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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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3
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation. Genes (Basel) 2020; 11:genes11111241. [PMID: 33105659 PMCID: PMC7716205 DOI: 10.3390/genes11111241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/10/2020] [Accepted: 10/20/2020] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.
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Key KN, Banta JA, Gluesenkamp AG, Hertweck KL, Placyk JS. CONSERVATION BIOLOGY OF A SOUTHWESTERN ENDEMIC, THE TEXAS GARTER SNAKE, THAMNOPHIS SIRTALIS ANNECTENS: AN INTEGRATIVE PERSPECTIVE. SOUTHWEST NAT 2019. [DOI: 10.1894/0038-4909-64-1-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kayla N. Key
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - Joshua A. Banta
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | | | - Kate L. Hertweck
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - John S. Placyk
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
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Hernández‐Leal MS, Suárez‐Atilano M, Piñero D, González‐Rodríguez A. Regional patterns of genetic structure and environmental differentiation in willow populations ( Salix humboldtiana Willd.) from Central Mexico. Ecol Evol 2019; 9:9564-9579. [PMID: 31534675 PMCID: PMC6745842 DOI: 10.1002/ece3.5475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/11/2019] [Accepted: 07/01/2019] [Indexed: 11/05/2022] Open
Abstract
AIM To infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico. LOCATION Central Mexico. METHODS We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA. RESULTS Both cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution. MAIN CONCLUSIONS The genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.
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Affiliation(s)
- Mariana S. Hernández‐Leal
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMéxico
- Departamento de Ecología de la Biodiversidad, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Marco Suárez‐Atilano
- Departamento de Ecología de la Biodiversidad, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Antonio González‐Rodríguez
- Instituto de Investigaciones en Ecosistemas y SustentabilidadUniversidad Nacional Autónoma de MéxicoMoreliaMéxico
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Molecular phylogeny of Macrosiphini (Hemiptera: Aphididae): An evolutionary hypothesis for the Pterocomma-group habitat adaptation. Mol Phylogenet Evol 2018; 121:12-22. [DOI: 10.1016/j.ympev.2017.12.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 10/25/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
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Salvador de Jesús-Bonilla V, García-París M, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process. INVERTEBR SYST 2018. [DOI: 10.1071/is17072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.
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Laopichienpong N, Muangmai N, Supikamolseni A, Twilprawat P, Chanhome L, Suntrarachun S, Peyachoknagul S, Srikulnath K. Assessment of snake DNA barcodes based on mitochondrial COI and Cytb genes revealed multiple putative cryptic species in Thailand. Gene 2016; 594:238-247. [PMID: 27632899 DOI: 10.1016/j.gene.2016.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 08/24/2016] [Accepted: 09/11/2016] [Indexed: 12/21/2022]
Abstract
DNA barcodes of mitochondrial cytochrome c oxidase I (COI), cytochrome b (Cytb) genes, and their combined data sets were constructed from 35 snake species in Thailand. No barcoding gap was detected in either of the two genes from the observed intra- and interspecific sequence divergences. Intra- and interspecific sequence divergences of the COI gene differed 14 times, with barcode cut-off scores ranging over 2%-4% for threshold values differentiated among most of the different species; the Cytb gene differed 6 times with cut-off scores ranging over 2%-6%. Thirty-five specific nucleotide mutations were also found at interspecific level in the COI gene, identifying 18 snake species, but no specific nucleotide mutation was observed for Cytb in any single species. This suggests that COI barcoding was a better marker than Cytb. Phylogenetic clustering analysis indicated that most species were represented by monophyletic clusters, suggesting that these snake species could be clearly differentiated using COI barcodes. However, the two-marker combination of both COI and Cytb was more effective, differentiating snake species by over 2%-4%, and reducing species numbers in the overlap value between intra- and interspecific divergences. Three species delimitation algorithms (general mixed Yule-coalescent, automatic barcoding gap detection, and statistical parsimony network analysis) were extensively applied to a wide range of snakes based on both barcodes. This revealed cryptic diversity for eleven snake species in Thailand. In addition, eleven accessions from the database previously grouped under the same species were represented at different species level, suggesting either high genetic diversity, or the misidentification of these sequences in the database as a consequence of cryptic species.
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Affiliation(s)
- Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Arrjaree Supikamolseni
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Panupon Twilprawat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sunutcha Suntrarachun
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU), Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU), Thailand.
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Folt B, Garrison N, Guyer C, Rodriguez J, Bond JE. Phylogeography and evolution of the Red Salamander (Pseudotriton ruber). Mol Phylogenet Evol 2016; 98:97-110. [PMID: 26872531 DOI: 10.1016/j.ympev.2016.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 01/04/2016] [Accepted: 01/28/2016] [Indexed: 11/27/2022]
Abstract
Phylogeographic studies frequently result in the elevation of subspecific taxa to species given monophyly, or the synonymy of subspecies that are not monophyletic. However, given limited or incongruent datasets, retention of subspecies can be useful to describe hypothesized incipient species or to illustrate interesting biological phenomena driving morphological diversity. Four subspecific taxa have been used to describe largely allopatric geographic variation within the species Pseudotriton ruber, a plethodontid salamander occupying stream and spring habitats across eastern North America: P. r. vioscai occurs in lowland Coastal Plain habitats, while P. r. ruber, P. r. nitidus, and P. r. schencki occupy upland regions in and around the Appalachian Mountains. Pseudotriton ruber co-occurs through its distribution with the aposematic newt Notophthalmus viridescens, and both species are hypothesized to be part of a Müllerian mimicry complex. In this study, we sequenced regions of two mitochondrial (cytochrome b, NADH dehydrogenase subunit 2) and one single copy nuclear protein-coding gene (pro-opiomelanocortin) from individuals sampled across much of the distribution of P. ruber and then used maximum-likelihood and Bayesian phylogenetic inference to test the monophyly of subspecies, reconstruct biogeographic history, and make inferences about morphological evolution. Phylogeographic hypotheses from mitochondrial and nuclear datasets described structure among populations of P. ruber which separated Coastal Plain and upland Appalachian populations, but subspecies were not monophyletic. Biogeographic reconstruction estimated the ancestor of all populations to have occupied and initially diverged in the Coastal Plain during the Pliocene (∼3.6mya), before one lineage subsequently invaded upland areas of Appalachia. Bold bright coloration of high elevation subspecies P. r. nitidus and P. r. schencki appears to have evolved twice. We hypothesize that the Müllerian mimicry complex with N. viridescens and P. ruber may provide a selective mechanism driving the co-evolution of striking bright and dull morphological variation among populations of both species. While P. ruber subspecies were not consistent with our criteria for diagnosing species (monophyly) and therefore could not be elevated to species, we advocate for the retention of subspecies because they describe hypotheses about an incipient species (P. r. vioscai) and how Müllerian mimicry may shape morphological diversity of species.
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Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA.
| | - Nicole Garrison
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Craig Guyer
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Juanita Rodriguez
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Jason E Bond
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
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McVay JD, Flores-Villela O, Carstens B. Diversification of North American natricine snakes. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12558] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John D. McVay
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - Oscar Flores-Villela
- Facultad de Ciencias; Museo de Zoologia; Universidad Nacional Autonoma de Mexico; Circuito Extrior de CU Mexico DF 04510 Mexico
| | - Bryan Carstens
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
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12
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Separation of the bioclimatic spaces of Himalayan tree rhododendron species predicted by ensemble suitability models. Glob Ecol Conserv 2014. [DOI: 10.1016/j.gecco.2014.07.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Torstrom SM, Pangle KL, Swanson BJ. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy. Mol Phylogenet Evol 2014; 76:134-43. [DOI: 10.1016/j.ympev.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/08/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
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Kornilios P, Thanou E, Lymberakis P, Sindaco R, Liuzzi C, Giokas S. Mitochondrial phylogeography, intraspecific diversity and phenotypic convergence in the four-lined snake (Reptilia, Squamata). ZOOL SCR 2013. [DOI: 10.1111/zsc.12045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panagiotis Kornilios
- Section of Animal Biology; Department of Biology; School of Natural Sciences; University of Patras; GR-26500 Patras Greece
| | - Evanthia Thanou
- Section of Animal Biology; Department of Biology; School of Natural Sciences; University of Patras; GR-26500 Patras Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Knossou Ave. 71409, Crete Irakleio Greece
| | - Roberto Sindaco
- Museo Civico di Storia Naturale; via San Francesco di Sales 88, 10022 Carmagnola Torino Italy
| | - Cristiano Liuzzi
- Riserva Naturale dello Stato Le Cesine Oasi WWF; Masseria Cesine, 73029 Vernole Lecce Italy
| | - Sinos Giokas
- Section of Animal Biology; Department of Biology; School of Natural Sciences; University of Patras; GR-26500 Patras Greece
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Malaney JL, Cook JA. Using biogeographical history to inform conservation: the case of Preble's meadow jumping mouse. Mol Ecol 2013; 22:6000-17. [DOI: 10.1111/mec.12476] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Jason L. Malaney
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
| | - Joseph A. Cook
- Museum of Southwestern Biology; Department of Biology; University of New Mexico; Albuquerque NM 87131 USA
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Bergsten J, Nilsson AN, Ronquist F. Bayesian tests of topology hypotheses with an example from diving beetles. Syst Biol 2013; 62:660-73. [PMID: 23628960 PMCID: PMC3739882 DOI: 10.1093/sysbio/syt029] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/16/2013] [Accepted: 04/23/2013] [Indexed: 01/18/2023] Open
Abstract
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
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Affiliation(s)
- Johannes Bergsten
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Anders N. Nilsson
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Soto-Centeno JA, Barrow LN, Allen JM, Reed DL. Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence. Ecol Evol 2013; 3:1603-13. [PMID: 23789071 PMCID: PMC3686195 DOI: 10.1002/ece3.576] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/16/2013] [Accepted: 03/27/2013] [Indexed: 11/08/2022] Open
Abstract
We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma-830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial-interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.
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Affiliation(s)
- J Angel Soto-Centeno
- Department of Biology, University of Florida Gainesville, Florida, 32611 ; Florida Museum of Natural History, University of Florida Gainesville, Florida, 32611
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Janies DA, Studer J, Handelman SK, Linchangco G. A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets. Cladistics 2013; 29:560-566. [DOI: 10.1111/cla.12014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Daniel A. Janies
- Department of Bioinformatics and Genomics; College of Computing and Informatics; University of North Carolina at Charlotte; 9201 University City Blvd; Charlotte; NC; 28223; USA
| | - Jonathon Studer
- Case Western Reserve University School of Law; 11075 East Boulevard; Cleveland; OH; 44106; USA
| | - Samuel K. Handelman
- Department of Pharmacology; College of Medicine; The Ohio State University; 333 W. 10th Ave.; Columbus; OH; 43210; USA
| | - Gregorio Linchangco
- Department of Bioinformatics and Genomics; College of Computing and Informatics; University of North Carolina at Charlotte; 9201 University City Blvd; Charlotte; NC; 28223; USA
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JACKSON NATHAND, AUSTIN CHRISTOPHERC. Inferring the evolutionary history of divergence despite gene flow in a lizard species, Scincella lateralis (Scincidae), composed of cryptic lineages. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01929.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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NEWMAN CATHERINEE, RISSLER LESLIEJ. Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies. Mol Ecol 2011; 20:5295-312. [DOI: 10.1111/j.1365-294x.2011.05353.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Marino J, Bennett M, Cossios D, Iriarte A, Lucherini M, Pliscoff P, Sillero-Zubiri C, Villalba L, Walker S. Bioclimatic constraints to Andean cat distribution: a modelling application for rare species. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00744.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Brandley MC, Guiher TJ, Pyron RA, Winne CT, Burbrink FT. Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)? Mol Phylogenet Evol 2010; 57:552-60. [DOI: 10.1016/j.ympev.2010.07.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 07/22/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
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