Rosser, Neil; Kozak, Krzysztof M; Phillimore, Albert B; Mallet, James

    2015-06-30

    Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two

  16. INSTITUTION vs. ORGANIZATION. CONCEPTUAL DELIMITATIONS

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    Andrea Sveda ANGEL

    2011-06-01

    Full Text Available Both organizations and institutions are social structures. On the basis of the institutions arethe formal rules and at the basis of the organizations are the interactions between peoples withcommon aims. The evolution of the institutions is explained by the institutionalism with its twoorientations: the new institutionalism and the old institutionalism. The last one was preoccupied bythe transformation of the economy and by the evolution of the technology and the newinstitutionalism explains the existence of the institutions from the individual’s point of view.Organizations were and are studied in present days from different point of views: organizationalstructure and culture, organizational change and development. The organization was classifiedaccording to several factors: aim, size, legal form, or their operational domain. Thecharacterization of the organization through metaphors such as machines, culture, brain, ororganism proves their complexity and diversity. Regarding to the relations between institution andorganization, the relationship could be characterised as interdependence because the organizationscan determine instituional changes, by offering a framework for the application of the rules.

  17. ILLEGAL MIGRATION-CONCEPTUAL DELIMITATIONS

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    CRISTINA FLORINA POPESCU (PANAIT

    2013-05-01

    Full Text Available Illegal migration is a mobile phenomenon, which ignores national borders, a threat that originates outside the community and extends to Western societies. This phenomenon is becoming larger and irregular migrants are often in a precarious situation and exposed to the criminals involved in various manifestations of organized crime. The future risk factors of the illegal migration are the demographic bomb, because the population is decreasing in European countries and increasing rapidly in poorer countries, droughts, floods, deforestation, that cause conflicts between climate refugees , extreme poverty, totalitarian regimes, epidemics, can trigger millions of people, the elderly and the working population imbalance which leads to the permanent import of immigrants To combat this phenomenon, states must engage and cooperate with each other. Measures taken by states must balance their integration policy for immigrants, legally residents and asylum policy to comply with international conventions. Also, states must adopt anti-immigrant policies, consisting of subordination visa policy to the interests of international security and exchange of information and, not least, to continue the Schengen process, as a value of humanitarian law applied in the field. The aim of the research is to characterize this dangerous phenomenon for the society and the goal is to identify strategies to combat illegal migration.

  18. Systematics and natural history of Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) with descriptions of eight new species from Malaysia, Thailand, and Indonesia.

    Science.gov (United States)

    Grismer, L Lee; Wood, Perry L; Anuar, Shahrul; Riyanto, Awal; Ahmad, Norhayati; Muin, Mohd A; Sumontha, Montri; Grismer, Jesse L; Onn, Chan Kin; Quah, Evan S H; Pauwels, Olivier S A

    2014-10-31

    A well-supported and well-resolved phylogeny based on a concatenated data set from one mitochondrial and two nuclear genes, six morphological characters, and nine color pattern characters for 44 of the 50 species of the Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) is consistent with the previous taxonomy of Cnemaspis based solely on morphology and color pattern. Cnemaspis is partitioned into four major clades that collectively contain six species groups. The monophyly of all clades and species groups is strongly supported and they are parapatrically distributed across well-established, biogeographical regions ranging from southern Vietnam westward through southern Indochina, southward through the Thai-Malay Peninsula, then eastward to Borneo. Eight new species (Cnemaspis omari sp. nov. from the Thai-Malaysian border; C. temiah sp. nov. from Cameron Highlands, Pahang, Malaysia; C. stongensis sp. nov. from Gunung Stong, Kelantan, Malaysia; C. hangus sp. nov. from Bukit Hangus, Pahang, Malaysia; C. sundagekko sp. nov. from Pulau Siantan, Indonesia; C. peninsularis sp. nov. from southern Peninsular Malaysia and Singapore, and C. mumpuniae sp. nov. and C. sundainsula sp. nov. from Pulau Natuna Besar, Indonesia) are described based on morphology and color pattern and all but C. sundagekko sp. nov. are included in the phylogenetic analyses. Cnemaspis kendallii is polyphyletic and a composite of six species. An updated taxonomy consistent with the phylogeny is proposed for all 50 species and is based on 25 morphological and 53 color pattern characters scored across 594 specimens. Cladogenetic events and biogeographical relationships within Cnemaspis were likely influenced by this group's low vagility and the cyclical patterns of geographical and environmental changes in Sundaland over the last 25 million years and especially within the last 2.5 million years. The phylogeny indicates that nocturnality, diurnality, substrate preferences, and the presence of

  19. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex

    Science.gov (United States)

    Souza, Camila S.; Costa-Silva, Guilherme J.; Roxo, Fábio F.; Foresti, Fausto; Oliveira, Claudio

    2018-01-01

    Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species. PMID:29552028

  20. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex.

    Science.gov (United States)

    Souza, Camila S; Costa-Silva, Guilherme J; Roxo, Fábio F; Foresti, Fausto; Oliveira, Claudio

    2018-01-01

    Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs - a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis . Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

  1. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae Is Likely to Be a Species Complex

    Directory of Open Access Journals (Sweden)

    Camila S. Souza

    2018-03-01

    Full Text Available Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC and the Automatic Barcode Gap Discovery (ABGD for single locus species delimitation, and a Principal Component Analysis (PCA of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis, a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

  2. SALMONELLA SPECIES

    African Journals Online (AJOL)

    DR. AMINU

    ... of Salmonella species serotypes in relation to age and sex among children, ..... However, most antimicrobials show sufficient selective toxicity to be of value in ... salmonellosis should be given good attention (Barrow et al., 2007). To reduce ...

  3. Recircumscription of the Nepenthes alata group (Caryophyllales: Nepenthaceae, in the Philippines, with four new species

    Directory of Open Access Journals (Sweden)

    Martin Cheek

    2013-12-01

    Full Text Available An overview of Nepenthes in the Philippines is presented. Four new species, Nepenthes extincta sp. nov., N. kitanglad sp. nov., N. kurata sp. nov. and N. leyte sp. nov. are described and illustrated from the Philippines and placed in the Nepenthes alata group. An updated circumscription and key to the species of the group is provided. Delimitation and comparison with the Regiae group is given. All four of the newly described species are assessed as threatened using the International Union for the Conservation of Nature 2012 standard, and one, N. extincta sp. nov. is considered likely to be already extinct due to open-cast mining. Logging and conversion of forest habitat are thought to be the main threats to the other three species.

  4. Evolutionary relationships within the Phytophthora cactorum species complex in Europe.

    Science.gov (United States)

    Pánek, Matěj; Fér, Tomáš; Mráček, Jaroslav; Tomšovský, Michal

    2016-01-01

    The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of three genes (ITS region of ribosomal RNA gene, phenolic acid decarboxylase - Pheca I, and Cytochrome oxidase - Cox I), morphometric analysis and cardinal temperature data. The high proportion of clonal genotypes, low gene flow among groups, which was defined by the structure analysis, and low Nei's gene diversity confirms the homothallic life cycle of the groups. On the other hand, the ITS, Cox I and Pheca I sequence data support occasional hybridization between species. The structure K = 5 grouping revealed two groups of hybrid origin (C2 and F). While the C2 group resembles P. × serendipita, the F group includes Finnish isolates characterized by high oogonial abortion rates and slow growth. The morphological characters routinely used in identification of Phytophthora species are not useful for delimitation of species from the P. cactorum complex. Therefore, we discuss the status of P. hedraiandra as a separate species. The epitypification of P. cactorum is proposed. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  5. Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments.

    Science.gov (United States)

    Hauquier, Freija; Leliaert, Frederik; Rigaux, Annelien; Derycke, Sofie; Vanreusel, Ann

    2017-05-30

    Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200-500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations. Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species. Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with

  6. The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species.

    Science.gov (United States)

    Bernardes, Samuel C; Pepato, Almir R; von Rintelen, Thomas; von Rintelen, Kristina; Page, Timothy J; Freitag, Hendrik; de Bruyn, Mark

    2017-08-22

    The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution - from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species' potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus' early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet's closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.

  7. The species concept in a marine diatom: LSU rDNA–based phylogenetic differentiation in Skeletonema marinoi/dohrnii (Bacillariophyceae) is not reflected in morphology

    DEFF Research Database (Denmark)

    Ellegaard, Marianne; Godhe, Anna; Härnström, Karolina

    2008-01-01

    and Canada) included in the study showed differences in LSU rDNA sequence within the morphospecies, with differences seen even among clones established from a single plankton net sample. Morphologically, all clones were indistinguishable from each other and from the closely related species Skeletonema...... dohrnii. In the original description of these two species, they were differentiated by the structure of the girdle bands. However, the girdle band types of both species were found within single samples of almost all clones of S. marinoi in this study. The LSU-based phylogeny is consistent with the split...... into two species, and there may be a difference in their biogeographical distribution. We therefore do not at present suggest that the two species be merged. Questions regarding species delimitation and cryptic species within protists often arise from such studies that include data from both morphological...

  8. 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.

  9. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia.

    Science.gov (United States)

    Esselstyn, Jacob A; Maharadatunkamsi; Achmadi, Anang S; Siler, Cameron D; Evans, Ben J

    2013-10-01

    In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence. © 2013 John Wiley & Sons Ltd.

  10. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

  11. 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 characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised 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 unrecognised 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 formalised.

  12. Diagnóstico ambiental e delimitação de Áreas de Preservação Permanente em um assentamento rural = Environmental diagnosis and delimitation of PPAs (Permanent Preservation Areas in a rural settlement

    Directory of Open Access Journals (Sweden)

    Nelson Alexandre Fagundes

    2008-01-01

    Full Text Available Leia-se neste artigo a tentativa de diagnosticar, delimitar e situar as Áreas de Preservação Permanentes e de Reserva Legal dentro de um assentamento rural, do Incra; visando à experimentação de ferramentas de geoprocessamento para a restauração das matas ribeirinhas, pela delimitação destas áreas, respeitando a legislação ambiental vigente, e partindo de uma ampla avaliação ambiental descritiva da paisagem, encontrada no Projeto de Assentamento Federal Capela. Um diagnóstico da paisagem local é apresentado na forma de um memorial fotográfico. Neste trabalho, serão delimitadas e quantificadas somente asAPP’s de entorno de corpos d’água.This article aims to diagnose, demarcate and situate Permanent Preservation Areas and Legal Reserves within an Incra Rural Settlement. This effort was conducted while testing the effective application of geoprocessing tools in the restoration of riparian forests and the delimitation of these areas, in accordance withexisting environmental legislation, and based on a broad descriptive environmental evaluation of the local landscape, located at the Capela Federal Settlement Project. A landscape diagnosis is shown in a photographic memorial as well. For this study, only the PPAs surrounding water bodies will be delimited and quantified.

  13. Description of two new species of Rissoella Gray, 1847 (Mollusca, Gastropoda, Heterobranchia from Venezuela, with a key to the Caribbean species known for the genus

    Directory of Open Access Journals (Sweden)

    Manuel Caballer Gutierrez

    2011-07-01

    Full Text Available Two new species of the genus Rissoella Gray, 1847 are described from Venezuela, one from the National Park Morrocoy, Rissoella morrocoyensis sp. n. and the other from the Wildlife Refuge Isla de Aves, Rissoella venezolanicola sp. n. R. morrocoyensis sp. n. has a deep umbilicus (partly closed, preumbilical cord, black head, hypobranchial gland marked by a pale yellow boomerang-shaped ribbon and it lives on the leaves of the seagrass Thalassia testudinum Banks & König, 1805. R. venezolanicola sp. n. has an angled preumbilical cord which extends to the columella delimiting a trapezoid, a hypobranchial gland marked by a yellow quaver-shaped ribbon and protoconch with fuchsia highlights. It lives on the brown alga Dictyota spp. The records of Rissoella in the Caribbean are revised and illustrations, a comparative table and a key to the Caribbean species known for the genus are provided.

  14. The second species of Phanoperla (Plecoptera: Perlidae) from China, P. hainana sp. nov., from Hainan Island.

    Science.gov (United States)

    Li, Weihai; Qin, Xuefeng

    2016-09-08

    The genus Phanoperla Banks was originally established as a subgenus of Neoperla and its genus delimitation was not fully clear until the revisionary work by Zwick (1982). It currently contains 49 known species from the Oriental region (Banks 1938, 1939, Cao & Bae 2009, Cao et al. 2007, DeWalt et al. 2016, Jewett 1975, Kawai 1968, Stark 1983, 1987, Stark & Sheldon 2009, Sivec & Stark 2010, 2011, Stark & Sivec 2007, Sivec et al. 1988, Zwick 1982, Zwick 1986, Zwick & Sivec 1985). Although species of Phanoperla are not rare in many areas of Southeast Asia bordering China, especially Vietnam and India (Cao & Bae 2009, Mason & Stark 2015), P. pallipennis Banks, 1938 is the only known species of the genus known from China. In this paper, we describe a new species of Phanoperla from Hainan Island of the southernmost province of China. The northern portion of the island has a humid subtropical climate, whereas the remainder of the island has tropical monsoon climate.

  15. Genetic diversity of neotropical Myotis (chiroptera: vespertilionidae with an emphasis on South American species.

    Directory of Open Access Journals (Sweden)

    Roxanne J Larsen

    Full Text Available BACKGROUND: Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America. METHODOLOGY AND PRINCIPAL FINDINGS: Cytochrome-b sequences were generated and phylogenetically analyzed from 215 specimens, providing DNA sequence data for the most species of New World Myotis to date. Based on genetic data in our sample, and on comparisons with available DNA sequence data from GenBank, we estimate the number of species-level genetic lineages in South America alone to be at least 18, rather than the 15 species currently recognized. CONCLUSIONS: Our findings provide evidence that the perception of lower species richness in South American Myotis is largely due to a combination of cryptic morphological variation and insufficient sampling coverage in genetic-based systematic studies. A more accurate assessment of the level of diversity and species richness in New World Myotis is not only helpful for delimiting species boundaries, but also for understanding evolutionary processes within this globally distributed bat genus.

  16. The use of color infrared aerial photography in determining salt marsh vegetation and delimiting man-made structures of Lynnhaven Bay, Virginia. M.S. Thesis

    Science.gov (United States)

    Holman, R. E., III

    1974-01-01

    Color infrared aerial photography was found to be superior to color aerial photography in an ecological study of Lynnhaven Bay, Virginia. The research was divided into three phases: (1) Determination of the feasibility of correlating color infrared aerial photography with saline wetland species composition and zonation patterns, (2) determination of the accuracy of the aerial interpretation and problems related to the aerial method used; and (3) comparison of developed with undeveloped areas along Lynnhaven Bay's shoreline. Wetland species composition and plant community zonation bands were compared with aerial infrared photography and resulted in a high degree of correlation. Problems existed with changing physical conditions; time of day, aircraft angle and sun angle, making it necessary to use several different characteristics in wetland species identification. The main characteristics used were known zonation patterns, textural signatures and color tones. Lynnhaven Bay's shoreline was 61.5 percent developed.

  17. Unexpected high species diversity among European stalked puffballs – a contribution to the phylogeny and taxonomy of the genus Tulostoma (Agaricales

    Directory of Open Access Journals (Sweden)

    Mikael Jeppson

    2017-04-01

    Full Text Available A three-gene data set was generated to explore species diversity and delimitations within the stalked puffballs (Tulostoma, Agaricales in Europe. Data on species from other parts of the world were included for comparison of species concepts and distribution ranges. Sequence data from 26 type specimens are included. The phylogenetic analyses support Tulostoma as monophyletic. Eleven major clades, 37 minor clades, and 20 single branches were recovered and found to correspond to 30 described species and 27 species without scientific names. Five species are here described as new to science: Tulostoma calcareum, T. calongei, T. eckbladii, T. grandisporum, and T. pannonicum. In total we report 26 described, and 19 undescribed, species from Europe. An epitype for T. fimbriatum with ITS sequence data is selected to fix the name. The recovered tree topology was not in congruence with the current infrageneric classification of Tulostoma, suggesting that many of the morphological characters used for segregation of taxa are plesiomorphic or homoplasious. Spore ornamentation and hyphal structure of the peridium are found to be reliable characters for delimitation of species. The majority of the species occur in the dry, arid areas of southern and east central Europe but a few are shown to be restricted to humid temperate regions in the North. The study confirms that species with smooth or sub-smooth spores are restricted to dry and arid habitats whereas species with more strongly ornamented spores occur in humid habitats. Areas with steppe vegetation in Hungary and Spain are here identified as hot spots for Tulostoma species diversity.

  18. Endangered Species Day | Endangered Species Coalition

    Science.gov (United States)

    Annual Top 10 Report Protecting the Endangered Species Act Wildlife Voices Stand for Wolves Endangered Campaigns Wildlife Voices Protecting the Endangered Species Act Annual Top 10 Report Endangered Species Day Stand for Wolves Vanishing BOOK: A Wild Success The Endangered Species Act at 40 Endangered Species The

  19. A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China.

    Directory of Open Access Journals (Sweden)

    Xin Zhao

    Full Text Available The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens. Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.

  20. Leaf arrangements are invalid in the taxonomy of orchid species

    Directory of Open Access Journals (Sweden)

    Anna Jakubska-Busse

    2017-07-01

    Full Text Available The selection and validation of proper distinguishing characters are of crucial importance in taxonomic revisions. The modern classifications of orchids utilize the molecular tools, but still the selection and identification of the material used in these studies is for the most part related to general species morphology. One of the vegetative characters quoted in orchid manuals is leaf arrangement. However, phyllotactic diversity and ontogenetic changeability have not been analysed in detail in reference to particular taxonomic groups. Therefore, we evaluated the usefulness of leaf arrangements in the taxonomy of the genus Epipactis Zinn, 1757. Typical leaf arrangements in shoots of this genus are described as distichous or spiral. However, in the course of field research and screening of herbarium materials, we indisputably disproved the presence of distichous phyllotaxis in the species Epipactis purpurata Sm. and confirmed the spiral Fibonacci pattern as the dominant leaf arrangement. In addition, detailed analyses revealed the presence of atypical decussate phyllotaxis in this species, as well as demonstrated the ontogenetic formation of pseudowhorls. These findings confirm ontogenetic variability and plasticity in E. purpurata. Our results are discussed in the context of their significance in delimitations of complex taxa within the genus Epipactis.

  1. Two new mountainous species of Lactuca (Cichorieae, Asteraceae) from Iran, one presenting a new, possibly myrmecochorous achene variant.

    Science.gov (United States)

    Kilian, Norbert; Djavadi, Seyyedeh Bahereh; Eskandari, Majid

    2012-01-01

    It is shown that the concept of the Iranian endemic Lactuca polyclada in the sense of both its original author Boissier and its current use actually admixes two entirely different species, as was first noted by Beauverd a hundred years ago but has been neglected by later workers. One is a putative relative of Lactuca rosularis, the other was recognised by Beauverd as a member of the genus Cicerbita. The name Lactuca polyclada Boiss. is lectotypified here, maintaining its use as established by Beauverd for the Cicerbita species. Both species are morphologically delimited and mature achenes of Cicerbita polyclada are illustrated for the first time. The putative relative of Lactuca rosularis, a rare local endemic of the summit area of Kuh e-Dena, which has remained without a valid name by now, is described as a new species, Lactuca denaensis N. Kilian & Djavadi, and illustrated. A third member of the Lactuca rosularis group, Lactuca hazaranensis Djavadi & N. Kilian, discovered among a recent collection and apparently being a rare chasmophyte of the Hazaran mountain massif in the province of Kerman, Iran, is described as a species new to science, illustrated and delimited from the other two species. This new species has peculiar achenes representing a hitherto unknown variant: the body of the beaked achenes is divided into two segments by a transversal constriction in the distal third. The proximal segment contains the embryo, the distal segment is solid with a lipid-containing yellow tissue. The easily detachable pappus and the equally easily detachable beak potentially obstruct dispersal by wind. Since detachment of the beak also exposes the lipid-containing tissue of the distal segment, its potential as an elaiosome and myrmecochory as a possible mode of dispersal are discussed.

  2. Two new mountainous species of Lactuca (Cichorieae, Asteraceae from Iran, one presenting a new, possibly myrmecochorous achene variant

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    Norbert Kilian

    2012-04-01

    Full Text Available It is shown that the concept of the Iranian endemic Lactuca polyclada in the sense of both its original author Boissier and its current use actually admixes two entirely different species, as was first noted by Beauverd a hundred years ago but has been neglected by later workers. One is a putative relative of L. rosularis, the other was recognised by Beauverd as a member of the genus Cicerbita. The name L. polyclada Boiss. is lectotypified here, maintaining its use as established by Beauverd for the Cicerbita species. Both species are morphologically delimited and mature achenes of Cicerbita polyclada are illustrated for the first time. The putative relative of Lactuca rosularis, a rare local endemic of the summit area of Kuh e-Dena, which has remained without a valid name by now, is described as a new species, Lactuca denaensis N. Kilian & Djavadi, and illustrated. A third member of the Lactuca rosularis group, L. hazaranensis Djavadi & N. Kilian, discovered among a recent collection and apparently being a rare chasmophyte of the Hazaran mountain massif in the province of Kerman, Iran, is described as a species new to science, illustrated and delimited from the other two species. This new species has peculiar achenes representing a hitherto unknown variant: the body of the beaked achenes is divided into two segments by a transversal constriction in the distal third. The proximal segment contains the embryo, the distal segment is solid with a lipid-containing yellow tissue. The easily detachable pappus and the equally easily detachable beak potentially obstruct dispersal by wind. Since detachment of the beak also exposes the lipid-containing tissue of the distal segment, its potential as an elaiosome and myrmecochory as a possible mode of dispersal are discussed.

  3. Speciation on the rocks: integrated systematics of the Heteronotia spelea species complex (Gekkota; Reptilia from Western and Central Australia.

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    Mitzy Pepper

    Full Text Available The isolated uplands of the Australian arid zone are known to provide mesic refuges in an otherwise xeric landscape, and divergent lineages of largely arid zone taxa have persisted in these regions following the onset of Miocene aridification. Geckos of the genus Heteronotia are one such group, and have been the subject of many genetic studies, including H. spelea, a strongly banded form that occurs in the uplands of the Pilbara and Central Ranges regions of the Australian arid zone. Here we assess the systematics of these geckos based on detailed examination of morphological and genetic variation. The H. spelea species complex is a monophyletic lineage to the exclusion of the H. binoei and H. planiceps species complexes. Within the H. spelea complex, our previous studies based on mtDNA and nine nDNA loci found populations from the Central Ranges to be genetically divergent from Pilbara populations. Here we supplement our published molecular data with additional data gathered from central Australian samples. In the spirit of integrative species delimitation, we combine multi-locus, coalescent-based lineage delimitation with extensive morphological analyses to test species boundaries, and we describe the central populations as a new species, H. fasciolatus sp. nov. In addition, within the Pilbara there is strong genetic evidence for three lineages corresponding to northeastern (type, southern, and a large-bodied melanic population isolated in the northwest. Due to its genetic distinctiveness and extreme morphological divergence from all other Heteronotia, we describe the melanic form as a new species, H. atra sp. nov. The northeastern and southern Pilbara populations are morphologically indistinguishable with the exception of a morpho-type in the southeast that has a banding pattern resembling H. planiceps from the northern monsoonal tropics. Pending more extensive analyses, we therefore treat Pilbara H. spelea as a single species with

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

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    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.

  5. O processo de reconhecimento das indicações geográficas de alimentos e bebidas brasileiras: regulamento de uso, delimitação da área e diferenciação do produto The process of geographical indications recognition for food and beverages in Brazil: regulation of use, delimitation aerea and product differentiation

    Directory of Open Access Journals (Sweden)

    Maria Emília Rodrigues Valente

    2013-01-01

    Full Text Available As denominações de origem e as indicações de procedência compõem as espécies de indicação geográfica (IG previstas pela legislação brasileira e têm sido vistas como formas de mobilização e valorização dos territórios e de agregação de valor aos produtos típicos e de qualidade diferenciada. O presente trabalho teve como objetivo caracterizar a condução das etapas de elaboração do regulamento de uso, delimitação da área e comprovação da notoriedade e da relação entre produto e meio geográfico das IGs brasileiras. A metodologia adotada foi pesquisa survey, realizada por meio de questionários semiestruturados. Os resultados revelaram que, apesar das lacunas da legislação brasileira sobre IGs, vários órgãos têm viabilizado o processo de construção das IGs brasileiras atuando de forma decisiva nas etapas de elaboração do regulamento de uso (universidades, ONGs, INPI, delimitação da área (universidades, Embrapa, Emater, IMA, comprovação da notoriedade (SEBRAE e da relação entre meio geográfico e qualidade (universidades. A comprovação da influência do território nas características qualitativas do produto constitui, atualmente, o principal entrave ao desenvolvimento das denominações de origem no País.The appellations of origin and indication of source are species of geographical indication (GI provided by the Brazilian industrial property law that could be seen as one of the ways of mobilization and recovering of the rural territories adding value to local products with differentiated quality. This study aimed to characterize the stages of the construction of the regulations of use of GI, the geographical area delimitation, the evidence of reputation and the relationship between product and geographical environment of GIs in Brazil. The survey research was the methodology adopted conducted through semi-structured questionnaires. The results showed that despite the shortcomings of the Brazilian

  6. The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa.

    Science.gov (United States)

    Gonçalves, Duarte Vasconcelos; Martínez-Freiría, Fernando; Crochet, Pierre-André; Geniez, Philippe; Carranza, Salvador; Brito, José Carlos

    2018-01-01

    Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P. schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonization. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use

  7. 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.

  8. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora.

    Science.gov (United States)

    Spinks, Phillip Q; Thomson, Robert C; Zhang, YaPing; Che, Jing; Wu, Yonghua; Shaffer, H Bradley

    2012-06-01

    Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Revision of Gymnotus (Gymnotiformes: Gymnotidae) from the Upper Madeira Basin of Bolivia and Peru, with descriptions of two new species.

    Science.gov (United States)

    Craig, Jack M; Correa-roldÁn, Vanessa; Ortega, HernÁn; Crampton, William G R; Albert, James S

    2018-04-20

    Banded Knifefishes (Gymnotus, Gymnotidae) comprise the most species-rich genus of Neotropical electric fishes, with 41 species currently described from throughout the humid Neotropics, from Mexico to Argentina. Despite substantial alpha-taxonomic work in recent years, the diversity of Gymnotus in some regions remains poorly understood. Here we describe the Gymnotus fauna of the Upper Madeira basin of Bolivia and Peru from examination of more than 240 adult specimens. Species are delimited and described using body proportions (traditional morphometrics), fin-ray, squamation and laterosensory-pore counts (meristics), quantitative shape differences (geometric morphometrics), osteological traits, and color patterns. Comparisons of standardized linear measures as well as multivariate statistical methods validate the presence in the Upper Madeira basin of three previously described species, two with wide-spread geographic distributions throughout Greater Amazonia (G. carapo and G. coropinae), and one (G. chaviro) endemic to southwestern Amazonia. We also diagnose and describe two new species that are endemic to the Upper Madeira basin: G. eyra n. sp., morphologically most similar to G. mamiraua from lowland Amazonia, and G. riberalta n. sp., morphologically most similar to G. pantanal from the Paraguay-Paraná basin. The five Gymnotus species from the Upper Madeira basin are not monophyletic, each species being more closely related to a different species from another region; i.e. the Gymnotus species from the Upper Madeira represents a polyphyletic assemblage. These descriptions to 43 the number of valid Gymnotus species.

  10. Multi-gene phylogeny of the genus Lobaria: Evidence of species-pair and allopatric cryptic speciation in East Asia.

    Science.gov (United States)

    Cornejo, Carolina; Scheidegger, Christoph

    2015-12-01

    Accurate species delimitation has critical implications for ecological and conservation studies. The lichen genus Lobaria is widely distributed in old-growth forests. Particularly in East Asia, this genus includes many rare and poorly known taxa that are circumscribed as morpho- or chemospecies, as well as species-pairs. To critically examine the relationships between species identified via morphological and chemical criteria, phylogenetic species recognition (PSR) was applied to the genus Lobaria. Morphological and chemical patterns of 87 individuals were examined and three independent nuclear loci were sequenced. The East Asian L. meridionalis-group was additionally studied using split decomposition and haplotype network analysis. The genus Lobaria and most of its species were strongly supported statistically. Split decomposition and haplotype networks suggest complex evolutionary histories of species within the East Asian L. meridionalis-group. Phylogenetic analyses confirmed the monophyly of the genus Lobaria, including L. anomala. Within Lobaria, three major clades were found. These clades associate with different photobionts and comprise 18 known species and 5 undescribed species. Several chemical compounds were found to be neither stable nor invariant characters. Some taxa of the L. meridionalis-group appear to be monophyletic but remain as allopatric cryptic species. In three clades, this study found evidence for diversification processes between isidiate and nonisidiate specimens (species-pair). These findings are discussed in the context of evolutionary hypotheses for speciation processes. © 2015 Botanical Society of America.

  11. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes.

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    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.

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

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    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

  13. Species concept and speciation

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    Amal Y. Aldhebiani

    2018-03-01

    Full Text Available Defining and recognizing a species has been a controversial issue for a long time. To determine the variation and the limitation between species, many concepts have been proposed. When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa. In this paper some of species concepts are discussed starting from the typological species concepts to the phylogenetic concept. Positive and negative aspects of these concepts are represented in addition to their application. Keywords: Species concept, Species limitation, Species, Taxonomy, Classification

  14. The role of biotic interactions in plant community assembly: What is the community species pool?

    Science.gov (United States)

    Švamberková, Eva; Vítová, Alena; Lepš, Jan

    2017-11-01

    resident species were able to persist in competition. Comparison of realized vegetation composition with the corresponding species pool greatly underestimates the potential impact of the biotic filter if the delimitation of the species pool is based on the realized niches of species and co-occurrence patterns.

  15. Zonas de influência portuárias - hinterlands: conceituação e metodologias para sua delimitação Ports influence zones - hinterlands: concepts and methodologies for their delimitation

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    Nélio Domingues Pizzolato

    2010-01-01

    Full Text Available O processo de desenvolvimento de contêineres e o desenvolvimento de redes de transporte intermodal têm provocado crescente competição no setor portuário e vêm, no mundo inteiro, interferindo nas zonas de influência dos portos (hinterlands. Essas hinterlands estão deixando de ser cativas de um determinado porto para serem de múltipla influência de dois ou mais portos. O presente trabalho apresenta um estudo cujo objetivo é caracterizar a dinâmica portuária à luz da desenvolvimento de contêineres, mapear a discussão acerca do conceito de hinterlands e apresentar metodologias para sua delimitação. Essa contextualização conceitual e metodológica encontra-se ilustrada com sua aplicação ao caso do terminal de contêineres do porto de Rio Grande com apoio de Sistemas de Informação Geográfica (SIG. Como resultado, os autores concluem que a delimitação de hinterlands é essencial para auxiliar o planejamento do desenvolvimento portuário por parte de Autoridades Portuárias e Terminais Privativos num cenário de crescente competição.The containerization process and the development of intermodal transport networks have lead to a competitive scenario in the port sector and have modified their hinterlands all over the world. Those hinterlands are no longer captive areas of one port but competitive areas among two or more ports. The objectives of the present study are to characterize the port development due to the containerization process, to map the discussion on the concept of ports' hinterlands, and to present methodologies for their delimitation. Using Geographical Information Systems (GIS, this conceptual and methodological context allows the application of a methodology in a case study that embraces the container terminal of the port of Rio Grande. As a result, the authors conclude that the delimitation of hinterlands, in a growing competitive scenario, is essential to assist the port planning and development by Port

  16. Species accounts. Chapter 4

    Science.gov (United States)

    Margaret K. Trani; W. Mark Ford; Brian R., eds. Chapman

    2007-01-01

    Narrative accounts for each species are presented by several authors in a consistent format to convey specific information relative to that mammal. The orders are arranged phylogenetically; families and species are arranged alphabetically to facilitate finding a particular species.

  17. 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

  18. Ecological interpretations of the leaf anatomy of amphibious species of Aeschynomene L. (Leguminosae - Papilionoideae

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    FM Leme

    Full Text Available We present the leaf anatomy of seven amphibious species of Aeschynomene L. (Papilionoideae, Leguminosae, interpreting their structures and ecological functions, and also, providing information on which their taxonomy can be based, especially of morphologically similar species. We evaluated Aeschynomene americana, A. ciliata, A. evenia, A. denticulata, A. fluminensis, A. rudis and A. sensitiva. The anatomy corroborates the separation of the series Americanae, Fluminenses, Indicae and Sensitivae, with the shape of the petiole, types of trichomes and quantity of vascular units in the petiole as main characteristics to delimit the species. The petiole shape varies from cylindric in A. americana, A. sensitiva and A. fluminensis, to triangular in A. evenia and quadrangular in A. rudis, A. denticulata and A. ciliata. We observed four types of trichomes: hydathode trichome, long conic trichome, short conic trichome and bulb-based trichome. The hydathode trichome was the most common, except for A. americana and A. fluminensis. Species with higher affinity with water share similar adaptive characteristics, including hydathode trichomes described for the first time for the genus. This article adds unseen descriptions for the genus and on the adaptation factors of the amphibious species.

  19. Ecological interpretations of the leaf anatomy of amphibious species of Aeschynomene L. (Leguminosae - Papilionoideae).

    Science.gov (United States)

    Leme, F M; Scremin-Dias, E

    2014-02-01

    We present the leaf anatomy of seven amphibious species of Aeschynomene L. (Papilionoideae, Leguminosae), interpreting their structures and ecological functions, and also, providing information on which their taxonomy can be based, especially of morphologically similar species. We evaluated Aeschynomene americana, A. ciliata, A. evenia, A. denticulata, A. fluminensis, A. rudis and A. sensitiva. The anatomy corroborates the separation of the series Americanae, Fluminenses, Indicae and Sensitivae, with the shape of the petiole, types of trichomes and quantity of vascular units in the petiole as main characteristics to delimit the species. The petiole shape varies from cylindric in A. americana, A. sensitiva and A. fluminensis, to triangular in A. evenia and quadrangular in A. rudis, A. denticulata and A. ciliata. We observed four types of trichomes: hydathode trichome, long conic trichome, short conic trichome and bulb-based trichome. The hydathode trichome was the most common, except for A. americana and A. fluminensis. Species with higher affinity with water share similar adaptive characteristics, including hydathode trichomes described for the first time for the genus. This article adds unseen descriptions for the genus and on the adaptation factors of the amphibious species.

  20. Comparative genetics of hybrid incompatibility: sterility in two Solanum species crosses.

    Science.gov (United States)

    Moyle, Leonie C; Nakazato, Takuya

    2008-07-01

    The genetic basis of hybrid sterility can provide insight into the genetic and evolutionary origins of species barriers. We examine the genetics of hybrid incompatibility between two diploid plant species in the plant clade Solanum sect. Lycopersicon. Using a set of near-isogenic lines (NILs) representing the wild species Solanum pennellii (formerly Lycopersicon pennellii) in the genetic background of the cultivated tomato S. lycopersicum (formerly L. esculentum), we found that hybrid pollen and seed infertility are each based on a modest number of loci, male (pollen) and other (seed) incompatibility factors are roughly comparable in number, and seed-infertility QTL act additively or recessively. These findings are remarkably consistent with our previous analysis in a different species pair, S. lycopersicum x S. habrochaites. Data from both studies contrast strongly with data from Drosophila. Finally, QTL for pollen and seed sterility from the two Solanum studies were chromosomally colocalized, indicating a shared evolutionary history for these QTL, a nonrandom genomic distribution of loci causing sterility, and/or a proclivity of certain genes to be involved in hybrid sterility. We show that comparative mapping data can delimit the probable timing of evolution of detected QTL and discern which sterility loci likely evolved earliest among species.

  1. 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.

  2. Revision of the Metallactus kollari species-group with a new diagnosis of the genus (Coleoptera: Chrysomelidae: Cryptocephalinae).

    Science.gov (United States)

    Sassi, Davide

    2018-04-20

    The genus Metallactus has been controversial since its introduction due to the ambiguous nature of the original diagnosis. This has caused some confusion in the taxonomy of Neotropical Pachybrachina. In this work the morphology of endophallus, which is useful for the characterization of species groups in several groups of Coleoptera, including Cryptocephalinae, has been analyzed. This has proven to be a good resource also in the taxonomic treatment of the species belonging to the genus Metallactus. After a careful survey on most of the species described so far, the endophallus shape in Metallactus turned out to be remarkably distinctive and very promising in the delimitation of species groups. The present work includes: a) a new diagnosis of the genus Metallactus on the basis of the aedeagal anatomy; b) the designation of the type species of the nominal genus; c) the revision of a first species-group of the genus, including the type species, hereinafter called Metallactus kollari species-group. Before this revision, catalogues had been reporting 13 species attributable to this group, in the present work three species have been synonymized and seven have been described as new to science. Therefore, the group includes 17 species. The species described as new are: Metallactus rileyi n. sp., M. bellatrix n. sp., M. longicornis n. sp.; M. londonpridei n. sp., M. regalini n. sp., M. bezoar n. sp., M. guarani n. sp. The new synonymies are as follows: Metallactus albipes Suffrian, 1866 (= M. nigrofasciatus Suffrian, 1866 n. syn.), M. albifrons Suffrian, 1866 (= M. flavofrontalis Jacoby, 1907 n. syn.), M. dodecastictus Suffrian, 1866 (= Griburius nigritarsis Jacoby, 1907 n. syn.). The lectotypes of all previously described species have been designated. The new synonymies, the name-bearing type fixations and designations and the nomenclatural acts have been critically discussed. An identification key for the species-group is also provided.

  3. Agroforestry Species Switchboard

    DEFF Research Database (Denmark)

    Kindt, R.; John, I.; Ordonez, J.

    2016-01-01

    The current version of the Agroforestry Species Switchboard documents the presence of a total of 26,135 plant species (33,813 species including synonyms) across 19 web-based databases. When available, hyperlinks to information on the selected species in particular databases are provided. In total...

  4. New or little-known species of Chaetocladius s. str. Kieffer, 1911 (Diptera: Chironomidae: Orthocladiinae) from the Amur River basin (Russian Far East).

    Science.gov (United States)

    Makarchenko, Eugenyi A; Makarchenko, Marina A; Semenchenko, Alexander A

    2017-03-27

    Chironomids of the subgenus Chaetocladius s. str. from the Amur River basin are revised using both morphological characters and molecular data. Three new species, C. egorych sp. nov., C. lopatinskiy sp. nov. and C. yavorskayae sp. nov., are described and figured. The pupa of C. fedotkin is described for the first time. Adult males of C. ligni and C. piger, little-known in the Far East, are redescribed and annotated, and key to males of the Chaetocladius s. str. from the Amur River basin is provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between 5 species in the subgenus produced K2P genetic distances of 8.3-12.6%, values well associated with interspecific variation. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str.

  5. 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.

  6. New species of titi monkey, genus Callicebus Thomas, 1903 (Primates, Pitheciidae, from Southern Amazonia, Brazil

    Directory of Open Access Journals (Sweden)

    Julio César Dalponte

    2014-01-01

    Full Text Available The genus Callicebus is one of the most diverse Neotropical primate groups, with 31 recognized species. However, large knowledge gaps still exist regarding the diversity of this genus. Such gaps are gradually being filled due to recent intensification of sampling efforts. Several geographic distributions have been better delimited, and six new species have been described in the last 15 years. The goal of the present study is to describe a new species of Callicebus belonging to the Callicebus moloch species group, recently discovered in an area previously considered to be part of the geographic distribution of C. cinerascens. Data collection was conducted through direct observations, specimen collection and interviews with local residents during four expeditions. Specimens were deposited in the mammalian collection of the Museu Paraense Emílio Goeldi.. For a comparative evaluation, we examined specimens of the other species of the Callicebus moloch species group, especially the geographically neighboring forms, C. bernhardi and C. cinerascens. We examined 10 chromatic characters of the fur. In addition to body mass, we verified the conventional external variables and 26 craniometric variables. The new species differs from all other Amazonian Callicebus by an exclusive combination of characters, being easily distinguished by the light gray line of the forehead, dark ocher sideburns and throat, dark gray portions of the torso and flanks, and uniformly orange tail. The geographic distribution of the new species is limited by the Roosevelt and Aripuanã rivers, in the states of Mato Grosso and Amazonas, Brazil. Approximately 25% (1,246.382 ha of this area falls within conservation areas, with five areas of sustainable use (746,818 ha and three of integral protection (499,564 ha. Furthermore, a considerable portion of the distribution area is located within indigenous lands (1,555.116 ha - 32%. Therefore, 57% (2,801.498 ha of the occurrence area of

  7. Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of

  8. 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

  9. On the Bennelongia barangaroo lineage (Crustacea, Ostracoda in Western Australia, with the description of seven new species

    Directory of Open Access Journals (Sweden)

    Koen Martens

    2013-11-01

    Full Text Available The ostracod genus Bennelongia De Deckker & McKenzie, 1981 is endemic to Australia and New Zealand. Extensive sampling in Western Australia (WA revealed a high specific and largely undescribed diversity. Here, we describe seven new species belonging to the B. barangaroo lineage: B. timmsi sp. nov., B. gnamma sp. nov., B. hirsuta sp. nov., B. ivanae sp. nov., B. mcraeae sp. nov., B. scanloni sp. nov. and B. calei sp. nov., and confirm the presence of an additional species, B. dedeckkeri, in WA. For five of these eight species, we could construct molecular phylogenies and parsimonious networks based on COI sequences. We also tested for cryptic diversity and specific status of clusters with a statistical method based on the evolutionary genetic species concept, namely Birky’s 4 theta rule. The analyses support the existence of these five species and a further three cryptic species in the WA B. barangaroo lineage. The molecular evidence was particularly relevant because most species described herein have very similar morphologies and can be distinguished from each other only by the shape, size and position of the antero-ventral lapel on the right valve, and, in sexual populations, by the small differences in shape of the hemipenes and the prehensile palps in males. Four species of the WA B. barangaroo lineage occur in small temporary rock pools (gnammas on rocky outcrops. The other four species are mainly found in soft bottomed seasonal water bodies. One of the latter species, B. scanloni sp. nov., occurs in both claypans and deeper rock pools (pit gnammas. All species, except for B. dedeckkeri, originally described from Queensland, have quite clearly delimited distributions in WA. With the seven new species described here, the genus Bennelongia now comprises 25 nominal species but several more await formal description.

  10. 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

  11. The status of the Lutzomyia longipalpis species complex and possible implications for Leishmania transmission

    Directory of Open Access Journals (Sweden)

    Uribe Sandra

    1999-01-01

    Full Text Available The sand fly Lutzomyia longipalpis sensu latu has been identified as the principal vector of American visceral leishmaniasis, a potentially fatal disease that primarily affects children in several countries of South and Central America. Over the past several years increases have occurred both in the number of reported cases and the population at risk: approximately 1.6 million people reside in highly endemic areas with 16,000 cases reported annually. Several studies have attempted to relate the epidemiology of this disease to variability in Lu. longipalpis that is now recognized to be a complex of at least three sibling species. Morphological variation in this species was first noted by Mangabeira (1969. Since then physiological and biochemical differences have been reported by several investigators. Recent reports in Costa Rica of the presence of Lu. longipalpis in a focus of cutaneous leishmaniasis caused by Leishmania chagasi may be an additional indication of variability in this species. While existing evidence indicates that the morphospecies Lu. longipalpis may represent a complex of sibling species, genetic, epidemiological and ecological distinctions have not been fully resolved. Thus, delimitation of systematic boundaries within the complex and corresponding to geographic distributions and roles in transmission remain unresolved. The purpose of this review is to summarize from the literature observations of polymorphism in this morphospecies and consider what significance this reported variability may have to the epidemiology of visceral leishmaniasis.

  12. Leaf Protein Electrophoresis and Taxonomy of Species of Jatropha L. (Euphorbiaceae

    Directory of Open Access Journals (Sweden)

    Olaniran Temitope OLADIPO

    2012-08-01

    Full Text Available The systematic relationship existing among members of the all important genus Jatropha was studied using leaf protein electrophoresis. The aim was to identify possible taxonomic importance of the protein profile in the estimation and elucidation of the taxonomic affinity of the six species of Jatropha (Jatropha curcas Linn., J. podagrica Hook., J. gossypifolia Linn., J. mutifida Linn., J. tanjorensis Ellis & Saroja and J. integerrima Linn. found in Nigeria. The species were screened for total protein banding patterns using gel electrophoresis. Young leaves (0.8 g of the plants were washed with distilled water and macerated with sterile mortar and pestle in 0.8% Phosphate Buffer-Saline (PBS containing 0.4 M NaCl at pH 8.0. Results reveal that protein banding pattern was taxon specific. Generic band occurs at 8.3. The highest number of interspecific bands (4 exists between J. podagrica and J. multifida. Variations exist not only in the number of bands but also in the intensity of the bands. Sokal and Sneath coefficient of similarity ranges between 11.1-44.4 %. Single linkage Cluster Analysis (SLCA of the relative mobility values of the protein in the taxa shows partial agreement with current sub generic and sectional delimitation of the species based on morphology and anatomy of the species.

  13. Revision of the Malagasy Camponotus edmondi species group (Hymenoptera, Formicidae, Formicinae): integrating qualitative morphology and multivariate morphometric analysis.

    Science.gov (United States)

    Rakotonirina, Jean Claude; Csősz, Sándor; Fisher, Brian L

    2016-01-01

    The Malagasy Camponotus edmondi species group is revised based on both qualitative morphological traits and multivariate analysis of continuous morphometric data. To minimize the effect of the scaling properties of diverse traits due to worker caste polymorphism, and to achieve the desired near-linearity of data, morphometric analyses were done only on minor workers. The majority of traits exhibit broken scaling on head size, dividing Camponotus workers into two discrete subcastes, minors and majors. This broken scaling prevents the application of algorithms that uses linear combination of data to the entire dataset, hence only minor workers were analyzed statistically. The elimination of major workers resulted in linearity and the data meet required assumptions. However, morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. Prior species hypotheses and the goodness of clusters were tested on raw data by confirmatory linear discriminant analysis. Due to the small sample size available for some species, a factor known to reduce statistical reliability, hypotheses generated by exploratory analyses were tested with extreme care and species delimitations were inferred via the combined evidence of both qualitative (morphology and biology) and quantitative data. Altogether, fifteen species are recognized, of which 11 are new to science: Camponotus alamaina sp. n. , Camponotus androy sp. n. , Camponotus bevohitra sp. n. , Camponotus galoko sp. n. , Camponotus matsilo sp. n. , Camponotus mifaka sp. n. , Camponotus orombe sp. n. , Camponotus tafo sp. n. , Camponotus tratra sp. n. , Camponotus varatra sp. n. , and Camponotus zavo sp. n. Four species are redescribed: Camponotus echinoploides Forel, Camponotus edmondi André, Camponotus ethicus Forel, and Camponotus robustus Roger. Camponotus edmondi ernesti Forel, syn. n. is synonymized under Camponotus edmondi . This revision also includes an identification key to

  14. Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus.

    Directory of Open Access Journals (Sweden)

    Peter G Foster

    Full Text Available Specimens of neotropical Anopheles (Nyssorhynchus were collected and identified morphologically. We amplified three genes for phylogenetic analysis-the single copy nuclear white and CAD genes, and the COI barcode region. Since we had multiple specimens for most species we were able to test how well the single or combined genes were able to corroborate morphologically defined species by placing the species into exclusive groups. We found that single genes, including the COI barcode region, were poor at confirming species, but that the three genes combined were able to do so much better. This has implications for species identification, species delimitation, and species discovery, and we caution that single genes are not enough. Higher level groupings were partially resolved with some well-supported groupings, whereas others were found to be either polyphyletic or paraphyletic. There were examples of known groups, such as the Myzorhynchella Section, which were poorly supported with single genes but were well supported with combined genes. From this we can infer that more sequence data will be needed in order to show more higher-level groupings with good support. We got unambiguously good support (0.94-1.0 Bayesian posterior probability from all DNA-based analyses for a grouping of An. dunhami with An. nuneztovari and An. goeldii, and because of this and because of morphological similarities we propose that An. dunhami be included in the Nuneztovari Complex. We obtained phylogenetic corroboration for new species which had been recognised by morphological differences; these will need to be formally described and named.

  15. Endangered Species Act

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The purpose of the Endangered Species Act (ESA) is to protect and recover imperiled species and the ecosystems upon which they depend. The U.S. Fish and Wildlife...

  16. Endangered Species Protection Bulletins

    Science.gov (United States)

    Endangered Species Protection Bulletins set forth geographically specific pesticide use limitations for the protection of threatened and endangered (listed) species and their designated critical habitat. Find out how to get and use Bulletins.

  17. 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.

  18. Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding.

    Science.gov (United States)

    Hawlitschek, Oliver; Porch, Nick; Hendrich, Lars; Balke, Michael

    2011-02-09

    DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data. The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n. In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.

  19. The ichthyofauna of upper rio Capivari: defining conservation strategies based on the composition and distribution of fish species

    Directory of Open Access Journals (Sweden)

    Paulo dos Santos Pompeu

    Full Text Available Although the rio Capivari basin is recognized as an area of great importance for the ichthyofauna, it lacks virtually every basic requirement for the definition of appropriate conservation strategies, since not even its species composition is known. The objective of this work is to determine the composition and distribution of fish species in the upper rio Capivari basin, relating them to the local physical features, and to evaluate the effectiveness of proposed conservations units, delimited based on areas of native vegetation remains, on the conservation of local ichthyofauna. During 2007, 50 different watercourses were sampled with gillnets, cast nets and kick nets. A total of 1308 individuals belonging to 41 species were captured. Degree of conservation, altitude and width were the parameters that best explained fish species richness. Considering the recently proposed boundaries for potential conservation units in the region only 15 or 20 out of 41 species would be found in the State Park and Environmental Protection Area respectively. In practice, the proposed conservation units would not be effective tools for fish conservation, since it would be located in mountainous areas of high altitude, of headwaters streams and where few species are found. In such context, the conservation of specific stretches of larger rivers is critical.

  20. Systematics of Nothopsini (Serpentes, Dipsadidae), with a new species of Synophis from the Pacific Andean slopes of southwestern Ecuador

    Science.gov (United States)

    Pyron, R. Alexander; Guayasamin, Juan M.; Peñafiel, Nicolás; Bustamante, Lucas; Arteaga, Alejandro

    2015-01-01

    Abstract Within Dipsadinae, some recent authors have recognized a tribe Nothopsini containing the genera Diaphorolepis, Emmochliophis, Nothopsis, Synophis, and Xenopholis, on the basis of a number of putative morphological synapomorphies. However, molecular results suggest that Nothopsis, Synophis, and Xenopholis do not form a monophyletic group, while the remaining taxa are unsampled in recent molecular phylogenies. Here, DNA-sequence data for some Diaphorolepis and Synophis species are provided for the first time, as well as additional new sequences for Nothopsis and some Synophis species. Including these and other existing data for nothopsine species, previous studies showing that Nothopsini is not a natural group are corroborated. Nothopsini Cope, 1871 is restricted to Nothopsis. Diaphorolepidini Jenner, 1981 is resurrected and re-delimited to include only Diaphorolepis, Emmochliophis, and Synophis. Finally, Xenopholis remains Dipsadinae incertae sedis. Known material of Diaphorolepidini is reviewed to generate revised and expanded descriptions and diagnoses at the tribe, genus, and species level. Numerous cryptic species are likely present in Synophis bicolor and Synophis lasallei. Finally, a new population from the low-elevation cloud forests of SW Ecuador is reported upon, which is genetically and morphologically distinct from all other species, that is here named Synophis zaheri sp. n. PMID:26798284

  1. Delimiting Cladosporium from morphologically similar genera

    NARCIS (Netherlands)

    Crous, P.W.; Braun, U.; Schubert, K.; Groenewald, J.Z.

    2007-01-01

    The genus Cladosporium is restricted to dematiaceous hyphomycetes with a coronate scar type, and Davidiella teleomorphs. In the present study numerous cladosporium-like taxa are treated, and allocated to different genera based on their morphology and DNA phylogeny derived from the LSU nrRNA gene.

  2. 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...

  3. ON DELIMITING AFRICAN PHILOSOPHY AND THE ...

    African Journals Online (AJOL)

    Ike Odimegwu

    Hermeneutical Investigation of the Conditions of its Possibility” - an extract was published in .... defining African philosophy in terms of sages raises the problem that the difference ... beings. Universalism. This is a philosophical view that is rooted in the idea of logic and .... hegemony whether cultural and/or economical.

  4. Some Problems of Pedophilia Crimes Delimitation

    Directory of Open Access Journals (Sweden)

    Kuznetsova I. A.

    2013-10-01

    Full Text Available The article deals with the analysis of the changes contributed by the lawmaker to the RF Criminal Code. Here are distinguished contradictory and collision norms, the problems of their qualification. Some scientific points of view are quoted. The authors offer the ways of solving problematic issues connected with strengthening of the responsibility for crimes of sexual character committed in relation to non-adults

  5. Species diversity modulates predation

    NARCIS (Netherlands)

    Kratina, P.; Vos, M.; Anholt, B.R.

    2007-01-01

    Predation occurs in a context defined by both prey and non-prey species. At present it is largely unknown how species diversity in general, and species that are not included in a predator's diet in particular, modify predator–prey interactions.Therefore we studied how both the density and diversity

  6. Species choice, provenance and species trials among native Brazilian species

    Energy Technology Data Exchange (ETDEWEB)

    Drumond, M A

    1982-01-01

    Six papers from the conference are presented. Drumond, M.A., Potential of species native to the semi-arid tropics, 766-781, (Refs. 18), reports on Anadenanthera macrocarpa, Mimosa species, Schinopsis brasiliensis, Spondias tuberosa, Ziziphus joazeiro, Cnidoscolus phyllacanthus, Bursera leptophleos (leptophloeos), Tabebuia impetiginosa, Astronium urundeuva, and Mimosa caesalpinia. Monteiro, R.F.R., Speltz, R.M., Gurgel, J.T. do A.; Silvicultural performance of 24 provenances of Araucaria angustifolia in Parana, 814-824, (Refs. 8). Pires, C.L. da S., Kalil Filho, A.N., Rosa, P.R.F. da, Parente, P.R., Zanatto, A.C.S.; Provenance trials of Cordia alliodora in the State of Sao Paulo, 988-995, (Refs. 9). Nogueira, J.C.B., Siqueira, A.C.M.F., Garrido, M.A.O., Gurgel Garrido, L.M. do A., Rosa, P.R.F., Moraes, J.L. de, Zandarin, M.A., Gurgel Filho, O.A., Trials of some native species in various regions of the State of Sao Paulo, 1051-1063, (Refs. 9) describes Centrolobium tomentosum, Peltophorum dubium, Tabebuia vellosoi, Cariniana legalis, and Balfourodendron riedelianum. Batista, M.P., Borges, J.F., Franco, M.A.B.; Early growth of a native species in comparison with exotics in northeastern Para, Brazil, 1105-1110, (Refs. 3). Jacaranda copaia is compared with Gmelina arborea, Pinus caribaea various hondurensis, Eucalyptus deglupta, and E. urophylla. Lima, P.C.F., Souza, S.M. de, Drumond, M.A.; Trials of native forest species at Petrolina, Pernambuco, 1139-1148, (Refs. 8), deals with Anadenanthera macrocarpa, Piptadenia obliqua, Pithecellobium foliolosum, Astronium urundeuva, Schinopsis brasiliensis, Cassia excelsa, Caesalpinia pyramidalis, Parkia platycephala, Pseudobombax simplicifolium, Tabebuia impetiginosa, Caesalpinia ferrea, and Aspidosperma pyrifolium. 18 references.

  7. DNA barcoding of Vietnamese bent-toed geckos (Squamata: Gekkonidae: Cyrtodactylus) and the description of a new species.

    Science.gov (United States)

    Nguyen, Sang Ngoc; Yang, Jun-Xiao; Le, Thanh-Ngan Thi; Nguyen, Luan Thanh; Orlov, Nikolai L; Hoang, Chung Van; Nguyen, Truong Quang; Jin, Jie-Qiong; Rao, Ding-Qi; Hoang, Thao Ngoc; Che, Jing; Murphy, Robert W; Zhang, Ya-Ping

    2014-03-26

    Species of bent-toed gecko (Cyrtodactylus) in Vietnam have been described at a rate of nearly four species per year since 2007 mostly based on morphological data. A tool that guides species delimitation will accelerate the rate of documentation, and at a time when the recognition of species greatly benefits conservation. We use DNA barcoding using COI (550 bp) to re-examine the levels of genetic divergence and taxonomic status of 21 described species of Vietnamese bent-toed geckos. Tree-based analyses resolve all sampled species and identify potential undescribed taxa. Kimura 2-parameter genetic distances between the described species average 21.0±4.2% and range from 4.3% to 28.7%. Further, our analyses discover two potentially new species from Vietnam, two from Laos and one from China. Herein we describe the new species Cyrtodactylus puhuensis sp. nov. from Vietnam on the basis of both genetics and morphology. Genetically, it differs from the remaining species by an average K2P distance of 24.0±1.8%. Morphologically, the new species is diagnosed by its medium-size (snout-vent length 79.24 mm and tail length 82.59 mm, for the single known individual), in having a series of moderately enlarged transverse subcaudals and a series of moderately enlarged femoral scales that extend from precloacal scales, in possessing femoral scales without pores, with males having five precloacal pores, and in exhibiting 8 supralabials, 10 infralabials, 23 narrow subdigital lamellae on its fourth toe, and 36 transverse ventrals.

  8. Separation of chemical species

    International Nuclear Information System (INIS)

    Rentzepis, P.M.

    1977-01-01

    Isotopic separation is accomplished by (1) a second photon irradiation step for selective ionization of a first isotopic species and (2) selective precipitation of a generally immiscible liquid from the saturating vapor phase on the ionized species. The first photon corresponds with a sharply defined spectral portion of the irradiation which exclusively excites the first species to a vibrational level. The second photon further excites this species to its ionization level. Selective precipitation is by coulombic attraction between the ionized species and the vapor. The procedure is applicable to any vapor phase ionizable material

  9. A unified model of avian species richness on islands and continents.

    Science.gov (United States)

    Kalmar, Attila; Currie, David J

    2007-05-01

    How many species in a given taxon should be found in a delimited area in a specified place in the world? Some recent literature suggests that the answer to this question depends strongly on the geographical, evolutionary, and ecological context. For example, current theory suggests that species accumulate as a function of area differently on continents and islands. Species richness-climate relationships have been examined separately on continents and on islands. This study tests the hypotheses that (1) the functional relationship between richness and climate is the same on continents and islands; (2) the species-area slope depends on distance-based isolation; (3) species-area relationships differ among land bridge islands, oceanic islands, and continents; (4) richness differs among biogeographic regions independently of climate and isolation. We related bird species numbers in a worldwide sample of 240 continental parcels and 346 islands to several environmental variables. We found that breeding bird richness varies similarly on islands and on continents as a function of mean annual temperature, an area x precipitation interaction, and the distance separating insular samples from the nearest continent (R2 = 0.86). Most studies to date have postulated that the slope of the species-area relationship depends upon isolation. In contrast, we found no such interaction. A richness-environment relationship derived using Old World sites accurately predicts patterns of richness in the New World and vice versa (R2 = 0.85). Our results suggest that most of the global variation in richness is not strongly context-specific; rather, it reflects a small number of general environmental constraints operating on both continents and islands.

  10. Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

    Directory of Open Access Journals (Sweden)

    Paul De Barro

    Full Text Available BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010. Only two species proposed in Dinsdale et al. (2010 departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED and Middle East - Asia Minor 1 (MEAM1, showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of

  11. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae).

    Science.gov (United States)

    Eckert, Andrew J; Shahi, Hurshbir; Datwyler, Shannon L; Neale, David B

    2012-08-01

    Plant populations arrayed across sharp environmental gradients are ideal systems for identifying the genetic basis of ecologically relevant phenotypes. A series of five uplifted marine terraces along the northern coast of California represents one such system where morphologically distinct populations of lodgepole pine (Pinus contorta) are distributed across sharp soil gradients ranging from fertile soils near the coast to podzolic soils ca. 5 km inland. A total of 92 trees was sampled across four coastal marine terraces (N = 10-46 trees/terrace) located in Mendocino County, California and sequenced for a set of 24 candidate genes for growth and responses to various soil chemistry variables. Statistical analyses relying on patterns of nucleotide diversity were employed to identify genes whose diversity patterns were inconsistent with three null models. Most genes displayed patterns of nucleotide diversity that were consistent with null models (N = 19) or with the presence of paralogs (N = 3). Two genes, however, were exceptional: an aluminum responsive ABC-transporter with F(ST) = 0.664 and an inorganic phosphate transporter characterized by divergent haplotypes segregating at intermediate frequencies in most populations. Spatially variable natural selection along gradients of aluminum and phosphate ion concentrations likely accounted for both outliers. These results shed light on some of the genetic components comprising the extended phenotype of this ecosystem, as well as highlight ecotones as fruitful study systems for the detection of adaptive genetic variants.

  12. Spatiotemporal variation in the reproductive ecology of two parapatric subspecies of Oenothera cespitosa (Onagraceae).

    Science.gov (United States)

    Artz, Derek R; Villagra, Cristian A; Raguso, Robert A

    2010-09-01

    • Flowering plants that rely on pollinators for most of their reproduction may experience unpredictable and inconsistent availability of effective pollinators throughout their reproductive lifetime. We investigated the reproductive ecology of two subspecies of the tufted evening primrose, Oenothera cespitosa, which occupy geographically and edaphically distinct habitats in western North America: O. cespitosa subsp. navajoensis inhabits sandstone soils on open sites or rocky slopes in the Colorado Plateau and O. cespitosa subsp. cespitosa grows in clay soils on talus slopes and exposed rocky ridges in the western Great Plains and northern Rocky Mountains of the United States. • Pollen augmentation and selfing experiments, floral visitor observations, and single-visit effectiveness experiments were conducted over 4 years to examine the breeding system and spatiotemporal variation in pollinator behavior, assemblage, and abundance at different populations for each subspecies. • Both subspecies of O. cespitosa were self-incompatible and pollen-limited, suggesting that the relative abundance, effectiveness, and movement patterns of different insects as pollinators influenced the quality and quantity of seed production in these plants. Medium-sized vespertine hawkmoths (Hyles lineata, Sphinx vashti) were effective pollinators when present, as were large matinal bees (Anthophora affabilis, A. dammersi, Xylocopa tabaniformis androleuca), whereas small oligolectic Lasioglossum bees primarily functioned as pollen thieves in the evening and morning. • These findings highlight the importance of variability of pollinator composition and abundance in the evolution of plant breeding systems and reproductive success at varying spatial and temporal scales.

  13. A new species of Hatchet-faced Treefrog Sphaenorhynchus Tschudi (Anura: Hylidae) from Quadrilátero Ferrífero, Minas Gerais, southeastern Brazil.

    Science.gov (United States)

    Araujo-Vieira, Katyuscia; Lacerda, João Victor A; Pezzuti, Tiago L; Leite, Felipe Sá Fortes; De Assis, Clodoaldo Lopes; Cruz, Carlos Alberto G

    2015-12-21

    A new species of Sphaenorhynchus is described from the Municipality of Mariana, State of Minas Gerais, Brazil. It is characterized by the vocal sac moderately developed, single, subgular, with longitudinal folds; white canthal and dorsolateral lines delimited below by a dorsolateral black line from the tip of snout extending beyond the eye to gradually disappearing up to the flanks; and premaxilla and maxilla almost completely edentulous, each bearing 1-5 extremely small teeth. It is most similar with Sphaenorhynchus orophilus, from which it can be distinguished by having a less robust forearm in males; glandular subcloacal dermal fold; premaxilla and maxilla almost completely edentulous; and larvae with large marginal papillae in the oral disc. The new species occurs in natural ponds over ironstone outcrops (known as canga) on flat terrain, where males call from the floating vegetation.

  14. Microhyla laterite sp. nov., A New Species of Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae from a Laterite Rock Formation in South West India.

    Directory of Open Access Journals (Sweden)

    K S Seshadri

    Full Text Available In recent times, several new species of amphibians have been described from India. Many of these discoveries are from biodiversity hotspots or from within protected areas. We undertook amphibian surveys in human dominated landscapes outside of protected areas in south western region of India between years 2013-2015. We encountered a new species of Microhyla which is described here as Microhyla laterite sp. nov. It was delimited using molecular, morphometric and bioacoustics comparisons. Microhyla laterite sp. nov. appears to be restricted to areas of the West coast of India dominated by laterite rock formations. The laterite rock formations date as far back as the Cretaceous-Tertiary boundary and are considered to be wastelands in-spite of their intriguing geological history. We identify knowledge gaps in our understanding of the genus Microhyla from the Indian subcontinent and suggest ways to bridge them.

  15. Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species.

    Directory of Open Access Journals (Sweden)

    Haw Chuan Lim

    Full Text Available Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5% bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

  16. Historical Biogeography of Five Characidium Fish Species: Dispersal from the Amazon Paleobasin to Southeastern South America.

    Science.gov (United States)

    Poveda-Martínez, Daniel; Sosa, Chrystian C; Chacón-Vargas, Katherine; García-Merchán, Víctor Hugo

    2016-01-01

    Characidium is a Neotropical fish genus. Its distribution ranges from eastern Panama to northern Argentina, and it is an important component of the Neotropical ichthyofauna present in the major rivers of South America. We here provide an approximation to the dispersal and historical distributions of Characidium. The biogeographic history of five species of the genus was analyzed through nuclear RAG-2 and mitochondrial 16S genes and a time-calibrated phylogenetic analysis using three outgroup species. A biogeographical reconstruction was performed to estimate ancestral geographic ranges and infer the historical events that impacted the geographic distributions of Characidium species. Our results showed Characidium as a monophyletic group. The molecular clock suggests that the most recent common ancestor of Characidium originated during the Eocene, about 50.2 Mya. In addition, different dispersion and vicariance events could be inferred, which possibly gave rise to the present geographical distribution of the genus. Our results point to the rise of the Andean mountains and sea fluctuations as being important events in the formations and delimitation of different rivers, which influenced the distribution of South American ichthyofauna.

  17. 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)

  18. 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.

  19. Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).

    Science.gov (United States)

    Beck, James B; Semple, John C

    2015-06-01

    The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010. Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species. Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species. These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

  20. A new species of Casmaria H. Adams & A. Adams, 1853 (Gastropoda, Cassidae from the Philippines identified by molecular data

    Directory of Open Access Journals (Sweden)

    Alexander Fedosov

    2014-03-01

    Full Text Available The genus Casmaria H. Adams & A. Adams, 1853 (family Cassidae is widespread in the tropical Indo-Pacific and has been documented from some Atlantic localities as well. Two Casmaria species, C. erinaceus (Linnaeus, 1758 and C. ponderosa (Gmelin, 1791, are common in Indo-Pacific shallow-water sandy bottom communities and are characterized by high morphological variability; both species encompass multiple, often sympatric forms of uncertain status. In the present study we carry out a phylogenetic analysis of some Philippine Casmaria morphs and demonstrate that one of the distinctive morphs earlier assigned to Casmaria ponderosa is in fact a different species, which we describe as Casmaria boblehmani sp. nov. The smooth form of Casmaria ponderosa, C. ponderosa ponderosa, and the solid nodulose form, widely called “form nodulosa” despite being strikingly different in shell morphology, are shown to be conspecific. Studied specimens of these two morphs even from different localities share the same haplotype of the CO1 gene. In light of these new data on the morphological variability of Casmaria species, we discuss criteria of species delimitation in the genus Casmaria and possible affinities of Casmaria boblehmani sp. nov. within the genus.

  1. 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.

  2. 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.

  3. Integrating Morphology, Breeding Ground and Mitochondrial COI Gene Analysis for Species Identification of Bellamya lithophaga (Gastropoda: Viviparidae in China.

    Directory of Open Access Journals (Sweden)

    Youzhu Cheng

    2014-06-01

    Full Text Available Angiostrongylus cantonensis is a zoonotic public health concern that causes human severe eosinophilic meningitis in Southeast Asia and China. As a medically important intermediate host of A. cantonensis, Bellamya lithophaga (Gastropoda: Viviparidae is often confused with other morphologically similar sibling species of genus Bellamya, such as B. aeruginosa and B. purificata in the past. Hence, the aim of the present study was to investigate evidences to discriminate these equivocal Bellamya species.This study was carried out by getting Bellamya snail samples from Fujian Province in the South-East of China. The snail morphological features, breeding grounds and phylogenetic relationship according to mitochondrial cytochrome c oxidase subunit I (COI gene marker were analyzed.Based on external morphology, radular shape and cusp formula, as well as major breeding environment, B. lithophaga could be distinguished from B. aeruginosa, B. purificata. The phylogenetic tree also unconfirmed that B. lithophaga belongs to a different genetic clade from other morphologically similar species.Our findings demonstrate the significant differences in B. lithophaga and other sibling species, which supports the traditional species delimitation in the genus Bellamya.

  4. Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.

    Science.gov (United States)

    Yu, Xiang-Qin; Drew, Bryan T; Yang, Jun-Bo; Gao, Lian-Ming; Li, De-Zhu

    2017-01-01

    Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

  5. Integrative taxonomy of Leptonetela spiders (Araneae, Leptonetidae, with descriptions of 46 new species

    Directory of Open Access Journals (Sweden)

    Chun-Xia Wang

    2017-11-01

    Full Text Available Extreme environments, such as subterranean habitats, are suspected to be responsible for morphologically inseparable cryptic or sibling species and can bias biodiversity assessment. A DNA barcode is a short, standardized DNA sequence used for taxonomic purposes and has the potential to lessen the challenges presented by a biotic inventory. Here, we investigate the diversity of the genus Leptonetela Kratochvíl, 1978 that is endemic to karst systems in Eurasia using DNA barcoding. We analyzed 624 specimens using one mitochondrial gene fragment (COI. The results show that DNA barcoding is an efficient and rapid species identification method in this genus. DNA barcoding gap and automatic barcode gap discovery (ABGD analyses indicated the existence of 90 species, a result consistent with previous taxonomic hypotheses, and supported the existence of extreme male pedipalpal tibial spine and median apophysis polymorphism in Leptonetela species, with direct implications for the taxonomy of the group and its diversity. Based on the molecular and morphological evidence, we delimit and diagnose 90 Leptonetela species, including the type species Leptonetela kanellisi (Deeleman-Reinhold, 1971. Forty-six of them are previously undescribed. The female of Leptonetela zhai Wang & Li, 2011 is reported for the first time. Leptonetela tianxinensis (Tong & Li, 2008 comb. nov. is transferred from the genus Leptoneta Simon, 1872; the genus Guineta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela gigachela (Lin & Li, 2010 comb. nov. is transferred from Guineta. The genus Sinoneta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela notabilis (Lin & Li, 2010 comb. nov. and Leptonetela sexdigiti (Lin & Li, 2010 comb. nov. are transferred from Sinoneta; Leptonetela sanchahe Wang & Li nom. nov. is proposed as a replacement name for Sinoneta palmata (Chen et al., 2010 because Leptonetela palmata is preoccupied.

  6. Integrative taxonomy of Leptonetela spiders (Araneae, Leptonetidae), with descriptions of 46 new species.

    Science.gov (United States)

    Wang, Chun-Xia; Xu, Xin; Li, Shu-Qiang

    2017-11-18

    Extreme environments, such as subterranean habitats, are suspected to be responsible for morphologically inseparable cryptic or sibling species and can bias biodiversity assessment. A DNA barcode is a short, standardized DNA sequence used for taxonomic purposes and has the potential to lessen the challenges presented by a biotic inventory. Here, we investigate the diversity of the genus Leptonetela Kratochvíl, 1978 that is endemic to karst systems in Eurasia using DNA barcoding. We analyzed 624 specimens using one mitochondrial gene fragment ( COI ). The results show that DNA barcoding is an efficient and rapid species identification method in this genus. DNA barcoding gap and automatic barcode gap discovery (ABGD) analyses indicated the existence of 90 species, a result consistent with previous taxonomic hypotheses, and supported the existence of extreme male pedipalpal tibial spine and median apophysis polymorphism in Leptonetela species, with direct implications for the taxonomy of the group and its diversity. Based on the molecular and morphological evidence, we delimit and diagnose 90 Leptonetela species, including the type species Leptonetela kanellisi (Deeleman-Reinhold, 1971). Forty-six of them are previously undescribed. The female of Leptonetela zhai Wang & Li, 2011 is reported for the first time. Leptonetela tianxinensis (Tong & Li, 2008) comb. nov. is transferred from the genus Leptoneta Simon, 1872; the genus Guineta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela; Leptonetela gigachela (Lin & Li, 2010) comb. nov. is transferred from Guineta . The genus Sinoneta Lin & Li, 2010 syn. nov. is a junior synonym of Leptonetela ; Leptonetela notabilis (Lin & Li, 2010) comb. nov. and Leptonetela sexdigiti (Lin & Li, 2010) comb. nov. are transferred from Sinoneta ; Leptonetela sanchahe Wang & Li nom. nov. is proposed as a replacement name for Sinoneta palmata (Chen et al., 2010) because Leptonetela palmata is preoccupied.

  7. Chapter 16: Species Diversity

    African Journals Online (AJOL)

    zargaran

    2012-05-03

    May 3, 2012 ... rarefaction method was recorded in Pardanan, with 28 oak gall wasps species. Furthermore, the highest amount of Gini-Simpson and Shannon entropy index were recorded in Sardasht, while the highest evenness was recorded in Shalmash. Differences in the local distribution of oak species, especially.

  8. The Origin of Species

    NARCIS (Netherlands)

    Darwin, Charles

    2005-01-01

    In The Origin of Species Darwin outlined his theory of evolution, which proposed that species had been evolving and differentiating over time under the influence of natural selection. On its publication it became hugely influential, bringing about a seismic shift in the scientific view of humanitys

  9. Aquatic species and habitats

    Science.gov (United States)

    Danny C. Lee; James R. Sedell; Bruce E. Rieman; Russell F. Thurow; Jack E. Williams

    1998-01-01

    Continuing human activities threaten the highly prized aquatic resources of the interior Columbia basin. Precipitous declines in native species, particularly Pacific salmon, and a large influx of introduced species have radically altered the composition and distribution of native fishes. Fortunately, areas of relatively high aquatic integrity remain, much of it on...

  10. Support your local species

    DEFF Research Database (Denmark)

    Stärk, Johanna

    Nearly a quarter of all animal species within the European Union are threatened with extinction. Protecting many of these species will require the full spectrum of conservation actions from in-situ to ex-situ management. Holding an estimated 44% of EU Red Listed terrestrial vertebrates, zoos hereby...

  11. Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists.

    Science.gov (United States)

    Zhao, Yan; Yi, Zhenzhen; Gentekaki, Eleni; Zhan, Aibin; Al-Farraj, Saleh A; Song, Weibo

    2016-01-01

    Ciliates comprise a highly diverse protozoan lineage inhabiting all biotopes and playing crucial roles in regulating microbial food webs. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. Here, we use the species-rich taxon Frontonia and employ both nuclear and mitochondrial loci. We attempt to assess the level of genetic diversity and evaluate the potential of each marker in delineating species of Frontonia. Morphological features and ecological characteristics are also integrated into genetic results, in an attempt to resolve conflicts of species identification based on morphological and molecular methods. Our studies reveal: (1) the mitochondrial cox1 gene, nuclear ITS1 and ITS2 as well as the hypervariable D2 region of LSU rDNA are promising candidates for species delineation; (2) the cox1 gene provides the best resolution for analyses below the species level; (3) the V2 and V4 hypervariable regions of SSU rDNA, and D1 of LSU rDNA as well as the 5.8S rDNA gene do not show distinct barcoding gap due to overlap between intra- and inter-specific genetic divergences; (4) morphological character-based analysis shows promise for delimitation of Frontonia species; and (5) all gene markers and character-based analyses demonstrate that the genus Frontonia consists of three groups and monophyly of the genus Frontonia is questionable. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

    Science.gov (United States)

    Pfeiffer, John M.; Johnson, Nathan A.; Randklev, Charles R.; Howells, Robert G.; Williams, James D.

    2016-01-01

    The Central Texas endemic freshwater mussel, Quadrula mitchelli (Simpson in Dall, 1896), had been presumed extinct until relict populations were recently rediscovered. To help guide ongoing and future conservation efforts focused on Q. mitchelli we set out to resolve several uncertainties regarding its evolutionary history, specifically its unknown generic position and untested species boundaries. We designed a molecular matrix consisting of two loci (cytochrome c oxidase subunit I and internal transcribed spacer I) and 57 terminal taxa to test the generic position of Q. mitchelli using Bayesian inference and maximum likelihood phylogenetic reconstruction. We also employed two Bayesian species validation methods to test five a priori species models (i.e. hypotheses of species delimitation). Our study is the first to test the generic position of Q.mitchelli and we found robust support for its inclusion in the genusFusconaia. Accordingly, we introduce the binomial, Fusconaia mitchelli comb. nov., to accurately represent the systematic position of the species. We resolved F. mitchelli individuals in two well supported and divergent clades that were generally distinguished as distinct species using Bayesian species validation methods, although alternative hypotheses of species delineation were also supported. Despite strong evidence of genetic isolation within F. mitchelli, we do not advocate for species-level status of the two clades as they are allopatrically distributed and no morphological, behavioral, or ecological characters are known to distinguish them. These results are discussed in the context of the systematics, distribution, and conservation ofF. mitchelli.

  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. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

    Directory of Open Access Journals (Sweden)

    Luz E. Ochoa-Sánchez

    2017-08-01

    Full Text Available The genus Stenotrophomonas (Gammaproteobacteria has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR, opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc. Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs. The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They

  15. Novel intron markers to study the phylogeny of closely related mammalian species

    Directory of Open Access Journals (Sweden)

    Castresana Jose

    2010-11-01

    Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

  16. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

    Science.gov (United States)

    Szczecińska, Monika; Sawicki, Jakub

    2015-09-15

    The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete

  17. Signal complexity and modular organization of the courtship behaviours of two sibling species of wolf spiders (Araneae: Lycosidae).

    Science.gov (United States)

    Chiarle, Alberto; Isaia, Marco

    2013-07-01

    In this study, we compare the courtship behaviours of Pardosa proxima and P. vlijmi, two species of wolf spiders up to now regarded as "ethospecies", by means of motion analysis methodologies. In particular, we investigate the features of the signals, aiming at understanding the evolution of the courtship and its role in species delimitation and speciation processes. In our model, we highlight a modular structure of the behaviours and the presence of recurring units and phases. According to other similar cases concerning animal communication, we observed one highly variable and one stereotyped phase for both species. The stereotyped phase is here regarded as a signal related to species identity or an honest signal linked directly to the quality of the signaler. On the contrary, the variable phase aims to facilitate signal detection and assessment by the female reducing choice costs or errors. Variable phases include cues arisen from Fisherian runaway selection, female sensory exploitation and remaining of past selections. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Extragastric Helicobacter species

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Hynes, S.; Wadstrom, T.

    2002-01-01

    The genus Helicobacter has expanded at a rapid pace and no fewer than 31 species have been named since the proposal of the genus in 1989. Of these 31 species, 22 are principally associated with extragastric niches and there is increasing interest in the role of these taxa in diseases of humans...... and animals. Substantial evidence attests to certain species playing a role in the pathogenesis of enteric, hepatic and biliary disorders and some taxa demonstrate zoonotic potential. The importance of extragastric Helicobacters is likely to be an important topic for research in the near future. Here...

  19. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Phylogeography and systematics of the westernmost Italian Dolichopoda species (Orthoptera, Rhaphidophoridae)

    Science.gov (United States)

    Allegrucci, Giuliana; Rampini, Mauro; Di Russo, Claudio; Lana, Enrico; Cocchi, Sara; Sbordoni, Valerio

    2014-01-01

    Abstract The genus Dolichopoda (Orthoptera; Rhaphidopohoridae) is present in Italy with 9 species distributed from northwestern Italy (Piedmont and Liguria) to the southernmost Apennines (Calabria), occurring also in the Tyrrhenian coastal areas and in Sardinia. Three morphologically very close taxa have been described in Piedmont and Liguria, i.e., D. ligustica ligustica, D. ligustica septentrionalis and D. azami azami. To investigate the delimitation of the northwestern species of Dolichopoda, we performed both morphological and molecular analyses. Morphological analysis was carried out by considering diagnostic characters generally used to distinguish different taxa, as the shape of epiphallus in males and the subgenital fig in females. Molecular analysis was performed by sequencing three mitochondrial genes, 12S rRNA, 16S rRNA, partially sequenced and the entire gene of COI. Results from both morphological and molecular analyses highlighted a very homogeneous group of populations, although genetically structured. Three haplogroups geographically distributed could be distinguished and based on these results we suggest a new taxonomic arrangement. All populations, due to the priority of description, should be assigned to D. azami azami Saulcy, 1893 and to preserve the names ligustica and septentrionalis, corresponding to different genetic haplogroups, we assign them to D. azami ligustica stat. n. Baccetti & Capra, 1959 and to D. azami septentrionalis stat. n. Baccetti & Capra, 1959. PMID:25197209

  1. Phylogeography and systematics of the westernmost Italian Dolichopoda species (Orthoptera, Rhaphidophoridae

    Directory of Open Access Journals (Sweden)

    Giuliana Allegrucci

    2014-08-01

    Full Text Available The genus Dolichopoda (Orthoptera; Rhaphidopohoridae is present in Italy with 9 species distributed from northwestern Italy (Piedmont and Liguria to the southernmost Apennines (Calabria, occurring also in the Tyrrhenian coastal areas and in Sardinia. Three morphologically very close taxa have been described in Piedmont and Liguria, i.e., D. ligustica ligustica, D. ligustica septentrionalis and D. azami azami.To investigate the delimitation of the northwestern species of Dolichopoda, we performed both morphological and molecular analyses. Morphological analysis was carried out by considering diagnostic characters generally used to distinguish different taxa, as the shape of epiphallus in males and the subgenital plate in females. Molecular analysis was performed by sequencing three mitochondrial genes, 12S rRNA, 16S rRNA, partially sequenced and the entire gene of COI.Results from both morphological and molecular analyses highlighted a very homogeneous group of populations, although genetically structured. Three haplogroups geographically distributed could be distinguished and based on these results we suggest a new taxonomic arrangement. All populations, due to the priority of description, should be assigned to D. azami azami Saulcy, 1893 and to preserve the names ligustica and septentrionalis, corresponding to different genetic haplogroups, we assign them to D. azami ligustica Baccetti & Capra, 1959, stat. n. and to D. azami septentrionalis Baccetti & Capra, 1959, stat. n.

  2. 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

  3. 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.

  4. The species in primatology.

    Science.gov (United States)

    Groves, Colin

    2014-01-01

    Biologists of the late eighteenth and early nineteenth centuries all bandied about the term "species," but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit-appropriately, for the man who wrote a book called The Origin of Species - was Charles Darwin: "Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: "Hereafter, we shall be compelled to acknowledge that the only distinction between species and well-marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected"(1:484-5.) Copyright © 2014 Wiley Periodicals, Inc.

  5. Hierarchical species distribution models

    Science.gov (United States)

    Hefley, Trevor J.; Hooten, Mevin B.

    2016-01-01

    Determining the distribution pattern of a species is important to increase scientific knowledge, inform management decisions, and conserve biodiversity. To infer spatial and temporal patterns, species distribution models have been developed for use with many sampling designs and types of data. Recently, it has been shown that count, presence-absence, and presence-only data can be conceptualized as arising from a point process distribution. Therefore, it is important to understand properties of the point process distribution. We examine how the hierarchical species distribution modeling framework has been used to incorporate a wide array of regression and theory-based components while accounting for the data collection process and making use of auxiliary information. The hierarchical modeling framework allows us to demonstrate how several commonly used species distribution models can be derived from the point process distribution, highlight areas of potential overlap between different models, and suggest areas where further research is needed.

  6. Endangered Species: Pesticide Restrictions

    Science.gov (United States)

    Our goal is to protect threatened and endangered species and their habitats, without placing unnecessary burden on agriculture and pesticide users. Pesticide limitations are developed to ensure safe use of pesticides in order to meet this goal.

  7. Threatened & Endangered Species Occurrences

    Data.gov (United States)

    Kansas Data Access and Support Center — The database consists of a single statewide coverage of location records for 54 species contained in the Kansas Natural Heritage Inventory database of the Kansas...

  8. Sub specie aeternitatis

    Directory of Open Access Journals (Sweden)

    Laura Gioeni

    2012-10-01

    Full Text Available Per delineare il rapporto tra etica ed estetica nell'architettura e rispondere alla domanda principale «che cosa è o dovrebbe essere un buon architetto?», il saggio discute la tesi di Wittgenstein secondo cui «l'opera d'arte è l'oggetto visto sub specie aeternitatis e la vita buona è il mondo visto sub specie aeternitatis. Questa è la connessione tra arte ed etica».

  9. Hydrographic and hydrogeological basin of Entre-Ribeiros: probable recharge zone delimitation and environmental impact assessment Bacia hidrográfica e hidrogeológica de Entre-Ribeiros: zonas prováveis de recarga e análise dos impactos ambientais históricos

    Directory of Open Access Journals (Sweden)

    Vitor V. Vasconcelos

    2012-06-01

    Full Text Available The probable recharge zone delimitation of Entre-Ribeiros Basin (Northwest of the state of Minas Gerais / Brazil is proposed in this study. The delimitation is based upon stratigraphy, geomorphology, geo-environmental domains and hydrogeology studies. Combining the recharge zone map with the land use variation between 1975 and 2008, the occupation trends of possible recharge zones are identified. Concluding, the environmental impacts for this basin are discussed.Apresenta-se uma proposta de delimitação das prováveis zonas de recarga da Bacia Hidrográfica de Entre-Ribeiros (Noroeste de Minas Gerais/Brasil. A delimitação teve como subsídio estudos de litoestratigrafia, geomorfologia, unidades geoambientais e hidrogeologia. A partir da delimitação proposta, e conjugando-se à análise da ocupação do solo entre o período de 1975 a 2008, procura-se identificar as tendências de ocupação das zonas prováveis de recarga. Por fim, tecem-se comentários sobre os impactos ambientais decorrentes da ocupação dessas áreas.

  10. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  11. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  12. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  13. Aquatic Nuisance Species Locator

    Science.gov (United States)

    Data in this map has been collected by the United States Geological Survey's Nonindigenous Aquatic Species program located in Gainesville, Florida (http://nas.er.usgs.gov/default.aspx). This dataset may have some inaccuracies and is only current to June 15, 2012. The species identified in this dataset are not inclusive of all aquatic nuisance species, but rather a subset identified to be at risk for transport by recreational activities such as boating and angling. Additionally, the locations where organisims have been identified are also not inclusive and should be treated as a guide. Organisms are limited to the following: American bullfrog, Asian clam, Asian shore crab, Asian tunicate, Australian spotted jellyfish, Chinese mitten crab, New Zealand mudsnail, Colonial sea squirt, Alewife, Bighead carp, Black carp, Flathead catfish, Grass carp, Green crab, Lionfish, Northern snakehead, Quagga mussel, Round Goby, Ruffe, Rusty crayfish, Sea lamprey, Silver carp, Spiny water flea, Veined rapa whelk, Zebra mussel

  14. [Comparative leaf anatomy and phylogenetic relationships of 11 species of Laeliinae with emphasis on Brassavola (Orchidaceae)].

    Science.gov (United States)

    Noguera-Savelli, Eliana; Jáuregui, Damelis

    2011-09-01

    Brassavola inhabits a wide altitude range and habitat types from Northern Mexico to Northern Argentina. Classification schemes in plants have normally used vegetative and floral characters, but when species are very similar, as in this genus, conflicts arise in species delimitation, and alternative methods should be applied. In this study we explored the taxonomic and phylogenetic value of the anatomical structure of leaves in Brassavola; as ingroup, seven species of Brassavola were considered, and as an outgroup Guarianthe skinneri, Laelia anceps, Rhyncholaelia digbyana and Rhyncholaelia glauca were evaluated. Leaf anatomical characters were studied in freehand cross sections of the middle portion with a light microscope. Ten vegetative anatomical characters were selected and coded for the phylogenetic analysis. Phylogenetic reconstruction was carried out under maximum parsimony using the program NONA through WinClada. Overall, Brassavola species reveal a wide variety of anatomical characters, many of them associated with xeromorphic plants: thick cuticle, hypodermis and cells of the mesophyll with spiral thickenings in the secondary wall. Moreover, mesophyll is either homogeneous or heterogeneous, often with extravascular bundles of fibers near the epidermis at both terete and flat leaves. All vascular bundles are collateral, arranged in more than one row in the mesophyll. The phylogenetic analysis did not resolve internal relationships of the genus; we obtained a polytomy, indicating that the anatomical characters by themselves have little phylogenetic value in Brassavola. We concluded that few anatomical characters are phylogenetically important; however, they would provide more support to elucidate the phylogenetic relantionships in the Orchidaceae and other plant groups if they are used in conjunction with morphological and/or molecular characters.

  15. 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

  16. 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.

  17. 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.

  18. Phylogenetic reconstruction at the species and intraspecies levels in the genus Pisum (L.) (peas) using a histone H1 gene.

    Science.gov (United States)

    Zaytseva, Olga O; Bogdanova, Vera S; Kosterin, Oleg E

    2012-08-10

    A phylogenetic analysis of the genus Pisum (peas), embracing diverse wild and cultivated forms, which evoke problems with species delimitation, was carried out based on a gene coding for histone H1, a protein that has a long and variable functional C-terminal domain. Phylogenetic trees were reconstructed on the basis of the coding sequence of the gene His5 of H1 subtype 5 in 65 pea accessions. Early separation of a clear-cut wild species Pisum fulvum is well supported, while cultivated species Pisum abyssinicum appears as a small branch within Pisum sativum. Another robust branch within P. sativum includes some wild and almost all cultivated representatives of P. sativum. Other wild representatives form diverse but rather subtle branches. In a subset of accessions, PsbA-trnH chloroplast intergenic spacer was also analysed and found less informative than His5. A number of accessions of cultivated peas from remote regions have a His5 allele of identical sequence, encoding an electrophoretically slow protein product, which earlier attracted attention as likely positively selected in harsh climate conditions. In PsbA-trnH, a 8bp deletion was found, which marks cultivated representatives of P. sativum. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae

    Directory of Open Access Journals (Sweden)

    Marko Prous

    2017-09-01

    arctica Lindqvist, 1959, syn. n., Pachynematus incisus Lindqvist, 1970, syn. n., Pachynematus intermedius Verzhutskii, 1974, syn. n., and P. mongololaricis Haris, 2003, syn. n. with P. malaisei (Lindqvist, 1952; Nematus anderschi Zaddach, 1876, syn. n., P. inocreata Konow, 1902, syn. n., and P. discolor Lindqvist, 1975, syn. n. with P. nigricans (Eversmann, 1847; Lygaeonematus tenuicornis Lindqvist, 1955, syn. n. with P. paralella (Hartig, 1840; Lygaeonematus concolor Lindqvist, 1952, syn. n. with P. pseudocoactula (Lindqvist, 1952; P. flavipicta Lindqvist, 1975, syn. n., P. flavopleura Haris, 2002, syn. n., P. mongoloexigua Haris, 2002, syn. n., and P. mongolofausta Haris, 2003, syn. n. with P. punctifrons (Thomson, 1871; P. listoni Lacourt, 1998, syn. n. with P. sootryeni Lindqvist, 1955; P. gaunitzi Lindqvist, 1968, syn. n. with P. testacea (Jurine, 1807; and Nematus breviusculus Eversmann, 1847, syn. n. with Euura melanocephalus (Hartig, 1837. The valid name of Pachynematus (Pikonema carpathiensis Haris, 2001 is Nematinus carpathiensis (Haris, 2001 comb. n. Lectotypes are designated for 43 taxa. An illustrated electronic key made with Lucid and a traditional dichotomous key are provided to facilitate identification of the species. Species belonging to the carinata (previously Lygaeotus, micronematica (previously Lygaeophora, and rufipes (also known as thalictri or aquilegiae groups are not keyed to the species level, because additional research is needed to delimit the species more reliably in these groups. Phylogeny of Pristiphora is reconstructed based on one mitochondrial (COI and two nuclear (NaK and TPI genes. Remarkably, around 50–60% (depending on the exclusion or inclusion of the carinata, micronematica, and rufipes groups of the species cannot be reliably identified based on COI barcodes. Limited data from nuclear genes indicate a better identification potential (about 20% remain problematic.

  20. 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

  1. Unravelling the Biodiversity and Molecular Phylogeny of Needle Nematodes of the Genus Longidorus (Nematoda: Longidoridae) in Olive and a Description of Six New Species.

    Science.gov (United States)

    Archidona-Yuste, Antonio; Navas-Cortés, Juan A; Cantalapiedra-Navarrete, Carolina; Palomares-Rius, Juan E; Castillo, Pablo

    2016-01-01

    The genus Longidorus includes a remarkable group of invertebrate animals of the phylum Nematoda comprising polyphagous root-ectoparasites of numerous plants including several agricultural crops and trees. Damage is caused by direct feeding on root cells as well as by transmitting nepoviruses that cause disease on those crops. Thus, correct identification of Longidorus species is essential to establish appropriate control measures. We provide the first detailed information on the diversity and distribution of Longidorus species infesting wild and cultivated olive soils in a wide-region in southern Spain that included 159 locations from which 449 sampling sites were analyzed. The present study doubles the known biodiversity of Longidorus species identified in olives by including six new species (Longidorus indalus sp. nov., Longidorus macrodorus sp. nov., Longidorus onubensis sp. nov., Longidorus silvestris sp. nov., Longidorus vallensis sp. nov., and Longidorus wicuolea sp. nov.), two new records for wild and cultivate olives (L. alvegus and L. vineacola), and two additional new records for wild olive (L. intermedius and L. lusitanicus). We also found evidence of some geographic species associations to western (viz. L. alvegus, L. intermedius, L. lusitanicus, L. onubensis sp. nov., L. vineacola, L. vinearum, L. wicuolea sp. nov.) and eastern distributions (viz. L. indalus sp. nov.), while only L. magnus was detected in both areas. We developed a comparative study by considering morphological and morphometrical features together with molecular data from nuclear ribosomal RNA genes (D2-D3 expansion segments of 28S, ITS1, and partial 18S). Results of molecular and phylogenetic analyses confirmed the morphological hypotheses and allowed the delimitation and discrimination of six new species of the genus described herein and four known species. Phylogenetic analyses of Longidorus spp. based on three molecular markers resulted in a general consensus of these species

  2. Man as a Species.

    Science.gov (United States)

    Solem, Alan; And Others

    Written in 1964, the document represents experimental material of the Anthropology Curriculum Study Project. The objectives of the project were to discuss the evolution of man as distinguished from the evolution of other species and as related to culture, and to emphasize human diversity. Three brief essays are presented. The first, "The…

  3. Coevolution of Symbiotic Species

    OpenAIRE

    Leok, Boon Tiong Melvin

    1996-01-01

    This paper will consider the coevolution of species which are symbiotic in their interaction. In particular, we shall analyse the interaction of squirrels and oak trees, and develop a mathematical framework for determining the coevolutionary equilibrium for consumption and production patterns.

  4. Synonymization of key pest species within the Bactrocera dorsalis species complex (Diptera: Tephritidae): taxonomic changes based on a review of 20 years of integrative morphological, molecular, cytogenetic, behavioural and chemoecological data

    International Nuclear Information System (INIS)

    Schutze, Mark K.

    2015-01-01

    . Throughout the paper, we emphasize the value of independent and multidisciplinary tools in delimiting species, particularly in complicated cases involving morphologically cryptic taxa. (author)

  5. [Floral structure of two species of Trachycarpea (Arecaceae)].

    Science.gov (United States)

    Guevara, Lorena I; Jáuregui, Damelis J; Stauffer, Fred W

    2014-09-01

    Copernicia and Washingtonia are two genera of the Trachycarpeae for which no subtribal classification has been proposed, mainly because of the lack of resolution in phylogenetic studies. Morphology and anatomy of flowers whithin Coryphoideae have proven useful for taxa delimitation and supporting relationships among their members. A description of the morphological and anatomical structure of flowers of C. tectorum and W. filifera is presented in order to explore reproductive characters that may clarify their classification within the subfamily and to contribute with floral biology studies. Flowers of cultivated specimens of both taxa and developing fruits of C. tectorum were fixed in FAA, dissected for morphological analysis, and parafin-embedded flowers and fruits were serially sectioned for obtaining permanent slides, using conventional techniques and safranin-fast green staining. All procedures were carried out in the Laboratory of Morpho-Anatomy, Agronomy Faculty of the Universidad Central de Venezuela (UCV). Both species have hermaphroditic flowers. C. tectorum flowers have a thick and pubescent perianth, six stamens with filaments forming a tube fused to the corolla, with rounded projections and an acute apex where the anthers are inserted. W. filifera flowers have an irregularly dentate calyx, and a shortly acuminate corolla, six stamens united by their filaments to the corolla which at the same time are briefly fused to the gynoecium. Cells with druse crystals in the staminal tube are reported for C. tectorum. Only one of the carpels of the gynoecium of C. tectorum develops at fruit stage, and a layer of abundant raphide cells forming a crustaceous endocarp in mature fruits, was found. W. filifera presents the perianth mesophyll with few layers of thick walled cells and schlerenchymatic tissue, gynoecium with apically fused carpels in the ventral region of ovary, free at the base and the apex of the style, where the ventral sutures are opened. C. tectorum

  6. Hypocrea rufa/Trichoderma viride: a reassessment, and description of five closely related species with and without warted conidia.

    Science.gov (United States)

    Jaklitsch, Walter M; Samuels, Gary J; Dodd, Sarah L; Lu, Bing-Sheng; Druzhinina, Irina S

    2006-01-01

    The type species of the genus Hypocrea (Hypocreaceae, Hypocreales, Ascomycota, Fungi), H. rufa, is re-defined and epitypified using a combination of phenotype (morphology of teleomorphs and anamorphs, and characteristics in culture) and phylogenetic analyses of the translation-elongation factor 1alpha gene. Its anamorph, T. viride, the type species of Trichoderma, is re-described and epitypified. Eidamia viridescens is combined as Trichoderma viridescens and is recognised as one of the most morphologically and phylogenetically similar relatives of T. viride. Its teleomorph is newly described as Hypocrea viridescens. Contrary to frequent citations of H. rufa and T. viride in the literature, this species is relatively rare. Although both T. viride and T. viridescens have a wide geographic distribution, their greatest genetic diversity appears to be in Europe and North America. Hypocrea vinosa is characterised and its anamorph, T. vinosum sp. nov., is described. Conidia of T. vinosum are subglobose and warted. The new species T. gamsii is proposed. It shares eidamia-like morphology of conidiophores with T. viridescens, but it has smooth, ellipsoidal conidia that have the longest L/W ratio that we have seen in Trichoderma. Trichoderma scalesiae, an endophyte of trunks of Scalesia pedunculata in the Galapagos Islands, is described as new. It only produces conidia on a low-nutrient agar to which filter paper has been added. Additional phylogenetically distinct clades are recognised and provisionally delimited from the species here described. Trichoderma neokoningii, a T. koningii-like species, is described from a collection made in Peru on a fruit of Theobroma cacao infected with Moniliophthora roreri.

  7. Phylogenetic assessment of global Suillus ITS sequences supports morphologically defined species and reveals synonymous and undescribed taxa.

    Science.gov (United States)

    Nguyen, Nhu H; Vellinga, Else C; Bruns, Thomas D; Kennedy, Peter G

    The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. We present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available inPUBLIC databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America. We found that species boundaries delimited by morphological data are broadly congruent with those based on ITS sequences. However, some species appear to have been described several times under different names, several species groups cannot be resolved by ITS sequences alone, and undescribed taxa are apparent, especially in Asia. Therefore, we elevated S. tomentosus var. discolor to S. discolor; proposed synonymies of S. neoalbidipes with S. glandulosipes, S. borealis with S. brunnescens, Boletus serotinus and B. solidipes with Suillus elbensis, S. lactifluus with S. granulatus, S. himalayensis with S. americanus; and proposed usage of the names S. clintonianus in the place of the North American S. grevillei, S. weaverae for North American S. granulatus, S. ampliporus in the place of the North American S. cavipes, and S. elbensis in place of the North American S. viscidus. We showed that the majority of Suillus species have strong affinities for particular host genera. Although deep node support was low, geographic differentiation was apparent, with species from North America, Eurasia, and Asia often forming their own clades. Collectively, this comprehensive genus-level phylogenetic integration of currently available Suillus ITS molecular data and metadata will aid future taxonomic and ecological work on an

  8. Positive feedback in species communities

    NARCIS (Netherlands)

    Gerla, D.J.

    2012-01-01

    Sometimes the eventual population densities in a species community depend on the initial densities or the arrival times of species. If arrival times determine species composition, a priority effect has occurred. Priority effects may occur if the species community exhibits alternative stable states

  9. The functional biogeography of species

    DEFF Research Database (Denmark)

    Carstensen, Daniel W.; Dalsgaard, Bo; Svenning, Jens-Christian

    2013-01-01

    Biogeographical systems can be analyzed as networks of species and geographical units. Within such a biogeographical network, individual species may differ fundamentally in their linkage pattern, and therefore hold different topological roles. To advance our understanding of the relationship betw...... to distributions at the local community level. We finally discuss how our biogeographical species roles may correspond to the stages of the taxon cycle and other prominent theories of species assembly.......Biogeographical systems can be analyzed as networks of species and geographical units. Within such a biogeographical network, individual species may differ fundamentally in their linkage pattern, and therefore hold different topological roles. To advance our understanding of the relationship...... between species traits and large-scale species distribution patterns in archipelagos, we use a network approach to classify birds as one of four biogeographical species roles: peripherals, connectors, module hubs, and network hubs. These roles are based upon the position of species within the modular...

  10. Autecology of broadleaved species

    OpenAIRE

    Gonin, Pierre; Larrieu, Laurent; Coello, Jaime; Marty, Pauline; Lestrade , Marine; Becquey, Jacques; Claessens, Hugues

    2013-01-01

    Anyone involved in timber production needs some knowledge of autecology. With the renewed interest in hardwoods in the last 20 years, they are increasingly being introduced by planting or encouraged in natural stands. The results in terms of growth have not always met foresters’ expectations, due to technical problems and especially because the species are not always suited to the different sites. While the principle of establishing hardwoods is not in question, it is important to be aware of...

  11. Palynotaxonomy of Brazilian Viguiera (Asteraceae Species Palinotaxonomia de espécies brasileiras de Viguiera (Asteraceae-Heliantheae

    Directory of Open Access Journals (Sweden)

    Mara Angelina Galvão Magenta

    2010-12-01

    Full Text Available With the aim of improving inter-specific delimitation of the genus Viguiera Kunth in Brazil, a palynological analysis was undertaken with 27 taxa, representing around 77% of all occurring species. Samples were obtained from herbarium specimens and the pollen grains were analyzed through light and scanning electron microscopy. Characteristics, including the shape of the pollen grains, polar and equatorial diameter, aperture measurements, surface ornamentation and exine thickness, were registered and compared. The pollen grains were medium-sized (25 - 50 mm, isopolar and oblate spheroidal (prolate spheroidal in V. aspilioides Baker. The observed values corroborated the synonymity of some species and also highlighted certain micro-morphological differences, such as polar diameter and the dimensions of the colpus and endoaperture, thus confirming the groups of species delimitation obtained by morphologic and phylogenetic analyses.Com a finalidade de obter subsídios para a delimitação interespecífica do gênero Viguiera Kunth no Brasil, foi efetuado um estudo palinológico com 27 táxons, representando cerca de 77% das espécies ocorrentes. As amostras foram obtidas de material herborizado e o grão de pólen foi analisado sob microscopias óptica e eletrônica de varredura. Os grãos de pólen foram caracterizados quanto à forma, às dimensões e tipo da abertura, à ornamentação da superfície e à espessura da exina. Os grãos de pólen são médios (25 - 50mm, isopolares, oblato-esferoidais (prolato-esferoidais em V. aspilioides Baker, tricolporados, endoabertura lalongada, sexina espinhosa. Os valores obtidos corroboraram a sinonimização de algumas espécies e diferenças micro-morfológicas, tais como os valores do diâmetro polar, as dimensões do colpo e da endoabertura confirmaram algumas delimitações de grupos de espécies obtidas em análises filogenéticas de morfologia.

  12. Prior indigenous technological species

    Science.gov (United States)

    Wright, Jason T.

    2018-01-01

    One of the primary open questions of astrobiology is whether there is extant or extinct life elsewhere the solar system. Implicit in much of this work is that we are looking for microbial or, at best, unintelligent life, even though technological artefacts might be much easier to find. Search for Extraterrestrial Intelligence (SETI) work on searches for alien artefacts in the solar system typically presumes that such artefacts would be of extrasolar origin, even though life is known to have existed in the solar system, on Earth, for eons. But if a prior technological, perhaps spacefaring, species ever arose in the solar system, it might have produced artefacts or other technosignatures that have survived to present day, meaning solar system artefact SETI provides a potential path to resolving astrobiology's question. Here, I discuss the origins and possible locations for technosignatures of such a prior indigenous technological species, which might have arisen on ancient Earth or another body, such as a pre-greenhouse Venus or a wet Mars. In the case of Venus, the arrival of its global greenhouse and potential resurfacing might have erased all evidence of its existence on the Venusian surface. In the case of Earth, erosion and, ultimately, plate tectonics may have erased most such evidence if the species lived Gyr ago. Remaining indigenous technosignatures might be expected to be extremely old, limiting the places they might still be found to beneath the surfaces of Mars and the Moon, or in the outer solar system.

  13. 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.

  14. Estimating Effects of Species Interactions on Populations of Endangered Species.

    Science.gov (United States)

    Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

    2016-04-01

    Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

  15. CHROMOSOMES OF WOODY SPECIES

    Directory of Open Access Journals (Sweden)

    Julio R Daviña

    2000-01-01

    Full Text Available Chromosome numbers of nine subtropical woody species collected in Argentina and Paraguay are reported. The counts tor Coutarea hexandra (2n=52, Inga vera subsp. affinis 2n=26 (Fabaceae and Chorisia speciosa 2n=86 (Bombacaceae are reported for the first time. The chromosome number given for Inga semialata 2n=52 is a new cytotype different from the previously reported. Somatic chromosome numbers of the other taxa studied are: Sesbania punicea 2n=12, S. virgata 2n=12 and Pilocarpus pennatifolius 2n=44 from Argentina

  16. Cupreoboletus (Boletaceae, Boletineae), a new monotypic genus segregated from Boletus sect. Luridi to reassign the Mediterranean species B. poikilochromus.

    Science.gov (United States)

    Gelardi, Matteo; Simonini, Giampaolo; Ercole, Enrico; Davoli, Paolo; Vizzini, Alfredo

    2015-01-01

    Cupreoboletus is erected as a new monospecific genus of Boletaceae to accommodate the thermophilic southern European species Boletus poikilochromus, characterized by discoloration toward copper-red tints overall, hymenophore forming tiny crystals on drying, a pervasive and long lasting sweet odor and presence of pseudocystidia. Macro- and microscopic descriptions of the species based on re-examination of the type material and recent Italian collections including additional topotypical samples are provided and accompanied by photos and line drawings of the main anatomical structures. In addition, an epitype specimen is selected. Phylogenetic relationships were inferred from multigene molecular analysis based on partial sequences of the nuc rDNA 28S D1/D2 (28S) and internal transcribed spacer (ITS) regions and genes for ribosomal RNA polymerase II subunits 1 (rpb1) and 2 (rpb2) and translation-elongation factor 1-α (tef1α). Ecological context, geographical range and delimitation from closely allied taxa also were elucidated. B. martaluciae is treated as a synonym of C. poikilochromus according to the morphological and molecular comparative study. © 2015 by The Mycological Society of America.

  17. Save Our Species: Protecting Endangered Species from Pesticides.

    Science.gov (United States)

    Environmental Protection Agency, Washington, DC.

    This full-size poster profiles 11 wildlife species that are endangered. Color illustrations of animals and plants are accompanied by narrative describing their habitats and reasons for endangerment. The reverse side of the poster contains information on the Endangered Species Act, why protecting endangered and threatened species is important, how…

  18. New species of Malaysian ferns

    NARCIS (Netherlands)

    Holttum, R.E.

    1962-01-01

    The present paper includes descriptions of several new species of ferns found among recent collections from various parts of Malaysia; also two new combinations of names of species which are of interest on account of their taxonomic history.

  19. Endangered Species Act Critical Habitat

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Critical habitat (CH) is designated for the survival and recovery of species listed as threatened or endangered under the Endangered Species Act (ESA). Critical...

  20. New Malesian species of Viscaceae

    NARCIS (Netherlands)

    Barlow, Bryan A.

    1996-01-01

    Three new Malesian species of Viscaceae are described. Ginalloa flagellaris Barlow is distinguished as a species from New Guinea and New Britain, previously included within G. arnottiana Korthals. Viscum exile Barlow is recognized as a new species endemic to Celebes, related to V. ovalifolium.

  1. Lichen species preference by reindeer

    Energy Technology Data Exchange (ETDEWEB)

    Holleman, D F; Luick, J R

    1977-08-01

    The preference by reindeer for five species of lichens commonly found on Central Alaska rangelands was tested under controlled laboratory conditions. Results indicate that reindeer are strongly selective species in their lichen grazing habits. The five tested species ranged as follows in order of decreasing acceptibility: Caldonia alpestris, C. rangiferina, Stereocaulon paschale, Cetraria richardsonii, and Peltigera aphthosa.

  2. 75 FR 78974 - Endangered Species

    Science.gov (United States)

    2010-12-17

    ...-XA086 Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and exporting of endangered and threatened species (50 CFR 222-226). Permit...

  3. California Endangered Species Resource Guide.

    Science.gov (United States)

    California State Dept. of Education, Los Angeles.

    This document was developed in response to California Senate Bill No. 885, "The Endangered Species Education Project," that called for a statewide program in which schools adopt a local endangered species, research past and current efforts to preserve the species' habitat, develop and implement an action plan to educate the community…

  4. 76 FR 2348 - Endangered Species

    Science.gov (United States)

    2011-01-13

    .... 15596] Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... requested permit has been issued under the authority of the Endangered Species Act of 1973, as amended (ESA... endangered and threatened species (50 CFR parts 222-226). The North Carolina Aquarium at Fort Fisher has been...

  5. Electrosmog and species conservation

    Energy Technology Data Exchange (ETDEWEB)

    Balmori, Alfonso, E-mail: abalmorimartinez@gmail.com

    2014-10-15

    Despite the widespread use of wireless telephone networks around the world, authorities and researchers have paid little attention to the potential harmful effects of mobile phone radiation on wildlife. This paper briefly reviews the available scientific information on this topic and recommends further studies and specific lines of research to confirm or refute the experimental results to date. Controls must be introduced and technology rendered safe for the environment, particularly, threatened species. - Highlights: • Studies have shown effects in both animals and plants. • Two thirds of the studies reported ecological effects. • There is little research in this area and further research is needed. • The technology must be safe. • Controls should be introduced to mitigate the possible effects.

  6. Management of invasive species

    DEFF Research Database (Denmark)

    Schou, Jesper Sølver; Jensen, Frank

    impact of the establishment of this invasive species is a substantial increase in the number of allergy cases, which we use as a measure of the physical damage. As valuation methods, we use both the cost-of-illness method and the benefit transfer method to quantify the total gross benefits of the two...... policy actions. Based on the idea of an invasion function, we identify the total and average net benefit under both prevention and mitigation. For both policy actions, the total and average net benefits are significantly positive irrespective of the valuation method used; therefore, both prevention...... and mitigation are beneficial policy actions. However, the total and average net benefits under mitigation are larger than the benefits under prevention, implying that the former policy action is more beneficial. Despite this result, we conclude that prevention, not mitigation, shall be used because...

  7. Prices and species diversity

    DEFF Research Database (Denmark)

    Sauer, Johannes

    of biodiversity and the appropriate incorporation in stochastic fron-tier models to achieve more realistic measures of production efficiency. We use the empirical example of tobacco production drawing from as well as affecting species diversity in the surrounding forests. We apply a shadow profit distance......In recent decades a significant amount of literature has been produced concerned with establishing a link between production efficiency and environmental efficiency with respect to quantitative modelling. This has been mainly addressed by focusing on the incorporation of undesirable outputs...... or the incorporation of environmentally det-rimental inputs. However, while the debate with respect to linear programming based DEA modelling is already at an advanced stage the corresponding one with respect to stochastic frontier modelling still needs considerable efforts. This contribution fo-cuses on the case...

  8. Reactive Oxygen Species

    DEFF Research Database (Denmark)

    Franchina, Davide G.; Dostert, Catherine; Brenner, Dirk

    2018-01-01

    T cells are a central component of defenses against pathogens and tumors. Their effector functions are sustained by specific metabolic changes that occur upon activation, and these have been the focus of renewed interest. Energy production inevitably generates unwanted products, namely reactive...... and transcription factors, influencing the outcome of the T cell response. We discuss here how ROS can directly fine-tune metabolism and effector functions of T cells....... oxygen species (ROS), which have long been known to trigger cell death. However, there is now evidence that ROS also act as intracellular signaling molecules both in steady-state and upon antigen recognition. The levels and localization of ROS contribute to the redox modeling of effector proteins...

  9. Introduced species as evolutionary traps

    Science.gov (United States)

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  10. Insular species swarm goes underground

    DEFF Research Database (Denmark)

    P. S. Reboleira, Ana Sofia; Enghoff, Henrik

    2014-01-01

    Two new species of the genus Cylindroiulus Verhoeff, 1894, C. julesvernei and C. oromii, are described from the subterranean ecosystem of Madeira Island, Portugal. Species are illustrated with photographs and diagrammatic drawings. The new species belong to the Cylindroiulus madeirae......-group, an insular species swarm distributed in the archipelagos of Madeira and the Canary Islands. We discuss the differences between the new species and their relatives and present information on the subterranean environment of Madeira. An updated overview of the subterranean biodiversity of millipedes...

  11. Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera.

    Science.gov (United States)

    Richards, Leigh R; Rambau, Ramugondo V; Lamb, Jennifer M; Taylor, Peter J; Yang, Fengtang; Schoeman, M Corrie; Goodman, Steven M

    2010-09-01

    The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.

  12. Ring species as demonstrations of the continuum of species formation

    DEFF Research Database (Denmark)

    Pereira, Ricardo José Do Nascimento; Wake, David B.

    2015-01-01

    In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier......? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012......). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper...

  13. Species of Wadicosa (Araneae, Lycosidae): a new species from Madagascar.

    Science.gov (United States)

    Kronestedt, Torbjörn

    2017-05-10

    Since establishing the wolf spider genus Wadicosa Zyuzin, 1985 (Zyuzin 1985), eleven species have been accepted in it, either by transfer from Lycosa Latreille, 1804 or Pardosa C.L. Koch, 1847 or by original designation (WSC 2017). However, according to Kronestedt (1987), additional species wait to be formally transferred to Wadicosa. The genus is restricted to the Old World, with one species, Wadicosa jocquei Kronestedt, 2015, recently described from Madagascar and surrounding islands.

  14. Native species that can replace exotic species in landscaping

    Directory of Open Access Journals (Sweden)

    Elisabeth Regina Tempel Stumpf

    2015-08-01

    Full Text Available Beyond aesthetics, the contemporary landscaping intends to provide other benefits for humans and environment, especially related to the environmental quality of urban spaces and conservation of the species. A trend in this direction is the reduction in the use of exotic plants in their designs, since, over time, they can become agents of replacement of native flora, as it has occurred in Rio Grande do Sul with many species introduced by settlers. However, the use of exotic species is unjustifiable, because the flora diversity of the Bioma Pampa offers many native species with appropriate features to the ornamental use. The commercial cultivation and the implantation of native species in landscaped areas constitute innovations for plant nurseries and landscapers and can provide a positive reduction in extractivism, contributing to dissemination, exploitation and preservation of native flora, and also decrease the impact of chemical products on environment. So, this work intends to identify native species of Bioma Pampa with features and uses similar to the most used exotic species at Brazilian landscaping. The species were selected from consulting books about native plants of Bioma Pampa and plants used at Brazilian landscaping, considering the similarity on habit and architecture, as well as characteristics of leafs, flowers and/or fruits and environmental conditions of occurrence and cultivation. There were identified 34 native species able to properly replace exotic species commonly used. The results show that many native species of Bioma Pampa have interesting ornamental features to landscape gardening, allowing them to replace exotic species that are traditionally cultivated.

  15. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    McPheron, Bruce A.

    2000-01-01

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  16. Confronting species distribution model predictions with species functional traits.

    Science.gov (United States)

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  17. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Monika Szczecińska

    2015-09-01

    Full Text Available Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2 enabled the molecular delimitation of closely-related Pulsatilla

  18. Balance of bacterial species in the gut

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Balance of bacterial species in the gut. Protective. Lactobacillus species. Bifidobacterium species. Selected E. coli. Saccharomyces boulardii. Clostridium butyricum.

  19. Quantifying the invasiveness of species

    Directory of Open Access Journals (Sweden)

    Robert Colautti

    2014-04-01

    Full Text Available The success of invasive species has been explained by two contrasting but non-exclusive views: (i intrinsic factors make some species inherently good invaders; (ii species become invasive as a result of extrinsic ecological and genetic influences such as release from natural enemies, hybridization or other novel ecological and evolutionary interactions. These viewpoints are rarely distinguished but hinge on distinct mechanisms leading to different management scenarios. To improve tests of these hypotheses of invasion success we introduce a simple mathematical framework to quantify the invasiveness of species along two axes: (i interspecific differences in performance among native and introduced species within a region, and (ii intraspecific differences between populations of a species in its native and introduced ranges. Applying these equations to a sample dataset of occurrences of 1,416 plant species across Europe, Argentina, and South Africa, we found that many species are common in their native range but become rare following introduction; only a few introduced species become more common. Biogeographical factors limiting spread (e.g. biotic resistance, time of invasion therefore appear more common than those promoting invasion (e.g. enemy release. Invasiveness, as measured by occurrence data, is better explained by inter-specific variation in invasion potential than biogeographical changes in performance. We discuss how applying these comparisons to more detailed performance data would improve hypothesis testing in invasion biology and potentially lead to more efficient management strategies.

  20. Uncommon Species and Other Features

    Data.gov (United States)

    Vermont Center for Geographic Information — The Vermont Fish and Wildlife Department's Natural Heritage Inventory (NHI) maintains a database of uncommon, rare, threatened and endangered species and natural...

  1. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  2. 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.

  3. 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

  4. Notes on Magnoliaceae with a revision of Pachylarnax and Elmerrillia and the Malesian species of Manglietia and Michelia

    NARCIS (Netherlands)

    Nooteboom, H.P.

    1985-01-01

    After the general chapters, mainly based on literature and dealing with wood anatomy, characters of the leaf epidermis and foliar sclereids, embryology and chromosome numbers, phytochemistry, and characters of the fruit, the generic delimitation of subfamily Magnolioideae is discussed. Paramichelia

  5. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  6. Fuzzy species among recombinogenic bacteria

    Directory of Open Access Journals (Sweden)

    Fraser Christophe

    2005-03-01

    Full Text Available Abstract Background It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species. Results Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'. Conclusion A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.

  7. Limnephilid taxa revised by speciation traits: Rhadicoleptus, Isogamus, Melampophylax genera, Chaetopteryx rugulosa, Psilopteryx psorosa species groups, Drusus bolivari, Annitella kosciuszkii species complexes (Trichoptera: Limnephilidae

    Directory of Open Access Journals (Sweden)

    Oláh, J.

    2015-06-01

    Full Text Available Speciation traits of paramere, paraproct and aedeagus were applied to find initial split criteria with fine structure analysis in order to prepare diverged trait matrices for delimiting phylogenetic incipient species of unsettled limnephilid taxa in the early stages of reproductive isolation. A brief history is presented how this phenotypic taxonomic tool of the speciation traits was discovered and applied in caddisfly taxonomy. The theoretical basis was elaborated for the phenotypic speciation trait by reviewing several relevant topics in the sciences of taxonomy, molecular genetics and phylogenetics. Perspectives of integrative taxonomy is discussed in context of phenotype versus genotype, immensely complex phenotype versus phenomic challenge, taxonomic impediment versus genetic expedient, taxonomic adaptation of genetic vocabulary versus genetic sophistication and virtualization, New Systematics of Huxley and Mayr versus New Taxonomy of Wheeler. Debates on magic trait, speciation phenotype, speciation trait and super traits are discussed concluding that evolution works with phenotype and why the cryptic species concept is irrelevant. Briefly summarized how speciation traits evolve in sexual selection, through accelerated reproductive isolation with genital evolution through sex-limited speciation traits, including minor sex chromosomes. Why neutral molecular markers are blind compared to the adaptive speciation traits sensitized by fine structure analysis and backed by the potential of high-tech and high-throughput phenotyping and cyber-infrastructure broadly accessible and fed by computable phenotype descriptions. What sort of genetics could really help taxonomy to describe biodiversity of the over 100 million unknown taxa? Collecting new and re-examining old type materials deposited in various collections, the following taxonomic actions were elaborated by speciation traits. Drusus bolivari new species complex has been erected with

  8. 76 FR 74778 - Endangered Species

    Science.gov (United States)

    2011-12-01

    .... 16439] Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... has been issued under the authority of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and exporting of endangered and...

  9. [Yeast species in vulvovaginitis candidosa].

    Science.gov (United States)

    Nemes-Nikodém, Éva; Tamási, Béla; Mihalik, Noémi; Ostorházi, Eszter

    2015-01-04

    Vulvovaginal candidiasis is the most common mycosis, however, the available information about antifungal susceptibilities of these yeasts is limited. To compare the gold standard fungal culture with a new molecular identification method and report the incidence of yeast species in vulvovaginitis candidosa. The authors studied 370 yeasts isolated from vulvovaginal candidiasis and identified them by phenotypic and molecular methods. The most common species was Candida albicans (85%), followed by Candida glabrata, and other Candida species. At present there are no recommendations for the evaluation of antifungal susceptibility of pathogenic fungal species occurring in vulvovaginal candidiasis and the natural antifungal resistance of the different species is known only. Matrix Assisted Laser Desorption Ionization Time of Flight identification can be used to differentiate the fluconazole resistant Candida dubliniensis and the sensitive Candida albicans strains.

  10. Enolonium Species-Umpoled Enolates

    DEFF Research Database (Denmark)

    Arava, Shlomy; Kumar, Jayprakash N.; Maksymenko, Shimon

    2017-01-01

    Enolonium species/iodo(III) enolates of carbonyl compounds have been suggested to be intermediates in a wide variety of hypervalent iodine induced chemical transformations of ketones, including α-C-O, α-C-N, α-C-C, and alpha-carbon- halide bond formation, but they have never been characterized. We...... report that these elusive umpoled enolates may be made as discrete species that are stable for several minutes at-78 degrees C, and report the first spectroscopic identification of such species. It is shown that enolonium species are direct intermediates in C-O, C-N, C-Cl, and C-C bond forming reactions....... Our results open up chemical space for designing a variety of new transformations. We showcase the ability of enolonium species to react with prenyl, crotyl, cinnamyl, and allyl silanes with absolute regioselectivity in up to 92% yield....

  11. The South African fruit fly action plan: area-wide suppression and exotic species surveillance

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, Brian N., E-mail: barnesb@arc.agric.z [ARC Infruitec-Nietvoorbij Institute for Fruit, Vine and Wine, Stellenbosch (South Africa); Venter, Jan-Hendrik, E-mail: janhendrikv@nda.agric.z [Directorate Plant Health, Pretoria (South Africa)

    2006-07-01

    Two species of tephritid fruit flies of economic importance, Mediterranean fruit fly (Medfly, Ceratitis capitata [Wiedemann]) and Natal fruit fly (C. rosa Karsch) cause economic losses in the South African deciduous fruit industry of approximately US$3 million per annum. A third species, marula fruit fly, C. cosyra (Walker), causes damage to citrus and sub-tropical fruits in the north-eastern part of the country. In 1999 a sterile insect technique (SIT) programme against Medfly was initiated over 10,000 ha of table grapes with a goal of cost-effective, ecologically compatible suppression of Medfly. The SIT programme was extended to two other fruit production areas in 2004. Although results in all three SIT areas have been mixed, populations of wild Medflies, as well as associated pesticide usage and control costs, have been reduced since the start of sterile fly releases. Reasons for the partial degree of success and the relatively slow expansion of Medfly SIT to other areas include economic, operational and cultural factors, as well as certain fruit production practices. Before fruit fly-free areas can be created, deficiencies in the ability to mass-rear Natal fruit fly need to be overcome so that an SIT programme against this species can be initiated. Any fruit fly suppression or eradication campaign will be severely compromised by any introductions into South Africa of exotic fruit fly species. The risk of such introductions is increasing as trade with and travel to the country increases. A Plant Health Early Warning Systems Division has been initiated to formulate fruit fly detection and action plans. Melon fly (Bactrocera cucurbitae [Coquillett]), Asian fruit fly (B. invadens Drew, Tsurutu and White) and peach fruit fly (B. zonata [Saunders]), which are all well established in parts of Africa and/or Indian Ocean islands, have been identified as presenting the highest risk for entering and becoming established in South Africa. An exotic fruit fly surveillance

  12. Is Homo heidelbergensis a distinct species? New insight on the Mauer mandible.

    Science.gov (United States)

    Mounier, Aurélien; Marchal, François; Condemi, Silvana

    2009-03-01

    The discovery of new fossils in Africa, Asia, and Europe, and the recognition of a greater diversity in the middle Pleistocene fossil record, has led to a reconsideration of the species Homo heidelbergensis. This nomen, formulated by Schoetensack in 1908 to describe the Mauer jaw (Germany), was almost forgotten during most of the past century. Numerous fossils have been attributed to it but no consensus has arisen concerning their classification. The holotype anatomical traits are still poorly understood, and numerous fossils with no mandibular remains have been placed in the taxon. Some researchers propose H. heidelbergensis as an Afro-European taxon that is ancestral to both modern humans and Neandertals whereas others think it is a strictly European species that is part of the Neandertal lineage. We focus on the validity of H. heidelbergensis, using the traditional basis of species recognition: anatomical description. We provide a comparative morphological analysis using 47 anatomical traits of 36 Pleistocene fossils from Africa, Asia, and Europe and 35 extant human mandibles. We re-examine the mandibular features of Mauer and discuss the specimen's inclusion in H. heidelbergensis, as well as alternative evolutionary theories. To lend objectivity to specimen grouping, we use multiple correspondence analysis associated with hierarchical classification that creates clusters corresponding to phenetic similarities between jaws. Our phenetic and comparative morphological analyses support the validity of H. heidelbergensis as a taxon. A set of morphological features can be statistically identified for the definition of the species. Some traits can be used to delimit H. heidelbergensis in an evolutionary framework (e.g., foramina mentale posteriorly positioned, horizontal retromolar surface). Those traits are also present on African (e.g., Tighenif) and European (e.g., Sima de los Huesos) specimens that show a close relationship with the Mauer mandible. Therefore, the

  13. The South African fruit fly action plan: area-wide suppression and exotic species surveillance

    International Nuclear Information System (INIS)

    Barnes, Brian N.; Venter, Jan-Hendrik

    2006-01-01

    Two species of tephritid fruit flies of economic importance, Mediterranean fruit fly (Medfly, Ceratitis capitata [Wiedemann]) and Natal fruit fly (C. rosa Karsch) cause economic losses in the South African deciduous fruit industry of approximately US$3 million per annum. A third species, marula fruit fly, C. cosyra (Walker), causes damage to citrus and sub-tropical fruits in the north-eastern part of the country. In 1999 a sterile insect technique (SIT) programme against Medfly was initiated over 10,000 ha of table grapes with a goal of cost-effective, ecologically compatible suppression of Medfly. The SIT programme was extended to two other fruit production areas in 2004. Although results in all three SIT areas have been mixed, populations of wild Medflies, as well as associated pesticide usage and control costs, have been reduced since the start of sterile fly releases. Reasons for the partial degree of success and the relatively slow expansion of Medfly SIT to other areas include economic, operational and cultural factors, as well as certain fruit production practices. Before fruit fly-free areas can be created, deficiencies in the ability to mass-rear Natal fruit fly need to be overcome so that an SIT programme against this species can be initiated. Any fruit fly suppression or eradication campaign will be severely compromised by any introductions into South Africa of exotic fruit fly species. The risk of such introductions is increasing as trade with and travel to the country increases. A Plant Health Early Warning Systems Division has been initiated to formulate fruit fly detection and action plans. Melon fly (Bactrocera cucurbitae [Coquillett]), Asian fruit fly (B. invadens Drew, Tsurutu and White) and peach fruit fly (B. zonata [Saunders]), which are all well established in parts of Africa and/or Indian Ocean islands, have been identified as presenting the highest risk for entering and becoming established in South Africa. An exotic fruit fly surveillance

  14. 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. lamellatus Mont. (New World clade).

  15. New molecular data shed light on the global phylogeny and species limits of the Rhipicephalus sanguineus complex.

    Science.gov (United States)

    Hekimoğlu, Olcay; Sağlam, İsmail K; Özer, Nurdan; Estrada-Peña, Agustin

    2016-07-01

    The Rhipicephalus sanguineus complex is a group of closely related tick species distributed all around the world. In this study, using mitochondrial 16S ribosomal DNA, new specimens of R sanguineus sensu lato from Turkey and Rhipicephalus camicasi from Kenya, were evaluated together with available sequences of this complex in GenBank. Our objectives were to delimit the complex, re-evaluate its global phylogeny and develop a reconstruction of its biogeographic history. Given Turkey's geographical location and its neighboring status within Africa, Asia and Europe, molecular information of R. sanguineus s.l. species from this region could have important implications both on a regional and global scale. Phylogenetic trees obtained with three methods (Bayesian, Maximum Likelihood and Maximum Parsimony) were highly similar and consensus trees gave the same branching patterns and similar node support values. A total of four different clades with up to 9 Operational Taxonomic Units formed strong monophyletic groups. Biogeographic reconstructions demonstrated the importance of populations in Middle East (Turkey) in the spread of the group from Europe to Africa and Asia. Data supported previous conclusions on the existence of two species of R. sanguineus s.l. in South America and the strong molecular similarity between R. camicasi and the so-called tropical lineage of R. sanguineus s.l. These results point to the need of a re-evaluation of most specimens designated as R. sanguineus s.l. in East Europe, Middle East, Africa and Asia after an adequate re-description of this taxon. Copyright © 2016 Elsevier GmbH. All rights reserved.

  16. Species associations structured by environment and land-use history promote beta-diversity in a temperate forest.

    Science.gov (United States)

    Murphy, Stephen J; Audino, Livia D; Whitacre, James; Eck, Jenalle L; Wenzel, John W; Queenborough, Simon A; Comita, Liza S

    2015-03-01

    Patterns of diversity and community composition in forests are controlled by a combination of environmental factors, historical events, and stochastic or neutral mechanisms. Each of these processes has been linked to forest community assembly, but their combined contributions to alpha and beta-diversity in forests has not been well explored. Here we use variance partitioning to analyze approximately 40,000 individual trees of 49 species, collected within 137 ha of sampling area spread across a 900-ha temperate deciduous forest reserve in Pennsylvania to ask (1) To what extent is site-to-site variation in species richness and community composition of a temperate forest explained by measured environmental gradients and by spatial descriptors (used here to estimate dispersal-assembly or unmeasured, spatially structured processes)? (2) How does the incorporation of land-use history information increase the importance attributed to deterministic community assembly? and (3) How do the distributions and abundances of individual species within the community correlate with these factors? Environmental variables (i.e., topography, soils, and distance to stream), spatial descriptors (i.e., spatial eigenvectors derived from Cartesian coordinates), and land-use history variables (i.e., land-use type and intensity, forest age, and distance to road), explained about half of the variation in both species richness and community composition. Spatial descriptors explained the most variation, followed by measured environmental variables and then by land- use history. Individual species revealed variable responses to each of these sets of predictor variables. Several species were associated with stream habitats, and others were strictly delimited across opposing north- and south-facing slopes. Several species were also associated with areas that experienced recent (i.e., indicate that deterministic factors, including environmental and land-use history variables, are important drivers

  17. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  18. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  19. Species interactions and plant polyploidy.

    Science.gov (United States)

    Segraves, Kari A; Anneberg, Thomas J

    2016-07-01

    Polyploidy is a common mode of speciation that can have far-reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole-genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species. © 2016 Botanical Society of America.

  20. Scale dependence in species turnover reflects variance in species occupancy.

    Science.gov (United States)

    McGlinn, Daniel J; Hurlbert, Allen H

    2012-02-01

    Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

  1. Species-area relationships are controlled by species traits.

    Science.gov (United States)

    Franzén, Markus; Schweiger, Oliver; Betzholtz, Per-Eric

    2012-01-01

    The species-area relationship (SAR) is one of the most thoroughly investigated empirical relationships in ecology. Two theories have been proposed to explain SARs: classical island biogeography theory and niche theory. Classical island biogeography theory considers the processes of persistence, extinction, and colonization, whereas niche theory focuses on species requirements, such as habitat and resource use. Recent studies have called for the unification of these two theories to better explain the underlying mechanisms that generates SARs. In this context, species traits that can be related to each theory seem promising. Here we analyzed the SARs of butterfly and moth assemblages on islands differing in size and isolation. We tested whether species traits modify the SAR and the response to isolation. In addition to the expected overall effects on the area, traits related to each of the two theories increased the model fit, from 69% up to 90%. Steeper slopes have been shown to have a particularly higher sensitivity to area, which was indicated by species with restricted range (slope = 0.82), narrow dietary niche (slope= 0.59), low abundance (slope= 0.52), and low reproductive potential (slope = 0.51). We concluded that considering species traits by analyzing SARs yields considerable potential for unifying island biogeography theory and niche theory, and that the systematic and predictable effects observed when considering traits can help to guide conservation and management actions.

  2. Multiple mechanisms enable invasive species to suppress native species.

    Science.gov (United States)

    Bennett, Alison E; Thomsen, Meredith; Strauss, Sharon Y

    2011-07-01

    Invasive plants represent a significant threat to ecosystem biodiversity. To decrease the impacts of invasive species, a major scientific undertaking of the last few decades has been aimed at understanding the mechanisms that drive invasive plant success. Most studies and theories have focused on a single mechanism for predicting the success of invasive plants and therefore cannot provide insight as to the relative importance of multiple interactions in predicting invasive species' success. We examine four mechanisms that potentially contribute to the success of invasive velvetgrass Holcus lanatus: direct competition, indirect competition mediated by mammalian herbivores, interference competition via allelopathy, and indirect competition mediated by changes in the soil community. Using a combination of field and greenhouse approaches, we focus on the effects of H. lanatus on a common species in California coastal prairies, Erigeron glaucus, where the invasion is most intense. We found that H. lanatus had the strongest effects on E. glaucus via direct competition, but it also influenced the soil community in ways that feed back to negatively influence E. glaucus and other native species after H. lanatus removal. This approach provided evidence for multiple mechanisms contributing to negative effects of invasive species, and it identified when particular strategies were most likely to be important. These mechanisms can be applied to eradication of H. lanatus and conservation of California coastal prairie systems, and they illustrate the utility of an integrated set of experiments for determining the potential mechanisms of invasive species' success.

  3. Hybridization relics complicate barcode-based identification of species in earthworms.

    Science.gov (United States)

    Dupont, L; Porco, D; Symondson, W O C; Roy, V

    2016-07-01

    Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation. © 2016 John Wiley & Sons Ltd.

  4. Blind to morphology: Genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

    KAUST Repository

    Pinzón, Jorge H C

    2013-04-05

    Aim: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. Location: Indo-Pacific, Red Sea, Arabian/Persian Gulf. Methods: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. Results: Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. Main conclusions: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the

  5. A molecular phylogeny of Afromontane dwarf geckos (Lygodactylus) reveals a single radiation and increased species diversity in a South African montane center of endemism.

    Science.gov (United States)

    Travers, Scott L; Jackman, Todd R; Bauer, Aaron M

    2014-11-01

    Afromontane habitats throughout eastern sub-Saharan Africa support remarkable levels of microendemism. However, despite being the subject of decades of research interest, biogeographical patterns of diversification throughout this disjunct montane system still remain largely unknown. We examined the evolutionary relationships of diurnal dwarf geckos (Lygodactylus) from several Afromontane regions throughout southeastern Africa, focusing primarily on two species groups (rex and bonsi groups). Using both mitochondrial and nuclear markers, we generate a molecular phylogeny containing all members of the rex and bonsi groups, to evaluate the monophyly of these groups along with previous biogeographic hypotheses suggesting independent southward invasions into the greater Drakensberg Afromontane center of endemism in northeastern South Africa by each group. Our results provide no support for these taxonomic and biogeographic hypotheses, and instead reveal geographically circumscribed patterns of diversification. One clade is restricted to the highlands of southern Malawi and northern Mozambique and the other to the greater Drakensberg region of northeastern South Africa and Swaziland. Interestingly, L. bernardi from the Nyanga Highlands of eastern Zimbabwe is nested within the primarily savanna-dwelling capensis group. We use Bayesian species delimitation methods to evaluate species limits within the greater Drakensberg clade, which support the elevation of the subspecies of L. ocellatus and L. nigropunctatus, thus bringing the total to eight species within a relatively confined geographic area. These results further highlight the greater Drakensberg Afromontane region as both an important center of endemism, as well as a center of diversification contributing to the accumulation of southern Africa's rich species diversity. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Blind to morphology: Genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

    KAUST Repository

    Pinzó n, Jorge H C; Sampayo, Eugenia M.; Cox, Evelyn F.; Chauka, Leonard J.; Chen, Chaolun Allen; Voolstra, Christian R.; LaJeunesse, Todd C.

    2013-01-01

    Aim: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. Location: Indo-Pacific, Red Sea, Arabian/Persian Gulf. Methods: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. Results: Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. Main conclusions: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the

  7. Evolution of mutualism between species

    Energy Technology Data Exchange (ETDEWEB)

    Post, W.M.; Travis, C.C.; DeAngelis, D.L.

    1980-01-01

    Recent theoretical work on mutualism, the interaction between species populations that is mutually beneficial, is reviewed. Several ecological facts that should be addressed in the construction of dynamic models for mutualism are examined. Basic terminology is clarified. (PSB)

  8. Phase Two Protected Species Valuation

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nonmarket valuation research has produced economic value estimates for a variety of threatened, endangered, and rare species around the world. Although over 40 value...

  9. 76 FR 1405 - Endangered Species

    Science.gov (United States)

    2011-01-10

    ... the understanding of the pelagic ecology of these species and allow more reliable assessments of... permit: (1) Was applied for in good faith, (2) will not operate to the disadvantage of such endangered or...

  10. Infrared spectra of mineral species

    CERN Document Server

    Chukanov, Nikita V

    2014-01-01

    This book details more than 3,000 IR spectra of more than 2,000 mineral species collected during last 30 years. It features full descriptions and analytical data of each sample for which IR spectrum was obtained.

  11. THE USE OF CASSAVA SPECIES

    African Journals Online (AJOL)

    User

    The plant is propagated from mature stems, which .... USE OF CASSAVA SPECIES AND ALUM IN WASTE WATER TREATMENT, .... acidity, total suspended solids, dissolved oxygen and ..... Rural Areas, MSc Thesis, Department of Water.

  12. Achromobacter species in cystic fibrosis

    DEFF Research Database (Denmark)

    Hansen, C R; Pressler, T; Ridderberg, W

    2013-01-01

    Achromobacter species leads to chronic infection in an increasing number of CF patients. We report 2 cases of Achromobacter ruhlandii cross-infection between patients after well-described indirect contact....

  13. Species Typing in Dermal Leishmaniasis

    Science.gov (United States)

    Dujardin, Jean-Claude

    2015-01-01

    SUMMARY Leishmania is an infectious protozoan parasite related to African and American trypanosomes. All Leishmania species that are pathogenic to humans can cause dermal disease. When one is confronted with cutaneous leishmaniasis, identification of the causative species is relevant in both clinical and epidemiological studies, case management, and control. This review gives an overview of the currently existing and most used assays for species discrimination, with a critical appraisal of the limitations of each technique. The consensus taxonomy for the genus is outlined, including debatable species designations. Finally, a numerical literature analysis is presented that describes which methods are most used in various countries and regions in the world, and for which purposes. PMID:25672782

  14. The Candida Pathogenic Species Complex

    Science.gov (United States)

    Turner, Siobhán A.; Butler, Geraldine

    2014-01-01

    Candida species are the most common causes of fungal infection. Approximately 90% of infections are caused by five species: Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei. Three (C. albicans, C. tropicalis, and C. parapsilosis) belong to the CTG clade, in which the CTG codon is translated as serine and not leucine. C. albicans remains the most commonly isolated but is decreasing relative to the other species. The increasing incidence of C. glabrata is related to its reduced susceptibility to azole drugs. Genome analysis suggests that virulence in the CTG clade is associated with expansion of gene families, particularly of cell wall genes. Similar independent processes took place in the C. glabrata species group. Gene loss and expansion in an ancestor of C. glabrata may have resulted in preadaptations that enabled pathogenicity. PMID:25183855

  15. Phase One Protected Species Valuation

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Nonmarket valuation research has produced economic value estimates for a variety of threatened, endangered, and rare species around the world. Although over 40 value...

  16. Theoretical microbial ecology without species

    Science.gov (United States)

    Tikhonov, Mikhail

    2017-09-01

    Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic and mounting experimental evidence raises the intriguing question whether this perspective is appropriate for the microbial world. Here an alternative formalism is proposed that does not require postulating the existence of species as fundamental ecological variables and provides a naturally hierarchical description of community dynamics. This formalism allows approaching the species problem from the opposite direction. While the classical models treat a world of imperfectly clustered organism types as a perturbation around well-clustered species, the presented approach allows gradually adding structure to a fully disordered background. The relevance of this theoretical construct for describing highly diverse natural ecosystems is discussed.

  17. Species selection for smallholder aquaculture

    OpenAIRE

    Brummett, R.E.

    1996-01-01

    Systems for selection of species for smallholder aquaculture are presented. These are: food fits; management decisions; and economic criteria. Food fits suggests categorizing pond food resources into a few categories based loosely on the instrinsic traits of food which effect their selectivity by predators. Using management decision techniques, potential polycultures might also be compared with each other and with monoculture. Under economic criteria (and for species known in local markets), ...

  18. Endangered Lilium Species of Turkey

    Directory of Open Access Journals (Sweden)

    Sevim Demir

    2018-01-01

    Full Text Available Turkey, which is among the major gene centers of the world and has a special place in plant genetic diversity. However, many plant genetic resources, including geophytes, are under genetic erosion because of the environmental and other problems and therefore face with the danger of extinction. Lilium ciliatum is endemic to North East Anatolia. IUCN (International Union for the Conservation of Natural Resources Red List Category of this species is Endangered (EN. Lilium ciliatum naturally grown in Zigana pass, Bayburt, Trabzon, Bulancak, Giresun and Gümüşhane is endangered and major threats of L. ciliatum are road construction and human disturbance related to ecotourism and recreation. It was reported that Lilium carniolicum naturally grown in Turkey is endangered although it isn’t in the IUCN Red List. Distribution areas of L. carniolicum are Trabzon, Rize, Artvin and it is also endemic to North East Anatolia. These species have high potential for use as ornamental plants with their colorful big flowers. In addition, the bulbs of these species are also used in the cosmetic industry and medicine. These are the main properties that increase the importance of L. ciliatum and L. carniolicum species. Therefore it is very important to protect the habitats of these species, ensure the continuity of their generations. The disappearance of these endemic species from our country means to disappear from the world. This review has been given in order to give some information about the endangered Lilium species of Turkey and conservation actions on these species in Turkey flora and take attention to the issue.

  19. Collective behaviour across animal species.

    Science.gov (United States)

    DeLellis, Pietro; Polverino, Giovanni; Ustuner, Gozde; Abaid, Nicole; Macrì, Simone; Bollt, Erik M; Porfiri, Maurizio

    2014-01-16

    We posit a new geometric perspective to define, detect, and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques, and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. These results offer a first glimpse at the transformative potential of machine learning for ethology, similar to its impact on robotics, where it enabled robots to recognize objects and navigate the environment.

  20. Thromboelastography in Selected Avian Species

    DEFF Research Database (Denmark)

    Andersen, Sophie Susanna Strindberg; Nielsen, Tenna W; Ribeiro, Ângela M

    2015-01-01

    Currently available assay methods and reagents are not optimized for evaluating avian hemostasis; therefore, assessing avian coagulopathies is challenging. Recently, thromboelastography (TEG), which measures the viscoelastic properties of blood, has been used clinically in mammalian species...... to diagnose and characterize hemostatic disorders. To evaluate TEG in healthy individuals of 6 avian species, we modified existing mammalian TEG protocols to allow analysis of citrated, avian whole-blood samples collected from scarlet ibis (Eudocimus ruber) (n = 13), American flamingos ( Phoenicopterus ruber...

  1. The nature of plant species.

    Science.gov (United States)

    Rieseberg, Loren H; Wood, Troy E; Baack, Eric J

    2006-03-23

    Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.

  2. Proposta de um modelo de delimitação geométrica para a injeção ventro-glútea Propuesta de un modelo de delimitación geométrica para inyección ventroglútea A proposal for a geometrical delimitation model for ventro-gluteal injection

    Directory of Open Access Journals (Sweden)

    Abel Silva de Meneses

    2007-10-01

    -experimental study of non-equivalent control group type, carried out with anatomical parts of corpses to verify the precision of punction between traditional delimitation using hand as reference and the geometrical model which was constituted by tracing imaginary lines across bone structures of the hip, making a configuration of a triangle whose barycenter points the punction site. The study demonstrated that the punction site delimited by the geometrical technique keeped proportion of the envolved structures, and matched with the muscular womb of the ventrogluteal area in 100% of punctions. In another hand, in the traditional technique the punction site varied in 39.9% of punctions.

  3. Interfaces entre o pensamento filosófico e linguístico: algumas reflexões teóricas sobre a delimitação do objeto de estudo da linguística=Interfaces between the philosofic and linguistic thought: some theoretical reflections about the delimitation of the object of study of the linguistic

    Directory of Open Access Journals (Sweden)

    Denilson Pereira de Matos

    2012-07-01

    Full Text Available Este trabalho objetiva abordar, no entrelaçamento entre linguística e filosofia, a ciência filosofia da linguagem no que se refere às duas orientações do pensamento filosófico-linguístico que buscam a resolução do problema de isolamento e delimitação da linguagem como objeto de estudo, a saber: o subjetivismo idealista e o objetivismo abstrato. São apontadas as principais proposições destas linhas mestras, seguidas de uma breve reflexão bakhtiniana sobre elas. Tal estudo é norteado pelo capítulo quarto, ‘Das Orientações do Pensamento Filosófico-linguístico’, da obra Marxismo e Filosofia da Linguagem de Mikhail Bakhtin. Algumas exemplificações são feitas, visando justificar as reflexões propostas.This work aims to approach, in the intertwining between linguistic and philosophy, the science phylosophy of the language with regard to two guidelines of the linguistic-philosophic thought which aim the resolution of the problem of the isolation and delimitation of the language as study object, to know, the idealist subjetivism and the abstract objetivism. The main proposals of these master lines followed by a brief bakhtinian reflection about them are pointed. Such study is guided by the chapter four, ‘Guidelines of the linguistic-Philosofic Thought’, of the classic Marxism and Language Philosophy by Mikhail Bakhtin. Some exemplifications are made in order to justify these reflections.

  4. The Colletotrichum gloeosporioides species complex.

    Science.gov (United States)

    Weir, B S; Johnston, P R; Damm, U

    2012-09-15

    The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity

  5. Comparative studies on the histology and ultrastructure of the siphons of two species of Tellinidae (Mollusca: Bivalvia from Brazil

    Directory of Open Access Journals (Sweden)

    João E.V.V. Vitonis

    2012-06-01

    Full Text Available Despite the great importance of the siphons for infaunal bivalves, only a few studies have examined their tissues using histology techniques or scanning electron microscopy. In the present study, the siphons of Tellina lineata Turton, 1819 and Macoma biota Arruda & Domaneschi, 2005 were investigated. The siphon walls are composed by a series of muscle sheets of longitudinal ("L", circular ("C" and radial ("R" fibers, with a clear pattern common to both species: there is a main median longitudinal layer (Lm, and two peripheral circular layers, one inner (Ci and one outer (Co, near the epithelia. A median circular layer (Cm separates an internal (Lmi from an outer (Lmo median longitudinal layer. Further, the Co is split by a thin outer longitudinal layer (Lo, forming Coi and Coo layers, the former being obliquely oriented. Thin radial fibers (R delimit clear packages of Lmi and Lmo fibers. In each siphon, there are six longitudinal nerve cords, running within the Lmi layer, adjacent to the Cm. The inhalant and exhalant siphons of M. biota are very similar in structure, but the Lmo of the exhalant siphon is almost twice as thick as its Lmi, while in the inhalant siphon these layers have similar thicknesses; the Coi is very thick, especially in the exhalant siphon. The inhalant siphon of T. lineata is very similar to that of M. biota, differing only with respect to the thickness of the Coi, which in the former species is not as well developed as in the latter. The Lmo of the exhalant siphon of T. lineata is by far the most developed layer, with the Lmi represented only by uniseriate small cells; in the vicinities of the nerve cords, the Cm is split in two layers. The epithelia of both siphons of M. biota and T. lineata bear ciliated receptors, which were difficult to observe as they were frequently covered with mucus. It was possible to observe that cilia are present in both species, differing in length and in the number per receptor between the

  6. Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

    Science.gov (United States)

    Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

    Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies. We present a new phylogeny of Angraecum based on chloroplast sequence data (matk, rps16, trnL), nuclear ribosomal (ITS2) and 39 morphological characters from 194 Angraecinae species of which 69 were newly sampled. Using this phylogeny, we evaluated the monophyly of the sections of Angraecum as defined by Garay and investigated the patterns of species diversification within the genus. We used maximum parsimony and bayesian analyses to generate phylogenetic trees and dated divergence times of the phylogeny. We analyzed diversification patterns within Angraecinae and Angraecum with an emphasis on four floral characters (flower color, flower size, labellum position, spur length) using macroevolutionary models to evaluate which characters or character states are associated with speciation rates, and inferred ancestral states of these characters. The phylogenetic analysis showed the polyphyly of Angraecum sensu lato and of all Angraecum sections except sect. Hadrangis, and that morphology can be consistent with the phylogeny. It appeared that the characters (flower color, flower size, spur length) formerly used by many authors to delineate Angraecum groups were insufficient to do so. However, the newly described character, position of the labellum (uppermost and lowermost), was the main character delimiting clades within a monophyletic Angraecum sensu stricto. This character also appeared to be associated with speciation rates in

  7. Terrestrial animals as invasive species and as species at risk from invasions

    Science.gov (United States)

    Deborah M. Finch; Dean Pearson; Joseph Wunderle; Wayne Arendt

    2010-01-01

    Including terrestrial animal species in the invasive species strategy plan is an important step in invasive species management. Invasions by nonindigenous species threaten nearly 50 percent of imperiled native species in the United States and are the Nation's second leading cause of species endangerment. Invasion and conversion of native habitats by exotic species...

  8. Malassezia Species and Pityriasis Versicolor

    Directory of Open Access Journals (Sweden)

    Gulin Rodoplu

    2016-01-01

    Full Text Available Malassezia species are found in part of the normal human cutaneous commensal flora, however it has been known for many years that the Malassezia yeasts are associated with a number of different human diseases ranging from pityriasis versicolor to seborrhoeic dermatitis. In addition, since the 1980s, they have been reported as causing opportunistic systemic infections. The taxonomy of Malassezia spp. has recently been modified to include 13 obligatorily lipophilic species, plus one non-obligatorily lipophilic species, which only rarely colonizes human hosts and currently the genus consist 14 species as M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. slooffiae, M. restricta, M. dermatis, M. japonica, M. nana, M. yamatoensis, M. caprae, M. equina, M. cuniculi. Fastidious growth requirements of Malassezia yeasts defied the initial attempts to culture these organisms and their true identification and the relationship between different species only became apparent with the application of modern molecular techniques. The causative fungus is seen especially in such seborrheic areas as the scalp, face, trunk and upper back. Under the influence of various exogenous or endogenous predisposing factors, these yeasts change from the blastospore form to the mycelial form and become pathogenic. Diagnosis of pityriasis versicolor which is caused by Malassezia species is generally easy and lies on the basis of its clinical appearance and can be confirmed by mycological examination. The diagnosisis is mainly based on direct examination with potassium hydroxide (KOH and demonstration that represents pseudohyphae and blastoconidia as the typical %u201Cspaghetti and meatballs%u201D pattern. Characteristic features of the genus Malassezia include a distinctive morphology and an affinity for lipids in culture. Culture is necessary to recover the infecting strain, especially for epidemiologic purposes and also to test its antifungal susceptibility

  9. Phenotypic covariance at species' borders.

    Science.gov (United States)

    Caley, M Julian; Cripps, Edward; Game, Edward T

    2013-05-28

    Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

  10. Global population genetic structure and biogeography of the oceanic copepods Eucalanus hyalinus and E. spinifer

    DEFF Research Database (Denmark)

    Goetze, Erica

    2005-01-01

    Although theory dictates that limited gene flow between populations is a necessary precursor to speciation under allopatric and parapatric models, it is currently unclear how genetic differentiation between conspecific populations can arise in open-ocean plankton species. I examined two recently...

  11. Nupela species (Naviculales: Bacillariophyceae from Colombian lowland waters including N. acaciensis nov. sp. and N. catatumbensis nov. sp.

    Directory of Open Access Journals (Sweden)

    Silvia Sala

    2014-03-01

    Full Text Available The genus Nupela comprises ca. 50 species that generally have a distribution restricted by bioclimatic frontiers. As part of an integrated analysis of the diatom flora of Colombia, in this study we focused our interest on the genus Nupela from lowland waters. Periphyton samples were collected from 150 sites of lotic water bodies in Colombia, taking into account hidrogeomorfological variability. In each sampling station, periphyton samples were obtained by scraping, and temperature, pH, dissolved oxygen and conductivity variables were measured. Samples were processed by both light microscopy (LM; Carl Zeiss Axio Scope.A1 and scanning electron microscopy (SEM; FEI-Quanta 450 and a Jeol JSM-6360 LV. The genus Nupela was found in 28 sites. Five taxa were identified, described and illustrated from tropical or subtropical environments: N. lesothensis, N. praecipua y N. subpallavicinii; these were new records for Colombia, and N. acaciensis and N. catatumbensis two new species for science. N. acaciensis is characterized by raphe branches of both valves equally long combined with cymbelloid symmetry, striae built by 2 transapically elongated areolae that delimit a longitudinal line at each hemivalve. N. catatumbensis is characterized by the presence of a well developed raphe in both valves; valves lanceolate with subcapitated to capitated ends and cymbelloid symmetry, striae built by 3-4 transapically elongated areolae, interestriae elevated as transapical ribs and internal proximal raphe ends hook-shaped. The genus Nupela was widely distributed in the studied basins but showed different distribution patterns: N. acaciensis and N. subpallavicini had a restricted distribution, while N. catatumbensis, N. lesothensis and N. praecipua had a wider distribution, and were collected in sites with significant variations in their ecomorphology, altitude, temperature, pH and electrolyte content.

  12. Aspergillus fumigatus and Related Species

    Science.gov (United States)

    Sugui, Janyce A.; Kwon-Chung, Kyung J.; Juvvadi, Praveen R.; Latgé, Jean-Paul; Steinbach, William J.

    2015-01-01

    The genus Aspergillus contains etiologic agents of aspergillosis. The clinical manifestations of the disease range from allergic reaction to invasive pulmonary infection. Among the pathogenic aspergilli, Aspergillus fumigatus is most ubiquitous in the environment and is the major cause of the disease, followed by Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus nidulans, and several species in the section Fumigati that morphologically resemble A. fumigatus. Patients that are at risk for acquiring aspergillosis are those with an altered immune system. Early diagnosis, species identification, and adequate antifungal therapy are key elements for treatment of the disease, especially in cases of pulmonary invasive aspergillosis that often advance very rapidly. Incorporating knowledge of the basic biology of Aspergillus species to that of the diseases that they cause is fundamental for further progress in the field. PMID:25377144

  13. URBAN DETECTION, DELIMITATION AND MORPHOLOGY: COMPARATIVE ANALYSIS OF SELECTIVE "MEGACITIES"

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    B. Alhaddad

    2012-08-01

    Full Text Available Over the last 50 years, the world has faced an impressive growth of urban population. The walled city, close to the outside, an "island"for economic activities and population density within the rural land, has led to the spread of urban life and urban networks in almost all the territory. There was, as said Margalef (1999, "a topological inversion of the landscape". The "urban" has gone from being an island in the ocean of rural land vastness, to represent the totally of the space in which are inserted natural and rural "systems". New phenomena such as the fall of the fordist model of production, the spread of urbanization known as urban sprawl, and the change of scale of the metropolis, covering increasingly large regions, called "megalopolis" (Gottmann, 1961, have characterized the century. However there are no rigorous databases capable of measuring and evaluating the phenomenon of megacities and in general the process of urbanization in the contemporary world. The aim of this paper is to detect, identify and analyze the morphology of the megacities through remote sensing instruments as well as various indicators of landscape. To understand the structure of these heterogeneous landscapes called megacities, land consumption and spatial complexity needs to be quantified accurately. Remote sensing might be helpful in evaluating how the different land covers shape urban megaregions. The morphological landscape analysis allows establishing the analogies and the differences between patterns of cities and studying the symmetry, growth direction, linearity, complexity and compactness of the urban form. The main objective of this paper is to develop a new methodology to detect urbanized land of some megacities around the world (Tokyo, Mexico, Chicago, New York, London, Moscow, Sao Paulo and Shanghai using Landsat 7 images.

  14. Expanding Basic Fuzzy Logic with Truth Constants for Component Delimiters

    Czech Academy of Sciences Publication Activity Database

    Haniková, Zuzana

    2012-01-01

    Roč. 197, 16 June (2012), s. 95-107 ISSN 0165-0114 R&D Projects: GA ČR GEICC/08/E018 Institutional research plan: CEZ:AV0Z10300504 Keywords : mathematics * non-classical logics * algebra * basic fuzzy logic BL * propositional constants Subject RIV: BA - General Mathematics Impact factor: 1.749, year: 2012

  15. Delimiting coefficient alpha from internal consistency and unidimensionality

    NARCIS (Netherlands)

    Sijtsma, K.

    2015-01-01

    I discuss the contribution by Davenport, Davison, Liou, & Love (2015) in which they relate reliability represented by coefficient α to formal definitions of internal consistency and unidimensionality, both proposed by Cronbach (1951). I argue that coefficient α is a lower bound to reliability and

  16. 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 linguistic structure overlaps the subjectivity of the actor, i. e., the premise that the strength of linguistic structure organization acts on the possible individual operation/style.

  17. Towards a delimitation of southwestern Nigeria into hydrological regions

    Science.gov (United States)

    Ogunkoya, O. O.

    1988-05-01

    Fifteen third-order drainage basins (1:50,000) on the Basement Complex rocks of southwestern Nigeria are classified into hydrological regions using hydrologic response parameters of average daily mean specific discharge ( QA); daily mean specific discharges equalled or exceeded 90% ( Q90), 50% ( Q50) and 10% ( Q10) of the study period; variability index of flow ( VI); recession constant ( K) of flow from peak discharge at the end of the rainy season to minimum discharge in the dry season; total annual runoff ( RO); total runoff within the dry season ( DSRO); dry season runoff as a percentage of total annual runoff (% DSRO); runoff coefficient ( ROC); and, number of days during the study period when there was no flow ( NFD). An ordination technique and a classification algorithm derived from cluster analysis technique and incorporating the analysis of variance (ANOVA) tests to determine the level of significance of the homogeneity of derived classes, were used to classify the fifteen basins into five hydrologically homogeneous regions. The constituent basins of each region were observed to share common basin geology. It was observed that those drainage basins having at least 50% of their basin area underlain by quartzitic rocks form two groups and have the most desirable or optimal hydrologic response patterns, desirability or optimality being in terms of ability to potentially meet water resource development requirements (i.e. high perennial discharge, low variability and large groundwater contribution to stream flow). The basins predominantly underlain by granite-gneisses and amphibolitic rocks have much poorer hydrologic response patterns. Hydrological regionalization in southwestern Nigeria appears to be influenced by drainage basin geology while percentage area of the basin underlain by massive quartzites could be used as an index of occurrence of desirable hydrologic response pattern.

  18. Delimiting Coefficient a from Internal Consistency and Unidimensionality

    Science.gov (United States)

    Sijtsma, Klaas

    2015-01-01

    I discuss the contribution by Davenport, Davison, Liou, & Love (2015) in which they relate reliability represented by coefficient a to formal definitions of internal consistency and unidimensionality, both proposed by Cronbach (1951). I argue that coefficient a is a lower bound to reliability and that concepts of internal consistency and…

  19. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis.

    Science.gov (United States)

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-07-01

    Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5'- and 3'-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients.Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3'-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5'-UTR polymorphisms).For neither the 3'- nor the 5'-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance.The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold, in our population. These data circumscribe the influence of these polymorphisms in the clinical outcome of 5-FU and question their use for establishing 5-FU dosage, above all when additional genetic factors are not considered.

  20. Just Imaginary: Delimiting Social Inclusion in Higher Education

    Science.gov (United States)

    Gale, Trevor; Hodge, Steven

    2014-01-01

    This paper explores the notion of a "just imaginary" for social inclusion in higher education. It responds to the current strategy of OECD nations to expand higher education and increase graduate numbers, as a way of securing a competitive advantage in the global knowledge economy. The Australian higher education system provides the case…

  1. On Delimiting African Philosophy and the Equalization Scheme ...

    African Journals Online (AJOL)

    One of these dimensions is African Philosophy where lots of African scholars have invested their time and mind on examining the African universe and bringing forth various descriptions of the African life. And in line with this, some schools of thought in African Philosophy have developed. It seems to me that these schools ...

  2. 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

  3. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

    Science.gov (United States)

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

    2015-06-19

    The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

  4. What is a Species? An Endless Debate

    Indian Academy of Sciences (India)

    Srimath

    a research scholar in ... perspectives are collectively termed as Phylogenetic Species ... tors view the origin of the species they study”. ..... explosion of molecular data has been the major driving force in unearthing cryptic species, it is no ...

  5. Vegetation composition and structure influences bird species ...

    African Journals Online (AJOL)

    Vegetation composition and structure influences bird species community ... variables on bird species diversity and richness of respective foraging guilds, and ... of the species assessed: (1) increasing closed cover due to woody plant density, ...

  6. Alien species recorded in the United Arab Emirates: an initial list of terrestrial and freshwater species

    Directory of Open Access Journals (Sweden)

    Pritpal Soorae

    2015-10-01

    Full Text Available Little is documented on the alien terrestrial and freshwater species in the United Arab Emirates. To address this, an assessment of terrestrial and freshwater alien species was conducted using various techniques such as a questionnaire, fieldwork data, networking with relevant people, and a detailed literature review. The results of the initial assessment show that there are 146 alien species recorded in the following seven major taxonomic groups: invertebrates 49 species, freshwater fish five species, amphibian one species, reptiles six species, birds 71 species, mammals six species and plants eight species. To inform decision makers a full list of the 146 species identified in this assessment is presented. 

  7. Man...An Endangered Species?

    Science.gov (United States)

    Department of the Interior, Washington, DC.

    The general theme of this 1968 yearbook is that man is a threatened species, facing overpopulation and unbridled technology - both self induced. The presentation is broad, relating to many aspects of conservation and natural resources in the United States in a descriptive, non-technical style. The yearbook is divided into major topics: Land…

  8. Phylogenetic relationships among Maloideae species

    Science.gov (United States)

    The Maloideae is a highly diverse sub-family of the Rosaceae containing several agronomically important species (Malus sp. and Pyrus sp.) and their wild relatives. Previous phylogenetic work within the group has revealed extensive intergeneric hybridization and polyploidization. In order to develop...

  9. Botrytis species on bulb crops

    NARCIS (Netherlands)

    Lorbeer, J.W.; Seyb, A.M.; Boer, de M.; Ende, van den J.E.

    2007-01-01

    Abstract. A number of Botrytis species are pathogens of bulb crops. Botrytis squamosa (teleomorph=Botrytotinia squamosa) causal agent of botrytis leaf blight and B. allii the causal agent of botrytis neck rotare two of the most important fungal diseases of onion. The taxonomics of several of the

  10. Endangered Species: An Educator's Handbook.

    Science.gov (United States)

    Smith, Jean, M., Comp.

    Presented are two articles, an annotated bibliography, and other information useful in teaching about endangered species, especially those found in Florida. The articles provide an ethical rationale, teaching suggestions, and a discussion of the value of wildlife. Descriptions of over 100 pertinent books, periodicals, movies, and filmstrips are in…

  11. Molecular Epidemiology of Fonsecaea Species

    NARCIS (Netherlands)

    Najafzadeh, M.J.; Sun, J.; Vicente, V.A.; Klaassen, C.H.W.; Bonifaz, A.; Gerrits van den Ende, A.H.G.; Menken, S.B.J.; de Hoog, G.S.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin,

  12. SARS – virus jumps species

    Indian Academy of Sciences (India)

    SARS – virus jumps species. Coronavirus reshuffles genes; Rotteir et al, Rotterdam showed the virus to jump from cats to mouse cells after single gene mutation ? Human disease due to virus jumping from wild or domestic animals; Present favourite animal - the cat; - edible or domestic.

  13. Species recovery in the United States: Increasing the effectiveness of the Endangered Species Act

    Science.gov (United States)

    Daniel M. Evans; Judy P. Che-Castaldo; Deborah Crouse; Frank W. Davis; Rebecca Epanchin-Niell; Curtis H. Flather; R. Kipp Frohlich; Dale D. Goble; Ya-Wei Li; Timothy D. Male; Lawrence L. Master; Matthew P. Moskwik; Maile C. Neel; Barry R. Noon; Camille Parmesan; Mark W. Schwartz; J. Michael Scott; Byron K. Williams

    2016-01-01

    The Endangered Species Act (ESA) has succeeded in shielding hundreds of species from extinction and improving species recovery over time. However, recovery for most species officially protected by the ESA - i.e., listed species - has been harder to achieve than initially envisioned. Threats to species are persistent and pervasive, funding has been insufficient...

  14. Optimal conservation of migratory species.

    Directory of Open Access Journals (Sweden)

    Tara G Martin

    Full Text Available BACKGROUND: Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea-regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity bringing into question the utility and efficiency of current conservation efforts. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. CONCLUSIONS/SIGNIFICANCE: We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of

  15. Synopsis of the Oxyethira flavicornis species group with new Japanese Oxyethira species (Trichoptera, Hydroptilidae

    Directory of Open Access Journals (Sweden)

    Oláh, J.

    2013-06-01

    Full Text Available A brief synopsis of the Oxyethira flavicornis species group is produced by the examination of type materials. Diagrammatic drawings with similar style were prepared for all the known and for the new species. Short description of genus Oxyethira, subgenus Oxyethira, species group of Oxyethira flavicornis are presented together with the description of five species clusters: O. datra new species cluster, O. ecornuta new species cluster, O. flavicornis new species cluster, O. hiroshima new species cluster, O. tiunovae new species cluster. Five new species are described from the O. flavicornis species group: O chitosea sp. n., O. hena sp. n., O. hiroshima sp. n., O. kakida sp. n., O. mekunna sp. n. One new species is described from the Oxyethira grisea species group: Oxyethira ozea sp. n. and two new species from the Oxyethira ramosa species group: Oxyethira miea sp. n., Oxyethira okinawa sp. n.

  16. Floral reward in Ranunculaceae species

    Directory of Open Access Journals (Sweden)

    Bożena Denisow

    2016-04-01

    Full Text Available Floral reward is important in ecological and evolutionary perspectives and essential in pollination biology. For example, floral traits, nectar and pollen features are essential for understanding the functional ecology, the dynamics of pollen transport, competition for pollinator services, and patterns of specialization and generalization in plant–pollinator interactions. We believe to present a synthetic description in the field of floral reward in Ranunculaceae family important in pollination biology and indicating connections bet