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Lyu B, Liu Q, Wu Y, Nguyen TQ, Che J, Nguyen SN, Myers EA, Burbrink FT, Guo P, Wang J. Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae). Ecol Evol 2024; 14:e11278. [PMID: 38628918 PMCID: PMC11019134 DOI: 10.1002/ece3.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.
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Affiliation(s)
- Bing Lyu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Truong Q. Nguyen
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Vietnam Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Sang N. Nguyen
- Institute of Tropical BiologyVietnam Academy of Science and TechnologyHo Chi Minh CityVietnam
| | - Edward A. Myers
- Department of HerpetologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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Burbrink FT, Harrington SM, Bobo D, Myers EA. Considering admixture when producing draft genomes: an example in North American ratsnakes (Pantherophis alleghaniensis/Pantherophis obsoletus). G3 (BETHESDA, MD.) 2023; 13:jkad113. [PMID: 37228097 PMCID: PMC10411579 DOI: 10.1093/g3journal/jkad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Sean M Harrington
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Dean Bobo
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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Jablonski D, Ribeiro-Júnior MA, Simonov E, Šoltys K, Meiri S. A new, rare, small-ranged, and endangered mountain snake of the genus Elaphe from the Southern Levant. Sci Rep 2023; 13:4839. [PMID: 36964263 PMCID: PMC10038995 DOI: 10.1038/s41598-023-30878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 03/02/2023] [Indexed: 03/26/2023] Open
Abstract
The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years and is virtually unstudied due to its extreme rarity. We studied these snakes' morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia.
| | | | - Evgeniy Simonov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Katarína Šoltys
- Department of Microbiology and Virology, Comenius University in Bratislava, Bratislava, Slovakia
- Comenius University Science Park, Bratislava, Slovakia
| | - Shai Meiri
- The School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
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5
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Hidalgo-Licona LF, Gutiérrez-Mayén MG, Sandoval-Ruiz CA, de la Vega-Pérez AD, Chollet-Villalpando JG. Ecogeographic and Morphometric Variation in the Mexican Pine Snake, Pituophis deppei (Squamata: Colubridae). ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/h2021105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Luis Fernando Hidalgo-Licona
- Maestría en Ciencias Biológicas, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México;
| | - María Guadalupe Gutiérrez-Mayén
- Laboratorio de Herpetología, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México;
| | - César Antonio Sandoval-Ruiz
- Laboratorio de Artropodología y Salud, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Blvd. Valsequillo y Av. San Claudio, Edificio BIO 1, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, México; Ema
| | - Anibal Díaz de la Vega-Pérez
- Consejo Nacional de Ciencia y Tecnología, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Carretera Tlaxcala-Puebla km 1.5 C.P. 90062, Tlaxcala, México;
| | - Jorge Guillermo Chollet-Villalpando
- Instituto de Ecología, A.C. Red de Biodiversidad y Sistemática, Carretera Antigua a Coatepec 351, El Haya, Xalapa Enríquez, 91070 Veracruz, México;
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6
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Nikolakis ZL, Orton RW, Crother BI. Fine‐scale population structure within an Eastern Nearctic snake complex (
Pituophis melanoleucus
). ZOOL SCR 2021. [DOI: 10.1111/zsc.12522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Richard W. Orton
- Department of Biology University of Texas at Arlington Arlington Texas USA
| | - Brian I. Crother
- Department of Biology Southeastern Louisiana University Hammond Louisina USA
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7
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Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data. J HERPETOL 2021. [DOI: 10.1670/20-040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Flowers JR, Beane JC. Helminths of the Eastern Rat Snake, Pantherophis alleghaniensis Holbrook (Squamata: Colubridae), from North Carolina, U.S.A. COMP PARASITOL 2021. [DOI: 10.1654/copa-d-21-00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- James R. Flowers
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Dr., Raleigh, North Carolina 27607, U.S.A. (e-mail: )
| | - Jeffrey C. Beane
- North Carolina State Museum of Natural Sciences, 1626 Mail Service Center, Raleigh, North Carolina 27699-1626, U.S.A. (e-mail: )
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9
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Weinell JL, Barley AJ, Siler CD, Orlov NL, Ananjeva NB, Oaks JR, Burbrink FT, Brown RM. Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.
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Affiliation(s)
- Jeffrey L Weinell
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Anthony J Barley
- Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Nikolai L Orlov
- Zoological Institute, Russian Academy of Science, Universitetskaya nab., St. Petersburg, Russia
| | - Natalia B Ananjeva
- Zoological Institute, Russian Academy of Science, Universitetskaya nab., St. Petersburg, Russia
| | - Jamie R Oaks
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
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10
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Out of the Hengduan Mountains: Molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae). Mol Phylogenet Evol 2020; 152:106927. [PMID: 32771547 DOI: 10.1016/j.ympev.2020.106927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 06/30/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023]
Abstract
The Asian water snake genus Trimerodytes (formerly Sinonatrix) is endemic to East and Southeast Asia. Although several species have been included in various phylogenetic studies previously, the evolution and relationships among members of this genus as a whole remain unexplored. In this study, we report the sequencing two protein-coding mitochondrial gene fragments (MTCYB and ND2) and three nuclear genes (c-mos, NT3, and Rag1), reconstruct interspecific phylogeny, and explore biogeography for the genus Trimerodytes. Both Bayesian inference and maximum likelihood analyses consistently recover the monophyly of Trimerodytes with strong support, with T. yapingi the sister-group to the remaining species. The divergence date and ancestral area estimation suggest that Trimerodytes likely originated in Hengduan Mountains (eastern Tibetan Plateau) in western China at 23.93 Ma (95% HPD: 17.09-31.30), and intraspecific divergence began at about 4.23 Ma (95% HPD: 2.74-6.10). Analyses support the validity of T. yunnanensis.
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11
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Murtskhvaladze M, Tarkhnishvili D, Anderson CL, Kotorashvili A. Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection. PLoS One 2020; 15:e0233680. [PMID: 32511235 PMCID: PMC7279592 DOI: 10.1371/journal.pone.0233680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.
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Affiliation(s)
- Marine Murtskhvaladze
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - David Tarkhnishvili
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Cort L. Anderson
- School of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- L. Sakvarelidze National Center for Disease Control and Public Health, Tbilisi, Georgia
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12
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Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia. Mol Phylogenet Evol 2018; 133:82-91. [PMID: 30594733 DOI: 10.1016/j.ympev.2018.12.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 11/21/2022]
Abstract
Understanding the influence of geographical events and climate changes on genetic diversity is essential in explaining current patterns of genetic structure and geographic distribution of organisms. We inferred phylogenetic relationships, investigated historical demography, explored the evolutionary history, and clarified intraspecific taxonomy of Protobothrops mucrosquamatus, which is one of the commonest and most wide-ranging Asian pitvipers. A total of 184 samples from 54 localities were sequenced and analyzed for two mitochondrial gene fragments and two nuclear genes. Phylogenetic reconstruction based on mtDNA sequences revealed the existence of a minimum of five geographically structured and well-supported lineages within P. mucrosquamatus. Based on the mtDNA gene tree, and the geographic relationship between populations allied by matrilineal lineages, a complex longitudinal and latitudinal diversification pattern was uncovered in P. mucrosquamatus. The estimated date of the origin of the species (about 5.3 Ma) and divergence of the intraspecific lineages match the rapid uplifting of Qinghai-Xizang Plateau, and is also consistent with those of some other co-distributed Asian pitvipers. Formation of the two island lineages (Taiwan and Hainan) was generally congruent with the first isolation of the islands, but the two lineages showed different relationships with the continental Asian populations in comparison with some other pitvipers. Population historical demographic analyses, based on three methods, showed that all lineages have experienced slight population expansion in and around the Dali Glacial. Tests of intraspecific taxonomy indicated that no cryptic taxon is present within this widely distributed snake.
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13
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Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Mol Phylogenet Evol 2018; 129:214-225. [PMID: 30189319 DOI: 10.1016/j.ympev.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022]
Abstract
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux. The number of species has increased from 23 to 51 over the last thirty years, predominately within three of the nine genera (Lampropeltis, Pantherophis, Pituophis). The remaining six depauperate genera (Arizona, Bogertophis, Cemophora, Pseudelaphe, Rhinocheilus, and Senticolis) have been poorly represented in phylogenetic studies. To estimate evolutionary relationships and determine if the dichotomy in depauperate and speciose genera within Lampropeltini is a function of taxon sampling or truly represents the lineage diversity, we estimated the phylogeny of this group using nuclear and mitochondrial loci in a concatenated and coalescent framework with the largest sampling of the six depauperate genera to date. In addition, we estimated the divergence dates among the genera to assess whether the instability of Lampropeltini phylogenetic relationships is due to an adaptive radiation. While some nodes still remain unresolved, the generic-level relationships we recovered agree with those of a recent next-generation study that used a much larger set of loci for fewer individuals. We also tested two putative species, Arizona pacata and Pseudelaphe phaescens, for the first time phylogenetically and find evidence that they are distinct lineages. Overall, we find that the taxonomic and genetic diversity are not correlated in Lampropeltini and that representing putative diversity in phylogenies will lead to a better estimate of evolutionary histories, especially in groups with complex radiations.
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14
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Salvi D, Mendes J, Carranza S, Harris DJ. Evolution, biogeography and systematics of the western Palaearctic Zamenis
ratsnakes. ZOOL SCR 2018. [DOI: 10.1111/zsc.12295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences; University of L'Aquila; L'Aquila Italy
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
| | - Joana Mendes
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
- Institute of Evolutionay Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | - Salvador Carranza
- Institute of Evolutionay Biology (CSIC-Universitat Pompeu Fabra); Barcelona Spain
| | - David James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vairão Vila do Conde Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
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15
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Phylogeography of the Japanese ratsnake, Elaphe climacophora (Serpentes: Colubridae): impacts of Pleistocene climatic oscillations and sea-level fluctuations on geographical range. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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16
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Myers EA, Burgoon JL, Ray JM, Martínez-Gómez JE, Matías-Ferrer N, Mulcahy DG, Burbrink FT. Coalescent Species Tree Inference of Coluber and Masticophis. COPEIA 2017. [DOI: 10.1643/ch-16-552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT. Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Mol Phylogenet Evol 2017; 111:206-218. [DOI: 10.1016/j.ympev.2017.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/07/2017] [Accepted: 03/20/2017] [Indexed: 11/15/2022]
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18
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A Novel Pattern of Yolk Processing in Developing Snake Eggs (Colubridae: Lampropeltini) and its Functional and Evolutionary Implications. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:462-475. [DOI: 10.1002/jez.b.22750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 12/24/2022]
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19
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20
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Kim YK, Blackburn DG. Fetal Membrane Ultrastructure and Development in the Oviparous MilksnakeLampropeltis triangulum(Colubridae) with Reference to Function and Evolution in Snakes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:290-302. [DOI: 10.1002/jez.b.22684] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 05/31/2016] [Accepted: 06/10/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Young K. Kim
- Department of Biology and Electron Microscopy Facility; Trinity College; Hartford Connecticut
| | - Daniel G. Blackburn
- Department of Biology and Electron Microscopy Facility; Trinity College; Hartford Connecticut
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21
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Guo P, Liu Q, Zhu F, Zhong GH, Chen X, Myers EA, Che J, Zhang L, Ziegler T, Nguyen TQ, Burbrink FT. Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri(Schmidt, 1925) (Reptilia: Serpentes: Viperidae). Mol Ecol 2016; 25:2920-36. [DOI: 10.1111/mec.13658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Guo
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Qin Liu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Fei Zhu
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Guang H. Zhong
- College of Life Sciences and Food Engineering; Yibin University; Yibin 644007 China
| | - Xin Chen
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Edward A. Myers
- Department of Biology; The Graduate School and University Center; The City University of New York; 365 5th Avenue New York NY 10016 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Menglun Mengla Yunnan 666303 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Thomas Ziegler
- AG Zoologischer Garten Köln; Riehler Strasse 173 D-50735 Cologne Germany
| | - Truong Q. Nguyen
- Institute of Ecology and Biological Resources; Vietnam Academy of Science and Technology; 18 Hoang Quoc Viet Street Hanoi Vietnam
| | - Frank T. Burbrink
- Department of Herpetology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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22
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Kim YK, Blackburn DG. Ultrastructure of the fetal membranes of the oviparous kingsnake,Lampropeltis getula(Colubridae) as revealed by scanning electron microscopy. J Morphol 2015; 276:1467-81. [DOI: 10.1002/jmor.20435] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Young K. Kim
- Department of Biology and Electron Microscopy Facility; Trinity College; Hartford Connecticut 06106
| | - Daniel G. Blackburn
- Department of Biology and Electron Microscopy Facility; Trinity College; Hartford Connecticut 06106
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23
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Ruane S, Torres-Carvajal O, Burbrink FT. Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis). PLoS One 2015; 10:e0128543. [PMID: 26083467 PMCID: PMC4470684 DOI: 10.1371/journal.pone.0128543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/28/2015] [Indexed: 01/02/2023] Open
Abstract
The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.
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Affiliation(s)
- Sara Ruane
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
- * E-mail:
| | - Omar Torres-Carvajal
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Frank T. Burbrink
- Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY, 10314, United States of America
- The Graduate Center, City University of New York, 365 5 Avenue, New York, NY, 10016, United States of America
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24
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Ruane S. Using geometric morphometrics for integrative taxonomy: an examination of head shapes of milksnakes (genusLampropeltis). Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12245] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Sara Ruane
- Department of Biology; College of Staten Island/CUNY Graduate Center; 2800 Victory Blvd. Staten Island NY 10314
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25
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Chen X, Jiang K, Guo P, Huang S, Rao D, Ding L, Takeuchi H, Che J, Zhang YP, Myers EA, Burbrink FT. Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods. Mol Phylogenet Evol 2014; 70:130-6. [DOI: 10.1016/j.ympev.2013.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/03/2013] [Accepted: 09/07/2013] [Indexed: 11/29/2022]
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26
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Ruane S, Bryson RW, Pyron RA, Burbrink FT. Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses. Syst Biol 2013; 63:231-50. [DOI: 10.1093/sysbio/syt099] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Myers EA, Rodríguez-Robles JA, DeNardo DF, Staub RE, Stropoli A, Ruane S, Burbrink FT. Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province. Mol Ecol 2013; 22:5418-29. [DOI: 10.1111/mec.12478] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 11/30/2022]
Affiliation(s)
- E. A. Myers
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
| | - J. A. Rodríguez-Robles
- School of Life Sciences; University of Nevada; 4505 Maryland Parkway Las Vegas NV 89154-4004 USA
| | - D. F. DeNardo
- School of Life Sciences; Arizona State University; Tempe AZ 85287-4501 USA
| | | | - A. Stropoli
- Science, Math and Engineering; Staten Island Technical High School; 485 Clawson Street Staten Island New York 10306 USA
| | - S. Ruane
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
| | - F. T. Burbrink
- Department of Biology; The Graduate School; City University of New York; NY 10016 USA
- Department of Biology; 6S-143; College of Staten Island; 2800 Victory Boulevard Staten Island NY 10314 USA
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28
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Zimkus BM, Gvoždík V. Sky Islands of the Cameroon Volcanic Line: a diversification hot spot for puddle frogs (Phrynobatrachidae:Phrynobatrachus). ZOOL SCR 2013. [DOI: 10.1111/zsc.12029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Breda M. Zimkus
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology; Harvard University; Cambridge; MA; USA
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29
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Allen WL, Baddeley R, Scott-Samuel NE, Cuthill IC. The evolution and function of pattern diversity in snakes. Behav Ecol 2013. [DOI: 10.1093/beheco/art058] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol 2013; 13:93. [PMID: 23627680 PMCID: PMC3682911 DOI: 10.1186/1471-2148-13-93] [Citation(s) in RCA: 962] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. RESULTS The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. CONCLUSIONS We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA
| | - Frank T Burbrink
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 5th Ave., New York, NY 10016, USA
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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31
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Siler CD, Oliveros CH, Santanen A, Brown RM. Multilocus phylogeny reveals unexpected diversification patterns in Asian wolf snakes (genusLycodon). ZOOL SCR 2013. [DOI: 10.1111/zsc.12007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cameron D. Siler
- Department of Biology; University of South Dakota; Vermillion; SD; 57069; USA
| | - Carl H. Oliveros
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence; KS; 66045-7561; USA
| | - Anssi Santanen
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence; KS; 66045-7561; USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence; KS; 66045-7561; USA
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Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka. Mol Phylogenet Evol 2012; 66:969-78. [PMID: 23261713 DOI: 10.1016/j.ympev.2012.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 11/27/2012] [Accepted: 12/05/2012] [Indexed: 11/20/2022]
Abstract
Snake diversity in the island of Sri Lanka is extremely high, hosting at least 89 inland (i.e., non-marine) snake species, of which at least 49 are endemic. This includes the endemic genera Aspidura, Balanophis, Cercaspis, Haplocercus, and Pseudotyphlops, which are of uncertain phylogenetic affinity. We present phylogenetic evidence from nuclear and mitochondrial loci showing the relationships of 40 snake species from Sri Lanka (22 endemics) to the remaining global snake fauna. To determine the phylogenetic placement of these species, we create a molecular dataset containing 10 genes for all global snake genera, while also sampling all available species for genera with endemic species occurring in Sri Lanka. Our sampling comprises five mitochondrial genes (12S, 16S, cyt-b, ND2, and ND4) and five nuclear genes (BDNF, c-mos, NT3 RAG-1, and RAG-2), for a total of up to 9582bp per taxon. We find that the five endemic genera represent portions of four independent colonizations of Sri Lanka, with Cercaspis nested within Colubrinae, Balanophis in Natricinae, Pseudotyphlops in Uropeltidae, and that Aspidura+Haplocercus represents a distinct, ancient lineage within Natricinae. We synonymize two endemic genera that render other genera paraphyletic (Haplocercus with Aspidura, and Cercaspis with Lycodon), and discover that further endemic radiations may be present on the island, including a new taxon from the blindsnake family Typhlopidae, suggesting a large endemic radiation. Despite its small size relative to other islands such as New Guinea, Borneo, and Madagascar, Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island's biodiversity, with numerous undescribed species in multiple lineages.
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33
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Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae). Mol Phylogenet Evol 2012; 66:254-61. [PMID: 23044403 DOI: 10.1016/j.ympev.2012.09.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 09/18/2012] [Accepted: 09/26/2012] [Indexed: 11/20/2022]
Abstract
Numerous taxa show ancient intertropical disjunct distributions. Many can be explained by well-known processes of historical vicariance, such as the breakup of Gondwanaland. Others, such as Asian-Neotropical divergences are not as well understood. To clarify the phylogenetic position and understand biogeographic and temporal origins of the geographically disjunct and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis (n=1) and Sibynophis (n=9; Colubridae), we inferred a time-calibrated phylogeny with additional 107 taxa representing the superfamily Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085 bp). We used this tree to estimate ancestral areas for the group. The results show that Scaphiodontophis is sister to Sibynophis, both originated in the late Eocene/Oligocene in Asia and likely dispersed through Beringia to the New World, but unlike other snake groups left no extant species in temperate North America. Current recognition of Scaphiodontophiinae renders Colubrinae paraphyletic, and we resurrect the previously named subfamily Sibynophiinae to encompass both genera and use the tribes Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to highlight the geographically distinct areas occupied by these taxa. These results suggest that intercontinental dispersal with extinction in intermediate areas can explain puzzling patterns of ancient intertropical disjunct distributions.
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A New Species of the Genus Elaphe (Squamata: Colubridae) from Zoige County, Sichuan, China. ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Two Naturally Occurring Intergeneric Hybrid Snakes (Pituophis catenifer sayi×Pantherophis vulpinus;Lampropeltini, Squamata) from the Midwestern United States. J HERPETOL 2012. [DOI: 10.1670/10-260] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Guo P, Liu Q, Xu Y, Jiang K, Hou M, Ding L, Alexander Pyron R, Burbrink FT. Out of Asia: Natricine snakes support the Cenozoic Beringian Dispersal Hypothesis. Mol Phylogenet Evol 2012; 63:825-33. [DOI: 10.1016/j.ympev.2012.02.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 02/16/2012] [Accepted: 02/22/2012] [Indexed: 11/15/2022]
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37
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Iverson JB, Young CA, Akre TSB, Griffiths CM. Reproduction by Female Bullsnakes (Pituophis catenifer sayi) in the Nebraska Sandhills. SOUTHWEST NAT 2012. [DOI: 10.1894/0038-4909-57.1.58] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pyron RA, Burbrink FT. Trait-dependent diversification and the impact of palaeontological data on evolutionary hypothesis testing in New World ratsnakes (tribe Lampropeltini). J Evol Biol 2012; 25:497-508. [PMID: 22226034 DOI: 10.1111/j.1420-9101.2011.02440.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For studies investigating trait evolution, there are at least two important questions. First, have traits under consideration influenced cladogenesis and extinction in the group? Second, how do fossil data alter inferences about trait evolution or diversification-rate dynamics? However, relatively few studies have assessed these questions. Here, we use recently developed methods to test for trait-dependent diversification in the New World colubrid snake tribe Lampropeltini. We also integrate data from fossil taxa into phylogenetic estimation of evolutionary parameters using a simple Monte Carlo randomization test. These analyses suggest that ecological conditions in temperate regions are tied to higher rates of cladogenesis, but that body size is not related to diversification in the group. We also find that the inclusion of fossil taxa alters absolute estimates of size and the rate of size evolution, but not the overall pattern of ecomorphological diversification, as well as estimates of evolutionary rates, particularly extinction.
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Affiliation(s)
- R A Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
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39
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Fenwick AM, Greene HW, Parkinson CL. The serpent and the egg: unidirectional evolution of reproductive mode in vipers? J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00646.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Tibetan Plateau Relict Snakes of the Genus Thermophis and Their Relationship to New World Relict Snakes. ASIAN HERPETOL RES 2011. [DOI: 10.3724/sp.j.1245.2011.00161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Burbrink FT, Yao H, Ingrasci M, Bryson RW, Guiher TJ, Ruane S. Speciation at the Mogollon Rim in the Arizona Mountain Kingsnake (Lampropeltis pyromelana). Mol Phylogenet Evol 2011; 60:445-54. [DOI: 10.1016/j.ympev.2011.05.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 05/06/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
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42
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Wood DA, Vandergast AG, Lemos Espinal JA, Fisher RN, Holycross AT. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data. Mol Ecol 2011; 20:3856-78. [PMID: 21851436 DOI: 10.1111/j.1365-294x.2011.05211.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.
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Affiliation(s)
- Dustin A Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101, USA.
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44
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Friedman M, Schaffer L. Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides). MITOCHONDRIAL DNA 2011; 22:22-27. [PMID: 21699370 DOI: 10.3109/19401736.2011.588218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.
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Affiliation(s)
- Michael Friedman
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, USA
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Pyron RA, Burbrink FT, Colli GR, de Oca ANM, Vitt LJ, Kuczynski CA, Wiens JJ. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol Phylogenet Evol 2010; 58:329-42. [PMID: 21074626 DOI: 10.1016/j.ympev.2010.11.006] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 10/28/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
The superfamily Colubroidea (> 2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5814bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean=67% per species), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.
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Affiliation(s)
- R Alexander Pyron
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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Arboreal habitat structure affects route choice by rat snakes. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2010; 197:119-29. [PMID: 20957373 DOI: 10.1007/s00359-010-0593-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/20/2010] [Accepted: 10/02/2010] [Indexed: 02/02/2023]
Abstract
In arboreal habitats gaps between branches and branch structure profoundly affect the ability of animals to move; hence, an ability to perceive such attributes could facilitate choosing routes that enhance the speed and ease of locomotion. Although many snakes are arboreal, no previous study has determined whether they can perceive structural variation of branches that is mechanically relevant to their locomotion. We tested whether the gap distance, location, and attributes of two destination perches on the far side of a crossable gap affected the route travelled by North American rat snakes (Pantherophis), which are proficient climbers. Snakes usually chose routes with shorter gaps. Within a horizontal plane, the snakes usually went straight rather than crossing an equal distance gap with a 90° turn, which was consistent with our finding that crossing a straight gap was easier. However, decreasing the distance of the gap with a 90° turn eliminated the preference for going straight. Additional factors, such as the width of the landing surface and the complexity of branching of the destination perches, resulted in non-random route choice. Thus, many of the observed biases in route choice suggested abilities to perceive structural variation and select routes that are mechanically beneficial.
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48
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Kikuchi DW, Pfennig DW. High-model abundance may permit the gradual evolution of Batesian mimicry: an experimental test. Proc Biol Sci 2009; 277:1041-8. [PMID: 19955153 DOI: 10.1098/rspb.2009.2000] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In Batesian mimicry, a harmless species (the 'mimic') resembles a dangerous species (the 'model') and is thus protected from predators. It is often assumed that the mimetic phenotype evolves from a cryptic phenotype, but it is unclear how a population can transition through intermediate phenotypes; such intermediates may receive neither the benefits of crypsis nor mimicry. Here, we ask if selection against intermediates weakens with increasing model abundance. We also ask if mimicry has evolved from cryptic phenotypes in a mimetic clade. We first present an ancestral character-state reconstruction showing that mimicry of a coral snake (Micrurus fulvius) by the scarlet kingsnake (Lampropeltis elapsoides) evolved from a cryptic phenotype. We then evaluate predation rates on intermediate phenotypes relative to cryptic and mimetic phenotypes under conditions of both high- and low-model abundances. Our results indicate that where coral snakes are rare, intermediate phenotypes are attacked more often than cryptic and mimetic phenotypes, indicating the presence of an adaptive valley. However, where coral snakes are abundant, intermediate phenotypes are not attacked more frequently, resulting in an adaptive landscape without a valley. Thus, high-model abundance may facilitate the evolution of Batesian mimicry.
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Affiliation(s)
- David W Kikuchi
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
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Burbrink FT, Pyron RA. HOW DOES ECOLOGICAL OPPORTUNITY INFLUENCE RATES OF SPECIATION, EXTINCTION, AND MORPHOLOGICAL DIVERSIFICATION IN NEW WORLD RATSNAKES (TRIBE LAMPROPELTINI)? Evolution 2009; 64:934-43. [DOI: 10.1111/j.1558-5646.2009.00888.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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ALEXANDER PYRON R, BURBRINK FT. Body size as a primary determinant of ecomorphological diversification and the evolution of mimicry in the lampropeltinine snakes (Serpentes: Colubridae). J Evol Biol 2009; 22:2057-67. [DOI: 10.1111/j.1420-9101.2009.01820.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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