Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of m...
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| Published in | Molecular ecology Vol. 22; no. 13; pp. 3495 - 3510 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Blackwell Scientific Publications
01.07.2013
Blackwell Publishing Ltd Blackwell |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0962-1083 1365-294X 1365-294X |
| DOI | 10.1111/mec.12324 |
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| Abstract | Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data‐rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5‐gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists. |
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| AbstractList | Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data‐rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5‐gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists. Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists. [PUBLICATION ABSTRACT] Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists.Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists. |
| Author | Brown, R. M. Siler, C. D. Oaks, J. R. Diesmos, A. C. Welton, L. J. |
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| Copyright | 2013 John Wiley & Sons Ltd 2014 INIST-CNRS 2013 John Wiley & Sons Ltd. Copyright © 2013 John Wiley & Sons Ltd |
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| Keywords | nuclear DNA species delimitation Taxonomy Tropical zone Philippines Conservation Diversity Mitochondrial DNA Phylogeny Cryptic Vertebrata Southeast Asia Sauria Genetics Reptilia conservation genetics |
| Language | English |
| License | CC BY 4.0 2013 John Wiley & Sons Ltd. |
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| Notes | http://dx.doi.org/10.1111/mec.12324 istex:5BDAB6238432F6AE79199D61C7BB5526BA13A120 Fulbright and Fulbright-Hayes Fellowships University of Kansas Biodiversity Institute Appendix S1 Specimen voucher numbers, identification and geographic location of samples for this study. Appendix S2 Description of *BEAST methodology for inferring BP&P starting topologies. Appendix S3 Description of BP&P species delimitation methodology.Fig. S1 Mitochondrial (left) and concatenated nuclear (right) maximum likelihood phylogenetic estimates. Only bootstrap support >70% is indicated. Fig. S2 Individual maximum likelihood gene trees for the four nuclear loci sampled. Only bootstrap support >70% is indicated. Fig. S3 Mitochondrial and nuclear (ND1-ND2, DGL-α, L52, L74, PRLR) statistical haplotype networks inferred by TCS (Clement et al. ). Fig. S4 Distance-based (neighbour-joining) nuclear haplotype network as inferred by the NeighborNet algorithm of splitstree. Input standardized distance matrix created with the program pofad. Fig. S5 Distruct visualization (Rosenberg ) visualization of structure analyses and summarized geographic distribution of major Varanus demes (Pritchard et al. ) for K = 6 populations. Fig. S6 Bayesian estimates of the Varanus salvator Complex species tree as inferred by the program *beast. Fig. S7 Recognized major faunal regions and island groups of the Philippines, including distributions of Varanus species.Table S1 Individual loci, original publications and polymerase chain reaction (PCR) thermal profiles for each. Annealing temperature was varied to improve amplification for problematic samples. Table S2 Loci and associated primers sequenced for this study. Thermal profiles for PCR and cycle sequencing reactions vary only by annealing temperature (55-58º) across primers and samples. Table S3 Estimated models of evolution by data partition, as inferred by jmodeltest. Final models selected by AIC and applied for partitioned, model-based analyses. Table S4 Summary of results among loci for tests of neutrality using Tajima's D (Tajima ). NSF - No. DEB 0804115 ArticleID:MEC12324 NSF Biotic Surveys and Inventories - No. DEB 0743491 ark:/67375/WNG-0XZ0FMSM-4 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 |
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| SubjectTerms | Amphibia. Reptilia Animal populations Animals Asia, Southeastern Bayes Theorem Bayesian analysis Biodiversity Biogeography Biological and medical sciences Biological evolution Boundaries conservation genetics Conservation of Natural Resources data collection DNA, Mitochondrial - genetics Evolution, Molecular Evolutionary biology Fundamental and applied biological sciences. Psychology Genetic diversity Genetic Loci Genetic Speciation Genetic Variation Genetics of eukaryotes. Biological and molecular evolution Haplotypes India Lacertilia Lizards Lizards - classification Lizards - genetics mitochondrial DNA Molecular Sequence Data nuclear DNA Philippines Phylogenetics Phylogeny Phylogeography Population genetics, reproduction patterns Population structure Reptiles & amphibians Sequence Alignment Sequence Analysis, DNA South East Asia Southeast Asia species delimitation Species diversity Varanus Vertebrates: general zoology, morphology, phylogeny, systematics, cytogenetics, geographical distribution Water monitoring |
| Title | Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards |
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