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

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.

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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.

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

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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

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

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.

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.

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.

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

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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.

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

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...

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.

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

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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.

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

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.

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

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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.

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

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

2011-02-01

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

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

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

2017-01-01

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

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.

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...

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.

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.

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...

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

Identification and systems methodologies for territorial delimitation

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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

Delimiting communities in the Pacific Northwest.

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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...

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

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Andrea A. F. Mourão

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

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

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.

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

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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.

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

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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.

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

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).

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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.

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.

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

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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.

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

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

2010-11-30

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

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

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Flot Jean-François

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

Delimiting areas of endemism through kernel interpolation.

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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.

Delimiting areas of endemism through kernel interpolation.

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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.

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

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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

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.

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.

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.

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...

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

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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.

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

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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.

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.

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

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.

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...

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.

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.

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.

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

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.

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

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

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

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.

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.

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...

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...

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

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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.

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...

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.

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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.

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.

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.

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....

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

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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.

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.

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.

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.

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 ...

POSITIONINGS AND DELIMITATIONS CONCERNING THE PERFORMANCE AUDIT

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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.

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.

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.

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.

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

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

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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.

Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae of an Ecuadorian Mountain Forest Using DNA Barcoding.

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Birthe Thormann

Full Text Available Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs (n = 284-289. Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2 and 469-481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons, the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a

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...

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...

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...

CONCEPTUAL DELIMITATIONS OF CONTROLLING

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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

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

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.

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.

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

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.

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 ...

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

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.

Automatic delimitation of microwatershed using SRTM data of the NASA

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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

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.

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.

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.

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.

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.

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

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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.

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

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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.

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

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.

Development of Geospatial Map Based Portal for Delimitation of Mcd Wards

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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.

DEVELOPMENT OF GEOSPATIAL MAP BASED PORTAL FOR DELIMITATION OF MCD WARDS

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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.

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

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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

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)

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

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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).

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.

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

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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.

Stuttering-Psycholinguistic Approach

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

2012-01-01

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

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

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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.

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

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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

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

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

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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-...

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.

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

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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

CONCEPTUAL DELIMITATIONS ON SUSTAINABLE DEVELOPMENT

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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

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

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.

Barcode index number, taxonomic rank and modes of speciation: examples from fish.

Science.gov (United States)

Kartavtsev, Yuri Phedorovich

2018-05-01

Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R 2  ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.

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

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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.

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

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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.

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

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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.

COMPARISON OF WETLANDS DESIGNATED IN PROJECT ISOK AND BY DELIMITATION OF SOILS METHOD IN ŚRODA ŚLĄSKA DISTRICT

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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.

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.

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.

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

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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

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.

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

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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.

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

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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.

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

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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

STUTTERING-PSYCHOLINGUISTIC APPROACH

OpenAIRE

Maria Anca; Carolina Bodea Haţegan; Lăcrămioara Prihoi

2012-01-01

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

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...

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.

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

Science.gov (United States)

Ishitani, Y.

2017-12-01

Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

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)

Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions.

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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

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

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

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.

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

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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.

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

DEFF Research Database (Denmark)

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

2017-01-01

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

A review of the genus Bulbothrix Hale: the species with medullary salazinic acid lacking vegetative propagules

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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.

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...

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.

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.

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

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 species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the

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

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

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...

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.

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

Science.gov (United States)

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

2014-02-01

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

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.

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.

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

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

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

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.

Natural Constraints to Species Diversification.

Directory of Open Access Journals (Sweden)

Eric Lewitus

2016-08-01

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

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

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

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.

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.

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

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.

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

Directory of Open Access Journals (Sweden)

Pablo D Lavinia

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

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.

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.

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

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.

An approach to grouping species for ecological risk assessment

International Nuclear Information System (INIS)

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

1994-01-01

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

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

Science.gov (United States)

Youssef, Noha H; Elshahed, Mostafa S

2008-09-01

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

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

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.

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

Benchmarking novel approaches for modelling species range dynamics.

Science.gov (United States)

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

2016-08-01

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

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.

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.

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.

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.

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

Directory of Open Access Journals (Sweden)

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.

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

Directory of Open Access Journals (Sweden)

Edwards Scott V

2010-10-01

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

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.

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

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.

METHODOLOGY FOR AUTOMATICALLY DELIMITING PERMANENT PRESERVATION AREAS ALONG WATER COURSES - THE USE OF GIS IN THE HYDROLOGICAL BASIN OF THE SERGIPE RIVER, BRAZIL

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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.

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

An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert.

Science.gov (United States)

Larridon, Isabel; Walter, Helmut E; Guerrero, Pablo C; Duarte, Milén; Cisternas, Mauricio A; Hernández, Carol Peña; Bauters, Kenneth; Asselman, Pieter; Goetghebeur, Paul; Samain, Marie-Stéphanie

2015-09-01

Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively. Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas. Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity. © 2015 Botanical Society of America.

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

Science.gov (United States)

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

2014-01-01

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

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

International Nuclear Information System (INIS)

Daemmgen, Ulrich; Hutchings, Nicholas J.

2008-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2008-08-15

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

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

ENVIRONMENTAL IMPACTS AND DELIMITATION OF THE PRESERVATION AREA STANDING IN ESPINHARAS RIVER IN THE URBAN STRETCH OF THE CITY OF PATOS-PB

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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.

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

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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.

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

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.

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

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.

Chorological classification approach for species and ecosystem conservation practice

Science.gov (United States)

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

2018-01-01

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

Forgotten forests--issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study.

Science.gov (United States)

Särkinen, Tiina; Iganci, João R V; Linares-Palomino, Reynaldo; Simon, Marcelo F; Prado, Darién E

2011-11-24

South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be particularly useful for mapping

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

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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.

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.

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

Science.gov (United States)

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

Scale Expansion of Community Investigations and Integration of the Effects of Abiotic and Biotic Processes on Maintenance of Species Diversity

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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.

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

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Simon J Pittman

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

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

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Ieshko Evgeny Pavlovich

2012-12-01

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

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

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Stacey L Lance

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

Overestimation of molecular and modelling methods and underestimation of traditional taxonomy leads to real problems in assessing and handling of the world's biodiversity.

Science.gov (United States)

Löbl, Ivan

2014-02-27

Since the 1992 Rio Convention on Biological Diversity, the earth's biodiversity is a matter of constant public interest, but the community of scientists who describe and delimit species in mega-diverse animal groups, i.e. the bulk of global biodiversity, faces ever-increasing impediments. The problems are rooted in poor understanding of specificity of taxonomy, and overestimation of quantitative approaches and modern technology. A high proportion of the animal species still remains to be discovered and studied, so a more balanced approach to the situation is needed.

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.

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

Science.gov (United States)

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

2018-06-01

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

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

Science.gov (United States)

Liu, Haijian; Wu, Changshan

2018-06-01

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

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.

Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae endemic to the Brazilian Atlantic forest.

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Luciana A Fusinatto

Full Text Available Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP, and Genealogical Sorting Index (GSI, providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

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

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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.

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

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Muhammad Kamal

2011-10-01

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

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

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Robert J Elshire

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

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...

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

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

2011-01-01

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

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

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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.

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

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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.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

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 ...

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

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Frank Pennekamp

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

Evolutionary relationships within the Phytophthora cactorum species complex in Europe.

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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.

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

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

2015-01-01

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

Duox, Flotillin-2, and Src42A are required to activate or delimit the spread of the transcriptional response to epidermal wounds in Drosophila.

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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

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

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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.

A Landscape Approach to Invasive Species Management.

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Miguel Lurgi

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

A Landscape Approach to Invasive Species Management.

Science.gov (United States)

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

2016-01-01

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

Approaching a Postcolonial Arctic

DEFF Research Database (Denmark)

Jensen, Lars

2016-01-01

This article explores different postcolonially configured approaches to the Arctic. It begins by considering the Arctic as a region, an entity, and how the customary political science informed approaches are delimited by their focus on understanding the Arctic as a region at the service...... of the contemporary neoliberal order. It moves on to explore how different parts of the Arctic are inscribed in a number of sub-Arctic nation-state binds, focusing mainly on Canada and Denmark. The article argues that the postcolonial can be understood as a prism or a methodology that asks pivotal questions to all...... approaches to the Arctic. Yet the postcolonial itself is characterised by limitations, not least in this context its lack of interest in the Arctic, and its bias towards conventional forms of representation in art. The article points to the need to develop a more integrated critique of colonial and neo...

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

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

2009-01-01

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

When Ontogeny Matters: A New Japanese Species of Brittle Star Illustrates the Importance of Considering both Adult and Juvenile Characters in Taxonomic Practice.

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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

Forgotten forests - issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study

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Särkinen Tiina

2011-11-01

Full Text Available Abstract Background South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF biome using herbarium data of habitat specialist species. Results Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1 poor spatial resolution, and (2 poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Conclusions Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in

Forgotten forests - issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study

Science.gov (United States)

2011-01-01

Background South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species. Results Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data. Conclusions Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps in silico. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be

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

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Kristopher J. L. Irizarry

2016-01-01

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

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

Science.gov (United States)

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

2016-01-01

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

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.

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.

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.

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

Science.gov (United States)

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

2018-01-01

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

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

Science.gov (United States)

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

2018-05-03

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

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.

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

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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.

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

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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.

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

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

2017-12-01

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

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

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

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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.

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

DEFF Research Database (Denmark)

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

2012-01-01

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

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

International Nuclear Information System (INIS)

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

2011-01-01

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

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

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

2014-07-01

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

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

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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

Object-based semi-automatic approach for forest structure characterization using lidar data in heterogeneous Pinus sylvestris stands

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C. Pascual; A. Garcia-Abril; L.G. Garcia-Montero; S. Martin-Fernandez; W.B. Cohen

2008-01-01

In this paper, we present a two-stage approach for characterizing the structure of Pinus sylvestris L. stands in forests of central Spain. The first stage was to delimit forest stands using eCognition and a digital canopy height model (DCHM) derived from lidar data. The polygons were then clustered into forest structure types based on the DCHM data...

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

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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.

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

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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.

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

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

2015-06-01

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

Leaf arrangements are invalid in the taxonomy of orchid species

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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.

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

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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.

DELIMITATION OF THE DISCRETIONARY POWER FROM THE POWER EXCESS IN THE ACTIVITY OF THE STATE’S AUTHORITIES

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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.

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

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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.

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

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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.

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

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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.

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

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

2013-11-14

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

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

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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.

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

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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.

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

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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.

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

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

2013-01-01

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

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

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

2015-01-01

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

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

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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.

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

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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.

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

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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.

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

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

2018-05-01

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

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

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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.

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

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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.

Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

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Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

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.

Delimitação dos núcleos talâmicos pela eletrofisiologia estereotáxica Delimitation of the thalamic nuclei by stereotaxic electrophysiology

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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.

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

NARCIS (Netherlands)

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

2001-01-01

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

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

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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.

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

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Rita S. W. Yam

2015-04-01

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

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

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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.

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

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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.

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

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

2016-12-01

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

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

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Rui Zhou

2016-11-01

Full Text Available Over the past decades, urban growth boundaries (UGBs have been regarded as effective tools applied by planners and local governments to curb urban sprawl and guide urban smart growth. The UGBs help limit urban development to suitable areas and protect surrounding agricultural and ecological landscapes. At present, China’s Town and Country Planning Act officially requires the delimitation of UGBs in a city master planning outline and in central urban area planning. However, China’s practices in UGBs are usually determined by urban planners and local authorities, and lack a sound analytical basis. Consequently, Chinese UGBs are often proven to be inefficient for controlling urban expansion. In this paper, take the fast-growing Xinzhuang town of Changshu city, eastern China as an example, a new method towards establishing UGBs is proposed based on land-use change model (the Conversion of Land Use and its Effects at Small regional extent, CLUE-S. The results of our study show that the land-use change and urban growth simulation accuracy of CLUE-S model is high. The expansion of construction land and the decrease of paddy field would be the main changing trends of local land use, and a good deal of cultivated land and ecological land would be transformed into construction land in 2009–2027. There is remarkable discordance in the spatial distribution between the simulated UGBs based on the CLUE-S model and the planned UGBs based on the conventional method, where the simulated results may more closely reflect the reality of urban growth laws. Therefore, we believe that our method could be a useful planning tool for the delimitation of UGBs in Chinese cities.

A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach.

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Faurby, Søren; Svenning, Jens-Christian

2015-03-01

Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups. Copyright © 2014 Elsevier Inc. All rights reserved.

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

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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

Heartwood and sapwood in eucalyptus trees: non-conventional approach to wood quality.

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Cherelli, Sabrina G; Sartori, Maria Márcia P; Próspero, André G; Ballarin, Adriano W

2018-01-01

This study evaluated the quality of heartwood and sapwood from mature trees of three species of Eucalyptus, by means of the qualification of their proportion, determination of basic and apparent density using non-destructive attenuation of gamma radiation technique and calculation of the density uniformity index. Six trees of each species (Eucalyptus grandis - 18 years old, Eucalyptus tereticornis - 35 years old and Corymbia citriodora - 28 years old) were used in the experimental program. The heartwood and sapwood were delimited by macroscopic analysis and the calculation of areas and percentage of heartwood and sapwood were performed using digital image. The uniformity index was calculated following methodology which numerically quantifies the dispersion of punctual density values of the wood around the mean density along the radius. The percentage of the heartwood was higher than the sapwood in all species studied. The density results showed no statistical difference between heartwood and sapwood. Differently from the density results, in all species studied there was statistical differences between uniformity indexes for heartwood and sapwood regions, making justifiable the inclusion of the density uniformity index as a quality parameter for Eucalyptus wood.

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

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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.

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

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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.

From single-species advice to mixed-species management: taking the next step

DEFF Research Database (Denmark)

Vinther, Morten; Reeves, S.A.; Patterson, K.R.

2004-01-01

Fishery management advice has traditionally been given on a stock-by-stock basis. Recent problems in implementing this advice, particularly for the demersal fisheries of the North Sea, have highlighted the limitations of the approach. In the long term, it would be desirable to give advice...... that accounts for mixed-fishery effects, but in the short term there is a need for approaches to resolve the conflicting management advice for different species within the same fishery, and to generate catch or effort advice that accounts for the mixed-species nature of the fishery. This paper documents...... a recent approach used to address these problems. The approach takes the single-species advice for each species in the fishery as a starting point, then attempts to resolve it into consistent catch or effort advice using fleet-disaggregated catch forecasts in combination with explicitly stated management...

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

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

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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.

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.

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.

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

Science.gov (United States)

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

2012-10-01

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

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.

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

Science.gov (United States)

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

2004-01-01

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

SESAM – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

DEFF Research Database (Denmark)

Guisan, Antoine; Rahbek, Carsten

2011-01-01

Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts...

First endemic freshwater Gammarus from Crete and its evolutionary history-an integrative taxonomy approach.

Science.gov (United States)

Hupało, Kamil; Mamos, Tomasz; Wrzesińska, Weronika; Grabowski, Michał

2018-01-01

The Mediterranean islands are known as natural laboratories of evolution with a high level of endemic biodiversity. However, most biodiversity assessments have focused mainly on terrestrial and marine fauna, leaving the freshwater animals aside. Crete is one of the largest islands in the Mediterranean Basin, with a long history of isolation from the continental mainland. Gammarid amphipods are often dominant in macrozoobenthic communities in European inland waters. They are widely used in biomonitoring and exotoxicological studies. Herein, we describe Gammarus plaitisi sp. nov., endemic to Cretan streams, based on morphological characters and a set of molecular species delimitation methods using mitochondrial cytochrome oxidase subunit I and 16S rRNA genes as well as nuclear 28S rDNA, ITS1 and EF1-alpha genes. The divergence of the new species is strongly connected with the geological history of the island supporting its continental origin.

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

Science.gov (United States)

Maguilla, Enrique; Escudero, Marcial

2016-01-01

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

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

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Nicolas Casajus

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

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

Science.gov (United States)

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

2016-01-01

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

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.

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.

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.

Speciation history and widespread introgression in the European short-call tree frogs (Hyla arborea sensu lato, H. intermedia and H. sarda)

Czech Academy of Sciences Publication Activity Database

Gvoždík, Václav; Canestrelli, D.; García-París, M.; Moravec, J.; Nascetti, G.; Recuero, E.; Teixeira, J.; Kotlík, P.

2015-01-01

Roč. 83, February (2015), s. 143-155 ISSN 1055-7903 Institutional support: RVO:68081766 Keywords : Bayesian species delimitation * Cryptic species complex * Gene flow * Phylogeography * Species tree * Systematics * Hylidae Subject RIV: EG - Zoology Impact factor: 3.792, year: 2015

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).

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

Directory of Open Access Journals (Sweden)

Hannes Gaisberger

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

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.

Parametric analysis as a methodical approach that facilitates the exploration of the creative space in low-energy and zero-energy design projects

DEFF Research Database (Denmark)

Hansen, Hanne Tine Ring; Knudstrup, Mary-Ann

2008-01-01

-energy or zero-energy building design. The paper discusses professional differences between two of the main actors involved in integrated design processes; engineers and architects, as well as a methodical approach to investigation and delimitation of the creative space of a specific project. The paper......Most – if not all - methodical approaches found in literature that describe the creation of environmentally sustainable architecture agree on the importance of inter-disciplinarity and the early integration of building system strategies and the importance of the comfort of the user. Today most...

Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae).

Science.gov (United States)

Montagna, Matteo; Mereghetti, Valeria; Lencioni, Valeria; Rossaro, Bruno

2016-01-01

Rapid and efficient DNA-based tools are recommended for the evaluation of the insect biodiversity of high-altitude streams. In the present study, focused principally on larvae of the genus Diamesa Meigen 1835 (Diptera: Chironomidae), the congruence between morphological/molecular delimitation of species as well as performances in taxonomic assignments were evaluated. A fragment of the mitochondrial cox1 gene was obtained from 112 larvae, pupae and adults (Diamesinae, Orthocladiinae and Tanypodinae) that were collected in different mountain regions of the Alps and Apennines. On the basis of morphological characters 102 specimens were attributed to 16 species, and the remaining ten specimens were identified to the genus level. Molecular species delimitation was performed using: i) distance-based Automatic Barcode Gap Discovery (ABGD), with no a priori assumptions on species identification; and ii) coalescent tree-based approaches as the Generalized Mixed Yule Coalescent model, its Bayesian implementation and Bayesian Poisson Tree Processes. The ABGD analysis, estimating an optimal intra/interspecific nucleotide distance threshold of 0.7%-1.4%, identified 23 putative species; the tree-based approaches, identified between 25-26 entities, provided nearly identical results. All species belonging to zernyi, steinboecki, latitarsis, bertrami, dampfi and incallida groups, as well as outgroup species, are recovered as separate entities, perfectly matching the identified morphospecies. In contrast, within the cinerella group, cases of discrepancy arose: i) the two morphologically separate species D. cinerella and D. tonsa are neither monophyletic nor diagnosable exhibiting low values of between-taxa nucleotide mean divergence (0.94%); ii) few cases of larvae morphological misidentification were observed. Head capsule color is confirmed to be a valid character able to discriminate larvae of D. zernyi, D. tonsa and D. cinerella, but it is here better defined as a color gradient

Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries.

Science.gov (United States)

Dagnino, D; Minuto, L; Casazza, G

2017-11-01

Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

2457-IJBCS-Article-Sefiu Adekilekun Saheed

African Journals Online (AJOL)

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Inflorescence and floral morphological characters in twelve species of Cyperus – a genus known to have C3 and C4 photosynthetic species – were investigated in order to check their usefulness in delimiting species into photosynthetic groups. Plant species were collected from different locations within Southwestern.

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

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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.

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

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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.

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes

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Bruno F. Melo

2018-04-01

Full Text Available Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.

Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus)

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Smith, Chase; Johnson, Nathan A.; Pfeiffer, John M.; Gangloff, Michael M.

2018-01-01

Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent ‘Strophitus’ connasaugaensis and ‘Strophitus’ subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize

Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

Science.gov (United States)

Hoef-Emden, Kerstin

2012-01-01

A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

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Kerstin Hoef-Emden

Full Text Available A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene. In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC, have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

Pitfalls of Establishing DNA Barcoding Systems in Protists: The Cryptophyceae as a Test Case

Science.gov (United States)

Hoef-Emden, Kerstin

2012-01-01

A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5′-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed. PMID:22970104

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

OpenAIRE

Rodrigues, Paula; Venâncio, Armando; Lima, Nelson

2011-01-01

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

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

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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.

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

Science.gov (United States)

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

2011-01-01

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

Studies on the Erythropeltidaceae (Rhodophyceae-Bangiophycidae)

NARCIS (Netherlands)

Heerebout, G.R.

1968-01-01

From culture studies it appears that the species of Erythrocladia and Erythrotrichia have a great morphological variability. The delimitation of the species has been studied. In the genus Erythrocladia two species are recognized, in Erythrotrichia three, and in Porphyropsis two. In cultures of

A leitmotif of contemporary mycology has challenges and benefits for plant pathologists

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Multiple traditional species names for plant pathogenic fungi have been supplemented with new names that delimit formerly cryptic species. In other instances, isolates within a species are clearly differentiated by both phylogeny and distinctive pathogenic traits and are assigned sub-specific design...

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

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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

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

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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.

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

Science.gov (United States)

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

2018-02-15

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

Using a distribution and conservation status weighted hotspot approach to identify areas in need of conservation action to benefit Idaho bird species

Science.gov (United States)

Haines, Aaron M.; Leu, Matthias; Svancara, Leona K.; Wilson, Gina; Scott, J. Michael

2010-01-01

Identification of biodiversity hotspots (hereafter, hotspots) has become a common strategy to delineate important areas for wildlife conservation. However, the use of hotspots has not often incorporated important habitat types, ecosystem services, anthropogenic activity, or consistency in identifying important conservation areas. The purpose of this study was to identify hotspots to improve avian conservation efforts for Species of Greatest Conservation Need (SGCN) in the state of Idaho, United States. We evaluated multiple approaches to define hotspots and used a unique approach based on weighting species by their distribution size and conservation status to identify hotspot areas. All hotspot approaches identified bodies of water (Bear Lake, Grays Lake, and American Falls Reservoir) as important hotspots for Idaho avian SGCN, but we found that the weighted approach produced more congruent hotspot areas when compared to other hotspot approaches. To incorporate anthropogenic activity into hotspot analysis, we grouped species based on their sensitivity to specific human threats (i.e., urban development, agriculture, fire suppression, grazing, roads, and logging) and identified ecological sections within Idaho that may require specific conservation actions to address these human threats using the weighted approach. The Snake River Basalts and Overthrust Mountains ecological sections were important areas for potential implementation of conservation actions to conserve biodiversity. Our approach to identifying hotspots may be useful as part of a larger conservation strategy to aid land managers or local governments in applying conservation actions on the ground.

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

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Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd; Chen, Wei-Jen

2017-01-01

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

Directory of Open Access Journals (Sweden)

Pei-Chun Lo

Full Text Available The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species from one nuclear gene (RAG1 and one mitochondrial gene (COI; the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species; and the dataset with only COI gene sequences (308 samples from 51 currently recognized species. The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC. The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology. Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and

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

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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.

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.

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

Science.gov (United States)

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

2015-01-01

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

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.

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.

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.

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...

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)

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.

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

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex.

Science.gov (United States)

Fisch-Muller, Sonia; Mol, Jan H A; Covain, Raphaël

2018-01-01

Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and

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

Science.gov (United States)

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

2017-01-01

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

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.

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

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

Multilocus analysis of the Exophiala jeanselmei clade containing black yeasts involved in opportunistic disease in humans

NARCIS (Netherlands)

Zeng, J.; Feng, P.; Gerrits van den Ende, A.H.G.; Xi, L.; Harrak, M.J.; de Hoog, G.S.

2014-01-01

To confirm species delimitations in the ‘jeanselmei-clade’ in the Chaetothyriales, four independent markers were analysed, and phylogenetic trees were reconstructed using different algorithms. Reproductive isolation within the complex and reproductive modes in the species involved were determined,

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.

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.

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.

Revision of the genus Spermophora Hentz in Southeast Asia and on the Pacific Islands, with descriptions of three new genera (Araneae: Pholcidae)

NARCIS (Netherlands)

Huber, B.A.

2005-01-01

The main aim of the present paper is to delimit ‘true’ Spermophora, i.e. the group of species most closely related to the type species S. senoculata (Dugès). Apart from the type species, only three previously described species are included in this core group (S. estebani Simon, S. paluma Huber, S.

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

Science.gov (United States)

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

2014-12-01

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

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

Science.gov (United States)

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

2009-02-01

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

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

Directory of Open Access Journals (Sweden)

F. Manes

2009-11-01

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

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

Science.gov (United States)

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

2009-11-01

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

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

Science.gov (United States)

Fang, Yishan; Huang, Xinjian; Wang, Lishi

2015-01-06

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

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.

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

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

2017-01-01

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

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

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Adugna Abdi Woldesemayat

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

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

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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

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

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

2017-02-09

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

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

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

2017-09-01

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

A MULTIVARIATE APPROACH TO ANALYSE NATIVE FOREST TREE SPECIE SEEDS

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Alessandro Dal Col Lúcio

2006-03-01

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

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

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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

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

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

2017-01-01

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

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

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Miraemiliana Murat

2017-09-01

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

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

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

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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.

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

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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

Theoretical microbial ecology without species

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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.

A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes

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Daniel Toffoli

2008-01-01

Full Text Available DNA barcoding is a recently proposed global standard in taxonomy based on DNA sequences. The two main goals of DNA barcoding methodology are assignment of specimens to a species and discovery of new species. There are two main underlying assumptions: i reciprocal monophyly of species, and ii intraspecific divergence is always less than interspecific divergence. Here we present a phylogenetic analysis of the family Potamotrygonidae based on mitochondrial cytochrome c oxidase I gene, sampling 10 out of the 18 to 20 valid species including two non-described species. Potamotrygonidae systematics is still not fully resolved with several still-to-be-described species while some other species are difficult to delimit due to overlap in morphological characters and because of sharing a complex color patterns. Our results suggest that the family passed through a process of rapid speciation and that the species Potamotrygon motoro, P. scobina, and P. orbignyi share haplotypes extensively. Our results suggest that systems of identification of specimens based on DNA sequences, together with morphological and/or ecological characters, can aid taxonomic studies, but delimitation of new species based on threshold values of genetic distances are overly simplistic and misleading.

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

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

2007-02-01

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

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

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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.

Biological species in the viral world.

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Bobay, Louis-Marie; Ochman, Howard

2018-06-05

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

How many taxa can be recognized within the complex Tillandsia capillaris (Bromeliaceae, Tillandsioideae? Analysis of the available classifications using a multivariate approach

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Lucía Castello

2013-05-01

Full Text Available Tillandsia capillaris Ruiz & Pav., which belongs to the subgenus Diaphoranthema is distributed in Ecuador, Peru, Bolivia, northern and central Argentina, and Chile, and includes forms that are difficult to circumscribe, thus considered to form a complex. The entities of this complex are predominantly small-sized epiphytes, adapted to xeric environments. The most widely used classification defines 5 forms for this complex based on few morphological reproductive traits: T. capillaris Ruiz & Pav. f. capillaris, T. capillaris f. incana (Mez L.B. Sm., T. capillaris f. cordobensis (Hieron. L.B. Sm., T. capillaris f. hieronymi (Mez L.B. Sm. and T. capillaris f. virescens (Ruiz & Pav. L.B. Sm. In this study, 35 floral and vegetative characters were analyzed with a multivariate approach in order to assess and discuss different proposals for classification of the T. capillaris complex, which presents morphotypes that co-occur in central and northern Argentina. To accomplish this, data of quantitative and categorical morphological characters of flowers and leaves were collected from herbarium specimens and field collections and were analyzed with statistical multivariate techniques. The results suggest that the last classification for the complex seems more comprehensive and three taxa were delimited: T. capillaris (=T. capillaris f. incana-hieronymi, T. virescens s. str. (=T. capillaris f. cordobensis and T. virescens s. l. (=T. capillaris f. virescens. While T. capillaris and T. virescens s. str. co-occur, T. virescens s. l. is restricted to altitudes above 2000 m in Argentina. Characters previously used for taxa delimitation showed continuous variation and therefore were not useful. New diagnostic characters are proposed and a key is provided for delimiting these three taxa within the complex.

How many taxa can be recognized within the complex Tillandsia capillaris (Bromeliaceae, Tillandsioideae)? Analysis of the available classifications using a multivariate approach.

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Castello, Lucía V; Galetto, Leonardo

2013-01-01

Tillandsia capillaris Ruiz & Pav., which belongs to the subgenus Diaphoranthema is distributed in Ecuador, Peru, Bolivia, northern and central Argentina, and Chile, and includes forms that are difficult to circumscribe, thus considered to form a complex. The entities of this complex are predominantly small-sized epiphytes, adapted to xeric environments. The most widely used classification defines 5 forms for this complex based on few morphological reproductive traits: Tillandsia capillaris Ruiz & Pav. f. capillaris, Tillandsia capillaris f. incana (Mez) L.B. Sm., Tillandsia capillaris f. cordobensis (Hieron.) L.B. Sm., Tillandsia capillaris f. hieronymi (Mez) L.B. Sm. and Tillandsia capillaris f. virescens (Ruiz & Pav.) L.B. Sm. In this study, 35 floral and vegetative characters were analyzed with a multivariate approach in order to assess and discuss different proposals for classification of the Tillandsia capillaris complex, which presents morphotypes that co-occur in central and northern Argentina. To accomplish this, data of quantitative and categorical morphological characters of flowers and leaves were collected from herbarium specimens and field collections and were analyzed with statistical multivariate techniques. The results suggest that the last classification for the complex seems more comprehensive and three taxa were delimited: Tillandsia capillaris (=Tillandsia capillaris f. incana-hieronymi), Tillandsia virescens s. str. (=Tillandsia capillaris f. cordobensis) and Tillandsia virescens s. l. (=Tillandsia capillaris f. virescens). While Tillandsia capillaris and Tillandsia virescens s. str. co-occur, Tillandsia virescens s. l. is restricted to altitudes above 2000 m in Argentina. Characters previously used for taxa delimitation showed continuous variation and therefore were not useful. New diagnostic characters are proposed and a key is provided for delimiting these three taxa within the complex.

Do pseudo-absence selection strategies influence species distribution models and their predictions? An information-theoretic approach based on simulated data

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Guisan Antoine

2009-04-01

Full Text Available Abstract Background Multiple logistic regression is precluded from many practical applications in ecology that aim to predict the geographic distributions of species because it requires absence data, which are rarely available or are unreliable. In order to use multiple logistic regression, many studies have simulated "pseudo-absences" through a number of strategies, but it is unknown how the choice of strategy influences models and their geographic predictions of species. In this paper we evaluate the effect of several prevailing pseudo-absence strategies on the predictions of the geographic distribution of a virtual species whose "true" distribution and relationship to three environmental predictors was predefined. We evaluated the effect of using a real absences b pseudo-absences selected randomly from the background and c two-step approaches: pseudo-absences selected from low suitability areas predicted by either Ecological Niche Factor Analysis: (ENFA or BIOCLIM. We compared how the choice of pseudo-absence strategy affected model fit, predictive power, and information-theoretic model selection results. Results Models built with true absences had the best predictive power, best discriminatory power, and the "true" model (the one that contained the correct predictors was supported by the data according to AIC, as expected. Models based on random pseudo-absences had among the lowest fit, but yielded the second highest AUC value (0.97, and the "true" model was also supported by the data. Models based on two-step approaches had intermediate fit, the lowest predictive power, and the "true" model was not supported by the data. Conclusion If ecologists wish to build parsimonious GLM models that will allow them to make robust predictions, a reasonable approach is to use a large number of randomly selected pseudo-absences, and perform model selection based on an information theoretic approach. However, the resulting models can be expected to have

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

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

2015-06-01

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

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

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.

Echelon approach to areas of concern in synoptic regional monitoring

Science.gov (United States)

Myers, Wayne; Patil, Ganapati P.; Joly, Kyle

1997-01-01

Echelons provide an objective approach to prospecting for areas of potential concern in synoptic regional monitoring of a surface variable. Echelons can be regarded informally as stacked hill forms. The strategy is to identify regions of the surface which are elevated relative to surroundings (Relative ELEVATIONS or RELEVATIONS). These are areas which would continue to expand as islands with receding (virtual) floodwaters. Levels where islands would merge are critical elevations which delimit echelons in the vertical dimension. Families of echelons consist of surface sectors constituting separate islands for deeper waters that merge as water level declines. Pits which would hold water are disregarded in such a progression, but a complementary analysis of pits is obtained using the surface as a virtual mould to cast a counter-surface (bathymetric analysis). An echelon tree is a family tree of echelons with peaks as terminals and the lowest level as root. An echelon tree thus provides a dendrogram representation of surface topology which enables graph theoretic analysis and comparison of surface structures. Echelon top view maps show echelon cover sectors on the base plane. An echelon table summarizes characteristics of echelons as instances or cases of hill form surface structure. Determination of echelons requires only ordinal strength for the surface variable, and is thus appropriate for environmental indices as well as measurements. Since echelons are inherent in a surface rather than perceptual, they provide a basis for computer-intelligent understanding of surfaces. Echelons are given for broad-scale mammalian species richness in Pennsylvania.

Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

Science.gov (United States)

Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

2014-12-16

Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

Assessing species vulnerability to climate change

Science.gov (United States)

Pacifici, Michela; Foden, Wendy B.; Visconti, Piero; Watson, James E. M.; Butchart, Stuart H. M.; Kovacs, Kit M.; Scheffers, Brett R.; Hole, David G.; Martin, Tara G.; Akçakaya, H. Resit; Corlett, Richard T.; Huntley, Brian; Bickford, David; Carr, Jamie A.; Hoffmann, Ary A.; Midgley, Guy F.; Pearce-Kelly, Paul; Pearson, Richard G.; Williams, Stephen E.; Willis, Stephen G.; Young, Bruce; Rondinini, Carlo

2015-03-01

The effects of climate change on biodiversity are increasingly well documented, and many methods have been developed to assess species' vulnerability to climatic changes, both ongoing and projected in the coming decades. To minimize global biodiversity losses, conservationists need to identify those species that are likely to be most vulnerable to the impacts of climate change. In this Review, we summarize different currencies used for assessing species' climate change vulnerability. We describe three main approaches used to derive these currencies (correlative, mechanistic and trait-based), and their associated data requirements, spatial and temporal scales of application and modelling methods. We identify strengths and weaknesses of the approaches and highlight the sources of uncertainty inherent in each method that limit projection reliability. Finally, we provide guidance for conservation practitioners in selecting the most appropriate approach(es) for their planning needs and highlight priority areas for further assessments.

Territorial behaviour and dominance hierarchy of Anthracothorax nigricollis Vieillot 1817 (Aves: Trochilidae) on food resources

OpenAIRE

Araujo-Silva, Lucas Eduardo; Bessa, Eduardo [UNESP

2010-01-01

Dominant species are those which delimit and defend territories from other individuals of the same or different species. Subordinate species are those which, furtive and sneakily, use sources of nectar from other individuals. This study aimed to describe the aggressive interactions between species of hummingbirds, define which species are dominant and which are subordinate, investigate if the sharing of resources occurs during the visits, and compare the behaviour of the dominant species in d...

Karyotype analysis in Machaerium lunatum (Linn. f.) Ducke ...

African Journals Online (AJOL)

ADOWIE PERE

2017-12-11

Dec 11, 2017 ... Ducke (syn. Drepanocarpus lunatus (Linn. f.) G.F.W. Mey) belongs to the family Fabaceae-Papilionaceae. (Hutchinson and Dalziel 1954). It has about 130 species distributed from Mexico to Argentina which are difficult to delimit taxonomically (Rudd 1987) and 150 species distributed from Mexico to South.

A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago.

Science.gov (United States)

Clerc-Blain, Jessica L E; Starr, Julian R; Bull, Roger D; Saarela, Jeffery M

2010-01-01

Previous research on barcoding sedges (Carex) suggested that basic searches within a global barcoding database would probably not resolve more than 60% of the world's some 2000 species. In this study, we take an alternative approach and explore the performance of plant DNA barcoding in the Carex lineage from an explicitly regional perspective. We characterize the utility of a subset of the proposed protein-coding and noncoding plastid barcoding regions (matK, rpoB, rpoC1, rbcL, atpF-atpH, psbK-psbI) for distinguishing species of Carex and Kobresia in the Canadian Arctic Archipelago, a clearly defined eco-geographical region representing 1% of the Earth's landmass. Our results show that matK resolves the greatest number of species of any single-locus (95%), and when combined in a two-locus barcode, it provides 100% species resolution in all but one combination (matK + atpFH) during unweighted pair-group method with arithmetic mean averages (UPGMA) analyses. Noncoding regions were equally or more variable than matK, but as single markers they resolve substantially fewer taxa than matK alone. When difficulties with sequencing and alignment due to microstructural variation in noncoding regions are also considered, our results support other studies in suggesting that protein-coding regions are more practical as barcoding markers. Plastid DNA barcodes are an effective identification tool for species of Carex and Kobresia in the Canadian Arctic Archipelago, a region where the number of co-existing closely related species is limited. We suggest that if a regional approach to plant DNA barcoding was applied on a global scale, it could provide a solution to the generally poor species resolution seen in previous barcoding studies. © 2009 Blackwell Publishing Ltd.

Digital holography of particles: benefits of the 'inverse problem' approach

International Nuclear Information System (INIS)

Gire, J; Denis, L; Fournier, C; Soulez, F; Ducottet, C; Thiébaut, E

2008-01-01

The potential of in-line digital holography to locate and measure the size of particles distributed throughout a volume (in one shot) has been established. These measurements are fundamental for the study of particle trajectories in fluid flow. The most important issues in digital holography today are poor depth positioning accuracy, transverse field-of-view limitations, border artifacts and computational burdens. We recently suggested an 'inverse problem' approach to address some of these issues for the processing of particle digital holograms. The described algorithm improves axial positioning accuracy, gives particle diameters with sub-micrometer accuracy, eliminates border effects and increases the size of the studied volume. This approach for processing particle holograms pushes back some classical constraints. For example, the Nyquist criterion is no longer a restriction for the recording step and the studied volume is no longer confined to the field of view delimited by the sensor borders. In this paper we present a review of the limitations commonly found in digital holography. We then discuss the benefits of the 'inverse problem' approach and the influence of some experimental parameters in this framework

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.

Optimization of visual trapping methodology for the emerald ash borer, Agrilus planipennis

Science.gov (United States)

Joseph A. Francese; Damon J. Crook; Ivich Fraser; David R. Lance; Alan J. Sawyer; Victor C. Mastro

2009-01-01

As the emerald ash borer (EAB), Agrilus planipennis (Coleoptera: Buprestidae), spreads throughout the range of North American ash species, better tools are needed for the detection and delimitation of new infestations...

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

Science.gov (United States)

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

2015-04-01

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

A globally-distributed alien invasive species poses risks to United States imperiled species.

Science.gov (United States)

McClure, Meredith L; Burdett, Christopher L; Farnsworth, Matthew L; Sweeney, Steven J; Miller, Ryan S

2018-03-28

In the midst of Earth's sixth mass extinction event, non-native species are a driving factor in many imperiled species' declines. One of the most widespread and destructive alien invasive species in the world, wild pigs (Sus scrofa) threaten native species through predation, habitat destruction, competition, and disease transmission. We show that wild pigs co-occur with up to 87.2% of imperiled species in the contiguous U.S. identified as susceptible to their direct impacts, and we project increases in both the number of species at risk and the geographic extent of risks by 2025. Wild pigs may therefore present a severe threat to U.S. imperiled species, with serious implications for management of at-risk species throughout wild pigs' global distribution. We offer guidance for efficient allocation of research effort and conservation resources across species and regions using a simple approach that can be applied to wild pigs and other alien invasive species globally.

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

Directory of Open Access Journals (Sweden)

Michael Hiller

2012-10-01