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Sample records for maxillariinae species delimitation

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

    PubMed Central

    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

  2. Delimitating species in paleoanthropology.

    PubMed

    White, Tim D

    2014-01-01

    Evolutionary biologists created a large twentieth-century literature about delimiting biological species. Paleontologists contributed the unique complications of deep time. Toward century's end, one participant wrote: "In all probability more paper has been consumed on the questions of the nature and definition of the species than any other subject in evolutionary and systematic biology." PMID:24591140

  3. Active mountain building and the distribution of core Maxillariinae species in tropical Mexico and Central America

    USGS Publications Warehouse

    Kirby, Stephen H.

    2011-01-01

    The observation that southeastern Central America is a hotspot for orchid diversity has long been known and confirmed by recent systematic studies and checklists. An analysis of the geographic and elevation distribution demonstrates that the most widespread species of “core” Maxillariinae are all adapted to life near sea level, whereas the most narrowly endemic species are largely distributed in wet highland environments. Drier, hotter lowland gaps exist between these cordilleras and evidently restrict the dispersal of the species adapted to wetter, cooler conditions. Among the recent generic realignments of “core” Maxillariinae based on molecular phylogenetics, the Camaridium clade is easily the most prominent genus in Central America and is largely restricted to the highlands of Costa Rica and Panama, indicating that this region is the ancestral home of this genus and that its dispersal limits are drier, lowland cordilleran gaps. The mountains of Costa Rica and Panama are among the geologically youngest topographic features in the Neotropics, reflecting the complex and dynamic interactions of numerous tectonic plates. From consideration of the available geological evidence, I conclude that the rapid growth of the mountain ranges in Costa Rica and Panama during the late Cenozoic times created, in turn, very rapid ranges in ecological life zones and geographic isolation in that part of the isthmus. Thus, I suggest that these recent geologic events were the primary drivers for accelerated orchid evolution in southeastern Central America.

  4. The Species Delimitation Uncertainty Principle

    PubMed Central

    Adams, Byron J.

    2001-01-01

    If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present. PMID:19265874

  5. Species delimitation and global biosecurity.

    PubMed

    Boykin, Laura M; Armstrong, Karen F; Kubatko, Laura; De Barro, Paul

    2012-01-01

    Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, "tip to root", for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg's reciprocal monophyly, (P(AB)),1 (2) Rodrigo's (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might

  6. Species Delimitation and Global Biosecurity

    PubMed Central

    Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

    2012-01-01

    Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits

  7. Active mountain building and the distribution of “core” Maxillariinae species in tropical Mexico and Central America

    USGS Publications Warehouse

    Kirby, Stephen H.

    2011-01-01

    The observation that southeastern Central America is a hotspot for orchid diversity has long been known and confirmed by recent systematic studies and checklists. An analysis of the geographic and elevation distribution demonstrates that the most widespread species of “core” Maxillariinae are all adapted to life near sea level, whereas the most narrowly endemic species are largely distributed in wet highland environments. Drier, hotter lowland gaps exist between these cordilleras and evidently restrict the dispersal of the species adapted to wetter, cooler conditions. Among the recent generic realignments of “core” Maxillariinae based on molecular phylogenetics, the Camaridium clade is easily the most prominent genus in Central America and is largely restricted to the highlands of Costa Rica and Panama, indicating that this region is the ancestral home of this genus and that its dispersal limits are drier, lowland cordilleran gaps. The mountains of Costa Rica and Panama are among the geologically youngest topographic features in the Neotropics, reflecting the complex and dynamic interactions of numerous tectonic plates. From consideration of the available geological evidence, I conclude that the rapid growth of the mountain ranges in Costa Rica and Panama during the late Cenozoic times created, in turn, very rapid ranges in ecological life zones and geographic isolation in that part of the isthmus. Thus, I suggest that these recent geologic events were the primary drivers for accelerated orchid evolution in southeastern Central America.

  8. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)

    PubMed Central

    Leaché, Adam D.; Fujita, Matthew K.

    2010-01-01

    Genealogical data are an important source of evidence for delimiting species, yet few statistical methods are available for calculating the probabilities associated with different species delimitations. Bayesian species delimitation uses reversible-jump Markov chain Monte Carlo (rjMCMC) in conjunction with a user-specified guide tree to estimate the posterior distribution for species delimitation models containing different numbers of species. We apply Bayesian species delimitation to investigate the speciation history of forest geckos (Hemidactylus fasciatus) from tropical West Africa using five nuclear loci (and mtDNA) for 51 specimens representing 10 populations. We find that species diversity in H. fasciatus is currently underestimated, and describe three new species to reflect the most conservative estimate for the number of species in this complex. We examine the impact of the guide tree, and the prior distributions on ancestral population sizes (θ) and root age (τ0), on the posterior probabilities for species delimitation. Mis-specification of the guide tree or the prior distribution for θ can result in strong support for models containing more species. We describe a new statistic for summarizing the posterior distribution of species delimitation models, called speciation probabilities, which summarize the posterior support for each speciation event on the starting guide tree. PMID:20519219

  9. Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

    PubMed Central

    Yang, Ziheng; Rannala, Bruce

    2014-01-01

    A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation. PMID:25274273

  10. Unguided species delimitation using DNA sequence data from multiple Loci.

    PubMed

    Yang, Ziheng; Rannala, Bruce

    2014-12-01

    A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation. PMID:25274273

  11. Species delimitation: A case study in a problematic ant taxon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species delimitation has been invigorated as a discipline in systematics by an influx of new character sets, analytical methods, and conceptual advances. We use genetic data from 68 markers, combined with distributional, bioclimatic, and coloration information, to distinguish evolutionarily indepe...

  12. Rarity and Incomplete Sampling in DNA-Based Species Delimitation.

    PubMed

    Ahrens, Dirk; Fujisawa, Tomochika; Krammer, Hans-Joachim; Eberle, Jonas; Fabrizi, Silvia; Vogler, Alfried P

    2016-05-01

    DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including "singleton" representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by "clade addition" of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size ([Formula: see text]), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in [Formula: see text] among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in [Formula: see text] and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable [Formula: see text] This effect was less

  13. Delimiting Species without Nuclear Monophyly in Madagascar's Mouse Lemurs

    PubMed Central

    Weisrock, David W.; Rasoloarison, Rodin M.; Fiorentino, Isabella; Ralison, José M.; Goodman, Steven M.; Kappeler, Peter M.; Yoder, Anne D.

    2010-01-01

    Background Speciation begins when populations become genetically separated through a substantial reduction in gene flow, and it is at this point that a genetically cohesive set of populations attain the sole property of species: the independent evolution of a population-level lineage. The comprehensive delimitation of species within biodiversity hotspots, regardless of their level of divergence, is important for understanding the factors that drive the diversification of biota and for identifying them as targets for conservation. However, delimiting recently diverged species is challenging due to insufficient time for the differential evolution of characters—including morphological differences, reproductive isolation, and gene tree monophyly—that are typically used as evidence for separately evolving lineages. Methodology In this study, we assembled multiple lines of evidence from the analysis of mtDNA and nDNA sequence data for the delimitation of a high diversity of cryptically diverged population-level mouse lemur lineages across the island of Madagascar. Our study uses a multi-faceted approach that applies phylogenetic, population genetic, and genealogical analysis for recognizing lineage diversity and presents the most thoroughly sampled species delimitation of mouse lemur ever performed. Conclusions The resolution of a large number of geographically defined clades in the mtDNA gene tree provides strong initial evidence for recognizing a high diversity of population-level lineages in mouse lemurs. We find additional support for lineage recognition in the striking concordance between mtDNA clades and patterns of nuclear population structure. Lineages identified using these two sources of evidence also exhibit patterns of population divergence according to genealogical exclusivity estimates. Mouse lemur lineage diversity is reflected in both a geographically fine-scaled pattern of population divergence within established and geographically widespread taxa

  14. Phylogenetic species delimitation for crayfishes of the genus Pacifastacus

    PubMed Central

    Castelin, Magalie; Williams, Bronwyn W.; Olden, Julian D.; Abbott, Cathryn L.

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  16. Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the ge...

  17. Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae).

    PubMed

    Grummer, Jared A; Bryson, Robert W; Reeder, Tod W

    2014-03-01

    Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal-likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation (HME), smoothed harmonic mean estimation (sHME), path-sampling/thermodynamic integration (PS), and stepping-stone (SS) analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that HME and sHME perform poorly compared with PS and SS marginal-likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through PS and SS analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical data sets, harmonic and smoothed harmonic mean marginal-likelihood estimators provided much higher marginal-likelihood estimates

  18. Evaluation of a bayesian coalescent method of species delimitation.

    PubMed

    Zhang, Chi; Zhang, De-Xing; Zhu, Tianqi; Yang, Ziheng

    2011-12-01

    A Bayesian coalescent-based method has recently been proposed to delimit species using multilocus genetic sequence data. Posterior probabilities of different species delimitation models are calculated using reversible-jump Markov chain Monte Carlo algorithms. The method accounts for species phylogenies and coalescent events in both extant and extinct species and accommodates lineage sorting and uncertainties in the gene trees. Although the method is theoretically appealing, its utility in practical data analysis is yet to be rigorously examined. In particular, the analysis may be sensitive to priors on ancestral population sizes and on species divergence times and to gene flow between species. Here we conduct a computer simulation to evaluate the statistical performance of the method, such as the false negatives (the error of lumping multiple species into one) and false positives (the error of splitting one species into several). We found that the correct species model was inferred with high posterior probability with only one or two loci when 5 or 10 sequences were sampled from each population, or with 50 loci when only one sequence was sampled. We also simulated data allowing migration under a two-species model, a mainland-island model and a stepping-stone model to assess the impact of gene flow (hybridization or introgression). The behavior of the method was diametrically different depending on the migration rate. Low rates at < 0.1 migrants per generation had virtually no effect, so that the method, while assuming no hybridization between species, identified distinct species despite small amounts of gene flow. This behavior appears to be consistent with biologists' practice. In contrast, higher migration rates at ≥ 10 migrants per generation caused the method to infer one species. At intermediate levels of migration, the method is indecisive. Our results suggest that Bayesian analysis under the multispecies coalescent model may provide important insights into

  19. Improved Reversible Jump Algorithms for Bayesian Species Delimitation

    PubMed Central

    Rannala, Bruce; Yang, Ziheng

    2013-01-01

    Several computational methods have recently been proposed for delimiting species using multilocus sequence data. Among them, the Bayesian method of Yang and Rannala uses the multispecies coalescent model in the likelihood framework to calculate the posterior probabilities for the different species-delimitation models. It has a sound statistical basis and is found to have nice statistical properties in simulation studies, such as low error rates of undersplitting and oversplitting. However, the method suffers from poor mixing of the reversible-jump Markov chain Monte Carlo (rjMCMC) algorithms. Here, we describe several modifications to the algorithms. We propose a flexible prior that allows the user to specify the probability that each node on the guide tree represents a true speciation event. We also introduce modifications to the rjMCMC algorithms that remove the constraint on the new species divergence time when splitting and alter the gene trees to remove incompatibilities. The new algorithms are found to improve mixing of the Markov chain for both simulated and empirical data sets. PMID:23502678

  20. Pollinarium Morphology and Floral Rewards inBrazilian Maxillariinae (Orchidaceae)

    PubMed Central

    SINGER, RODRIGO B.; KOEHLER, SAMANTHA

    2004-01-01

    • Background and Aims There is strong support for the monophyly of the orchid subtribe Maxillariinae s.l., yet generic boundaries within it are unsatisfactory and need re‐evaluation. In an effort to assemble sets of morphological characters to distinguish major clades within this subtribe, the pollinarium morphology and floral rewards of representative Brazilian species of this subtribe were studied. • Methods The study was based on fresh material from 60 species and seven genera obtained from cultivated specimens. Variation of pollinarium structure and floral rewards was assessed using a stereomicroscope and by SEM analysis. • Key Results Four morphological types of pollinaria are described. Type 1 appears to be the most widespread and is characterized by a well‐developed tegula. Type 2 lacks a stipe and the pollinia are attached directly to the viscidium. Type 3 also lacks a stipe, and the viscidium is rigid and dark. In Type 4, the stipe consists of the whole median rostelar portion and, so far, is known only from Maxillaria uncata. Nectar, trichomes, wax‐like and resin‐like secretions are described as flower rewards for different groups of species within the genus Maxillaria. Data on the biomechanics and pollination biology are also discussed and illustrated. In Maxillariinae flowers with arcuate viscidia, the pollinaria are deposited on the scuttellum of their Hymenopteran pollinators. In contrast, some flowers with rounded to rectangular, pad‐like viscidia fix their pollinaria on the face of their pollinators. • Conclusions Pollinarium morphology and floral features related to pollination in Brazilian Maxillariinae are more diverse than previously suggested. It is hoped that the data presented herein, together with other data sources such as vegetative traits and molecular tools, will be helpful in redefining and diagnosing clades within the subtribe Maxillariinae. PMID:14644913

  1. A new approach to species delimitation in Septoria

    PubMed Central

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

    2013-01-01

    Septoria is a large genus of asexual morphs of Ascomycota causing leaf spot diseases of many cultivated and wild plants. Host specificity has long been a decisive criterium in species delimitation in Septoria, mainly because of the paucity of useful morphological characters and the high level of variation therein. This study aimed at improving the species delimitation of Septoria by adopting a polyphasic approach, including multilocus DNA sequencing and morphological analyses on the natural substrate and in culture. To this end 365 cultures preserved in CBS, Utrecht, The Netherlands, among which many new isolates obtained from fresh field specimens were sequenced. Herbarium material including many types was also studied. Full descriptions of the morphology in planta and in vitro are provided for 57 species. DNA sequences were generated for seven loci, viz. nuclear ITS and (partial) LSU ribosomal RNA genes, RPB2, actin, calmodulin, Btub, and EF. The robust phylogeny inferred showed that the septoria-like fungi are distributed over three main clades, establishing the genera Septoria s. str., Sphaerulina, and Caryophylloseptoria gen. nov. Nine new combinations and one species, Sphaerulina tirolensis sp. nov. were proposed. It is demonstrated that some species have wider host ranges than expected, including hosts from more than one family. Septoria protearum, previously only associated with Proteaceae was found to be also associated with host plants from six additional families of phanerogams and cryptogams. To our knowledge this is the first study to provide DNA-based evidence that multiple family-associations occur for a single species in Septoria. The distribution of host families over the phylogenetic tree showed a highly dispersed pattern for 10 host plant families, providing new insight into the evolution of these fungi. It is concluded that trans-family host jumping is a major force driving the evolution of Septoria and Sphaerulina. Taxonomic novelties: New

  2. Putting the Biological Species Concept to the Test: Using Mating Networks to Delimit Species

    PubMed Central

    Lagache, Lélia; Leger, Jean-Benoist; Daudin, Jean-Jacques; Petit, Rémy J.; Vacher, Corinne

    2013-01-01

    Although interfertility is the key criterion upon which Mayr’s biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating events between individuals. The results reveal two groups of interfertile individuals connected by only few mating events. These two groups were largely congruent with those determined using other criteria (morphological similarity, genotypic similarity and individual relatedness). Our study, therefore, shows that the analysis of mating networks is an effective method to delimit species based on the interfertility criterion, provided that adequate network data can be assembled. Our study also shows that although species boundaries are highly congruent across methods of species delimitation, they are not exactly the same. Most of the differences stem from assignment of individuals to an intermediate category. The discrepancies between methods may reflect a biological reality. Indeed, the interfertility criterion is an environment-dependant criterion as species abundances typically affect rates of hybridization under natural conditions. Thus, the methods of species delimitation based on the interfertility criterion are expected to give results slightly different from those based on environment-independent criteria (such as the genotypic similarity criteria). However, whatever the criterion chosen, the challenge we face when delimiting species is to summarize continuous but non-uniform variations in biological diversity. The grade of membership model that we use in this study appears as an appropriate tool. PMID:23818990

  3. Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

    PubMed Central

    Stielow, Benjamin; Bratek, Zoltan; Orczán, Akos Kund I.; Rudnoy, Szabolcs; Hensel, Gunnar; Hoffmann, Peter; Klenk, Hans-Peter; Göker, Markus

    2011-01-01

    Background 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. Methodology 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. Conclusions 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 19th 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. PMID:21311589

  4. Species Delimitation--a Geneious plugin for the exploration of species boundaries.

    PubMed

    Masters, Bradley C; Fan, Vicky; Ross, Howard A

    2011-01-01

    Species Delimitation is a plugin to the Geneious software to support the exploration of species boundaries in a gene tree. The user assigns taxa to putative species and the plugin computes statistics relating to the probability of the observed monophyly or exclusivity having occurred by chance in a coalescent process. It also assesses the within and between species genetic distances to infer the probability with which members of a putative species might be identified successfully with tree-based methods. PMID:21429114

  5. The unholy trinity: taxonomy, species delimitation and DNA barcoding.

    PubMed

    DeSalle, Rob; Egan, Mary G; Siddall, Mark

    2005-10-29

    Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings--Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'. PMID:16214748

  6. Phylogeny and species delimitations in European Dicranum (Dicranaceae, Bryophyta) inferred from nuclear and plastid DNA.

    PubMed

    Lang, Annick S; Bocksberger, Gaëlle; Stech, Michael

    2015-11-01

    DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plants have been published so far and GMYC analyses of bryophytes are missing. Dicranum is a large genus of mosses whose (morpho-)species are partly ill-defined and frequently confused. To infer molecular species delimitations, we reconstructed phylogenetic trees based on five chloroplast markers and nuclear ribosomal ITS sequences from 27 out of 30 species occurring in Europe. We applied the species delimitation methods GMYC and Poisson tree processes (PTP) in order to compare their discriminatory power with species boundaries inferred from the molecular phylogenetic reconstructions and with the morphological species concept. Phylogenetic circumscriptions were congruent with the morphological concept for 19 species, while eight species were molecularly not well delimited, mostly forming closely related species pairs. The automated species delimitation methods achieved similar results but tended to overestimate the number of potential species and exposed several incongruences between the morphological concept and inference from molecular phylogenetic reconstructions. It is concluded that GMYC and PTP methods potentially provide a useful and objective way of delimiting bryophyte species, but studies on further bryophyte data sets are necessary to infer whether incongruences might ensue from evolutionary processes and to test the suitability of these approaches. PMID:26149758

  7. DNA Barcoding and Species Boundary Delimitation of Selected Species of Chinese Acridoidea (Orthoptera: Caelifera)

    PubMed Central

    Huang, Jianhua; Zhang, Aibing; Mao, Shaoli; Huang, Yuan

    2013-01-01

    We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. “Best match (BM)”, “best close match (BCM)”, “all species barcodes (ASB)” and “back-propagation neural networks (BP-based method)” were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species. PMID:24376533

  8. The unholy trinity: taxonomy, species delimitation and DNA barcoding

    PubMed Central

    DeSalle, Rob; Egan, Mary G; Siddall, Mark

    2005-01-01

    Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this ‘DNA barcoding’ initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the ‘DNA barcoding’ initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the ‘DNA barcoding’ initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings—Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of ‘DNA barcoding’. PMID:16214748

  9. New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards

    PubMed Central

    Miralles, Aurélien; Vences, Miguel

    2013-01-01

    Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence Ctax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index Rtax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist

  10. RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa.

    PubMed

    Herrera, Santiago; Shank, Timothy M

    2016-07-01

    Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness are particularly problematic. In this study, we demonstrate the utility of restriction site associated DNA sequencing (RAD-seq) to objectively resolve unambiguous phylogenetic relationships in a recalcitrant group of deep-sea corals with divergences >80 million years. We infer robust species boundaries in the genus Paragorgia by testing alternative delimitation hypotheses using a Bayes Factors delimitation method. We present substantial evidence rejecting the current morphological species delimitation model for the genus and infer the presence of cryptic species associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences cannot be assessed in terms of absolute time, but are contingent on taxon-specific factors. We show that classical taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypotheses. Our results lead the way for addressing further questions in marine biogeography, community ecology, population dynamics, conservation, and evolution. PMID:26993764

  11. Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae).

    PubMed

    Ortiz, David; Francke, Oscar F

    2016-08-01

    Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic diversity and many species redundantly described. Most of these studies have relied only on COI, a mitochondrial marker that has proven its efficacy in animal studies, but which also might lead to an over-estimation of diversity. Here we present an integrative approach to species delimitation in Bonnetina, a poorly known group of tarantulas endemic to Mexico. We employed morphological evidence, as well as different setups with distance-based (Hard-Gap barcoding and ABGD) and tree-based (GMYC, PTP and BPP) molecular barcoding approaches, using one mitochondrial (COI) and one nuclear (ITS1) rapidly evolving loci. BPP is also used as a multi-locus method. We also explored the influence of ambiguous alignment choice and of coding gaps as characters in phylogenetic inference and in species delimitation with that marker. Different delimitation methods with COI gave moderately variable results and this gene exhibited a universal barcode gap. The ITS1 gene tree was well supported and robust to alignment choice; with this locus, coding gaps improved branch support and species delimitation with PTP. No universal barcode gap was found with ITS1, and single locus delimitations returned disparate results. However, this locus helped to highlight cases of under- and overestimations by COI. BPP gave solutions with many lineages, in single locus and combined analyses, especially with the recently implemented unguided methodology. We recognize 12 robustly supported species in our data set, of which seven remain undescribed, and three are morphologically cryptic. For COI Bonnetina species identification, we propose intra- and inter-specific thresholds of 2% and 6

  12. Species delimitation and phylogeny of a New Zealand plant species radiation

    PubMed Central

    Meudt, Heidi M; Lockhart, Peter J; Bryant, David

    2009-01-01

    Background Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago. Results New Zealand Ourisia are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of Ourisia produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties. Conclusion Ourisia radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters

  13. Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae).

    PubMed

    Andújar, C; Arribas, P; Ruiz, C; Serrano, J; Gómez-Zurita, J

    2014-09-01

    In species differentiation, characters may not diverge synchronously, and there are also processes that shuffle character states in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters; therefore, taxonomic delimitation can benefit from integrative approaches and objective strategies that account for character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy does not accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence and morphometry of pronotal shape in more than 500 specimens of Mesocarabus show that these characters are not fully congruent. For these data, a three-step operational strategy is proposed for species delimitation by (i) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (ii) corroborating candidate species with inconclusive lines of evidence and (iii) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach. PMID:24828576

  14. Revisiting species delimitation within the genus Oxystele using DNA barcoding approach

    PubMed Central

    Van Der Bank, Herman; Herbert, Dai; Greenfield, Richard; Yessoufou, Kowiyou

    2013-01-01

    Abstract The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus. PMID:24453566

  15. True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex

    PubMed Central

    2013-01-01

    Background Species are the fundamental units in evolutionary biology. However, defining them as evolutionary independent lineages requires integration of several independent sources of information in order to develop robust hypotheses for taxonomic classification. Here, we exemplarily propose an integrative framework for species delimitation in the “brown lemur complex” (BLC) of Madagascar, which consists of seven allopatric populations of the genus Eulemur (Primates: Lemuridae), which were sampled extensively across northern, eastern and western Madagascar to collect fecal samples for DNA extraction as well as recordings of vocalizations. Our data base was extended by including museum specimens with reliable identification and locality information for skull shape and pelage color analysis. Results Between-group analyses of principal components revealed significant heterogeneity in skull shape, pelage color variation and loud calls across all seven populations. Furthermore, post-hoc statistical tests between pairs of populations revealed considerable discordance among different data sets for different dyads. Despite a high degree of incomplete lineage sorting among nuclear loci, significant exclusive ancestry was found for all populations, except for E. cinereiceps, based on one mitochondrial and three nuclear genetic loci. Conclusions Using several independent lines of evidence, our results confirm the species status of the members of the BLC under the general lineage concept of species. More generally, the present analyses demonstrate the importance and value of integrating different kinds of data in delimiting recently evolved radiations. PMID:24159931

  16. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae).

    PubMed

    Niemiller, Matthew L; Near, Thomas J; Fitzpatrick, Benjamin M

    2012-03-01

    A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study. PMID:22380444

  17. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)

    PubMed Central

    2012-01-01

    Background Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. Results Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. Conclusions Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation. PMID:22353848

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

    PubMed

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

    2015-10-01

    The charismatic tropical Polyura Nawab butterflies are distributed across twelve biodiversity hotspots in the Indomalayan/Australasian archipelago. In this study, we tested an array of species delimitation methods and compared the results to existing morphology-based taxonomy. We sequenced two mitochondrial and two nuclear gene fragments to reconstruct phylogenetic relationships within Polyura using both Bayesian inference and maximum likelihood. Based on this phylogenetic framework, we used the recently introduced bGMYC, BPP and PTP methods to investigate species boundaries. Based on our results, we describe two new species Polyura paulettae Toussaint sp. n. and Polyura smilesi Toussaint sp. n., propose one synonym, and five populations are raised to species status. Most of the newly recognized species are single-island endemics likely resulting from the recent highly complex geological history of the Indomalayan-Australasian archipelago. Surprisingly, we also find two newly recognized species in the Indomalayan region where additional biotic or abiotic factors have fostered speciation. Species delimitation methods were largely congruent and succeeded to cross-validate most extant morphological species. PTP and BPP seem to yield more consistent and robust estimations of species boundaries with respect to morphological characters while bGMYC delivered contrasting results depending on the different gene trees considered. Our findings demonstrate the efficiency of comparative approaches using molecular species delimitation methods on empirical data. They also pave the way for the investigation of less well-known groups to unveil patterns of species richness and catalogue Earth's concealed, therefore unappreciated diversity. PMID:26021440

  19. Sexual Mimicry in Mormolyca ringens (Lindl.) Schltr. (Orchidaceae: Maxillariinae)

    PubMed Central

    SINGER, RODRIGO B.; FLACH, ADRIANA; KOEHLER, SAMANTHA; MARSAIOLI, ANITA J.; AMARAL, MARIA DO CARMO E.

    2004-01-01

    • Background and Aims Pollination through sexual mimicry, also known as pseudocopulation, has been suggested to occur in some genera of the Neotropical orchid subtribe Maxillariinae. However, it has been demonstrated so far only for Trigonidium obtusum. This study reports and illustrates pollination through sexual mimicry in Mormolyca ringens. • Methods A total of 70 h were dedicated to the observation of flowers and pollinator behaviour, which was photographically recorded. Flower features involved in pollinator attraction were studied using a stereomicroscope and by SEM analyses. Preliminary observations on the plant breeding system were made by manually self‐pollinating flowers. The chemical composition of the fragrance volatiles was determined by GC/MS analysis. • Key Results The flower features of M. ringens parallel those of other pseudocopulatory flowers. The labellum shape and indument are reminiscent of an insect. Sexually excited drones of Nannotrigona testaceicornis and Scaptotrigona sp. (both in the Apidae: Meliponini) attempt copulation with the labellum and pollinate the flower in the process. In both bee species, the pollinarium is attached to the scutellum. Pollinator behaviour may promote some degree of self‐pollination, but preliminary observations indicate that M. ringens flowers are self‐incompatible. Flowers are produced all the year round, which ties in with the production of bee males several times a year. The phylogenetic relationships of M. ringens are discussed and a number of morphological and phenological features supporting them are reported. • Conclusions It is expected that further research could bring to light whether other Maxillariinae species are also pollinated through sexual mimicry. When a definitive and robust phylogeny of this subtribe is available, it should be possible to determine how many times pseudocopulation evolved and its possible evolutionary history. PMID:15051623

  20. Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

    PubMed Central

    Shirley, Matthew H.; Vliet, Kent A.; Carr, Amanda N.; Austin, James D.

    2014-01-01

    Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted crocodile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial morphology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species delimitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnosing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split ± 6.5–7.5 Ma, which is congruent with intraspecies divergence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of comprehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the community of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group. PMID:24335982

  1. Characterization of the mitogenome of Uropsilus gracilis and species delimitation.

    PubMed

    Hou, Quanfen; Tu, Feiyun; Liu, Yang; Liu, Shaoying

    2016-05-01

    The species diversity within the genus Uropsilus were underestimated: 10 species among the genus Uropsilus have been proposed. In this study, the complete mitochondrial genome of U. gracilis, with the topotype, was determined. It is 16,536 bp in length, comprising of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and 1 control region. The composition and arrangement of its genes are similar to most other mammals. The total base composition of the mitogenome is A, 33.4%; T, 30.3%; C, 22.7% and G, 13.6%, with a rich content of A+T pattern. We performed the similarity comparison based on 13 PCGs of three species of Asiatic shrew-like mole, U. gracilis, U. sp. 1 and U. soricipes. Pairwise sequence alignment showed that similarity data of U. gracilis versus U. sorcipes are significantly higher than those of U. gracilis versus U. sp.1. This pointed toward a cryptic species (U. sp.1) from Jiajin Mountains rather than U. gracilis. PMID:25329296

  2. Species delimitation of Chinese hop-hornbeams based on molecular and morphological evidence.

    PubMed

    Lu, Zhiqiang; Zhang, Dan; Liu, Siyu; Yang, Xiaoyue; Liu, Xue; Liu, Jianquan

    2016-07-01

    Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants. PMID:27547308

  3. Species Delimitation and Phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): Cryptic Diversity in North American Tarantulas

    PubMed Central

    Hamilton, Chris A.; Formanowicz, Daniel R.; Bond, Jason E.

    2011-01-01

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

  4. Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs.

    PubMed

    Hotaling, Scott; Foley, Mary E; Lawrence, Nicolette M; Bocanegra, Jose; Blanco, Marina B; Rasoloarison, Rodin; Kappeler, Peter M; Barrett, Meredith A; Yoder, Anne D; Weisrock, David W

    2016-05-01

    Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse-jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species-tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species. PMID:26946180

  5. High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas.

    PubMed

    Hedin, Marshal

    2015-01-01

    A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era. PMID:25492722

  6. Species delimitation and phylogeny in the genus Nasutitermes (Termitidae: Nasutitermitinae) in French Guiana.

    PubMed

    Roy, Virginie; Constantino, Reginaldo; Chassany, Vincent; Giusti-Miller, Stephanie; Diouf, Michel; Mora, Philippe; Harry, Myriam

    2014-02-01

    Species delimitation and identification can be arduous for taxa whose morphologic characters are easily confused, which can hamper global biodiversity assessments and pest species management. Exploratory methods of species delimitation that use DNA sequence as their primary information source to establish group membership and estimate putative species boundaries are useful approaches, complementary to traditional taxonomy. Termites of the genus Nasutitermes make interesting models for the application of such methods. They are dominant in Neotropical primary forests but also represent major agricultural and structural pests. Despite the prevalence, pivotal ecological role and economical impact of this group, the taxonomy of Nasutitermes species mainly depends on unreliable characters of soldier external morphology. Here, we generated robust species hypotheses for 79 Nasutitermes colonies sampled throughout French Guiana without any a priori knowledge of species affiliation. Sequence analysis of the mitochondrial cytochrome oxidase II gene was coupled with exploratory species-delimitation tools, using the automatic barcode gap discovery method (ABGD) and a generalized mixed Yule-coalescent model (GMYC) to propose primary species hypotheses (PSHs). PSHs were revaluated using phylogenetic analyses of two more loci (mitochondrial 16S rDNA and nuclear internal transcribed spacer 2) leading to 16 retained secondary species hypotheses (RSSH). Seven RSSHs, represented by 44/79 of the sampled colonies, were morphologically affiliated to species recognized as pests in the Neotropics, where they represent a real invasive pest potential in the context of growing ecosystem anthropization. Multigenic phylogenies based on combined alignments (1426-1784 bp) were also reconstructed to identify ancestral ecological niches and major-pest lineages, revealing that Guyanese pest species do not form monophyletic groups. PMID:24372711

  7. A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets

    PubMed Central

    Fujisawa, Tomochika; Aswad, Amr; Barraclough, Timothy G.

    2016-01-01

    Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases. PMID:27055648

  8. A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets.

    PubMed

    Fujisawa, Tomochika; Aswad, Amr; Barraclough, Timothy G

    2016-09-01

    Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases. PMID:27055648

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

    PubMed

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

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. PMID:26484942

  10. Species delimitation and recognition in the Pediomelum megalanthum complex (Fabaceae) via multivariate morphometrics

    PubMed Central

    Egan, Ashley N.

    2015-01-01

    Abstract Pediomelum is a genus endemic to North America comprising about 26 species, including the megalanthum complex, which consists of Pediomelum megalanthum and its varieties retrorsum and megalanthum, Pediomelum mephiticum, and the recently described Pediomelum verdiense and Pediomelum pauperitense. Historically, species of the megalanthum complex have been variably recognized at the species or variety levels, dependent upon the relative importance of morphological characters as diagnostic of species. Ten quantitative morphological characters regarded as diagnostic at the species level were analyzed using multivariate morphometrics across these taxa in order to examine the discriminatory power of these characters to delineate species and to aid in species delimitation. The analyses support the recognition of Pediomelum megalanthum, Pediomelum mephiticum, and Pediomelum verdiense at the species level, Pediomelum retrorsum as a variety under Pediomelum megalanthum, and suggest the sinking of Pediomelum pauperitense into Pediomelum verdiense. The findings of the present study help quantify the power of certain characters at delimiting taxa and provide a basis for taxonomic revision of the Pediomelum megalanthum complex. PMID:25698894

  11. Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata).

    PubMed

    Prévot, Vanya; Jordaens, Kurt; Sonet, Gontran; Backeljau, Thierry

    2013-01-01

    Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected. PMID:23577154

  12. Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)

    PubMed Central

    Prévot, Vanya; Jordaens, Kurt; Sonet, Gontran; Backeljau, Thierry

    2013-01-01

    Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected. PMID:23577154

  13. Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

    PubMed Central

    Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

    2015-01-01

    The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

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

    PubMed

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

    2016-01-01

    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 evidence

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

    PubMed Central

    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

  16. Species delimitation without prior knowledge: DISSECT reveals extensive cryptic speciation in the Silene aegyptiaca complex (Caryophyllaceae).

    PubMed

    Toprak, Zeynep; Pfeil, Bernard E; Jones, Graham; Marcussen, Thomas; Ertekin, Alaattin Selçuk; Oxelman, Bengt

    2016-09-01

    Species delimitation is a major focus of biosystematics. In recent years, considerable progress has been achieved with the development of the multispecies coalescent (MSC) model, where species constitute the branches of the species tree or network. However, researchers are faced with the limitation that the MSC method of choice often requires a priori assignment of individuals to species. This not only introduces subjectivitiy into the analyses, but may also lead to meaningless species tree hypotheses, if the allele-to-species assignments are inaccurate. DISSECT is a recently introduced method that does not require a priori allele-to-species assignments, but instead examines the posterior probabilities of groupings (clusterings) of individuals under study. Using the DISSECT approach, we analysed genetic data from 75 individual plants belonging to the Silene aegyptiaca species complex that has previously been divided into 3-5 species. Marginal likelihood estimates from (*)BEAST analyses, run with predefined species classifications, strongly favour those compatible with the DISSECT result over those from morphology- and geography-based taxonomy. We found at least nine species, including several cryptic ones, for which no clear geographical or morphological patterns are correlated. However, the limited data and the possibility of unmodelled processes mean there is still much uncertainty about the true number of MSC species, and for taxonomic purposes, other criteria might be relevant. Nevertheless, we argue that the approach signifies an important step towards objective and testable species delimitations in any organismal group. In particular, it makes it possible to avoid biologically irrelevant species classifications. PMID:27233442

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

    PubMed

    Bagley, Justin C; Alda, Fernando; Breitman, M Florencia; Bermingham, Eldredge; van den Berghe, Eric P; Johnson, Jerald B

    2015-01-01

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

  18. Assessing Species Boundaries Using Multilocus Species Delimitation in a Morphologically Conserved Group of Neotropical Freshwater Fishes, the Poecilia sphenops Species Complex (Poeciliidae)

    PubMed Central

    Bagley, Justin C.; Alda, Fernando; Breitman, M. Florencia; Bermingham, Eldredge; van den Berghe, Eric P.; Johnson, Jerald B.

    2015-01-01

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

  19. The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species.

    PubMed

    Rato, Catarina; Harris, David James; Carranza, Salvador; Machado, Luís; Perera, Ana

    2016-01-01

    The lack of morphological diagnosable characters typical of cryptic species, poses a particular problem to taxonomists. This is especially true when taxa are closely related, sharing considerable amounts of ancestral polymorphism. Phylogenetic studies on the Moorish gecko species-complex, Tarentola mauritanica, uncovered extremely high levels of mtDNA diversity with six identified clades, including one from the Canary Islands identified as T. angustimentalis. Because of the conserved morphology of this species and its paraphyletic status with respect to T. angustimentalis, it was suggested that T. mauritanica is a cryptic species complex. Nevertheless, none of the nuclear loci used were reciprocally monophyletic regarding the mitochondrial lineages due to retention of ancestral polymorphism. In this study, we added three new intron markers to the already available dataset and used additional tools, namely phylogenetic gene trees, species tree and species limits within a Bayesian coalescent framework to confirm the support of the main lineages. Bayesian clustering analysis supports all six mtDNA lineages as independent groups, despite showing signs of ancestral polymorphism or possibly gene flow between the Maghreb/South Iberia and Central Morocco clades. The species tree recovered two major groups; one clustering taxa from Europe and Northern Maghreb and another one encompassing the lineages from Central/Southern Morocco, Central Morocco and Canary Islands, indicating that the ancestor of T. angustimentalis came from the Central/Southern Morocco region. Finally, Bayesian coalescent species delimitation analysis supports all six mitochondrial clades as "unconfirmed candidate species", pending morphological data to define them. PMID:26391222

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

    PubMed

    Terraneo, Tullia I; Benzoni, Francesca; Arrigoni, Roberto; Berumen, Michael L

    2016-09-01

    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. PMID:27321092

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Yamashita, Tsunemi; Rhoads, Douglas D

    2013-01-01

    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. PMID:23861878

  4. Species Delimitation and Morphological Divergence in the Scorpion Centruroides vittatus (Say, 1821): Insights from Phylogeography

    PubMed Central

    Yamashita, Tsunemi; Rhoads, Douglas D.

    2013-01-01

    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. PMID:23861878

  5. Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia.

    PubMed

    Sadowska-Deś, Anna D; Dal Grande, Francesco; Lumbsch, H Thorsten; Beck, Andreas; Otte, Jürgen; Hur, Jae-Seoun; Kim, Jung A; Schmitt, Imke

    2014-07-01

    The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia. PMID:24685499

  6. Parametric and non-parametric species delimitation methods result in the recognition of two new Neotropical woody bamboo species.

    PubMed

    Ruiz-Sanchez, Eduardo

    2015-12-01

    The Neotropical woody bamboo genus Otatea is one of five genera in the subtribe Guaduinae. Of the eight described Otatea species, seven are endemic to Mexico and one is also distributed in Central and South America. Otatea acuminata has the widest geographical distribution of the eight species, and two of its recently collected populations do not match the known species morphologically. Parametric and non-parametric methods were used to delimit the species in Otatea using five chloroplast markers, one nuclear marker, and morphological characters. The parametric coalescent method and the non-parametric analysis supported the recognition of two distinct evolutionary lineages. Molecular clock estimates were used to estimate divergence times in Otatea. The results for divergence time in Otatea estimated the origin of the speciation events from the Late Miocene to Late Pleistocene. The species delimitation analyses (parametric and non-parametric) identified that the two populations of O. acuminata from Chiapas and Hidalgo are from two separate evolutionary lineages and these new species have morphological characters that separate them from O. acuminata s.s. The geological activity of the Trans-Mexican Volcanic Belt and the Isthmus of Tehuantepec may have isolated populations and limited the gene flow between Otatea species, driving speciation. Based on the results found here, I describe Otatea rzedowskiorum and Otatea victoriae as two new species, morphologically different from O. acuminata. PMID:26265258

  7. Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

    PubMed Central

    Hernández-León, Sergio; Gernandt, David S.; Pérez de la Rosa, Jorge A.; Jardón-Barbolla, Lev

    2013-01-01

    Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities. PMID:23936218

  8. The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.

    PubMed

    Huang, Jen-Pan; Knowles, L Lacey

    2016-07-01

    With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status. PMID:26681696

  9. Marginal Likelihood Estimate Comparisons to Obtain Optimal Species Delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)

    PubMed Central

    Aydin, Zeynep; Marcussen, Thomas; Ertekin, Alaattin Selcuk; Oxelman, Bengt

    2014-01-01

    Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii. PMID:25216034

  10. Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).

    PubMed

    Miadlikowska, Jolanta; Richardson, David; Magain, Nicolas; Ball, Bernard; Anderson, Frances; Cameron, Robert; Lendemer, James; Truong, Camille; Lutzoni, François

    2014-07-11

    • Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America. PMID:25016011

  11. Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes

    PubMed Central

    Verovnik, Rudi; Wiemers, Martin

    2016-01-01

    Abstract The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the ‘Mamurra’ species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution. PMID:27408604

  12. DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes

    PubMed Central

    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. PMID:22412956

  13. Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes.

    PubMed

    Verovnik, Rudi; Wiemers, Martin

    2016-01-01

    The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the 'Mamurra' species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution. PMID:27408604

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

    PubMed

    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. PMID:22412956

  15. Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences.

    PubMed

    Ley, A C; Hardy, O J

    2010-11-01

    Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding. PMID:20813193

  16. Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses.

    PubMed

    Łukomska-Kowalczyk, Maja; Karnkowska, Anna; Milanowski, Rafał; Łach, Łukasz; Zakryś, Bożena

    2015-12-01

    Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genome amplification, we delimited species within the Phacus longicauda complex. Morphological and molecular characters were analyzed for 36 strains isolated from environmental samples (mainly from Poland). DNA was obtained from a small number of cells (20-30) isolated with a micropipette from every sample (i.e., without setting up laboratory cultures), and phylogenetic analyses were based on variation in nSSU rDNA. Apart from Phacus longicauda, three other species (Phacus circumflexus, Phacus helikoides, and Phacus tortus) were distinguished. Phacus cordata comb. nov. Zakryś et M. Łukomska and Phacus rotunda comb. nov. Zakryś et M. Łukomska had their taxonomic ranks changed and two species new to science, Phacus cristatus sp. nov. Zakryś et M. Łukomska and Phacus crassus sp. nov. Zakryś et M. Łukomska, were described. For all verified species, diagnostic descriptions were amended and epitypes designated. PMID:26987009

  17. Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin

    PubMed Central

    Hu, Chaochao; Sun, Zhonglou; Zhu, Xiaoxue; Meng, Tao; Meng, Xiuxiang; Zhang, Baowei

    2015-01-01

    The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras. PMID:26280166

  18. Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin.

    PubMed

    Pan, Tao; Wang, Hui; Hu, Chaochao; Sun, Zhonglou; Zhu, Xiaoxue; Meng, Tao; Meng, Xiuxiang; Zhang, Baowei

    2015-01-01

    The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras. PMID:26280166

  19. Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability.

    PubMed

    Stockman, Amy K; Bond, Jason E

    2007-08-01

    Species exhibiting morphological homogeneity and strong population structuring present challenging taxonomic problems: morphology-based approaches infer few species, whereas genetic approaches often indicate more. Morphologically cryptic, yet genetically divergent species groups require alternative approaches to delimiting species that assess adaptive divergence and ecological interchangeability of lineages. We apply such an approach to Promyrmekiaphila, a small genus (three nominal taxa) of trapdoor spiders endemic to northern California to define cohesion species (lineages that are genetically exchangeable and ecologically interchangeable). Genetic exchangeability is evaluated using standard phylogeographical techniques (e.g. nested clade analysis); ecological interchangeability is assessed using two GIS-based approaches. First, climatic values are extracted from layer data for each locality point and utilized in a principal components analysis followed by MANOVA. Second, niche-based distribution models of genetically divergent lineages are created using a maximum-entropy modelling approach; the amount of overlap among lineages is calculated and evaluated against a probability distribution of null overlap. Lineages that have significant amounts of predicted overlap are considered ecologically interchangeable. Based on a synthetic evaluation of ecological interchangeability, geographical concordance, and morphological differentiation, we conclude that Promyrmekiaphila comprises six cohesion species, five of which are cryptic (i.e. undetectable by conventional means). PMID:17688540

  20. DNA taxonomy in morphologically plastic taxa: algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales).

    PubMed

    Leliaert, Frederik; Verbruggen, Heroen; Wysor, Brian; De Clerck, Olivier

    2009-10-01

    DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis. In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmic methods of sequence-based species delineation were applied, including statistical parsimony network analysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequence analyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp species boundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflict between traditional and phylogenetic species definitions. Identical morphological forms were distributed in different clades (cryptic diversity), and at the same time most of the phylogenetic species contained a mixture of different morphologies (indicating intraspecific morphological variation). Sampling outside the morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy for this group, we propose to discard provisionally the misleading morphospecies and genus names, and refer to clade numbers within a single genus, Boodlea. PMID:19524052

  1. Friends or Relatives? Phylogenetics and Species Delimitation in the Controversial European Orchid Genus Ophrys

    PubMed Central

    Devey, Dion S.; Bateman, Richard M.; Fay, Michael F.; Hawkins, Julie A.

    2008-01-01

    Background and Aims Highly variable, yet possibly convergent, morphology and lack of sequence variation have severely hindered production of a robust phylogenetic framework for the genus Ophrys. The aim of this study is to produce this framework as a basis for more rigorous species delimitation and conservation recommendations. Methods Nuclear and plastid DNA sequencing and amplified fragment length polymorphism (AFLP) were performed on 85 accessions of Ophrys, spanning the full range of species aggregates currently recognized. Data were analysed using a combination of parsimony and Bayesian tree-building techniques and by principal co-ordinates analysis. Key Results Complementary phylogenetic analyses and ordinations using nuclear, plastid and AFLP datasets identify ten genetically distinct groups (six robust) within the genus that may in turn be grouped into three sections (treated as subgenera by some authors). Additionally, genetic evidence is provided for a close relationship between the O. tenthredinifera, O. bombyliflora and O. speculum groups. The combination of these analytical techniques provides new insights into Ophrys systematics, notably recognition of the novel O. umbilicata group. Conclusions Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation. The supposedly highly specific pseudocopulatory pollination syndrome of Ophrys is demonstrably ‘leaky’, suggesting that the genus has been substantially over-divided at the species level. PMID:18184645

  2. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

    USGS Publications Warehouse

    Leache, A.D.; Koo, M.S.; Spencer, C.L.; Papenfuss, T.J.; Fisher, R.N.; McGuire, J.A.

    2009-01-01

    Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation.We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.

  3. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

    PubMed Central

    Leaché, Adam D.; Koo, Michelle S.; Spencer, Carol L.; Papenfuss, Theodore J.; Fisher, Robert N.; McGuire, Jimmy A.

    2009-01-01

    Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG−1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical. PMID:19625623

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

    PubMed Central

    Kuchta, Shawn R.; Brown, Ashley D.; Converse, Paul E.; Highton, Richard

    2016-01-01

    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 structure and

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

    PubMed

    Kuchta, Shawn R; Brown, Ashley D; Converse, Paul E; Highton, Richard

    2016-01-01

    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 structure and

  6. Hidden diversity in the Andes: comparison of species delimitation methods in montane marsupials.

    PubMed

    Giarla, Thomas C; Voss, Robert S; Jansa, Sharon A

    2014-01-01

    Cryptic genetic diversity is a significant challenge for systematists faced with ever-increasing amounts of DNA sequence data. Computationally intensive coalescent-based analyses involving multiple unlinked loci are the only currently viable methods by which to assess the extent to which phenotypically similar populations (or metapopulations) are genetically distinct lineages. Although coalescent-based approaches have been tested extensively via simulations, few empirical studies have examined the impact of prior assumptions and dataset size on the ability to assess genetic isolation (evolutionary independence) using molecular data alone. Here, we consider the efficacy of two coalescent-based approaches (BPP and SpeDeSTEM) for testing the evolutionary independence of cryptic mtDNA haplogroups within three morphologically diagnosable species of Andean mouse opossums (Thylamys pallidior, T. sponsorius, and T. venustus). Fourteen anonymous nuclear loci, one X-linked nuclear intron, and one mitochondrial gene were analyzed for multiple individuals within each haplogroup of interest. We inferred individual gene trees for each locus and considered all of the nuclear loci jointly in a species-tree analysis. Using only the nuclear loci, we performed "species validation" tests for the cryptic mitochondrial lineages in SpeDeSTEM and BPP. For BPP, we also tested a wide range of prior assumptions, assessed performance of the rjMCMC algorithm, and examined how many loci were necessary to confidently delimit lineages. Results from BPP provided strong support for two independent evolutionary lineages each within T. pallidior, T. sponsorius, and T. venustus, whereas SpeDeSTEM results did not support splitting out mtDNA haplogroups as distinct evolutionary units. For most tests, BPP was robust to prior assumptions, although priors were shown to have an effect on both the strength of lineage recognition among T. venustus haplotypes and on the efficiency of the rjMCMC algorithm

  7. Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data

    PubMed Central

    2012-01-01

    Background Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). Results We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. Conclusions Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient

  8. Integrated Bayesian species delimitation and morphological diagnostics of chorioptic mange mites (Acariformes: Psoroptidae: Chorioptes).

    PubMed

    Bochkov, Andre V; Klimov, Pavel B; Hestvik, Gete; Saveljev, Alexander P

    2014-07-01

    The external morphology of adult and immature stages of mange mites of the genus Chorioptes was investigated with the aid of light and scanning electron microscopy. A molecular phylogeny of this genus was inferred based on six genes (18S, 28S rDNA, EF1-α, SRP54, HSP70, and CO1). The validity of four species (Ch. bovis, Ch. panda, Ch. texanus, and Ch. sweatmani sp. nov. described from the moose from Sweden, Finland, and Russia) was confirmed based on morphology and a Bayesian species delimitation analysis incorporating both gene tree uncertainties and incomplete lineage sorting via the coalescent process model in BPP. Sequence data for Ch. crewei and Ch. mydaus was not available but their morphology strongly suggests their validity. The six valid Chorioptes species are diagnosed using type and non-type specimens, and a key to species is provided. Ch. sweatmani differs from closely related Ch. texanus by the following features: in males, the body length, including the gnathosoma, is 380-405 μm (vs. 220-295 in Ch. texanus), the idiosoma is 3-4 times longer than setae cp (vs. 1.3-1.6 times longer), legs III are approximately three times longer than setae sRIII (vs. 1.8-2 times longer), the apical spur of tarsus III is curved (vs. straight), a spur near seta fIII base is not developed (vs. small but distinct); in females, setae h2 are 1.4-1.5 times shorter than legs IV (vs. about two times longer). Hosts and distribution records of Chorioptes species are summarized. PMID:24820039

  9. Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

    PubMed Central

    Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

    2013-01-01

    In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID

  10. Lactifluus volemus in Europe: Three species in one--Revealed by a multilocus genealogical approach, Bayesian species delimitation and morphology.

    PubMed

    Van de Putte, Kobeke; Nuytinck, Jorinde; De Crop, Eske; Verbeken, Annemieke

    2016-01-01

    This study provides morphological and molecular evidence (from nuclear ITS, LSU, and rpb2 DNA sequences) for three previously unrecognized species within the morphospecies Lactifluus volemus from Europe. Phylogenetic species are supported by both a multi-locus tree-based method and Bayesian species delimitation. Lactifluus volemus and Lactifluus oedematopus are provided with a new description, and a third species, Lactifluus subvolemus, is described as new to science. Lactifluus oedematopus can be easily recognized by its short pileipellis hairs. Both L. volemus and L. subvolemus have longer pileipellis hairs and can only be distinguished from each other based on cap colour. Intermediary colour forms, however, occur as well, and cannot be identified as either L. volemus or L. subvolemus without molecular data. Revealing that L. volemus--already considered extinct in the Netherlands and the Belgian Flemish region, and declining in other European countries--is actually a complex of three species that are even more vulnerable to extinction, this study emphasizes the fundamental role of taxonomy in species conservation. PMID:26693681

  11. Concordant species delimitation from multiple independent evidence: A case study with the Pachytriton brevipes complex (Caudata: Salamandridae).

    PubMed

    Wu, Yunke; Murphy, Robert W

    2015-11-01

    Mitochondrial DNA (mtDNA) sequence data are widely used to delimit species. However, owing to its strict maternal inheritance in most species, mtDNA tracks female dispersion and dispersal only. The accuracy of mtDNA-derived species delimitation is often not explicitly tested using other independent evidence, such as nuclear DNA (nDNA) data, morphological data, or ecological data. Because species are independent evolutionary lineages that can form testable hypotheses, we present a multi-evidence case study on species delimitation that combines statistical approaches with spatially explicit ecological analysis. Montane salamanders of the Pachytriton brevipes complex (Salamandridae) from southeastern China exhibit conservative morphology and variable color patterning that impede species diagnosis. Recent studies proposed splitting P. brevipes into four species based on deep mtDNA divergence but also found discordance between mtDNA and nDNA trees. In this study, we test evolutionary independence of these hypothesized species lineages using two coalescent-based Bayesian methods (Bayes factor and BP&P). Despite significant conflict between mtDNA gene tree and the species phylogeny, the results reinforce the inference of at least four species in the complex as opposed to the one species recognized for over 130 years. Correlative ecological niche modeling and statistical analysis of environmental data indicate that suitable habitats for each species are isolated by incompatible intervening lowland regions, so the likelihood of gene flow among species is very low, which means species lineages should maintain their evolutionary independence. We demonstrate that concordance among independent evidence confirms species status, which forms the basis for accurate assessment of regional biodiversity. PMID:26119130

  12. A Multilocus Species Delimitation Reveals a Striking Number of Species of Coralline Algae Forming Maerl in the OSPAR Maritime Area

    PubMed Central

    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. PMID:25111057

  13. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae).

    PubMed

    Schwarzfeld, Marla D; Sperling, Felix A H

    2015-12-01

    DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus. PMID:26265257

  14. Species delimitation in plants using the Qinghai–Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example

    PubMed Central

    Su, Xu; Wu, Guili; Li, Lili; Liu, Jianquan

    2015-01-01

    Background and Aims Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai–Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species. Methods A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced. Key Results Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two. Conclusions Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions. PMID:25987712

  15. The Mycetophila ruficollis Meigen (Diptera, Mycetophilidae) group in Europe: elucidating species delimitation with COI and ITS2 sequence data

    PubMed Central

    Jürgenstein, Siiri; Kurina, Olavi; Põldmaa, Kadri

    2015-01-01

    Abstract European species of the Mycetophila ruficollis group are compared on the basis of morphology and sequences of mitochondrial cytochrome oxidase subunit one (COI) and the ITS2 region of nuclear ribosomal DNA. The study represents the first evaluation of morphology-based species delimitation of closely related fungus gnat species by applying molecular information. Detailed descriptions and illustrations of the male terminalia are presented along with a key for the identification of all nine European species of the group. Phylogenetic analyses of molecular data generally supported the morphological species discrimination. The barcoding region of COI superseded ITS2 rDNA in resolving species. In the COI barcoding region interspecific differences ranged from 2.9 to 10.6% and the intraspecific distance from 0.08 to 0.8%. Only COI data distinguished between the similar and closely related Mycetophila ichneumonea and Mycetophila uninotata of which the latter was observed to include cryptic species. The host range of some species is suggested to be narrower than previously considered and to depend on the forest type. Presented evidence indicates the importance of analysing sequence data of morphologically very similar mycetophages reared from identified host fungi for elucidating species delimitation as well as their geographic and host ranges. New country records, viz. Estonia for Mycetophila evanida, Georgia for Mycetophila ichneumonea, Mycetophila idonea and Mycetophila ruficollis, and Norway for Mycetophila strobli, widen the known distribution ranges of these species. PMID:26167119

  16. A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone

    PubMed Central

    Dépraz, Aline; Hausser, Jacques; Pfenninger, Markus

    2009-01-01

    Background Mitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics. Results Both mitochondrial lineages have a distinct geographical distribution with a small zone of co-occurrence. In the same area, we detected two nuclear genotype clusters, each being highly significantly associated to one mitochondrial lineage. This association however had exceptions: a small number of individuals in the contact zone showed intermediate genotypes (4%) or cytonuclear disequilibrium (12%). Both mitochondrial lineage and nuclear cluster were statistically significant predictors for the shell shape indicating morphological divergence. Nevertheless, the lineage morphospaces largely overlapped (low posterior classification success rate of 69% and 78%, respectively): the two lineages are truly cryptic. Conclusion The integrative approach using multiple lines of evidence supported the hypothesis that the investigated Trochulus lineages are reproductively isolated species. In the small contact area, however, the lineages hybridise to a limited extent. This detection of a hybrid zone adds an instance to the rare reported cases of hybridisation in land snails. PMID:19622149

  17. Biogeographical history and coalescent species delimitation of Pacific island skinks (Squamata: Scincidae: Emoia cyanura species group)

    USGS Publications Warehouse

    Klein, Elaine; Harris, Rebecca; Fisher, Robert N.; Reeder, Tod

    2016-01-01

    In contrast to the expectations of a stepping-stone model, E. cyanura and E. impar each exhibit the genetic signature of a rapid radiation during the mid to late Pleistocene, with evidence for newly identified lineages, mainly on western islands. Of these recovered lineages, we propose three to be elevated to species status. These findings expand our understanding of endemic Pacific biota, which are subject to conservation threats from human impacts and climate change.

  18. Diagnostic survey of Malagasy Nesomyrmex species-groups and revision of hafahafa group species via morphology based cluster delimitation protocol

    PubMed Central

    Csősz, Sándor; Fisher, Brian L.

    2015-01-01

    Abstract Madagascar and its surrounding islands are among the world’s greatest biodiversity hotspots, harboring predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Building on the considerable efforts in recent years to inventory the Malagasy ant fauna, the myrmicine genus Nesomyrmex is reviewed and (1) subdivided into four major groups based on salient morphological features corroborated by numeric morphology: angulatus-, hafahafa-, madecassus- and sikorai-groups, and (2) the hafahafa species-group endemic to Madagascar is revised. Diversity within hafahafa species-group was assessed via hypothesis-free nest-centroid-clustering combined with gap statistic to assess the number of clusters and to determine the most probable boundaries between them. This combination of methods provides a highly automatized, objective species delineation protocol based on continuous morphometric data. Delimitations of clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis. These results suggest the existence of four morphologically distinct species, Nesomyrmex capricornis sp. n., Nesomyrmex hafahafa sp. n., Nesomyrmex medusus sp. n. and Nesomyrmex spinosus sp. n.; all are described and an identification key for their worker castes using morphometric data is provided. Two members of the newly outlined hafahafa species-group, Nesomyrmex hafahafa sp. n., Nesomyrmex medusus sp. n., are distributed along the southeastern coast Madagascar and occupy rather large ranges, but two other species, Nesomyrmex capricornis sp. n. and Nesomyrmex spinosus sp. n., are only known to occur in small and isolated forest, highlighting the importance of small forest patches for conserving arthropod diversity. PMID:26487823

  19. Integrative Taxonomy and Species Delimitation in Harvestmen: A Revision of the Western North American Genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

    PubMed Central

    Derkarabetian, Shahan; Hedin, Marshal

    2014-01-01

    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. PMID:25144370

  20. Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

    PubMed

    Dellicour, Simon; Flot, Jean-François

    2015-11-01

    Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases. PMID:25601944

  1. Species Delimitation Tests of Endemic Lepidium Papilliferum and Identification of other Possible Evolutionarily Significant Units (ESUs) in the Lepidium Montanum Complex (Brassicaceae) of Western North America

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lepidium papilliferum of southwest Idaho was previously treated as an infraspecific variety of Lepidium montanum. Chloroplast (cpDNA) sequences, nuclear ribosomal internal transcribed spacer (ITS) sequences, and AFLPs were used to test species delimitations and other possible evolutionarily signifi...

  2. 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

    EPA Science Inventory

    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...

  3. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation.

    PubMed

    Siriwut, Warut; Edgecombe, Gregory D; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

  4. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation

    PubMed Central

    Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

  5. Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host

    PubMed Central

    2013-01-01

    Background To understand the ecological and evolutionary consequences of species interactions in food webs necessitates that interactions are properly identified. Genetic analyses suggest that many supposedly generalist parasitoid species should rather be defined as multiple species with a more narrow diet, reducing the probability that such species may mediate indirect interactions such as apparent competition among hosts. Recent studies showed that the parasitoid Asecodes lucens mediate apparent competition between two hosts, Galerucella tenella and G. calmariensis, affecting both interaction strengths and evolutionary feedbacks. The same parasitoid was also recorded from other species in the genus Galerucella, suggesting that similar indirect effects may also occur for other species pairs. Methods To explore the possibility of such interactions, we sequenced mitochondrial and nuclear genetic markers to resolve the phylogeny of both host and parasitoid and to test the number of parasitoid species involved. We thus collected 139 Galerucella larvae from 8 host plant species and sequenced 31 adult beetle and 108 parasitoid individuals. Results The analysis of the Galerucella data, that also included sequences from previous studies, verified the five species previously documented as reciprocally monophyletic, but the Bayesian species delimitation for A. lucens suggested 3–4 cryptic taxa with a more specialised host use than previously suggested. The gene data analyzed under the multispecies coalescent model allowed us to reconstruct the species tree phylogeny for both host and parasitoid and we found a fully congruent coevolutionary pattern suggesting that parasitoid speciation followed upon host speciation. Conclusion Using multilocus sequence data in a Bayesian species delimitation analysis we propose that hymenopteran parasitoids of the genus Asecodes that infest Galerucella larvae constitute at least three species with narrow diet breath. The evolution of

  6. Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation.

    PubMed

    Del-Prado, Ruth; Cubas, Paloma; Lumbsch, H Thorsten; Divakar, Pradeep K; Blanco, Oscar; de Paz, Guillermo Amo; Molina, M Carmen; Crespo, Ana

    2010-07-01

    The species delimitation in fungi is currently in flux. A growing body of evidence shows that the morphology-based species circumscription underestimates the number of existing species. The large and ever growing number of DNA sequence data of fungi makes it possible to use these to identify potential cases of hidden species, which then need to be studied with extensive taxon samplings. We used Parmeliaceae, one of the largest families of lichenized fungi as a model. Intra- and interspecific distances derived from maximum-likelihood phylogenetic trees inferred from 491 nuclear ITS rDNA sequences were examined for five major clades of parmelioid lichens. The intra- and interspecific distances were well separated in most cases allowing the calculation of a threshold, with exceptions of highly deviating distances in a few cases. These situations are shown to be taxa in which the current delimitation needs revision. Thus the analysis of the distance distributions is shown to be a powerful tool for identifying species complexes. PMID:20399873

  7. Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus).

    PubMed

    Rissler, Leslie J; Apodaca, Joseph J

    2007-12-01

    Being able to efficiently and accurately delimit species is one of the most basic and important aspects of systematics because species are the fundamental unit of analysis in biogeography, ecology, and conservation. We present a rationale and approach for combining ecological niche modeling, spatially explicit analyses of environmental data, and phylogenetics in species delimitation, and we use our methodology in an empirical example focusing on Aneides flavipunctatus, the black salamander (Caudata: Plethodontidae), in California. We assess the relationships between genetic, environmental, and geographic distance among populations. We use 11 climatic variables and point locality data from public databases to create ecological niche models. The suitability of potential contact zones between parapatric lineages is also assessed using the data from ecological niche modeling. Phylogenetic analyses of portions of the mitochondrial genome reveal morphologically cryptic mitochondrial lineages in this species. In addition, we find that patterns of genetic divergence are strongly associated with divergence in the ecological niche. Our work demonstrates the ease and utility of using spatial analyses of environmental data and phylogenetics in species delimitation, especially for groups displaying fine-scaled endemism and cryptic species. PMID:18066928

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

    PubMed

    Drotz, Marcus K; Brodin, Tomas; Nilsson, Anders N

    2015-01-01

    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. PMID:26619278

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

    PubMed Central

    Drotz, Marcus K.; Brodin, Tomas; Nilsson, Anders N.

    2015-01-01

    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. PMID:26619278

  10. 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).

    PubMed

    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. PMID:21443956

  11. Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

    PubMed Central

    Krug, Patrick J.; Vendetti, Jann E.; Rodriguez, Albert K.; Retana, Jennifer N.; Hirano, Yayoi M.; Trowbridge, Cynthia D.

    2013-01-01

    DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed “species” each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The “circumtropical” Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The “monotypic” and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated. PMID:23876292

  12. Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera, Tenebrionidae, Ulomini), with the description of four new species

    PubMed Central

    Soldati, Laurent; Kergoat, Gael J.; Clamens, Anne-Laure; Jourdan, Hervé; Jabbour-Zahab, Roula; Condamine, Fabien L.

    2014-01-01

    Abstract New Caledonia is an important biodiversity hotspot with much undocumented biodiversity, especially in many insect groups. Here we used an integrative approach to explore species diversity in the tenebrionid genus Uloma (Coleoptera, Tenebrionidae, Ulomini), which encompasses about 150 species, of which 22 are known from New Caledonia. To do so, we focused on a morphologically homogeneous group by comparing museum specimens with material collected during several recent field trips. We also conducted molecular phylogenetic analyses based on a concatenated matrix of four mitochondrial and three nuclear genes for 46 specimens. The morphological study allowed us to discover and describe four new species that belong to the group of interest, the Uloma isoceroides group. Molecular analyses confirmed the species boundaries of several of the previously described species and established the validity of the four new species. The phylogenetic analyses also provided additional information on the evolutionary history of the group, highlighting that a species that was thought to be unrelated to the group was in fact a member of the same evolutionary lineage. Molecular species delimitation confirmed the status of the sampled species of the group and also suggested some hidden (cryptic) biodiversity for at least two species of the group. Altogether this integrative taxonomic approach has allowed us to better define the boundaries of the Uloma isoceroides species group, which comprises at least 10 species: Uloma isoceroides (Fauvel, 1904), Uloma opacipennis (Fauvel, 1904), Uloma caledonica Kaszab, 1982, Uloma paniei Kaszab, 1982, Uloma monteithi Kaszab, 1986, Uloma robusta Kaszab, 1986, Uloma clamensae sp. n., Uloma condaminei sp. n., Uloma jourdani sp. n., and Uloma kergoati sp. n. We advocate more studies on other New Caledonian groups, as we expect that much undocumented biodiversity can be unveiled through the use of similar approaches. PMID:25009426

  13. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data

    PubMed Central

    Feng, Xiuyan; Liu, Jian; Gong, Xun

    2016-01-01

    The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective. PMID:26913044

  14. Species as the basic units in evolution and biodiversity: How to define and delimit larger foraminiferal species in respect to paleogeography and biostratigraphy.

    NASA Astrophysics Data System (ADS)

    Hohenegger, J.

    2012-04-01

    Many concepts have been developed for the base of taxonomy, the biological species. Still there is confusion in these concepts between the 'substance' of a species, e.g. which factors makes a species (definition) and how to detect or recognize a species (delimitation). Concepts like morphospecies and chronospecies (= palaeospecies) that are mainly used for fossil specimens, and all methods based on molecular genetic methods belong to the group of concepts for delimitating species. The species can be defined as a pool of contemporarily interconnected genotypes. This pool can be homogeneous or be divided into geographically separated sub-pools. Interconnectivity within such pools is given by the potential to transfer complete genomes or exchange genome parts through asexual or sexual reproduction. A change in genotype frequencies over successive generations is caused by preferred or restricted genome transfer due to evolutionary factors. After establishment of new adaptive zones, evolutionary factors leads to species differentiation. Depending on number, duration of the onset and the further role of the new adaptive zones (stable or continuously changing), various methods of speciation - grouped into split off and split up speciation - can be established. True speciation is characterized by a complete loss of the potential to transfer genomes between the new species without the possibility to fuse (hybridise) when their adaptive zones come in contact or overlap. In case of a broad geographical distribution, the area might be differentiated into several adaptive zones, where transferability between subgroups is restricted or even lost. Temporarily disconnected adaptive zones can again become combined, reinstalling transferability between sub-pools of genotypes. Genotypically and morphologically different subgroups preserving transferability are thus not species; taxonomically, these structurally distinct subgroups can be treated as subspecies. Due to this uncertainty

  15. Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region.

    PubMed

    Shazib, Shahed Uddin Ahmed; Vďačný, Peter; Kim, Ji Hye; Jang, Seok Won; Shin, Mann Kyoon

    2016-09-01

    Morphological and molecular delimitation of Spirostomum species is currently under debate. We addressed species boundaries within the genus Spirostomum, using the ITS1-5.8S-ITS2 region and the secondary structure of the ITS2 molecule, and 18S and 28S (D1D2) sequences additionally. The Spirostomum ITS region is among the shortest within the ciliates hitherto studied. The Spirostomum ITS2 molecule matches the "ring model", but exhibits only two helices radiating from a common loop. According to comparative analyses, they very likely correspond to helices II and III of other eukaryotes. Our phylogenetic analyses of the ITS region revealed a complex genealogical structure within the genus Spirostomum. However, boundaries among Spirostomum species could not be unambiguously determined either by phylogenetic trees, networks or sequence divergence cutoffs, because ITS2 sequences transcended species boundaries of the following morphospecies: S. ambiguum, S. minus, S. subtilis and S. teres. According to molecular diversity analysis, this is very likely caused by polymorphism in S. minus and S. teres, and by the lack of variability in S. ambiguum and S. subtilis. No compensatory base changes (CBCs) were detected in helices of the ITS2 molecule between different Spirostomum species, documenting that CBC analysis per se is not able to effectively discriminate Spirostomum species. PMID:27261253

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

    PubMed

    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. PMID:24162075

  17. Species delimitation, phylogeny and evolutionary demography of co-distributed, montane frogs in the southern Brazilian Atlantic Forest.

    PubMed

    Firkowski, Carina R; Bornschein, Marcos R; Ribeiro, Luiz F; Pie, Marcio R

    2016-07-01

    The Brazilian Atlantic Forest (BAF) is recognized as one of the world's biodiversity hotspots, with even more species per unit of area than the Amazon, however the mechanisms that led to such astonishing diversity are yet to be fully understood. In this study, we investigate the diversification of two co-distributed frog genera associated with montane areas of southern BAF: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). Species delimitation methods using mitochondrial and nuclear loci supported the existence of a remarkable number of highly endemic species in each genus, most of which occupy only one or a few adjacent mountaintops. Their timing of diversification was highly congruent, supporting recent speciation events within the past 600 thousand years. Extended Bayesian skyline plots indicate that most populations have remained relatively stable in size across the evolutionary past, with recent growth after 0.15My, suggesting that the drastic changes found in previous studies on lowland frog species were not shared by these montane taxa. These results are consistent with the existence of a montane refugium in southern BAF, allowing species persistence through the climatic shifts experienced along the BAF during the Quaternary. PMID:27129900

  18. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).

    PubMed

    Satler, Jordan D; Carstens, Bryan C; Hedin, Marshal

    2013-11-01

    Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups. PMID:23771888

  19. Morphology delimits more species than molecular genetic clusters of invasive Pilosella

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Reliable identifications of invasive species are essential for effective management. Several species of Pilosella (syn. Hieracium, Asteraceae) hawkweeds invade North America, where unreliable identification hinders their control. Here we ask (i) do morphological traits dependab...

  20. An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring.

    PubMed

    Bond, Jason E; Stockman, Amy K

    2008-08-01

    Here we present an objective, repeatable approach to delineating species when populations are divergent and highly structured geographically using the Californian trapdoor spider species complex Aptostichus atomarius Simon as a model system. This system is particularly difficult because under strict criteria of geographical concordance coupled with estimates of genetic divergence, an unrealistic number of population lineages would qualify as species (20 to 60). Our novel phylogeographic approach, which is generally applicable but particularly relevant to highly structured systems, uses genealogical exclusivity to establish a topological framework to examine lineages for genetic and ecological exchangeability in an effort to delimit cohesion species. Both qualitative assessments of habitat and niche-based distribution modeling are employed to evaluate selective regime and ecological interchangeability among genetic lineages; adaptive divergence among populations is weighted more heavily than simple geographical concordance. Based on these analyses we conclude that five cohesion species should be recognized, three of which are new to science. PMID:18686196

  1. Islands in the desert: Species delimitation and evolutionary history of Pseudotetracha tiger beetles (Coleoptera: Cicindelidae: Megacephalini) from Australian salt lakes.

    PubMed

    López-López, Alejandro; Hudson, Peter; Galián, José

    2016-08-01

    The Australian salt lakes are a natural archipelago-like laboratory for investigating evolutionary and population processes. Their environmental conditions have not undergone relevant changes since the aridification of Australia 10-5 million years ago. The genus Pseudotetracha, a group of nocturnal tiger beetles found on these remote salt lakes, includes 20 described species. Recent studies based on molecular markers and cytogenetics hinted at the existence of cryptic species within this group. Here we use various species delimitation algorithms to detect a high number of cryptic and undescribed taxa, and challenge the validity of the taxonomic characters traditionally used for discerning species in this group. Our analyses show that the divergence dates of the clades, between 10 and 5 million years ago, correspond to the period in which Australia was undergoing an aridification process that probably isolated the ancestral Pseudotetracha populations to individual lakes or palaeodrainage basins. This implies an important role of the isolation, produced by the aridification of Australia, in the speciation and divergence of Pseudotetracha, which underwent a remarkable radiation as the populations became geographically restricted. PMID:27223998

  2. Molecular Divergence and Species Delimitation of the Cultivated Oyster Mushrooms: Integration of IGS1 and ITS

    PubMed Central

    Bhassu, Subha; Tan, Yee Shin; Vikineswary, Sabaratnam

    2014-01-01

    Identification of edible mushrooms particularly Pleurotus genus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivated Pleurotus species. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1 + ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species of P. nebrodensis and P. eryngii var. ferulae with other strains of P. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species' evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode. PMID:24587752

  3. Molecular divergence and species delimitation of the cultivated oyster mushrooms: integration of IGS1 and ITS.

    PubMed

    Avin, Farhat Ahmadi; Bhassu, Subha; Tan, Yee Shin; Shahbazi, Pedram; Vikineswary, Sabaratnam

    2014-01-01

    Identification of edible mushrooms particularly Pleurotus genus has been restricted due to various obstacles. The present study attempted to use the combination of two variable regions of IGS1 and ITS for classifying the economically cultivated Pleurotus species. Integration of the two regions proved a high ability that not only could clearly distinguish the species but also served sufficient intraspecies variation. Phylogenetic tree (IGS1+ITS) showed seven distinct clades, each clade belonging to a separate species group. Moreover, the species differentiation was tested by AMOVA and the results were reconfirmed by presenting appropriate amounts of divergence (91.82% among and 8.18% within the species). In spite of achieving a proper classification of species by combination of IGS1 and ITS sequences, the phylogenetic tree showed the misclassification of the species of P. nebrodensis and P. eryngii var. ferulae with other strains of P. eryngii. However, the constructed median joining (MJ) network could not only differentiate between these species but also offer a profound perception of the species' evolutionary process. Eventually, due to the sufficient variation among and within species, distinct sequences, simple amplification, and location between ideal conserved ribosomal genes, the integration of IGS1 and ITS sequences is recommended as a desirable DNA barcode. PMID:24587752

  4. Recent evolutionary history of Lost World endemics: population genetics, species delimitation, and phylogeography of sky-island treefrogs.

    PubMed

    Salerno, P E; Señaris, J C; Rojas-Runjaic, F J M; Cannatella, D C

    2015-01-01

    The tepuis of South America are massive flattop mountains with cliffs up to 1000m and summits up to 3100m. Tepuis hold enormous endemicity levels, but little is known about the origins of the endemic flora and fauna. Recently diverged lineages offer the possibility of understanding the origins of summit endemicity by examining population dynamics and dispersal. We examine species delimitation, clade relationships, and demographic patterns of three recently diverged lineages of Tepuihyla, an endemic treefrog clade. These three lineages represent two currently recognized species, T. edelcae and T. rodriguezi. Given the low divergences in both nuclear and mitochondrial genes among lineages, we find unexpectedly high numbers of unique nuclear haplotypes and moderate levels of lineage sorting. We also find support from multiple analyses for a cryptic, undescribed summit species within T. edelcae. We suggest that the genetic and distribution patterns of the four most recently diverged Tepuihyla lineages support a concurrent speciation event during the Pliocene, and suggest a biogeographic hypothesis in which a widespread climatic change made mid- and low-elevation habitat unsuitable for the common ancestor within the timeframe of their divergence. PMID:25450102

  5. Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon.

    PubMed

    Meyin A Ebong, Solange; Petit, Elsa; Le Gall, Philippe; Chen, Ping-Ping; Nieser, Nico; Guilbert, Eric; Njiokou, Flobert; Marsollier, Laurent; Guégan, Jean-François; Pluot-Sigwalt, Dominique; Eyangoh, Sara; Harry, Myriam

    2016-01-01

    Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for "DNA barcoding") and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41-45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and "DNA barcoding" reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy. PMID:27149077

  6. Molecular Species Delimitation and Morphology of Aquatic and Sub-Aquatic Bugs (Heteroptera) in Cameroon

    PubMed Central

    Le Gall, Philippe; Chen, Ping-Ping; Nieser, Nico; Guilbert, Eric; Njiokou, Flobert; Marsollier, Laurent; Guégan, Jean-François; Pluot-Sigwalt, Dominique; Eyangoh, Sara; Harry, Myriam

    2016-01-01

    Aquatic and semi-aquatic bugs (Heteroptera) represent a remarkable diversity and a resurging interest has been given to documenting at the species level these insects inhabiting Cameroon in Central Africa due to their potential implication in the transmission of the bacterium Mycobacterium ulcerans, the causal agent of Buruli ulcer, an emerging human disease. A survey was carried out over two years in Cameroon. Morphological analyses were done in two steps. A first step consisted in separating the specimens based on broadly shared characters into morphotypes. The specimens were then separated into two independent batches containing each the same representation of each morphotype. One batch (309 specimens) was used by taxonomy experts on aquatic bugs for species level identification and/or to reconcile nymph with their corresponding adult species. The second batch (188 specimens) was used to define species based on the COI DNA sequences (standard sequence used for “DNA barcoding”) and using the Automatic Barcode Gap Discovery (ABGD) method. The first morphological analysis step separated the specimens into 63 different morphotypes (49 adults and 14 nymphs), which were then found to belong to 54 morphological species in the infra-orders Gerromorpha and Nepomorpha based on the species-level morphological identification, and 41–45 putative molecular species according to the gap value retained in the ABGD. Integrating morphology and “DNA barcoding” reconciled all the specimens into 62 aquatic bug species in Cameroon. Generally, we obtained a good congruence between species a priori identified based on morphology from adult morphotypes and molecular putative species. Moreover, molecular identification has allowed the association of 86% of nymphs with adults. This work illustrates the importance of integrative taxonomy. PMID:27149077

  7. The Pollination Mechanism in Trigonidium obtusum Lindl (Orchidaceae: Maxillariinae): Sexual Mimicry and Trap‐flowers

    PubMed Central

    SINGER, RODRIGO B.

    2002-01-01

    The pollination process in Trigonidium obtusum Lindl. (Epidendroideae: Maxillariinae) is documented. The flowers are pollinated by sexually excited drones of Plebeia droryana (Meliponinae). When attempting to copulate either with sepals or petals, these bees slip on the waxy perianth surface and become trapped in the funnel‐like flower tube. Bees trying to escape from the flowers may instead access the space between the column and lip, fixing the pollinarium on their scutellum. Pollinarium‐bearing bees may pollinate the flowers when repeating the above‐mentioned steps, leaving pollinia on the concave stigmatic surface, thus effecting pollination. Recently removed pollinaria are too broad to enter the stigma but they begin to dehydrate and within 40 min of removal are small enough to fit the stigmatic cavity. This mechanism prevents insect‐mediated self‐pollination and promotes cross‐pollination. Preliminary evidence based on experiments with cultivated plants suggests that they are self‐compatible but that fruit set is pollinator‐dependent. The data obtained are discussed in a phylogenetic context. It is suggested that the pseudocopulatory syndrome in Trigonidium could have evolved from rewardless (food advertising) ancestors. Pseudocopulation in the context of the long flowering period of this orchid species (about 7 months) is understandable since the eusocial Plebeia bees produce fertile individuals several times a year. PMID:12099346

  8. A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

    PubMed

    Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

    2016-10-01

    Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. PMID:27444708

  9. Species delimitation and cryptic diversity in the moss genus Scleropodium (Brachytheciaceae).

    PubMed

    Carter, Benjamin E

    2012-06-01

    Cryptic lineage diversification is an important component of global biodiversity, but it presents challenges to our ability to catalog and understand that diversity. Because of their relative morphological simplicity and broad geographic distributions, bryophytes are an ideal study group for investigating this phenomenon. This study generated molecular data from 109 ingroup individuals to test morphological species circumscriptions and examine patterns of cryptic lineage diversification within the small north temperate moss genus Scleropodium (Brachytheciaceae). Maximum Parsimony and Bayesian phylogenetic analyses and statistical parsimony network analyses of ITS and chloroplast rps4, psbA2 and trnG regions indicate that the genus comprises six distinct molecular groups. Five of these molecular groups correspond to previously recognized species: S. californicum (Lesq.) Kindb., S. cespitans (Müll.) Koch, S. julaceum Lawton, S. obtusifolium (Mitt.) Kindb. in Macoun and S. touretii Brid. (Koch). However, the sixth group does not correspond to any existing species. Maximum parsimony and Bayesian posterior probability support for the monophyly of species varied widely and depended on both the dataset (ITS, chloroplast, combined) and the analysis method (Parsimony/Bayesian). Low phylogenetic resolution of species is attributable to the lack of informative DNA sequence vaiation and incongruent placements of three accessions in the chloroplast and ITS gene trees, both suggesting recent divergence within the genus. Re-examination of the herbarium vouchers for the sixth molecular group reveals that they form a group nested within the morphological circumscription of S. obtusifolium. One subtle morphological character (relative frequency of a costa spine) was identified that has utility in discriminating these two genetically distinct but morphologically very similar species. PMID:22421213

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

    PubMed Central

    2010-01-01

    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 mammals. Most of the species

  11. Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus).

    PubMed

    Reeves, Patrick A; Richards, Christopher M

    2011-01-01

    There is an emerging consensus that the intent of most species concepts is to identify evolutionarily distinct lineages. However, the criteria used to identify lineages differ among concepts depending on the perceived importance of various attributes of evolving populations. We have examined five different species criteria to ask whether the three taxonomic varieties of Humulus lupulus (hops) native to North America are distinct lineages. Three criteria (monophyly, absence of genetic intermediates, and diagnosability) focus on evolutionary patterns and two (intrinsic reproductive isolation and niche specialization) consider evolutionary processes. Phylogenetic analysis of amplified fragment length polymorphism (AFLP) data under a relaxed molecular clock, a stochastic Dollo substitution model, and parsimony identified all varieties as monophyletic, thus they satisfy the monophyly criterion for species delimitation. Principal coordinate analysis and a Bayesian assignment procedure revealed deep genetic subdivisions and little admixture between varieties, indicating an absence of genetic intermediates and compliance with the genotypic cluster species criterion. Diagnostic morphological and AFLP characters were found for all varieties, thus they meet the diagnosability criterion. Natural history information suggests that reproductive isolating barriers may have evolved in var. pubescens, potentially qualifying it as a species under a criterion of intrinsic reproductive isolation. Environmental niche modeling showed that the preferred habitat of var. neomexicanus is climatically unique, suggesting niche specialization and thus compliance with an ecological species criterion. Isolation by distance coupled with imperfect sampling can lead to erroneous lineage identification using some species criteria. Compliance with complementary pattern- and process-oriented criteria provides powerful corroboration for a species hypothesis and mitigates the necessity for comprehensive

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

    PubMed

    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. PMID:24875252

  13. Species delimitations in plants: lessons learned from potato taxonomy by a practicing taxonomist

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solanum section Petota has been the subject of intensive taxonomic work since the description of the cultivated potato in 1753. In total, there are 494 epithets for wild taxa and 626 epithets for cultivated taxa. Different taxonomists applied various taxonomic philosophies and species concepts to th...

  14. Comparative histology of floral elaiophores in the orchids Rudolfiella picta (Schltr.) Hoehne (Maxillariinae sensu lato) and Oncidium ornithorhynchum H.B.K. (Oncidiinae sensu lato)

    PubMed Central

    Davies, Kevin L.; Stpiczyńska, Malgorzata

    2009-01-01

    Background and Aims Floral elaiophores, although widespread amongst orchids, have not previously been described for Maxillariinae sensu lato. Here, two claims that epithelial, floral elaiophores occur in the genus Rudolfiella Hoehne (Bifrenaria clade) are investigated. Presumed elaiophores were compared with those of Oncidiinae Benth. and the floral, resin-secreting tissues of Rhetinantha M.A. Blanco and Heterotaxis Lindl., both genera formerly assigned to Maxillaria Ruiz & Pav. (Maxillariinae sensu stricto). Methods Putative, floral elaiophore tissue of Rudolfiella picta (Schltr.) Hoehne and floral elaiophores of Oncidium ornithorhynchum H.B.K. were examined by means of light microscopy, histochemistry, scanning electron microscopy and transmission electron microscopy. Key Results and Conclusions Floral, epithelial elaiophores are present in Rudolfiella picta, indicating, for the first time, that oil secretion occurs amongst members of the Bifrenaria clade (Maxillariinae sensu lato). However, whereas the elaiophore of R. picta is borne upon the labellar callus, the elaiophores of O. ornithorhynchum occur on the lateral lobes of the labellum. In both species, the elaiophore comprises a single layer of palisade secretory cells and parenchymatous, subsecretory tissue. Cell wall cavities are absent from both and there is no evidence of cuticular distension in response to oil accumulation between the outer tangential wall and the overlying cuticle in R. picta. Distension of the cuticle, however, occurs in O. ornithorhynchum. Secretory cells of R. picta contain characteristic, spherical or oval plastids with abundant plastoglobuli and these more closely resemble plastids found in labellar, secretory cells of representatives of Rhetinantha (formerly Maxillaria acuminata Lindl. alliance) than elaiophore plastids of Oncidiinae. In Rhetinantha, such plastids are involved in the synthesis of resin-like material or wax. Despite these differences, the elaiophore anatomy of

  15. Sodium channels as gateable non-photonic sensors for membrane-delimited reactive species

    PubMed Central

    Ojha, Navin K.; Nematian-Ardestani, Ehsan; Neugebauer, Sophie; Borowski, Benjamin; El-Hussein, Ahmed; Hoshi, Toshinori; Leipold, Enrico; Heinemann, Stefan H.

    2014-01-01

    Reactive oxygen species (ROS) and reactive oxygen intermediates (ROI) play crucial roles in physiological processes. While excessive ROS damages cells, small fluctuations in ROS levels represent physiological signals important for vital functions. Despite the physiological importance of ROS, many fundamental questions remain unanswered, such as which types of ROS occur in cells, how they distribute inside cells, and how long they remain in an active form. The current study presents a ratiometric sensor of intracellular ROS levels based on genetically engineered voltage-gated sodium channels (roNaV). roNaV can be used for detecting oxidative modification that occurs near the plasma membrane with a sensitivity similar to existing fluorescence-based ROS sensors. Moreover, roNaV has several advantages over traditional sensors because it does not need excitation light for sensing, and thus, can be used to detect phototoxic cellular modifications. In addition, the ROS dynamic range of roNaV is easily manipulated in real time by means of the endogenous channel inactivation mechanism. Measurements on ROS liberated from intracellular Lucifer Yellow and genetically encoded KillerRed has revealed an assessment of ROS lifetime in individual mammalian cells. Flashlight-induced ROS concentration decayed with two major time constants of about 10 and 1000 ms. PMID:24513256

  16. Sodium channels as gateable non-photonic sensors for membrane-delimited reactive species.

    PubMed

    Ojha, Navin K; Nematian-Ardestani, Ehsan; Neugebauer, Sophie; Borowski, Benjamin; El-Hussein, Ahmed; Hoshi, Toshinori; Leipold, Enrico; Heinemann, Stefan H

    2014-05-01

    Reactive oxygen species (ROS) and reactive oxygen intermediates (ROI) play crucial roles in physiological processes. While excessive ROS damages cells, small fluctuations in ROS levels represent physiological signals important for vital functions. Despite the physiological importance of ROS, many fundamental questions remain unanswered, such as which types of ROS occur in cells, how they distribute inside cells, and how long they remain in an active form. The current study presents a ratiometric sensor of intracellular ROS levels based on genetically engineered voltage-gated sodium channels (roNaV). roNaV can be used for detecting oxidative modification that occurs near the plasma membrane with a sensitivity similar to existing fluorescence-based ROS sensors. Moreover, roNaV has several advantages over traditional sensors because it does not need excitation light for sensing, and thus, can be used to detect phototoxic cellular modifications. In addition, the ROS dynamic range of roNaV is easily manipulated in real time by means of the endogenous channel inactivation mechanism. Measurements on ROS liberated from intracellular Lucifer Yellow and genetically encoded KillerRed have revealed an assessment of ROS lifetime in individual mammalian cells. Flashlight-induced ROS concentration decayed with two major time constants of about 10 and 1000 ms. PMID:24513256

  17. Coalescent-Based Species Delimitation Approach Uncovers High Cryptic Diversity in the Cosmopolitan Lichen-Forming Fungal Genus Protoparmelia (Lecanorales, Ascomycota)

    PubMed Central

    Singh, Garima; Dal Grande, Francesco; Divakar, Pradeep K.; Otte, Jürgen; Leavitt, Steven D.; Szczepanska, Katarzyna; Crespo, Ana; Rico, Víctor J.; Aptroot, André; Cáceres, Marcela Eugenia da Silva; Lumbsch, H. Thorsten; Schmitt, Imke

    2015-01-01

    Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence. PMID:25932996

  18. Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota).

    PubMed

    Singh, Garima; Dal Grande, Francesco; Divakar, Pradeep K; Otte, Jürgen; Leavitt, Steven D; Szczepanska, Katarzyna; Crespo, Ana; Rico, Víctor J; Aptroot, André; Cáceres, Marcela Eugenia da Silva; Lumbsch, H Thorsten; Schmitt, Imke

    2015-01-01

    Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal-arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods--BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence. PMID:25932996

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

    PubMed

    Blaimer, Bonnie B; Fisher, Brian L

    2013-01-01

    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. PMID:23874503

  20. Cambarus (Jugicambarus) adustus, a new species of crayfish from northeastern Kentucky delimited from the Cambarus (J.) aff. dubius species complex.

    PubMed

    Thoma, Roger F; Fetzner, James W Jr; Stocker, G Whitney; Loughman, Zachary J

    2016-01-01

    A new species of burrowing crayfish, Cambarus (Jugicambarus) adustus, is described from Lewis County in northeastern Kentucky, USA. The new species is most similar morphologically to C. dubius. Cambarus adustus coloration differs from C. dubius by lacking red, orange and blue hues, and instead is brown over the entire body surface. Morphological differences between C. dubius and C. adustus exist in the form I male gonopod, with C. adustus possessing a caudal knob, while C. dubius does not. In addition, the lateral carapace of C. adustus is distinctly tuberculate, whereas in C. dubius the carapace lacks extensive tuberculation. Cambarus (J.) adustus appears to have an extremely small geographic range (~19.5 km2), and as such we suggest its consideration for both state and federal levels of protection. PMID:27615965

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

    PubMed

    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. PMID:22764163

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

    PubMed Central

    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 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 (Ne) and speciation rate (SR; per lineage per million years) was less than or equal to 105, while interspecific variation in Ne was twofold or less. However, at higher but also biologically relevant values of Ne × SR and when Ne 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 Ne, SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results. PMID:22764163

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

    PubMed Central

    Liu, Jian; Zhou, Wei; Gong, Xun

    2015-01-01

    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

  4. Molecular phylogeny and taxonomy in leafmining flies (Diptera: Agromyzidae): Delimitation of Phytomyza fallén s. lat. and its species groups, with new insights on genitalic and host-use evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytomyza is the largest genus of leaf-mining flies (Agromyzidae), including over 530 species as previously delimited. Species of the very similar genus Chromatomyia are sometimes included in Phytomyza, and its status has been uncertain. Using 3,076 base pairs of DNA sequence from three genes (COI...

  5. Micromorphology of the Labellum and Floral Spur of Cryptocentrum Benth. and Sepalosaccus Schltr. (Maxillariinae: Orchidaceae)

    PubMed Central

    Davies, Kevin L.; Stpiczyńska, Malgorzata

    2007-01-01

    Background and Aims Gross vegetative and floral morphology, as well as modern molecular techniques, indicate that Cryptocentrum Benth. and Sepalosaccus Schltr. are related to Maxillaria Ruiz & Pav. However, they differ from Maxillaria in their possession of floral spurs and, in this respect, are atypical of Maxillariinae. The labellar micromorphology of Maxillaria, unlike that of the other two genera, has been extensively studied. In the present report, the labellar micromorphology of Cryptocentrum and Sepalosaccus is compared with that of Maxillaria and, for the first time, the micromorphology of the floral spur as found in Maxillariinae is described. Methods Labella and dissected floral spurs of Cryptocentrum and Sepalosaccus were examined using light microscopy (LM) and scanning electron microscopy (SEM). Key Results In each case, the labellum consists of a papillose mid-lobe (epichile), a cymbiform region (hypochile) and, proximally, a spur, which is pronounced in Cryptocentrum but short and blunt in Sepalosaccus. The inner epidermal surface of the spur of Cryptocentrum is glabrous or pubescent, and the bicellular hairs, where present, are unlike any hitherto described for Maxillariinae. Similar but unicellular hairs also occur in the floral spur of Sepalosaccus, whereas the glabrous epidermis lining the spur of C. peruvianum contains putative nectar pores. Conclusions The labellar micromorphology of Cryptocentrum and Sepalosaccus generally resembles that of Maxillaria. The floral spur of Cryptocentrum displays two types of organization in that the epidermal lining may be glabrous (possibly with nectar pores) or pubescent. This may have taxonomic significance and perhaps reflects physiological differences relating to nectar secretion. The trichomes found within the spurs of Cryptocentrum and Sepalosaccus more closely resemble the hairs of certain unrelated, nectariferous orchid taxa than those found in the largely nectarless genus Maxillaria, and this further

  6. Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa.

    PubMed

    Karanovic, Tomislav; Djurakic, Marko; Eberhard, Stefan M

    2016-03-01

    Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a

  7. Species delimitation using morphology, morphometrics, and molecules: definition of the Ophionscutellaris Thomson species group, with descriptions of six new species (Hymenoptera, Ichneumonidae).

    PubMed

    Schwarzfeld, Marla D; Sperling, Felix A H

    2014-01-01

    The diverse genus Ophion is almost entirely undescribed in the Nearctic region. In this paper we define the Ophionscutellaris species group. This species group is well-supported by analysis of DNA (ITS2, COI, and 28S D2-D3) and morphology. It includes the Palearctic species Ophionscutellaris and the Nearctic species Ophionidoneus. An integrative analysis of DNA, geometric wing morphometrics, classical morphometrics and qualitative morphology indicates that this species group contains a minimum of seven species in North America, although the full diversity of the group has likely not been sampled. Ophionclave Schwarzfeld, sp. n., Ophionaureus Schwarzfeld, sp. n., Ophionbrevipunctatus Schwarzfeld, sp. n., Ophiondombroskii Schwarzfeld, sp. n., Ophionkeala Schwarzfeld, sp. n. and Ophionimportunus Schwarzfeld, sp. n. are described, and a key to the known Nearctic species of the Ophionscutellaris group is provided. PMID:25589855

  8. Species delimitation using morphology, morphometrics, and molecules: definition of the Ophion scutellaris Thomson species group, with descriptions of six new species (Hymenoptera, Ichneumonidae)

    PubMed Central

    Schwarzfeld, Marla D.; Sperling, Felix A. H.

    2014-01-01

    Abstract The diverse genus Ophion is almost entirely undescribed in the Nearctic region. In this paper we define the Ophion scutellaris species group. This species group is well-supported by analysis of DNA (ITS2, COI, and 28S D2-D3) and morphology. It includes the Palearctic species Ophion scutellaris and the Nearctic species Ophion idoneus. An integrative analysis of DNA, geometric wing morphometrics, classical morphometrics and qualitative morphology indicates that this species group contains a minimum of seven species in North America, although the full diversity of the group has likely not been sampled. Ophion clave Schwarzfeld, sp. n., Ophion aureus Schwarzfeld, sp. n., Ophion brevipunctatus Schwarzfeld, sp. n., Ophion dombroskii Schwarzfeld, sp. n., Ophion keala Schwarzfeld, sp. n. and Ophion importunus Schwarzfeld, sp. n. are described, and a key to the known Nearctic species of the Ophion scutellaris group is provided. PMID:25589855

  9. Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation

    PubMed Central

    2013-01-01

    Background Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination. Results In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively. Conclusions We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence

  10. Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation.

    PubMed

    Pereira, Tiago José; Baldwin, James Gordon

    2016-05-01

    Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods. PMID:26926945

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

    PubMed

    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. PMID:26277215

  12. Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group

    PubMed Central

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

    2015-01-01

    The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units. PMID:26332320

  13. Using Different Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical Hyperdiverse Group.

    PubMed

    Costa-Silva, Guilherme J; Rodriguez, Mónica S; Roxo, Fábio F; Foresti, Fausto; Oliveira, Claudio

    2015-01-01

    The genus Rineloricaria is a Neotropical freshwater fish group with a long and problematic taxonomic history, attributed to the large number of species and the pronounced similarity among them. In the present work, taxonomic information and different molecular approaches were used to identify species boundaries and characterize independent evolutionary units. We analyzed 228 samples assembled in 53 distinct morphospecies. A general mixed yule-coalescent (GMYC) analysis indicated the existence of 70 entities, while BOLD system analyses showed the existence of 56 distinct BINs. When we used a new proposed integrative taxonomy approach, mixing the results obtained by each analysis, we identified 73 OTUs. We suggest that Rineloricaria probably has some complexity in the known species and several species not formally described yet. Our data suggested that other hyperdiverse fish groups with wide distributions can be further split into many new evolutionary taxonomic units. PMID:26332320

  14. Eriocaenus (Acari: Trombidiformes: Eriophyoidea), a new genus from Equisetum spp. (Equisetaceae): morphological and molecular delimitation of two morphologically similar species.

    PubMed

    Petanović, Radmila U; Amrine, James W; Chetverikov, Philipp E; Cvrković, Tatjana K

    2015-01-01

    Surveys conducted on horsetails, Equisetum spp. (Equisetaceae), in Serbia led to the discovery of a new eriophyoid mite genus while searching for a classical biological control agent against these weeds in New Zealand. Eriocaenus gen. n. is described based on the type species Aceria equiseti Farkas, 1960 (transferred to Eriophyes by Farkas 1965; herein reassigned to the new genus) and Eriocaenus ramosissimi n. sp., a new species discovered on Equisetum ramosissimum Desf. in Serbia. Eriocaenus equiseti (Farkas, 1960), previously only known from Hungary, was found in Serbia for the first time on Equisetum arvense L. and Equisetum telmateia Ehrh., and is redescribed. Species descriptions include line drawings as well as phase contrast (PCLM), differential interference contrast (DIC) and scanning electron (SEM) micrographs. The differential diagnosis between the two Eriocaenus species is supplemented by molecular differentiation of 28S rDNA sequences including D2 fragments for both mites. PMID:26623881

  15. Species delimitation and phylogenetic relationships in a genus of African weakly-electric fishes (Osteoglossiformes, Mormyridae, Campylomormyrus).

    PubMed

    Lamanna, Francesco; Kirschbaum, Frank; Ernst, Anja R R; Feulner, Philine G D; Mamonekene, Victor; Paul, Christiane; Tiedemann, Ralph

    2016-08-01

    African weakly-electric fishes (Mormyridae) are able to communicate through species-specific electric signals; this feature might have favoured the evolutionary radiation observed in this family (over 200 species) by acting as an effective pre-zygotic isolation mechanism. In the present study we used mitochondrial (cytb) and nuclear (rps7, scn4aa) markers in order to reconstruct a species-phylogeny and identify species boundaries for the genus Campylomormyrus, by applying inference methods based on the multispecies coalescent model. Additionally, we employed 16 microsatellite markers, landmark-based morphometric measurements, and electro-physiological analyses as independent lines of evidence to the results obtained from the sequence data. The results show that groups that are morphologically different are also significantly divergent at the genetic level, whereas morphologically similar groups, displaying dissimilar electric signals, do not show enough genetic diversity to be considered separate species. Furthermore, the data confirm the presence of a yet undescribed species within the genus Campylomormyrus. PMID:27143239

  16. Species delimitation under the general lineage concept: An empirical example using wild North American hops (cannabaceae: Humulus lupulus)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is an emerging consensus that the intent of most species concepts is to identify evolutionarily-distinct lineages. However, the criteria used to identify lineages differ between concepts depending on the perceived importance of various attributes of evolving populations. We have applied tests ...

  17. An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: a case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae).

    PubMed

    Hamilton, Chris A; Hendrixson, Brent E; Brewer, Michael S; Bond, Jason E

    2014-02-01

    The North American tarantula genus Aphonopelma provides one of the greatest challenges to species delimitation and downstream identification in spiders because traditional morphological characters appear ineffective for evaluating limits of intra- and interspecific variation in the group. We evaluated the efficacy of numerous molecular-based approaches to species delimitation within Aphonopelma based upon the most extensive sampling of theraphosids to date, while also investigating the sensitivity of randomized taxon sampling on the reproducibility of species boundaries. Mitochondrial DNA (cytochrome c oxidase subunit I) sequences were sampled from 682 specimens spanning the genetic, taxonomic, and geographic breadth of the genus within the United States. The effects of random taxon sampling compared traditional Neighbor-Joining with three modern quantitative species delimitation approaches (ABGD, P ID(Liberal), and GMYC). Our findings reveal remarkable consistency and congruence across various approaches and sampling regimes, while highlighting highly divergent outcomes in GMYC. Our investigation allowed us to integrate methodologies into an efficient, consistent, and more effective general methodological workflow for estimating species boundaries within the mygalomorph spider genus Aphonopelma. Taken alone, these approaches are not particularly useful - especially in the absence of prior knowledge of the focal taxa. Only through the incorporation of multiple lines of evidence, employed in a hypothesis-testing framework, can the identification and delimitation of confident species boundaries be determined. A key point in studying closely related species, and perhaps one of the most important aspects of DNA barcoding, is to combine a sampling strategy that broadly identifies the extent of genetic diversity across the distributions of the species of interest and incorporates previous knowledge into the "species equation" (morphology, molecules, and natural history

  18. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota).

    PubMed

    Truong, Camille; Divakar, Pradeep K; Yahr, Rebecca; Crespo, Ana; Clerc, Philippe

    2013-08-01

    In lichen-forming fungi, traditional taxonomical concepts are frequently in conflict with molecular data, and identifying appropriate taxonomic characters to describe phylogenetic clades remains challenging in many groups. The selection of suitable markers for the reconstruction of solid phylogenetic hypotheses is therefore fundamental. The lichen genus Usnea is highly diverse, with more than 350 estimated species, distributed in polar, temperate and tropical regions. The phylogeny and classification of Usnea have been a matter of debate, given the lack of phenotypic characters to describe phylogenetic clades and the low degree of resolution of phylogenetic trees. In this study, we investigated the phylogenetic relationships of 52 Usnea species from across the genus, based on ITS rDNA, nuLSU, and two protein-coding genes RPB1 and MCM7. ITS comprised several highly variable regions, containing substantial genetic signal, but also susceptible to causing bias in the generation of the alignment. We compared several methods of alignment of ITS and found that a simultaneous optimization of alignment and phylogeny (using BAli-phy) improved significantly both the topology and the resolution of the phylogenetic tree. However the resolution was even better when using protein-coding genes, especially RPB1 although it is less variable. The phylogeny based on the concatenated dataset revealed that the genus Usnea is subdivided into four highly-supported clades, corresponding to the traditionally circumscribed subgenera Eumitria, Dolichousnea, Neuropogon and Usnea. However, characters that have been used to describe these clades are often homoplasious within the phylogeny and their parallel evolution is suggested. On the other hand, most of the species were reconstructed as monophyletic, indicating that combinations of phenotypic characters are suitable discriminators for delimitating species, but are inadequate to describe generic subdivisions. PMID:23603312

  19. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves).

    PubMed

    Wang, Ning; Liang, Bin; Wang, Jichao; Yeh, Chia-Fen; Liu, Yang; Liu, Yanlin; Liang, Wei; Yao, Cheng-Te; Li, Shou-Hsien

    2016-09-01

    Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process. PMID:27233437

  20. Lineage delimitation and description of nine new species of bush frogs (Anura: Raorchestes, Rhacophoridae) from the Western Ghats Escarpment.

    PubMed

    Vijayakumar, S P; Dinesh, K P; Prabhu, Mrugank V; Shanker, Kartik

    2014-01-01

    Bush frogs of the genus Raorchestes are distributed mainly in the Western Ghats Escarpment of Peninsular India. The inventory of species in this genus is incomplete and there is ambiguity in the systematic status of species recognized by morphological criteria. To address the dual problem of taxon sampling and systematic uncertainty in bush frogs, we used a large-scale spatial sampling design, explicitly incorporating the geographic and ecological heterogeneity of the Western Ghats. We then used a hierarchical multi-criteria approach by combining mitochondrial phylogeny, genetic distance, geographic range, morphology and advertisement call to delimit bush frog lineages. Our analyses revealed the existence of a large number of new lineages with varying levels of genetic divergence. Here, we provide diagnoses and descriptions for nine lineages that exhibit divergence across multiple axes. The discovery of new lineages that exhibit high divergence across wide ranges of elevation and across the major massifs highlights the large gaps in historical sampling. These discoveries underscore the significance of addressing inadequate knowledge of species distribution, namely the "Wallacean shortfall", in addressing the problem of taxon sampling and unknown diversity in tropical hotspots. A biogeographically informed sampling and analytical approach was critical in detecting and delineating lineages in a consistent manner across the genus. Through increased taxon sampling, we were also able to discern a number of well-supported sub-clades that were either unresolved or absent in earlier phylogenetic reconstructions and identify a number of shallow divergent lineages which require further examination for assessment of their taxonomic status.  PMID:25544534

  1. Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences.

    PubMed

    Cao, De-Ping; Guo, Xian-Guang; Chen, Da-Li; Chen, Jian-Ping

    2011-07-01

    Leishmaniasis is a geographically widespread disease caused by protozoan parasites belonging to the genus Leishmania and transmitted by certain species of sand fly. This disease still remains endemic in China, especially in the west and northwest frontier regions. A recent ITS1 phylogeny of Chinese Leishmania isolates has challenged some aspects for their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within Chinese Leishmania isolates highlights the need for additional data and analyses. Here, we test the phylogenetic relationships among Chinese isolates and their relatives by analyzing kinetoplast cytochrome oxidase II (COII) gene sequences, including 14 Chinese isolates and three isolates from other countries plus 17 sequences retrieved from GenBank. The COII gene might have experienced little substitution saturation, and its evolutionary process was likely to have been stationary, reversible, and homogeneous. Both neighbor-joining and Bayesian analyses reveal a moderately supported group comprising ten newly determined isolates, which is closely related to Leishmania tarentolae and Endotrypanum monterogeii. In combination with genetic distance analysis as well as Bayesian hypothesis testing, this further corroborates the occurrence of an undescribed species of Leishmania. Our results also suggest that (1) isolate MHOM/CN/93/GS7 and isolate IPHL/CN/77/XJ771 are Leishmania donovani; (2) isolate MHOM/CN/84/JS1 is Leishmania tropica; (3) the status referring to an isolate MRHO/CN/62/GS-GER20 from a great gerbil in Gansu, China, as Leishmania gerbilli, formerly based on multilocus enzyme electrophoresis, is recognized; and (4) E. monterogeii is nested within the genus Leishmania, resulting in a paraphyletic Leishmania. In addition, the results of this study enrich our understanding of the heterogeneity and relationships of Chinese Leishmania isolates. PMID:21221640

  2. Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species.

    PubMed

    Welton, Luke J; Travers, Scott L; Siler, Cameron D; Brown, Rafe M

    2014-01-01

    We describe two new species of morphologically cryptic monitor lizards (genus Varanus) from the Philippine Archipelago:  Varanus dalubhasa sp. nov. and V. bangonorum sp. nov. These two distinct evolutionary lineages are members of the V. salvator species complex, and historically have been considered conspecific with the widespread, northern Philippine V. marmoratus. However, the new species each share closer phylogenetic affinities with V. nuchalis (and potentially V. palawanensis), than either does to one another or to V. marmoratus. Divergent from other recognized species within the V. salvator Complex of water monitors by as much as 3.5% pairwise genetic distance, these lineages are also distinguished by unique gular coloration, metrics of body size and scalation, their non-monophyly with "true" V. marmoratus, and insular allopatric distributions, suggesting biogeographically distinct and unique evolutionary histories. We compare the new species with the most geographically proximate and phenotypically relevant lineages.  Although we show that these new taxa are nearly indistinguishable morphologically from V. marmoratus, both species can be readily distinguished from their closest relatives (each's respective sister taxon, V. palawanensis and V. nuchalis) by traditional morphological characters.  Our findings underscore the high herpetological diversity and biogeographical complexity of vertebrates in the Philippines, and further emphasize the need for detailed study of species-level diversity, mechanisms of reproductive isolation, gene flow, and biologically relevant boundaries between taxa within the V. salvator Complex. PMID:25543631

  3. Checklist of the species of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) in fishes and turtles in Middle-America, and their delimitation based on sequences of the 28S rDNA.

    PubMed

    Pinacho-Pinacho, Carlos Daniel; Sereno-Uribe, Ana L; De León, Gerardo Pérez-Ponce; García-Varela, Martín

    2015-01-01

    Among the acanthocephalans, Neoechinorhynchus is one of the most speciose genera, with 116 described species distributed worldwide. The adults of Neoechinorhynchus are found in the intestine of freshwater and brackish water fish, as well as in freshwater turtles. In this study, a checklist of the congeneric species of Neoechinorhynchus occurring in Middle-American fish and turtles is presented. The checklist contains the records established in all published accounts, as well as novel data from survey work conducted in the region comprising Neotropical areas of Mexico, as well as some localities in Central America. The species delimitation criteria used to discriminate among species is based on molecular data. In the last years, a large database derived from sequences of the D2 + D3 domains of the large subunit of rDNA (28S) was generated for 262 specimens corresponding to nine species of Neoechinorhynchus. This molecular marker has shown to be useful in establishing species limits within Neoechinorhynchus and in resolving phylogenetic relationships at species level. Based on our results, the domains D2 + D3 of the 28S rDNA could be considered as potential DNA barcodes to complement mitochondrial DNA to discriminate among acanthocephalan species. PMID:26250025

  4. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens).

    PubMed

    de Lafontaine, Guillaume; Prunier, Julien; Gérardi, Sébastien; Bousquet, Jean

    2015-10-01

    The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor-derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes. PMID:26346701

  6. Phylogeny, species delimitation and convergence in the South American bothriurid scorpion genus Brachistosternus Pocock 1893: Integrating morphology, nuclear and mitochondrial DNA.

    PubMed

    Ojanguren-Affilastro, Andrés A; Mattoni, Camilo I; Ochoa, José A; Ramírez, Martín J; Ceccarelli, F Sara; Prendini, Lorenzo

    2016-01-01

    A phylogenetic analysis of the scorpion genus Brachistosternus Pocock, 1893 (Bothriuridae Simon, 1880) is presented, based on a dataset including 41 of the 43 described species and five outgroups, 116 morphological characters and more than 4150 base-pairs of DNA sequence from the nuclear 18S rDNA and 28S rDNA gene loci, and the mitochondrial 12S rDNA, 16S rDNA, and Cytochrome c Oxidase Subunit I gene loci. Analyses conducted using parsimony, Maximum Likelihood and Bayesian Inference were largely congruent with high support for most clades. The results confirmed the monophyly of Brachistosternus, the nominal subgenus, and subgenus Ministernus Francke, 1985, as in previous analyses based only on morphology, but differed in several other respects. Species from the plains of the Atacama Desert diverged basally whereas the high altitude Andean species radiated from a more derived ancestor, presumably as a consequence of Andean uplift and associated changes in climate. Species limits were assessed among species that contain intraspecific variation (e.g., different morphs), are difficult to separate morphologically, and/or exhibit widespread or disjunct distributions. The extent of convergence in morphological adaptation to life on sandy substrata (psammophily) and the complexity of the male genitalia, or hemispermatophores, was investigated. Psammophily evolved on at least four independent occasions. The lobe regions of the hemispermatophore increased in complexity on three independent occasions, and decreased in complexity on another three independent occasions. PMID:26321226

  7. Delimiting species by reproductive isolation: the genetic structure of epigean and hypogean Trichomycterus spp. (Teleostei, Siluriformes) in the restricted area of Torotoro (Upper Amazon, Bolivia).

    PubMed

    Renno, Jean-François; Gazel, Claude; Miranda, Guido; Pouilly, Marc; Berrebi, Patrick

    2007-11-01

    Genetic variability of Trichomycterus from the region of Torotoro (Bolivia, Upper Amazon), distributed in the same watershed where the habitat is structured by waterfalls, canyons and a cave, was studied by allozyme (twelve putative loci) and RFLP-mtDNA (DLoop and cytochrome b) analyses. Alloenzymatic variation studied by Correspondence Analysis and Maximum Likelihood Analysis revealed a four-group structure, which was largely congruent with the distribution of the 14 mtDNA haplotypes. Two of these four clusters (I and II) were differentiated by two diagnostic loci (IDH and G3PDH), two semi-diagnostic loci (PGM and 6PGDH) and consequently a very high F(st )value (estimator theta = 0.77). Therefore, clusters I and II are reproductively isolated. The distribution limit of these two (sibling) species does not correspond to those of the morphological species of Trichomycterus identified in this region: the epigean T. cf. barbouri and the hypogean T. chaberti. However, hypogean fish exhibited two mtDNA haplotypes, a private one and another shared with the epigean Trichomycterus from upstream reaches. PMID:17957496

  8. Exploiting comparative mapping among Brassica species to accelerate the physical delimitation of a genic male-sterile locus (BnRf) in Brassica napus.

    PubMed

    Xie, Yanzhou; Dong, Faming; Hong, Dengfeng; Wan, Lili; Liu, Pingwu; Yang, Guangsheng

    2012-07-01

    The recessive genic male sterility (RGMS) line 9012AB has been used as an important pollination control system for rapeseed hybrid production in China. Here, we report our study on physical mapping of one male-sterile locus (BnRf) in 9012AB by exploiting the comparative genomics among Brassica species. The genetic maps around BnRf from previous reports were integrated and enriched with markers from the Brassica A7 chromosome. Subsequent collinearity analysis of these markers contributed to the identification of a novel ancestral karyotype block F that possibly encompasses BnRf. Fourteen insertion/deletion markers were further developed from this conserved block and genotyped in three large backcross populations, leading to the construction of high-resolution local genetic maps where the BnRf locus was restricted to a less than 0.1-cM region. Moreover, it was observed that the target region in Brassica napus shares a high collinearity relationship with a region from the Brassica rapa A7 chromosome. A BnRf-cosegregated marker (AT3G23870) was then used to screen a B. napus bacterial artificial chromosome (BAC) library. From the resulting 16 positive BAC clones, one (JBnB089D05) was identified to most possibly contain the BnRf (c) allele. With the assistance of the genome sequence from the Brassica rapa homolog, the 13.8-kb DNA fragment covering both closest flanking markers from the BAC clone was isolated. Gene annotation based on the comparison of microcollinear regions among Brassica napus, B. rapa and Arabidopsis showed that five potential open reading frames reside in this fragment. These results provide a foundation for the characterization of the BnRf locus and allow a better understanding of the chromosome evolution around BnRf. PMID:22382487

  9. Delimiting Areas of Endemism through Kernel Interpolation

    PubMed Central

    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. PMID:25611971

  10. A network approach for identifying and delimiting biogeographical regions.

    PubMed

    Vilhena, Daril A; Antonelli, Alexandre

    2015-01-01

    Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify spatial biodiversity patterns, but algorithms based on similarity can be sensitive to common sampling biases in species distribution data. Here we apply a community detection approach from network theory that incorporates complex, higher-order presence-absence patterns. We demonstrate the performance of the method by applying it to all amphibian species in the world (c. 6,100 species), all vascular plant species of the USA (c. 17,600) and a hypothetical data set containing a zone of biotic transition. In comparison with current methods, our approach tackles the challenges posed by transition zones and succeeds in retrieving a larger number of commonly recognized biogeographical regions. This method can be applied to generate objective, data-derived identification and delimitation of the world's biogeographical regions. PMID:25907961

  11. Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru.

    PubMed

    Koch, Claudia; Flecks, Morris; Venegas, Pablo J; Bialke, Patrick; Valverde, Sebastian; Rödder, Dennis

    2016-01-01

    An integrative taxonomic approach based on morphology, molecular analyses, and climatic niche modeling was used to uncover cryptic diversity in the phyllodactylid gecko species Phyllodactylus reissii. At least three distinct species could be identified among the examined specimens from southern Ecuador and northern Peru. Phyllodactylus magister, described by Noble (1924) from arid Andean valleys of the Chinchipe and Marañón rivers in the Peruvian Department of Cajamarca and synonymized with P. reissii by Dixon & Huey (1970) is elevated from synonymy and a detailed redescription is provided. A new species of the genus Phyllodactylus from the Andean dry forest of the southern Marañón valley is identified and described herein. Phyllodactylus pachamama sp. nov. is differentiated from other South American congeners on the basis of mtDNA sequence divergence, morphological characters, and differences in the realized climatic niche. At least in Peru, P. reissii seems to primarily inhabit the northern coastal region west of the Andes, while the inter-Andean area along the Río Marañón and its tributaries seems to be inhabited mostly by other species of the genus, which are endemic to this area. The Andean valleys are underestimated in terms of biodiversity and lack thorough investigation and conservation actions. PMID:27615910

  12. Delimiting Cladosporium from morphologically similar genera

    PubMed Central

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

    2007-01-01

    The genus Cladosporium is restricted to dematiaceous hyphomycetes with a coronate scar type, and Davidiella teleomorphs. In the present study numerous cladosporium-like taxa are treated, and allocated to different genera based on their morphology and DNA phylogeny derived from the LSU nrRNA gene. Several species are introduced in new genera such as Hyalodendriella, Ochrocladosporium, Rachicladosporium, Rhizocladosporium, Toxicocladosporium and Verrucocladosporium. A further new taxon is described in Devriesia (Teratosphaeriaceae). Furthermore, Cladosporium castellanii, the etiological agent of tinea nigra in humans, is confirmed as synonym of Stenella araguata, while the type species of Stenella is shown to be linked to the Teratosphaeriaceae (Capnodiales), and not the Mycosphaerellaceae as formerly presumed. PMID:18490995

  13. Delimitation of the lung region with distributed ultrasound transducers

    NASA Astrophysics Data System (ADS)

    Cardona Cárdenas, Diego Armando; Furuie, Sérgio Shiguemi

    2016-04-01

    One technique used to infer and monitor patient's respiratory conditions is the electrical impedance tomography (EIT). This provides images with information about lung function. The EIT image contrast is dependent on the variation of electrical impedance, therefore, this image does not provide anatomical details in border regions of several organs. To contribute to a clinical solution, we propose a new method to delimit regions of interest such as the pulmonary region and to improve the reconstruction quality of the EIT. Using a Matlab Toolbox k-wave, the ultrasound propagation phenomenon in homogeneous medium without patient (Reference) and with thoracic models were simulated, separately via a set of several ultrasound transducers distributed around the chest. After pulse emission by a transducer (TR), all received signals were compared considering the two sets of signals. If the energy relation between parts of the signals does not exceed an empirical threshold (30% in this study), a partial mask is generated between the transmitter and the receptor. This process was repeated until all 128 transducers are considered as TR-emitters. The 128 transducers (150kHz) are uniformly distributed. The evaluation was made by visually comparing the resulting images with the respective simulated object. A simple approach was presented to delimit high contrast organs with ultrasound transducers distributed around the patient. This approach allows other lower contrast objects to become invisible by varying the threshold limit. The investigation, based on numerical simulations of ultrasonic propagation, has shown promising results in the delimitation of the pulmonary region.

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

    PubMed Central

    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

  15. On the difficulty to delimit disease risk hot spots

    NASA Astrophysics Data System (ADS)

    Charras-Garrido, M.; Azizi, L.; Forbes, F.; Doyle, S.; Peyrard, N.; Abrial, D.

    2013-06-01

    Representing the health state of a region is a helpful tool to highlight spatial heterogeneity and localize high risk areas. For ease of interpretation and to determine where to apply control procedures, we need to clearly identify and delineate homogeneous regions in terms of disease risk, and in particular disease risk hot spots. However, even if practical purposes require the delineation of different risk classes, such a classification does not correspond to a reality and is thus difficult to estimate. Working with grouped data, a first natural choice is to apply disease mapping models. We apply a usual disease mapping model, producing continuous estimations of the risks that requires a post-processing classification step to obtain clearly delimited risk zones. We also apply a risk partition model that build a classification of the risk levels in a one step procedure. Working with point data, we will focus on the scan statistic clustering method. We illustrate our article with a real example concerning the bovin spongiform encephalopathy (BSE) an animal disease whose zones at risk are well known by the epidemiologists. We show that in this difficult case of a rare disease and a very heterogeneous population, the different methods provide risk zones that are globally coherent. But, related to the dichotomy between the need and the reality, the exact delimitation of the risk zones, as well as the corresponding estimated risks are quite different.

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

    EPA Science Inventory

    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 ...

  17. Sharing the Space: Distribution, Habitat Segregation and Delimitation of a New Sympatric Area of Subterranean Rodents

    PubMed Central

    Kubiak, Bruno Busnello; Galiano, Daniel; de Freitas, Thales Renato Ochotorena

    2015-01-01

    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. PMID:25856399

  18. Automatic Match between Delimitation Line and Real Terrain Based on Least-Cost Path Analysis

    NASA Astrophysics Data System (ADS)

    Feng, C. Q.; Jiang, N.; Zhang, X. N.; Ma, J.

    2013-11-01

    Nowadays, during the international negotiation on separating dispute areas, manual adjusting is lonely applied to the match between delimitation line and real terrain, which not only consumes much time and great labor force, but also cannot ensure high precision. Concerning that, the paper mainly explores automatic match between them and study its general solution based on Least -Cost Path Analysis. First, under the guidelines of delimitation laws, the cost layer is acquired through special disposals of delimitation line and terrain features line. Second, a new delimitation line gets constructed with the help of Least-Cost Path Analysis. Third, the whole automatic match model is built via Module Builder in order to share and reuse it. Finally, the result of automatic match is analyzed from many different aspects, including delimitation laws, two-sided benefits and so on. Consequently, a conclusion is made that the method of automatic match is feasible and effective.

  19. Molecular Phylogeny of Tribe Theeae (Theaceae s.s.) and Its Implications for Generic Delimitation

    PubMed Central

    Zhang, Wei; Kan, Sheng-long; Zhao, Hong; Li, Zhen-yu; Wang, Xiao-quan

    2014-01-01

    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. PMID:24848365

  20. Testing Classical Species Properties with Contemporary Data: How "Bad Species" in the Brassy Ringlets (Erebia tyndarus complex, Lepidoptera) Turned Good.

    PubMed

    Gratton, Paolo; Trucchi, Emiliano; Trasatti, Alessandra; Riccarducci, Giorgio; Marta, Silvio; Allegrucci, Giuliana; Cesaroni, Donatella; Sbordoni, Valerio

    2016-03-01

    All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information. PMID:26568458

  1. Delimiting the distribution range of Indirana leithii (Boulenger, 1888) (Anura: Ranixalidae), an endemic threatened anuran of the Western Ghats, based on molecular and morphological analysis.

    PubMed

    Modak, Nikhil; Padhye, Anand; Dahanukar, Neelesh

    2014-01-01

    Indirana leithii (Boulenger, 1888) (Anura: Ranixalidae) is a frog species endemic to the Western Ghats and is categorized as Vulnerable according to IUCN red list. This species is currently considered to be widespread over the entire Western Ghats. Our study based on molecular data (using DNA sequence fragments of the mitochondrial 12S rRNA and 16S rRNA genes and the nuclear rhodopsin gene), morphological analysis of topotypic material as well as material collected from a wide range within the northern Western Ghats, suggests that the species has instead a restricted range in the state of Maharashtra. Specimens identified as I. leithii from the southern Western Ghats as well as from outside the Western Ghats probably belong to hitherto undescribed species. To facilitate future studies in understanding the nature of this species complex and provide better means for identification and delimitation of species we provide molecular, morphological and osteological characters of I. leithii from topotyic material. PMID:24870665

  2. How do societies and "corporate" groups delimit themselves? A puzzle common to social and medical anthropology.

    PubMed

    Zempléni, A

    1990-06-01

    Classic anthropological theories define the first but neglect the second condition of social life. When they assume that the universal effect of the incest taboo is the opening of the consanguinial groups to the others, to exchange, they do not explain the closure of their sphere of reciprocity, i.e., the delimitation of the society. Hence the question: How, by which means, are stateless societies delimited or do they delimit themselves? Among the Senoufo of Ivory Coast (Nafara), one of the main acts of male initiation ceremonies--to the Poro, which is the very basis of the Senoufo's ethnic identity--is a ritual intercourse between the neophytes and their symbolic mother who has just given birth to them. This rite materializes the initiatic axiom: Senoufo men reproduce themselves by incest. In this case, the prescription of ritual incest is a means by which the society "closes" the field of reciprocity "opened" by the prohibition of actual incest. The return of the forbidden--at the heart of the institution which reproduces its identity--is the basic principle of the ritual delimitation of this society. Despite appearances, the delimitation of the so-called "corporate groups"--for example, an African lineage--is neither more "natural" nor more jural than that of the society which contains them. The limits of these groups are traced and retraced notably in the course of traditional "therapies" and by means of etiological entities which share several common, distinctive properties. (1) They cannot operate outside of the group delimited by them. (2) They are polyvalent and their effects are permutable from one group-member to another. (3) They act periodically: they have to dismantle the group periodically from the inside in order to be able to delimit it constantly from the outside. This phenomenon of spatio-temporal inversion (inside-outside; periodic-continuous), observable in any process of ritual delimitation, deserves our attention insofar as its closer analysis

  3. DNA barcodes, species delimitation, and bioassessment: issues of diversity, analysis, and standardization

    EPA Science Inventory

    DNA barcoding has the capability to uncover cryptic diversity otherwise undetectable using morphology alone. For aquatic bioassessment, this opportunity to discover hidden biodiversity presents new data for incorporation into environmental monitoring programs. Unfortunately, the ...

  4. Region-growing segmentation to automatically delimit synthetic drumlins in 'real' DEMs

    NASA Astrophysics Data System (ADS)

    Eisank, Clemens; Smith, Mike; Hillier, John

    2013-04-01

    Mapping or 'delimiting' landforms is one of geomorphology's primary tools. Computer-based techniques, such as terrain segmentation, may potentially provide terrain units that are close to the size and shape of landforms. Whether terrain units represent landforms heavily depends on the segmentation algorithm, its settings and the type of underlying land-surface parameters (LSPs). We assess a widely used region-growing technique, i.e. the multiresolution segmentation (MRS) algorithm as implemented in object-based image analysis software, for delimiting drumlins. Supervised testing was based on five synthetic DEMs that included the same set of perfectly known drumlins at different locations. This, for the first time, removes subjectivity from the reference data. Five LSPs were tested, and four variants were computed for each using two pre- and post-processing options. The automated method (1) employs MRS to partition the input LSP into 200 ever coarser terrain unit patterns, (2) identifies the spatially best matching terrain unit for each reference drumlin, and (3) computes four accuracy metrics for quantifying the aerial match between delimited and reference drumlins. MRS performed best on LSPs that are regional, derived from a decluttered DEM and then normalized. Median scale parameters (SPs) for segments best delineating drumlins were relatively stable for the same LSP, but varied significantly between LSPs. Larger drumlins were generally delimited at higher SPs. MRS indicated high robustness against variations in the location and distribution of drumlins.

  5. Dynamic gap junctional communication: a delimiting model for tissue responses.

    PubMed Central

    Christ, G J; Brink, P R; Ramanan, S V

    1994-01-01

    Gap junctions are aqueous intercellular channels formed by a diverse class of membrane-spanning proteins, known as connexins. These aqueous pores provide partial cytoplasmic continuity between cells in most tissues, and are freely permeable to a host of physiologically relevant second messenger molecules/ionic species (e.g., Ca2+, IP3, cAMP, cGMP). Despite the fact that these second messenger molecules/ionic species have been shown to alter junctional patency, there is no clear basis for understanding how dynamic and transient changes in the intracellular concentration of second messenger molecules might modulate the extent of intercellular communication among coupled cells. Thus, we have modified the tissue monolayer model of Ramanan and Brink (1990) to account for both the up-regulatory and down-regulatory effects on junctions by second messenger molecules that diffuse through gap junctions. We have chosen the vascular wall as our morphological correlate because of its anisotropy and large investment of gap junctions. The model allows us to illustrate the putative behavior of gap junctions under a variety of physiologically relevant conditions. The modeling studies demonstrated that transient alterations in intracellular second messenger concentrations are capable of producing 50-125% changes in the number of cells recruited into a functional syncytial unit, after activation of a single cell. Moreover, the model conditions required to demonstrate such physiologically relevant changes in intercellular diffusion among coupled cells are commonly observed in intact tissues and cultured cells. Images FIGURE 2 PMID:7811948

  6. Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny.

    PubMed

    Egan, Ashley N; Vatanparast, Mohammad; Cagle, William

    2016-11-01

    Several taxonomic and phylogenetic studies have hypothesized polyphyly within Pueraria DC., a genus comprising 19 species (24 with varieties) including the highly invasive Pueraria montana var. lobata (Kudzu) introduced to the U.S.A. about 150years ago. Previous efforts to investigate monophyly of the genus have been hampered by limited taxon sampling or a lack of comprehensive evolutionary context that would enable definitive taxonomic associations. This work presents a comprehensive phylogenetic investigation of Pueraria within the context of tribe Phaseoleae (Leguminosae). Polyphyly was found to be more extensive than previously thought, with five distinct lineages spread across the tribe and spanning over 25mya of divergence strongly supported by two chloroplast and one nuclear marker, AS2, presented here as a phylogenetic marker for the first time. Our phylogenies support taxonomic revisions to rectify polyphyly within Pueraria, including the resurrection of Neustanthus, moving one species to Teyleria, and the creation of two new genera, Haymondia and Toxicopueraria (taxonomic revisions published elsewhere). PMID:27495827

  7. Generic Delimitations in Tuberous Periplocoideae (Apocynaceae) from Africa and Madagascar

    PubMed Central

    MEVE, ULRICH; LIEDE, SIGRID

    2004-01-01

    • Background and Aims The number of genera included in Apocynaceae subfamily Periplocoideae is a matter of debate. DNA sequences are used here as an independent dataset to clarify generic relationships and classification of the tuberous periplocoid genera and to address the question of the phylogenetic interpretation of pollinia formation in Schlechterella. • Methods Representatives of nearly all African and Malagasy genera of Periplocoideae possessing root tubers were analysed using ITS and plastid DNA sequence characters. • Key Results Sequence data from non‐coding molecular markers (ITS of nrDNA and the trnT‐L and trnL‐F spacers as well as the trnL intron of plastid DNA) give support for a broad taxonomic concept of Raphionacme including Pentagonanthus. Together with Schlechterella, which is sister to Raphionacme, all Raphionacme‐like taxa form a derived monophyletic group of somewhat diverse species. Sister to the Schlechterella/Raphionacme clade is a clade comprising Stomatostemma and the not truly tuberous vine Mondia. In the combined analysis, sister to these two clades combined is a clade formed by Petopentia natalensis and Periploca. • Conclusions The recent inclusion of the monotypic South African Petopentia in the monotypic Malagasy endemic Ischnolepis is to be rejected. The Malagasy Camptocarpus is sister to the remainder of Periplocoideae in the ITS and combined analyses, and a Malagasy origin for the subfamily is discussed. PMID:14980976

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

    NASA Astrophysics Data System (ADS)

    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.

  9. [A proposal for a geometrical delimitation model for ventro-gluteal injection].

    PubMed

    de Meneses, Abel Silva; Marques, Isaac Rosa

    2007-01-01

    This study aimed at presenting and comparing geometrical and traditional technique for intramuscular injection in the ventrogluteal area. This is a quasi-experimental study of non-equivalent control group type, carried out with anatomical parts of corpses to verify the precision of function between traditional delimitation using hand as reference and the geometrical model which was constituted by tracing imaginary lines across bone structures of the hip, making a configuration of a triangle whose barycenter points the punction site. The study demonstrated that the punction site delimited by the geometrical technique keeped proportion of the envolved structures, and matched with the muscular womb of the ventrogluteal area in 100% of punctions. In another hand, in the traditional technique the punction site varied in 39.9% of punctions. PMID:18041556

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

    PubMed

    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. PMID:25264114

  11. A Multilocus Genealogical Concordance Approach to Species Delimitation within the Fusarium graminearum Species Complex of Cereal Head Blight Pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium head blight (FHB) of wheat and barley currently ranks as one of the most destructive and economically devastating plant diseases worldwide. Outbreaks and epidemics of FHB pose a double threat to cereal production: (i) the disease is frequently responsible for poor seed quality and reductio...

  12. Delimitation of air space and outer space - Is such a boundary needed now?

    NASA Technical Reports Server (NTRS)

    Hosenball, S. N.

    1983-01-01

    A discussion is presented of the question of establishing a boundary between air space and outer space. Four theories and approaches for establishing a delimitation between air space and outer space are examined. Spatial approaches include demarcation based on the division of the atmosphere into layers, demarcation based on aerodynamic characteristics of flight instrumentalities (von Karman Line), demarcation according to the lowest perigee of an orbiting satellite, and demarcation based upon the earth's gravitational effects. The functionalist approach is based on the delimitation or definition of the air space/outer space regime by the purpose and activities for which an object is designed in air space or outer space. The arbitrarist approach is supported by those who wish to draw an arbitrary line between air space and outer space. It is proposed that a pragmatist approach will be more useful than the other three approaches. The pragmatist approach advocates not establishing a boundary between air space and outer space at the present time or in the immediate future. It is argued that there are at present no serious problems that can be resolved by the definition/delimitation of air space and outer space.

  13. Assessment of multiresolution segmentation for delimiting drumlins in digital elevation models

    NASA Astrophysics Data System (ADS)

    Eisank, Clemens; Smith, Mike; Hillier, John

    2014-06-01

    Mapping or "delimiting" landforms is one of geomorphology's primary tools. Computer-based techniques such as land-surface segmentation allow the emulation of the process of manual landform delineation. Land-surface segmentation exhaustively subdivides a digital elevation model (DEM) into morphometrically-homogeneous irregularly-shaped regions, called terrain segments. Terrain segments can be created from various land-surface parameters (LSP) at multiple scales, and may therefore potentially correspond to the spatial extents of landforms such as drumlins. However, this depends on the segmentation algorithm, the parameterization, and the LSPs. In the present study we assess the widely used multiresolution segmentation (MRS) algorithm for its potential in providing terrain segments which delimit drumlins. Supervised testing was based on five 5-m DEMs that represented a set of 173 synthetic drumlins at random but representative positions in the same landscape. Five LSPs were tested, and four variants were computed for each LSP to assess the impact of median filtering of DEMs, and logarithmic transformation of LSPs. The testing scheme (1) employs MRS to partition each LSP exhaustively into 200 coarser scales of terrain segments by increasing the scale parameter (SP), (2) identifies the spatially best matching terrain segment for each reference drumlin, and (3) computes four segmentation accuracy metrics for quantifying the overall spatial match between drumlin segments and reference drumlins. Results of 100 tests showed that MRS tends to perform best on LSPs that are regionally derived from filtered DEMs, and then log-transformed. MRS delineated 97% of the detected drumlins at SP values between 1 and 50. Drumlin delimitation rates with values up to 50% are in line with the success of manual interpretations. Synthetic DEMs are well-suited for assessing landform quantification methods such as MRS, since subjectivity in the reference data is avoided which increases the

  14. Assessment of multiresolution segmentation for delimiting drumlins in digital elevation models.

    PubMed

    Eisank, Clemens; Smith, Mike; Hillier, John

    2014-06-01

    Mapping or "delimiting" landforms is one of geomorphology's primary tools. Computer-based techniques such as land-surface segmentation allow the emulation of the process of manual landform delineation. Land-surface segmentation exhaustively subdivides a digital elevation model (DEM) into morphometrically-homogeneous irregularly-shaped regions, called terrain segments. Terrain segments can be created from various land-surface parameters (LSP) at multiple scales, and may therefore potentially correspond to the spatial extents of landforms such as drumlins. However, this depends on the segmentation algorithm, the parameterization, and the LSPs. In the present study we assess the widely used multiresolution segmentation (MRS) algorithm for its potential in providing terrain segments which delimit drumlins. Supervised testing was based on five 5-m DEMs that represented a set of 173 synthetic drumlins at random but representative positions in the same landscape. Five LSPs were tested, and four variants were computed for each LSP to assess the impact of median filtering of DEMs, and logarithmic transformation of LSPs. The testing scheme (1) employs MRS to partition each LSP exhaustively into 200 coarser scales of terrain segments by increasing the scale parameter (SP), (2) identifies the spatially best matching terrain segment for each reference drumlin, and (3) computes four segmentation accuracy metrics for quantifying the overall spatial match between drumlin segments and reference drumlins. Results of 100 tests showed that MRS tends to perform best on LSPs that are regionally derived from filtered DEMs, and then log-transformed. MRS delineated 97% of the detected drumlins at SP values between 1 and 50. Drumlin delimitation rates with values up to 50% are in line with the success of manual interpretations. Synthetic DEMs are well-suited for assessing landform quantification methods such as MRS, since subjectivity in the reference data is avoided which increases the

  15. Convex Non-Negative Matrix Factorization for Brain Tumor Delimitation from MRSI Data

    PubMed Central

    Ortega-Martorell, Sandra; Lisboa, Paulo J. G.; Vellido, Alfredo; Simões, Rui V.; Pumarola, Martí; Julià-Sapé, Margarida; Arús, Carles

    2012-01-01

    Background Pattern Recognition techniques can provide invaluable insights in the field of neuro-oncology. This is because the clinical analysis of brain tumors requires the use of non-invasive methods that generate complex data in electronic format. Magnetic Resonance (MR), in the modalities of spectroscopy (MRS) and spectroscopic imaging (MRSI), has been widely applied to this purpose. The heterogeneity of the tissue in the brain volumes analyzed by MR remains a challenge in terms of pathological area delimitation. Methodology/Principal Findings A pre-clinical study was carried out using seven brain tumor-bearing mice. Imaging and spectroscopy information was acquired from the brain tissue. A methodology is proposed to extract tissue type-specific sources from these signals by applying Convex Non-negative Matrix Factorization (Convex-NMF). Its suitability for the delimitation of pathological brain area from MRSI is experimentally confirmed by comparing the images obtained with its application to selected target regions, and to the gold standard of registered histopathology data. The former showed good accuracy for the solid tumor region (proliferation index (PI)>30%). The latter yielded (i) high sensitivity and specificity in most cases, (ii) acquisition conditions for safe thresholds in tumor and non-tumor regions (PI>30% for solid tumoral region; ≤5% for non-tumor), and (iii) fairly good results when borderline pixels were considered. Conclusions/Significance The unsupervised nature of Convex-NMF, which does not use prior information regarding the tumor area for its delimitation, places this approach one step ahead of classical label-requiring supervised methods for discrimination between tissue types, minimizing the negative effect of using mislabeled voxels. Convex-NMF also relaxes the non-negativity constraints on the observed data, which allows for a natural representation of the MRSI signal. This should help radiologists to accurately tackle one of the

  16. Comparative anatomy of the nectary spur in selected species of Aeridinae (Orchidaceae)

    PubMed Central

    Stpiczyńska, Małgorzata; Davies, Kevin L.; Kamińska, Magdalena

    2011-01-01

    Background and Aims To date, the structure of the nectary spur of Aeridinae has not been studied in detail, and data relating to the nectaries of ornithophilous orchids remain scarce. The present paper compares the structural organization of the floral nectary in a range of Aeridinae species, including both entomophilous and ornithophilous taxa. Methods Nectary spurs of Ascocentrum ampullaceum (Roxb.) Schltr. var. aurantiacum Pradhan, A. curvifolium (Lindl.) Schltr., A. garayi Christenson, Papilionanthe vandarum (Rchb.f.) Garay, Schoenorchis gemmata (Lindl.) J.J. Sm., Sedirea japonica (Rchb.f.) Garay & H.R. Sweet and Stereochilus dalatensis (Guillaumin) Garay were examined by means of light microscopy, scanning electron microscopy and transmission electron microscopy. Key Results and Conclusions The diverse anatomy of the nectary is described for a range of Aeridinae species. All species of Ascocentrum investigated displayed features characteristic of ornithophilous taxa. They have weakly zygomorphic, scentless, red or orange flowers, display diurnal anthesis, possess cryptic anther caps and produce nectar that is secluded in a relatively massive nectary spur. Unicellular, secretory hairs line the lumen at the middle part of the spur. Generally, however, with the exception of Papilionanthe vandarum, the nectary spurs of all entomophilous species studied here (Schoenorchis gemmata, Sedirea japonica, Stereochilus dalatensis) lack secretory trichomes. Moreover, collenchymatous secretory tissue, present only in the nectary spur of Asiatic Ascocentrum species, closely resembles that found in nectaries of certain Neotropical species that are hummingbird-pollinated and assigned to subtribes Maxillariinae Benth., Laeliinae Benth. and Oncidiinae Benth. This similarity in anatomical organization of the nectary, regardless of geographical distribution and phylogeny, indicates convergence. PMID:21183455

  17. Polarity of prismatic facets delimiting WC grains in WC-Co alloys.

    PubMed

    Lay, Sabine; Donnadieu, Patricia; Loubradou, Marc

    2010-07-01

    This study reports a determination of the polarity of WC facets in WC-Co alloys sintered at the liquid state. In these alloys, WC grains are delimited by basal facets and two sets of {10 10} prismatic facets, one set of facets being much more developed than the other. A variation of the shape is observed as a function of the composition of the alloy. High resolution transmission electron microscopy is used to investigate the polarity of the prismatic facets owing to the typical triangular patterns appearing on the images. The effect of the composition is investigated using two alloys with different carbon potentials and one containing VC and Cr(3)C(2) as grain growth inhibitors. The interpretation of the images shows that in all cases, the same set of prismatic planes is favoured. PMID:20206535

  18. Polarization radiation in the planetary atmosphere delimited by a heterogeneous diffusely reflecting surface

    NASA Technical Reports Server (NTRS)

    Strelkov, S. A.; Sushkevich, T. A.

    1983-01-01

    Spatial frequency characteristics (SFC) and the scattering functions were studied in the two cases of a uniform horizontal layer with absolutely black bottom, and an isolated layer. The mathematical model for these examples describes the horizontal heterogeneities in a light field with regard to radiation polarization in a three dimensional planar atmosphere, delimited by a heterogeneous surface with diffuse reflection. The perturbation method was used to obtain vector transfer equations which correspond to the linear and nonlinear systems of polarization radiation transfer. The boundary value tasks for the vector transfer equation that is a parametric set and one dimensional are satisfied by the SFC of the nonlinear system, and are expressed through the SFC of linear approximation. As a consequence of the developed theory, formulas were obtained for analytical calculation of albedo in solving the task of dissemination of polarization radiation in the planetary atmosphere with uniform Lambert bottom.

  19. Plate tectonics and offshore boundary delimitation: Tunisia-Libya case at the International Court of Justice

    NASA Astrophysics Data System (ADS)

    Stanley, Daniel Jean

    1982-03-01

    The first major offshore boundary dispute where plate tectonics constituted a significant argument was recently brought before the International Court of Justice by Libya and Tunisia concerning the delimitation of their continental shelves. Libya placed emphasis on this concept to determine natural prolongation of its land territory under the sea. Tunisia contested use of the entire African continental landmass as a reference unit and views geography, geomorphology and bathymetry as relevant as geology. The Court pronounced that “It is the outcome, not the evolution in the long-distant past, which is of importance.” Moreover, it is the present-day configuration of coasts and seabed that are the main factors, not geology.

  20. Automatic landmark detection and scan range delimitation for topogram images using hierarchical network

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Mantlic, Frederic; Zhou, Shaohua K.

    2010-03-01

    The topogram is a 2D projection image of human body formed using a Computed Tomography (CT) scanner. It could be used to delimitate the desired scan range for further precise 3D CT scan. In this paper, we present a robust and efficient system for automatically determining scan ranges and their associated anatomical landmarks for topogram images. The system could handle the cases when only about 50% of the desired regions are visible. The robustness of our system can be attributed to three key ingredients: 1. The detection is based on a hierarchical network; 2. Network optimization is based on sequentially optimizing a set of subnetworks; 3. The detection probability is further refined based on the detection context. Extensive experiments (including external testing) on over 1000 topogram images show that our approach works robustly and efficiently even on very challenging data.

  1. Assessment of multiresolution segmentation for delimiting drumlins in digital elevation models

    PubMed Central

    Eisank, Clemens; Smith, Mike; Hillier, John

    2014-01-01

    Mapping or “delimiting” landforms is one of geomorphology's primary tools. Computer-based techniques such as land-surface segmentation allow the emulation of the process of manual landform delineation. Land-surface segmentation exhaustively subdivides a digital elevation model (DEM) into morphometrically-homogeneous irregularly-shaped regions, called terrain segments. Terrain segments can be created from various land-surface parameters (LSP) at multiple scales, and may therefore potentially correspond to the spatial extents of landforms such as drumlins. However, this depends on the segmentation algorithm, the parameterization, and the LSPs. In the present study we assess the widely used multiresolution segmentation (MRS) algorithm for its potential in providing terrain segments which delimit drumlins. Supervised testing was based on five 5-m DEMs that represented a set of 173 synthetic drumlins at random but representative positions in the same landscape. Five LSPs were tested, and four variants were computed for each LSP to assess the impact of median filtering of DEMs, and logarithmic transformation of LSPs. The testing scheme (1) employs MRS to partition each LSP exhaustively into 200 coarser scales of terrain segments by increasing the scale parameter (SP), (2) identifies the spatially best matching terrain segment for each reference drumlin, and (3) computes four segmentation accuracy metrics for quantifying the overall spatial match between drumlin segments and reference drumlins. Results of 100 tests showed that MRS tends to perform best on LSPs that are regionally derived from filtered DEMs, and then log-transformed. MRS delineated 97% of the detected drumlins at SP values between 1 and 50. Drumlin delimitation rates with values up to 50% are in line with the success of manual interpretations. Synthetic DEMs are well-suited for assessing landform quantification methods such as MRS, since subjectivity in the reference data is avoided which increases the

  2. Plate tectonics and offshore boundary delimitation: Tunisia-Libya case at the International Court of Justice

    SciTech Connect

    Stanley, D.J.

    1983-03-01

    Advances in the technology for exploiting resources of the oceans, particularly recovery of hydrocarbons and minerals in deep water, is benefiting a growing number of nations. At the same time, however, economic and political pressures have induced concern and there is now a much increased emphasis on jurisdiction to divide the offshore areas between the 132 coastal nations. Negotiations affect research operations at sea and, in consequence, marine scientists have been made aware of offshore problems as highlighted by the Law of the Sea Treaty (UNCLOS III) and complications arising from the legal versus scientific definitions of continental shelves and margins. The first major offshore boundary case of international scope where plate tectonics has constituted a significant argument is the one recently brought before the International Court of Justice by Libya and Tunisia concerning the delimitation of their continental shelves. Of the two parties, Libya placed the greatest emphasis on this concept as a means to determine natural prolongation of its land territory into and under the sea. Tunisia contested Libya's use of the whole of the African continental landmass as a reference unit; in Tunisia's view, considerations of geography, geomorphology, and bathymetry are at least as relevant as are those of geology. In its landmark judgment (February 1982) - which almost certainly will have far-reaching consequences in future such boundary delimitation cases - the court pronounced that It is the outcome, not the evolution in the long-distant past, which is of importance, and that it is the present-day configuration of the coasts and sea bed which are the main factors to be considered, not geology.

  3. Delimiting the Problem of Generalizability of Research Results: An Example from a Trend Study of a Citizenship Education Project.

    ERIC Educational Resources Information Center

    Napier, John D.; Grant, Evelyn T.

    1984-01-01

    How social studies researchers can use National Assessment of Educational Progress Public Use Data File tapes to delimit the problem of generalizability of research results is described. An example using data from a trend study of a citizenship education project is used to demonstrate the procedure. (Author/RM)

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

    PubMed Central

    Aguilar, César; Wood Jr, Perry L.; Cusi, Juan C.; Guzmán, Alfredo; Huari, Frank; Lundberg, Mikael; Mortensen, Emma; Ramírez, César; Robles, Daniel; Suárez, Juana; Ticona, Andres; Vargas, Víctor J.; Venegas, Pablo J.; Sites Jr, Jack W.

    2013-01-01

    Abstract 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. PMID:24453545

  5. Protecting Endangered Species in the United States

    NASA Astrophysics Data System (ADS)

    Shogren, Jason F.; Tschirhart, John

    2001-05-01

    Protecting Endangered Species in the United States is a collection of original papers by economists, biologists and political scientists with a common theme--protecting species at risk while safeguarding social order is a policy challenge that entangles biology, politics, and economics. The volume begins by assessing the biological needs that define the endangered species problem. The authors then explore the political realities that delimit the debate--who pays the costs and receives the benefits, and how interest groups affect species protection. The book addresses the economic choices that must be confronted for effective protection strategies including incentive schemes to promote preservation on public and private land.

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

    PubMed Central

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

    2014-01-01

    Background and objectives 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. Methods 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. Results 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. Conclusion 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. PMID:27226844

  7. Application of LANDSAT data to delimitation of avalanche hazards in Montane Colorado

    NASA Technical Reports Server (NTRS)

    Knepper, D. H., Jr. (Principal Investigator)

    1977-01-01

    The author has identified the following significant results. Many avalanche hazard zones can be identified on LANDSAT imagery, but not consistently over a large region. Therefore, regional avalanche hazard mapping, using LANDSAT imagery, must draw on additional sources of information. A method was devised that depicts three levels of avalanche hazards according to three corresponding levels of certainty that active avalanches occur. The lowest level, potential avalanche hazards, was defined by delineating slopes steep enough to support avalanches at elevations where snowfall was likely to be sufficient to produce a thick snowpack. The intermediate level of avalanche hazard was interpreted as avalanche hazard zones. These zones have direct and indirect indicators of active avalanche activity and were interpreted from LANDSAT imagery. The highest level of known or active avalanche hazards was compiled from existing maps. Some landslides in Colorado were identified and, to a degree, delimited on LANDSAT imagery, but the conditions of their identification were highly variable. Because of local topographic, geologic, structural, and vegetational variations, there was no unique landslide spectral appearance.

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

    PubMed

    Qin, Feng; Wang, Yu-Fei; Ferguson, David K; Chen, Wen-Li; Li, Ya-Meng; Cai, Zhe; Wang, Qing; Ma, Hong-Zhen; Li, Cheng-Sen

    2015-01-01

    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. PMID:25763576

  9. Fitting C2 Continuous Parametric Surfaces to Frontiers Delimiting Physiologic Structures

    PubMed Central

    Bayer, Jason D.

    2014-01-01

    We present a technique to fit C2 continuous parametric surfaces to scattered geometric data points forming frontiers delimiting physiologic structures in segmented images. Such mathematical representation is interesting because it facilitates a large number of operations in modeling. While the fitting of C2 continuous parametric curves to scattered geometric data points is quite trivial, the fitting of C2 continuous parametric surfaces is not. The difficulty comes from the fact that each scattered data point should be assigned a unique parametric coordinate, and the fit is quite sensitive to their distribution on the parametric plane. We present a new approach where a polygonal (quadrilateral or triangular) surface is extracted from the segmented image. This surface is subsequently projected onto a parametric plane in a manner to ensure a one-to-one mapping. The resulting polygonal mesh is then regularized for area and edge length. Finally, from this point, surface fitting is relatively trivial. The novelty of our approach lies in the regularization of the polygonal mesh. Process performance is assessed with the reconstruction of a geometric model of mouse heart ventricles from a computerized tomography scan. Our results show an excellent reproduction of the geometric data with surfaces that are C2 continuous. PMID:24782911

  10. Utility of Surface Pollen Assemblages to Delimit Eastern Eurasian Steppe Types

    PubMed Central

    Qin, Feng; Wang, Yu-Fei; Ferguson, David K.; Chen, Wen-Li; Li, Ya-Meng; Cai, Zhe; Wang, Qing; Ma, Hong-Zhen; Li, Cheng-Sen

    2015-01-01

    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. PMID:25763576

  11. A refined concept of the Critoniopsis bogotana species group in Colombia with two new species (Vernonieae, Asteraceae)

    PubMed Central

    Robinson, Harold; Keeley, Sterling C.

    2015-01-01

    Abstract Critoniopsis bogotana is more precisely delimited, and two related Colombian species are described as new. The form of trichomes on the abaxial surfaces of the leaves is found to be of major importance. A short key to the Critoniopsis bogotana group is provided. PMID:25931974

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

    PubMed Central

    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

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

    PubMed

    Lozouet, Pierre; Krygelmans, Anouchka

    2016-01-01

    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). PMID:27394632

  14. Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

    PubMed

    Nadler, Steven A; DE León, Gerardo Pérez-Ponce

    2011-11-01

    Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases. PMID:21281559

  15. These lit areas are undeveloped: Delimiting China's urban extents from thresholded nighttime light imagery

    NASA Astrophysics Data System (ADS)

    Liu, Ying; Delahunty, Tina; Zhao, Naizhuo; Cao, Guofeng

    2016-08-01

    Nighttime light imagery is a powerful tool to study urbanization because it can provide a uniform metric, lit area, to delimit urban extents. However, lit area is much larger than actual urban area, so thresholds of digital number (DN) values are usually needed to reduce the lit area. The threshold varies greatly among different regions, but at present it is still not very clear what factors impact the changes of the threshold. In this study, urban extent by province for China is mapped using official statistical data and four intercalibrated and geometrically corrected nighttime light images between 2004 and 2010. Lit area in the imagery for most provinces is at least 94% greater than the official amount of urban area. Regression analyses show a significant correlation between optimal thresholds and GDP per capita, and larger thresholds more commonly indicate higher economic level. Size and environmental condition may explain a province's threshold that is disproportionate to GDP. Findings indicate one threshold DN is not appropriate for multiple (adjacent) province urban extent mapping, and optimal thresholds for one year may be notably different than the next. Province-level derived thresholds are not appropriate for other geographic levels. Brightness of nighttime lights is an advantage over imagery that relies on daylight reflection, and decreases in brightness indicate faster growth in the horizontal direction than the vertical. A province's optimal threshold does not always maintain an increase with population and economic growth. In the economically developed eastern provinces, urban population densities decreased (and this is seen in the brightness data), while urban population increased.

  16. Species Recognition and Cryptic Species in the Tuber indicum Complex

    PubMed Central

    Chen, Juan; Guo, Shun-Xing; Liu, Pei-Gui

    2011-01-01

    Morphological delimitation of Asian black truffles, including Tuber himalayense, T. indicum, T. sinense, T. pseudohimalayense, T. formosanum and T. pseudoexcavatum, has remained problematic and even phylogenetic analyses have been controversial. In this study, we combined five years of field investigation in China with morphological study and DNA sequences analyses (ITS, LSU and β-tubulin) of 131 Tuber specimens to show that T. pseudohimalayense and T. pseudoexcavatum are the same species. T. formosanum is a separate species based on its host plants and geographic distribution, combined with minor morphological difference from T. indicum. T. sinense should be treated as a synonym of T. indicum. Our results demonstrate that the present T. indicum, a single described morphological species, should include at least two separate phylogenetic species. These findings are of high importance for truffle taxonomy and reveal and preserve the richness of truffle diversity. PMID:21297969

  17. Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the Cladia aggregata Complex (Ascomycota, Lecanorales)

    PubMed Central

    Parnmen, Sittiporn; Rangsiruji, Achariya; Mongkolsuk, Pachara; Boonpragob, Kansri; Nutakki, Aparna; Lumbsch, H. Thorsten

    2012-01-01

    The Cladia aggregata complex is one of the phenotypically most variable groups in lichenized fungi, making species determination difficult and resulting in different classifications accepting between one to eight species. Multi-locus DNA sequence data provide an avenue to test species delimitation scenarios using genealogical and coalescent methods, employing gene and species trees. Here we tested species delimitation in the complex using molecular data of four loci (nuITS and IGS rDNA, protein-coding GAPDH and Mcm-7), including 474 newly generated sequences. Using a combination of ML and Bayesian gene tree topologies, species tree inferences, coalescent-based species delimitation, and examination of phenotypic variation we assessed the circumscription of lineages. We propose that results from our analyses support a 12 species delimitation scenario, suggesting that there is a high level of species diversity in the complex. Morphological and chemical characters often do not characterize lineages but show some degree of plasticity within at least some of the clades. However, clades can often be characterized by a combination of several phenotypical characters. In contrast to the amount of homoplasy in the morphological characters, the data set exhibits some geographical patterns with putative species having distribution patterns, such as austral, Australasian or being endemic to Australia, New Zealand or Tasmania. PMID:23272229

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. 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.

    PubMed

    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. PMID:25076129

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Delimitation of Russula Subgenus Amoenula in Korea Using Three Molecular Markers

    PubMed Central

    Park, Myung Soo; Fong, Jonathan J.; Lee, Hyun; Oh, Seung-Yoon; Jung, Paul Eunil; Min, Young Ju; Seok, Soon Ja

    2013-01-01

    Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula. PMID:24493939

  2. The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

    PubMed Central

    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. PMID:25076129

  3. The Species Problem in Myxomycetes Revisited.

    PubMed

    Walker, Laura M; Stephenson, Steven L

    2016-08-01

    Species identification in the myxomycetes (plasmodial slime molds or myxogastrids) poses particular challenges to researchers as a result of their morphological plasticity and frequent alteration between sexual and asexual life strategies. Traditionally, myxomycete morphology has been used as the primary method of species delimitation. However, with the increasing availability of genetic information, traditional myxomycete taxonomy is being increasingly challenged, and new hypotheses continue to emerge. Due to conflicts that sometimes occur between traditional and more modern species concepts that are based largely on molecular data, there is a pressing need to revisit the discussion surrounding the species concept used for myxomycetes. Biological diversity is being increasingly studied with molecular methods and data accumulates at ever-faster rates, making resolution of this matter urgent. In this review, currently used and potentially useful species concepts (biological, morphological, phylogenetic and ecological) are reviewed, and an integrated approach to resolve the myxomycete species problem is discussed. PMID:27351595

  4. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota).

    PubMed

    Alors, David; Lumbsch, H Thorsten; Divakar, Pradeep K; Leavitt, Steven D; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  5. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota)

    PubMed Central

    Alors, David; Lumbsch, H. Thorsten; Divakar, Pradeep K.; Leavitt, Steven D.; Crespo, Ana

    2016-01-01

    High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species. PMID:26863231

  6. New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands

    PubMed Central

    DiDomenico, Angela; Hedin, Marshal

    2016-01-01

    Abstract The western United States is home to numerous narrowly endemic harvestman taxa (Arachnida, Opiliones), including members of the genus Sitalcina Banks, 1911. Sitalcina is comprised of three species groups, including the monospecific Sitalcina californica and Sitalcina lobata groups, and the Sitalcina sura group with eight described species. All species in the Sitalcina sura group have very small geographic distributions, with group members distributed like disjunct “beads on a string” from Monterey south to southern California and southeast to the sky-island mountain ranges of southern Arizona. Here, molecular phylogenetic and species delimitation analyses were conducted for all described species in the Sitalcina sura group, plus several newly discovered populations. Species trees were reconstructed using multispecies coalescent methods implemented in *BEAST, and species delimitation was accomplished using Bayes Factor Delimitation (BFD). Based on quantitative species delimitation results supported by consideration of morphological characters, two new species (Sitalcina oasiensis sp. n., Sitalcina ubicki sp. n.) are described. We also provide a description of the previously unknown male of Sitalcina borregoensis Briggs, 1968. Molecular phylogenetic evidence strongly supports distinctive desert versus coastal clades, with desert canyon taxa from southern California more closely related to Arizona taxa than to geographically proximate California coastal taxa. We hypothesize that southern ancestry and plate tectonics have played a role in the diversification history of this animal lineage, similar to sclerophyllous plant taxa of the Madro-Tertiary Geoflora. Molecular clock analyses for the Sitalcina sura group are generally consistent with these hypotheses. We also propose that additional Sitalcina species await discovery in the desert canyons of southern California and northern Baja, and the mountains of northwestern mainland Mexico. PMID:27199607

  7. New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands.

    PubMed

    DiDomenico, Angela; Hedin, Marshal

    2016-01-01

    The western United States is home to numerous narrowly endemic harvestman taxa (Arachnida, Opiliones), including members of the genus Sitalcina Banks, 1911. Sitalcina is comprised of three species groups, including the monospecific Sitalcina californica and Sitalcina lobata groups, and the Sitalcina sura group with eight described species. All species in the Sitalcina sura group have very small geographic distributions, with group members distributed like disjunct "beads on a string" from Monterey south to southern California and southeast to the sky-island mountain ranges of southern Arizona. Here, molecular phylogenetic and species delimitation analyses were conducted for all described species in the Sitalcina sura group, plus several newly discovered populations. Species trees were reconstructed using multispecies coalescent methods implemented in *BEAST, and species delimitation was accomplished using Bayes Factor Delimitation (BFD). Based on quantitative species delimitation results supported by consideration of morphological characters, two new species (Sitalcina oasiensis sp. n., Sitalcina ubicki sp. n.) are described. We also provide a description of the previously unknown male of Sitalcina borregoensis Briggs, 1968. Molecular phylogenetic evidence strongly supports distinctive desert versus coastal clades, with desert canyon taxa from southern California more closely related to Arizona taxa than to geographically proximate California coastal taxa. We hypothesize that southern ancestry and plate tectonics have played a role in the diversification history of this animal lineage, similar to sclerophyllous plant taxa of the Madro-Tertiary Geoflora. Molecular clock analyses for the Sitalcina sura group are generally consistent with these hypotheses. We also propose that additional Sitalcina species await discovery in the desert canyons of southern California and northern Baja, and the mountains of northwestern mainland Mexico. PMID:27199607

  8. Species Detection and Identification in Sexual Organisms Using Population Genetic Theory and DNA Sequences

    PubMed Central

    Birky, C. William

    2013-01-01

    Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ≥4) or the same species (K/θ<4) with probability ≥0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes. PMID:23308113

  9. Use of electromagnetic induction surveys to delimit zones of contrasting tree development in an irrigated olive orchard in Southern Spain.

    NASA Astrophysics Data System (ADS)

    Pedrera, Aura; Vanderlinden, Karl; Jesús Espejo-Pérez, Antonio; Gómez, José Alfonso; Giráldez, Juan Vicente

    2014-05-01

    Olives are historically closely linked to Mediterranean culture and have nowadays important societal and economical implications. Improving yield and preventing infestation by soil-borne pathogens are crucial issues in maintaining olive cropping competitive. In order to assess both issues properly at the farm or field scale, accurate knowledge of the spatial distribution of soil physical properties and associated water dynamics is required. Conventional soil surveying is generally prohibitive at commercial farms, but electromagnetic induction (EMI) sensors, measuring soil apparent electrical conductivity (ECa) provide a suitable alternative. ECa depends strongly on soil texture and water content and has been used exhaustively in precision agriculture to delimit management zones. The aim of this study was to delimit areas with unsatisfactory tree development in an olive orchard using EMI, and to identify the underlying relationships between ECa and the soil properties driving the spatial tree development pattern. An experimental catchment in S. Spain dedicated to irrigated olive cropping was surveyed for ECa under dry and wet soil conditions (0.06 vs. 0.22 g/g, respectively), using a Dualem 21-S EMI sensor. In addition, ECa and gravimetric soil water content (SWC) was measured at 45 locations throughout the catchment during each survey. At each of these locations, soil profile samples were collected to determine textural class including coarse particles content, organic matter (OM), and bulk density. Measurements for dry soil conditions with the perpendicular coil configuration with a separation of 2.1 m (P2.1) were chosen to make a first assessment of the orchard-growth variability. According to the shape of the histogram, the P2.1 ECa values were classified to delimit three areas in the field for which canopy coverage was estimated. Combining the 4 ECa signals for the wet and dry surveys, a principal component (PC) analysis showed that 91% of the total variance

  10. Delimiting oceanographic provinces to determine drivers of mesoscale patterns in benthic megafauna: A case study in the Barents Sea

    NASA Astrophysics Data System (ADS)

    Lacharité, Myriam; Jørgensen, Lis Lindal; Metaxas, Anna; Lien, Vidar S.; Skjoldal, Hein Rune

    2016-08-01

    Communities of benthic megafauna in the deep waters of continental shelves (> 100 m) are important components of marine ecosystems. In high-latitude ecosystems, this fauna is increasingly impacted by human activities and climate variability. In this study, we provide baseline knowledge on the oceanographic conditions affecting its distribution in the Barents Sea in the vicinity of the Polar Front - an oceanic front occurring at the transition zone between the Atlantic and Arctic water masses. We used fields of temperature and currents from an ocean circulation model (Regional Ocean Modelling System - ROMS) to derive variables divided into 3 groups relevant to bottom fauna (temperature, water column structure and bottom currents) expressing either mean conditions or temporal variability over 10 years (2001-2010). Benthic megafauna was surveyed in summer 2011 at 139 sites. To analyze the relationship between spatial variability in the composition of benthic megafauna (i.e., β-diversity) and oceanographic conditions, we: (1) used generalized dissimilarity modelling (GDM) and (2) delimited oceanographic provinces (i.e., regions of similar conditions) for each group of variables using principal component analysis (PCA) followed by cluster analysis. Turnover in benthic megafauna was explained by 7 oceanographic variables (temperature: 4, water column structure: 2, bottom currents: 1), depth and geographic distance (56.7% of total deviance explained). Concurrently, patterns in oceanographic provinces among the 3 groups of variables coincided with results from the GDM, where provinces derived from temperature were sharply delimited relative to the other groups. We concluded that the spatial structure of the environment is important in the relationship between spatial variability of benthic megafauna and oceanographic conditions in shelf deep waters. Ocean models are powerful tools to study this relationship, but the way in which their inherent uncertainty affects the

  11. Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis

    PubMed Central

    Kerr, Kevin C R; Dove, Carla J

    2013-01-01

    The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin-1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence. PMID:23919139

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

    PubMed

    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. PMID:25593084

  13. Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species1

    PubMed Central

    Prebble, Jessica M.; Tate, Jennifer A.; Meudt, Heidi M.; Symonds, V. Vaughan

    2015-01-01

    Premise of the study: Microsatellite loci were developed as polymorphic markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) for use in species delimitation and population and conservation genetic studies. Methods and Results: Illumina MiSeq sequencing was performed on genomic DNA from seedlings of M. drucei. From trimmed paired-end sequences >400 bp, 484 microsatellite loci were identified. Twelve of 48 microsatellite loci tested were found to be polymorphic and consistently scorable when screened on 53 individuals from four populations representing the geographic range of M. drucei. They also amplify in all other species in the M. pygmaea species group, i.e., M. antarctica, M. brevis, M. glauca, and M. pygmaea, as well as 18 other Myosotis species. Conclusions: These 12 polymorphic microsatellite markers establish an important resource for research and conservation of the M. pygmaea species group and potentially other Southern Hemisphere Myosotis. PMID:26082880

  14. Integrating fuzzy logic and statistics to improve the reliable delimitation of biogeographic regions and transition zones.

    PubMed

    Olivero, Jesús; Márquez, Ana L; Real, Raimundo

    2013-01-01

    This study uses the amphibian species of the Mediterranean basin to develop a consistent procedure based on fuzzy sets with which biogeographic regions and biotic transition zones can be objectively detected and reliably mapped. Biogeographical regionalizations are abstractions of the geographical organization of life on Earth that provide frameworks for cataloguing species and ecosystems, for answering basic questions in biogeography, evolutionary biology, and systematics, and for assessing priorities for conservation. On the other hand, limits between regions may form sharply defined boundaries along some parts of their borders, whereas elsewhere they may consist of broad transition zones. The fuzzy set approach provides a heuristic way to analyse the complexity of the biota within an area; significantly different regions are detected whose mutual limits are sometimes fuzzy, sometimes clearly crisp. Most of the regionalizations described in the literature for the Mediterranean biogeographical area present a certain degree of convergence when they are compared within the context of fuzzy interpretation, as many of the differences found between regionalizations are located in transition zones, according to our case study. Compared with other classification procedures based on fuzzy sets, the novelty of our method is that both fuzzy logic and statistics are used together in a synergy in order to avoid arbitrary decisions in the definition of biogeographic regions and transition zones. PMID:22744774

  15. Testing the validity of Northern European species in the Chrysis ignita species group (Hymenoptera: Chrysididae) with DNA barcoding.

    PubMed

    Soon, Villu; Budrys, Eduardas; Orlovskytė, Svetlana; Paukkunen, Juho; Odegaard, Frode; Ljubomirov, Toshko; Saarma, Urmas

    2014-01-01

    Containing more than a hundred species, the Chrysis ignita species group is the largest and one of the most taxonomically challenging groups in its genus. It has not been possible to resolve the taxonomy of the group using traditional methods due to the lack of robust diagnostic morphological characters. Here we present the results of a molecular analysis designed to delimit species in the Chrysis ignita group for the first time; using mitochondrial sequence data for 364 in-group specimens consisting of all 18 species known to occur in Northern Europe. Two mitochondrial loci were analysed: a COI gene fragment, and a continuous DNA sequence consisting of 16S rRNA, tRNAVal, 12S rRNA and ND4. Two approaches were employed for delimiting species: (1) genetic distance analysis based on the standard COI barcode sequences and; (2) phylogenetic analysis of the COI fragment together with rRNA genes. Both analyses yielded trees with similar topology, but support values for nodes were higher using the second approach. Fifteen species were distinguished in all analyses: Chrysis angustula Schenck, 1856, C. brevitarsis Thomson, 1870, C. clarinicollis Linsenmaier, 1951, C. corusca Valkeila, 1971, C. fulgida Linnaeus, 1761, C. ignita (Linnaeus, 1758), C. impressa Schenck, 1856, C. iris Christ, 1791, C. leptomandibularis Niehuis, 2000, C. longula Abeille de Perrin, 1879, C. ruddii Shuckard, 1837, C. schencki Linsenmaier, 1968, C. subcoriacea Linsenmaier, 1959, C. terminata Dahlbom, 1854 and C. vanlithi Linsenmaier, 1959. The specific status of C. mediata Linsenmaier, 1951 and C. solida Haupt, 1957 was not resolved. Included unidentified specimens grouped in three clusters, two of which are distinctly delimited and apparently represent cryptic species. The specific status of the unidentified samples in the third cluster remained unclear. Moreover, our data suggest the existence of additional cryptic species currently lumped under the names C. pseudobrevitarsis Linsenmaier

  16. Genotype Delimitation in the Nod-Independent Model Legume Aeschynomene evenia

    PubMed Central

    Arrighi, Jean-François; Cartieaux, Fabienne; Chaintreuil, Clémence; Brown, Spencer; Boursot, Marc; Giraud, Eric

    2013-01-01

    Research on the nitrogen-fixing symbiosis has been so far focused on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some semi-aquatic Aeschynomene species present the distinctive feature to form nitrogen-fixing nodules on both roots and stems following elicitation by photosynthetic bradyrhizobia that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium-legume symbiosis. To decipher the molecular mechanisms of this unique Nod-independent nitrogen-fixing symbiosis, we previously identified A. evenia C. Wright as an appropriate model legume, because it displays all the requisites for molecular and genetic approaches. To advance the use of this new model legume species, here we characterized the intraspecific diversity found in A. evenia. For this, the accessions available in germplasm banks were collected and subjected to morphological investigations, genotyping with RAPD and SSR markers, molecular phylogenies using ITS and single nuclear gene sequences, and cross-compatibility tests. These combined analyses revealed an important intraspecific differentiation that led us to propose a new taxonomic classification for A. evenia comprising two subspecies and four varieties. The A. evenia ssp. evenia contains var. evenia and var. pauciciliata whereas A. evenia ssp. serrulata comprises var. serrulata and var. major. This study provides information to exploit efficiently the diversity encountered in A. evenia and proposes subsp. evenia as the most appropriate subspecies for future projects aimed at identifying plant determinants of the Nod-independent symbiotic process. PMID:23717496

  17. Species limits in polymorphic mimetic Eniclases net-winged beetles from New Guinean mountains (Coleoptera, Lycidae)

    PubMed Central

    Bocek, Matej; Bocak, Ladislav

    2016-01-01

    Abstract Species delimitation was compared in a group of closely related lineages of aposematically colored Eniclases (Coleoptera, Lycidae) using morphology, genetic distances, and Bayesian implementation of the Poisson Tree Processes model. A high diversity of net-winged beetles was found in previously unsampled regions of New Guinea and ten new species are described: Eniclases bicolor sp. n., Eniclases bokondinensis sp. n., Eniclases brancuccii sp. n., Eniclases elelimensis sp. n., Eniclases infuscatus sp. n., Eniclases niger sp. n., Eniclases pseudoapertus sp. n., Eniclases pseudoluteolus sp. n., Eniclases tikapurensis sp. n., and Eniclases variabilis sp. n. Different levels of genetic and morphological diversification were identified in various sister-species pairs. As a result, both morphological and molecular analyses are used to delimit species. Sister-species with uncorrected pairwise genetic divergence as low as 0.45% were morphologically distinct not only in color pattern, but also in the relative size of eyes. Conversely, differences in color pattern regardless of their magnitude did not necessarily indicate genetic distance and intraspecific mimicry polymorphism was common. Additionally, genetic divergence without morphological differentiation was detected in one sister-species pair. Low dispersal propensity, diverse mimicry patterns, and mimetic polymorphism resulted in complex diversification of Eniclases and uncertain species delimitation in recently diversified lineages. PMID:27408550

  18. Application of a GIS algorithm to delimit the areas protected against basic lava flow invasion on Tenerife Island

    NASA Astrophysics Data System (ADS)

    Gómez-Fernández, F.

    2000-12-01

    A GIS algorithm has been applied to analyse the maximum potential extent that lava flows can reach in order to delimit the areas topographically protected against flow invasion. The algorithm selected makes use of a special kind of spatial analysis functions called neighbourhood operators, in which the outcome depends on the values that one or more specified variables adopt in the surroundings of the element where analysis takes place. Assuming the maximum magnitude hypothesis, potential lava flow invasion areas can be calculated with spatial analysis functions in the context of two propagation regimes: persistent flow lengthening, and a combination of persistent flow lengthening and widening. To define the algorithm behaviour for each regime, a series of simple stochastic rules have been set to establish the way in which lava flow propagation can proceed. The algorithm has been applied on three source areas located in Tenerife Island characterised by their high probability of occurrence of basic effusive events. For each area, maximum potential flow extent has been calculated following both propagation regimes, with the aim of delimiting the areas that would potentially remain out of lava reach. No distance limits have been taken into account to carry out the calculation, as lava has on many occasions reached the coastline either in historic or geologic times. An additional hazard exposure level analysis has been possible in those areas where results indicated that flows could potentially arrive from more than one source. Algorithm performance assessment has been carried out in terms of accuracy by generating a series of 3D views and comparing the algorithm application results with those obtained from stochastic physical model simulation. Although the GIS algorithm applied does not distinguish the probability level of an area being invaded by lava, it has clearly identified on Tenerife the areas which are potentially safe from the flows that could originate at any

  19. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs.

    PubMed

    Chaverri, P; Salgado, C; Hirooka, Y; Rossman, A Y; Samuels, G J

    2011-01-01

    Neonectria is a cosmopolitan genus and it is, in part, defined by its link to the anamorph genus Cylindrocarpon. Neonectria has been divided into informal groups on the basis of combined morphology of anamorph and teleomorph. Previously, Cylindrocarpon was divided into four groups defined by presence or absence of microconidia and chlamydospores. Molecular phylogenetic analyses have indicated that Neonectriasensu stricto and Cylindrocarponsensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarponsensu lato do not form a monophyletic group and that the respective informal groups may represent distinct genera. In the present work, a multilocus analysis (act, ITS, LSU, rpb1, tef1, tub) was applied to representatives of the informal groups to determine their level of phylogenetic support as a first step towards taxonomic revision of Neonectriasensu lato. Results show five distinct highly supported clades that correspond to some extent with the informal Neonectria and Cylindrocarpon groups that are here recognised as genera: (1) N. coccinea-group and Cylindrocarpon groups 1 & 4 (Neonectria/Cylindrocarponsensu stricto); (2) N.rugulosa-group (Rugonectria gen. nov.); (3) N. mammoidea/N. veuillotiana-groups and Cylindrocarpon group 2 (Thelonectria gen. nov.); (4) N. radicicola-group and Cylindrocarpon group 3 (Ilyonectria gen. nov.); and (5) anamorph genus Campylocarpon. Characteristics of the anamorphs and teleomorphs correlate with the five genera, three of which are newly described. New combinations are made for species where their classification is confirmed by phylogenetic data. PMID:21523189

  20. Development of agroclimatic zoning model to delimit the potential growing areas for macaw palm (Acrocomia aculeata)

    NASA Astrophysics Data System (ADS)

    Falasca, Silvia; Ulberich, Ana; Pitta-Alvarez, Sandra

    2016-07-01

    The growing biodiesel production requires the use of new technologies and alternative feedstocks to maintain the growing demand of this biofuel. The macaw (Acrocomia aculeata) is a palm native to Argentina whose fruits present high oil content. Due to its tolerance to prolonged drought, it is a promising crop for biodiesel and biokerosene production. The aim of this work was to design an agroclimatic zoning model to define the potential growing areas from macaw in Argentina. To define the agroclimatic suitability to produce oil, it was necessary to identify the requirements, limits, and biometeorological tolerance for this palm. In order to define the agroclimatic fitness of this crop in Argentina, the meteorological data corresponding to the period 1981-2010 were employed. The agroclimatic indices were integrated in a Geographic Information System. The maps were superimposed and the overlapping regions delineated the agroclimatic zoning. The agroclimatic zonation classified zones with homogeneous characteristics responding to bioclimatic requirements of this species, resulting in optimal, very suitable, suitable, and nonsuitable areas for macaw cultivation. The authors designed an agroclimatic zoning model based on bibliography. This model can be used in any part of the world, employing the same agroclimatic indices presented in this work.

  1. Delimitation and functional characterization of the bidirectional THOX-DUOXA promoter regions in thyrocytes.

    PubMed

    Christophe-Hobertus, Christiane; Christophe, Daniel

    2010-04-12

    The THOX and DUOXA genes encode components of the oxidative machinery involved in thyroid hormone biosynthesis. Both of these genes are duplicated in mammalian genomes and are positioned in a head-to-head configuration, THOX1 facing DUOXA1 and THOX2 facing DUOXA2, respectively. The intergenic regions in both couples of genes exhibit dissimilar compositions, being highly GC-rich in the case of THOX1-DUOXA1 but not in the other case. In this study we localized precisely the transcription starts of all four genes using the RLM-RACE technique. It revealed that the distance between THOX1 and DUOXA1 transcription units is of about 70bp only, whereas THOX2 and DUOXA2 transcription starts are separated by 170bp. Analysis of these putative promoter regions revealed the presence of several potential binding sites for transcription factor Sp1 within the THOX1-DUOXA1 intergenic space, and of a TATA box and an Inr element in front of DUOXA2 and THOX2 genes, respectively. The putative promoter regions were inserted into a specifically designed vector harbouring two distinct reporter genes facing each other and their activity was investigated in transient transfection experiments in rat thyroid PCCl3 cells. Both regions exhibited bidirectional promoter activity in the assay. Gel shift experiments using extracts obtained from PCCl3 cells demonstrated the existence of at least one functional Sp1 binding site within the THOX1-DUOXA1 promoter. When Sp1 binding was abolished by mutation of the DNA sequence, a clear reduction in promoter activity in both THOX1 and DUOXA1 directions was observed in the functional assay. As these promoter sequences are well conserved in mammalian genomes, it appears very likely that the results we obtained here in the rat may be extended to the other species. PMID:20060878

  2. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs

    PubMed Central

    Chaverri, P.; Salgado, C.; Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.

    2011-01-01

    Neonectria is a cosmopolitan genus and it is, in part, defined by its link to the anamorph genus Cylindrocarpon. Neonectria has been divided into informal groups on the basis of combined morphology of anamorph and teleomorph. Previously, Cylindrocarpon was divided into four groups defined by presence or absence of microconidia and chlamydospores. Molecular phylogenetic analyses have indicated that Neonectria sensu stricto and Cylindrocarpon sensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarpon sensu lato do not form a monophyletic group and that the respective informal groups may represent distinct genera. In the present work, a multilocus analysis (act, ITS, LSU, rpb1, tef1, tub) was applied to representatives of the informal groups to determine their level of phylogenetic support as a first step towards taxonomic revision of Neonectria sensu lato. Results show five distinct highly supported clades that correspond to some extent with the informal Neonectria and Cylindrocarpon groups that are here recognised as genera: (1) N. coccinea-group and Cylindrocarpon groups 1 & 4 (Neonectria/Cylindrocarpon sensu stricto); (2) N. rugulosa-group (Rugonectria gen. nov.); (3) N. mammoidea/N. veuillotiana-groups and Cylindrocarpon group 2 (Thelonectria gen. nov.); (4) N. radicicola-group and Cylindrocarpon group 3 (Ilyonectria gen. nov.); and (5) anamorph genus Campylocarpon. Characteristics of the anamorphs and teleomorphs correlate with the five genera, three of which are newly described. New combinations are made for species where their classification is confirmed by phylogenetic data. PMID:21523189

  3. Genetic variation corroborates subspecific delimitation in the Namib fog-basking beetle, Onymacris unguicularis (Haag) (Tenebrionidae, Coleoptera)

    PubMed Central

    Lamb, Trip; Pollard, Rachel; Bond, Jason E.

    2013-01-01

    Abstract The fog-basking beetle, Onymacris unguicularis (Haag, 1875), is currently listed as a polytypic form comprising two subspecies. A flightless substrate specialist, the beetleis endemic to vegetationless dunes in the Namib, where southern populations constitute the nominate subspecies, O. u. unguicularis, and populations some 300 km to the north compose O. u. schulzeae Penrith, 1984. Their taxonomic descriptions are based on minor differences in pronotal and prosternal shape, and the phylogenetic validity of these subspecies has yet to be ascertained. Here we reassess the polytypic status of O. unguicularis by (1) examining diagnostic phenotypic characters in conjunction with a geometric morphometric analysis, and (2) conducting phylogenetic analysis of mitochondrial DNA sequences. Our results confirm pronotal and prosternal differences, which are complemented by geometric morphometric resolution of the subspecies. Phylogenetic analysis recovered two reciprocally monophyletic lineages that exhibit perfect phylogeographic congruence with phenotypic variation. Our genetic data identify southern and northern populations as distinct lineages, corroborate morphometric data regarding subspecific delimitation, and therefore support the recognition of O. u. unguicularis and O. u. schulzeae as valid taxa under the general lineage concept. PMID:24294097

  4. Species limits, interspecific hybridization and phylogeny in the cryptic land snail complex Pyramidula: The power of RADseq data.

    PubMed

    Razkin, Oihana; Sonet, Gontran; Breugelmans, Karin; Madeira, María José; Gómez-Moliner, Benjamín Juan; Backeljau, Thierry

    2016-08-01

    Restriction site-associated DNA sequencing (RADseq) was used to jointly assess phylogenetic relationships, interspecific hybridization and species delimitation in the cryptic, non-model land snail complex Pyramidula. A robust phylogeny was inferred using a matrix of concatenated sequences of almost 1,500,000bp long, containing >97,000 polymorphic sites. Maximum likelihood analyses fully resolved the phylogenetic relationships among species and drastically improved phylogenetic trees obtained from mtDNA and nDNA gene trees (COI, 16S rRNA, 5.8S rRNA, ITS2 and 28S rRNA sequence data). The best species delimitation scenario was selected on the basis of 875 unlinked single nucleotide polymorphisms, showing that nine Pyramidula species should be distinguished in Europe. Applying D-statistics provided no or weak evidence of interspecific hybridization among Pyramidula, except for some evidence of gene flow between two species. PMID:27177931

  5. A Good Compromise: Rapid and Robust Species Proxies for Inventorying Biodiversity Hotspots Using the Terebridae (Gastropoda: Conoidea)

    PubMed Central

    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. PMID:25003611

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

    NASA Astrophysics Data System (ADS)

    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

  7. Integrative taxonomy of Metrichia Ross (Trichoptera: Hydroptilidae: Ochrotrichiinae) microcaddisflies from Brazil: descriptions of twenty new species.

    PubMed

    Santos, Allan P M; Takiya, Daniela M; Nessimian, Jorge L

    2016-01-01

    Metrichia is assigned to the Ochrotrichiinae, a group of almost exclusively Neotropical microcaddisflies. Metrichia comprises over 100 described species and, despite its diversity, only one species has been described from Brazil so far. In this paper, we provide descriptions for 20 new species from 8 Brazilian states: M. acuminata sp. nov., M. azul sp. nov., M. bonita sp. nov., M. bracui sp. nov., M. caraca sp. nov., M. circuliforme sp. nov., M. curta sp. nov., M. farofa sp. nov., M. forceps sp. nov., M. formosinha sp. nov., M. goiana sp. nov., M. itabaiana sp. nov., M. longissima sp. nov., M. peluda sp. nov., M. rafaeli sp. nov., M. simples sp. nov., M. talhada sp. nov., M. tere sp. nov., M. ubajara sp. nov., and M. vulgaris sp. nov. DNA barcode sequences (577 bp of the mitochondrial gene COI) were generated for 13 of the new species and two previously known species of Metrichia resulting in 64 sequences. In addition, COI sequences were obtained for other genera of Ochrotrichiinae (Angrisanoia, Nothotrichia, Ochrotrichia, Ragatrichia, and Rhyacopsyche). DNA sequences and morphological data were integrated to evaluate species delimitations. K2P pairwise distances were calculated to generate a neighbor-joining tree. COI sequences also were submitted to ABGD and GMYC methods to assess 'potential species' delimitation. Analyses showed a conspicuous barcoding gap among Metrichia sequences (highest intraspecific divergence: 4.8%; lowest interspecific divergence: 12.6%). Molecular analyses also allowed the association of larvae and adults of Metrichia bonita sp. nov. from Mato Grosso do Sul, representing the first record of microcaddisfly larvae occurring in calcareous tufa (or travertine). ABGD results agreed with the morphological delimitation of Metrichia species, while GMYC estimated a slightly higher number of species, suggesting the division of two morphological species, each one into two potential species. Because this could be due to unbalanced sampling and the

  8. New diagnosis for species of Plutomurus Yosii (Collembola, Tomoceridae), with descriptions of two new species from Georgian caves.

    PubMed

    Barjadze, Shalva; Baquero, Enrique; Soto-Adames, Felipe N; Giordano, Rosanna; Jordana, Rafael

    2016-01-01

    Two new species of the genus Plutomurus, P. revazi sp. nov. from Prometheus and Satsurblia caves and P. eristoi sp. nov. from Satevzia Cave are described, illustrated and differentiated from other morphologically closely related species. A high variability in the number of teeth in the claw, unguiculus and mucro of P. revazi sp. nov. demonstrate that these characters are not useful for species diagnosis. However, dorsal chaetotaxy was shown to be stable character for this purpose. Analysis of DNA sequences for the COI and 28S genes is congruent with species-level groups delimited by chaetotaxy, and provide additional support for chaetotaxy as the most reliable morphological character system to distinguish species in Plutomurus. A key to species of the genus Plutomurus found in Georgia is provided, which for the first time includes characters of the macrochaetotaxy. PMID:27395573

  9. Taxonomy of the Colocasiomyia gigantea species group (Diptera, Drosophilidae), with descriptions of four new species from Yunnan, China

    PubMed Central

    Li, Nan-Nan; Toda, Masanori J.; Fu, Zhao; Chen, Ji-Min; Li, Su-Hua; Gao, Jian-Jun

    2014-01-01

    Abstract Species of the genus Colocasiomyia de Meijere feed/breed on inflorescences/infructescences of the plants from the families Araceae, Arecaceae and Magnoliaceae. Although most of them utilize plants from the subfamily Aroideae of Araceae, three species of the recently established C. gigantea species group make use of plants of the subfamily Monsteroideae. We describe four new species of the gigantea group found from Yunnan, China: Colocasiomyia longifilamentata Li & Gao, sp. n., C. longivalva Li & Gao, sp. n., C. hailini Li & Gao, sp. n., and C. yini Li & Gao, sp. n. The species delimitation is proved in virtue of not only morphology but also DNA barcodes, i.e., sequences of the partial mitochondrial COI (cytochrome c oxidase subunit I) gene. Some nucleotide sites with fixed status in the alignment of the COI sequences (658 sites in length) are used as “pure” molecular diagnostic characters to delineate species in the gigantea group. PMID:24843281

  10. Integrative taxonomy of Metrichia Ross (Trichoptera: Hydroptilidae: Ochrotrichiinae) microcaddisflies from Brazil: descriptions of twenty new species

    PubMed Central

    Takiya, Daniela M.; Nessimian, Jorge L.

    2016-01-01

    Metrichia is assigned to the Ochrotrichiinae, a group of almost exclusively Neotropical microcaddisflies. Metrichia comprises over 100 described species and, despite its diversity, only one species has been described from Brazil so far. In this paper, we provide descriptions for 20 new species from 8 Brazilian states: M. acuminata sp. nov., M. azul sp. nov., M. bonita sp. nov., M. bracui sp. nov., M. caraca sp. nov., M. circuliforme sp. nov., M. curta sp. nov., M. farofa sp. nov., M. forceps sp. nov., M. formosinha sp. nov., M. goiana sp. nov., M. itabaiana sp. nov., M. longissima sp. nov., M. peluda sp. nov., M. rafaeli sp. nov., M. simples sp. nov., M. talhada sp. nov., M. tere sp. nov., M. ubajara sp. nov., and M. vulgaris sp. nov. DNA barcode sequences (577 bp of the mitochondrial gene COI) were generated for 13 of the new species and two previously known species of Metrichia resulting in 64 sequences. In addition, COI sequences were obtained for other genera of Ochrotrichiinae (Angrisanoia, Nothotrichia, Ochrotrichia, Ragatrichia, and Rhyacopsyche). DNA sequences and morphological data were integrated to evaluate species delimitations. K2P pairwise distances were calculated to generate a neighbor-joining tree. COI sequences also were submitted to ABGD and GMYC methods to assess ‘potential species’ delimitation. Analyses showed a conspicuous barcoding gap among Metrichia sequences (highest intraspecific divergence: 4.8%; lowest interspecific divergence: 12.6%). Molecular analyses also allowed the association of larvae and adults of Metrichia bonita sp. nov. from Mato Grosso do Sul, representing the first record of microcaddisfly larvae occurring in calcareous tufa (or travertine). ABGD results agreed with the morphological delimitation of Metrichia species, while GMYC estimated a slightly higher number of species, suggesting the division of two morphological species, each one into two potential species. Because this could be due to unbalanced sampling and