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Das S, Greenbaum E, Brecko J, Pauwels OSG, Ruane S, Pirro S, Merilä J. Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family. Sci Rep 2024; 14:9489. [PMID: 38664489 PMCID: PMC11045840 DOI: 10.1038/s41598-024-60215-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.
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Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX, 79968, USA
| | - Jonathan Brecko
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium
- Royal Museum for Central Africa, Tervuren, Belgium
| | - Olivier S G Pauwels
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, Chicago, IL, USA
| | - Stacy Pirro
- Iridian Genomes Inc., Bethesda, MD, 20817, USA
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
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2
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Zhu F, Lu J, Sun K, Deng C, Xu Y. Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing. BMC Genom Data 2024; 25:23. [PMID: 38408920 PMCID: PMC10895795 DOI: 10.1186/s12863-024-01208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates. METHODS In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species. RESULTS A total of 51,849 nonredundant full-length transcript assemblies (with an N50 length of 2980 bp) from I. braminus were generated and fully annotated using various gene function databases. Our analysis provides preliminary evidence supporting a recent genome duplication event in I. braminus. Phylogenetic analysis indicated that the divergence of I. braminus subgenomes occurred approximately 11.5 ~ 15 million years ago (Mya). The full-length transcript resource generated as part of this research will facilitate transcriptome analysis and genomic evolution studies in the future.
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Affiliation(s)
- Fei Zhu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China.
| | - Jing Lu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Ke Sun
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
| | - Cao Deng
- Department of Bioinformatics, DNA Stories Bioinformatics Center, 610000, Chengdu, China
| | - Yu Xu
- School of Life Sciences, Guizhou Normal University, 550025, Guiyang, Guizhou, China
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3
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Pinto BJ, Nielsen SV, Sullivan KA, Behere A, Keating SE, van Schingen-Khan M, Nguyen TQ, Ziegler T, Pramuk J, Wilson MA, Gamble T. It's a trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex-determining gene in a lizard (Anguimorpha; Shinisauridae). Evolution 2024; 78:355-363. [PMID: 37952174 PMCID: PMC10834058 DOI: 10.1093/evolut/qpad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally to genetically influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades are not conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 with a novel ZW system on LG3. The linkage group, LG3, corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1 Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2, critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex-determining gene for Shinisaurus.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Stuart V Nielsen
- Department of Biological Sciences, Museum of Life Sciences, Louisiana State University-Shreveport, Shreveport, LA, United States
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Kathryn A Sullivan
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Ashmika Behere
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | | | - Truong Q Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Department of Biology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Jennifer Pramuk
- Former affiliation: Woodland Park Zoo, Seattle, WA, United States
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
- Center for Mechanisms of Evolution, Biodesign Institute, Tempe, AZ, United States
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
- Bell Museum of Natural History, University of Minnesota, St Paul, MN, United States
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5
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Hampton PM, Meik JM. Regionalization of the vertebral column and its correlation with heart position in snakes: Implications for evolutionary pathways and morphological diversification. Evol Dev 2024; 26:e12460. [PMID: 37804483 DOI: 10.1111/ede.12460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
Spinal regionalization has important implications for the evolution of vertebrate body plans. We determined the variation in the number and morphology of vertebrae across the vertebral column (i.e., vertebral formula) for 63 snake species representing 13 families using intracolumnar variation in vertebral shape. Vertebral counts were used to determine the position of the heart, pylorus, and left kidney for each species. Across all species we observed a conspicuous midthoracic transition in vertebral shape, indicating four developmental domains of the precloacal vertebral column (cervical, anterior thoracic, posterior thoracic, and lumbar). Using phylogenetic analyses, the boundary between the anterior and posterior thoracic vertebrae was correlated with heart position. No associations were found between shifts in morphology of the vertebral column and either the pylorus or left kidney. We observed that among taxa, the number of preapex and postapex vertebrae could change independently from one another and from changes in the total number of precloacal vertebrae. Ancestral state reconstruction of the preapex and postapex vertebrae illustrated several evolutionary pathways by which diversity in the vertebral column and heart position have been attained. In addition, no conspicuous pattern was observed among the heart, pylorus, or kidney indicating that their relative positions to each other evolve independently. We conclude that snakes exhibit four morphologically distinct regions of the vertebral column. We discuss the implications of the forebody and hindbody vertebral formula on the morphological diversification of snakes.
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Affiliation(s)
- Paul M Hampton
- Department of Biology, Colorado Mesa University, Grand Junction, Colorado, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
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6
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Sidharthan C, Roy P, Karanth KP. Molecular data reveals a new genus of blindsnakes within Asiatyphlopinae from India. J Genet 2024; 103:03. [PMID: 38258298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The genus Indotyphlops has a widespread distribution in the Indian landmass and Southeast Asia, with 20 reported species. The current classification within the genus is based on morphology. In this study, we sampled all the reported Indotyphlops species from subcontinental India, to resolve relationships within this genus and to understand biogeographic patterns that resulted in the widespread distribution. We generated sequences for five nuclear markers which were used in the global typhlopoid phylogeny and built phylogenetic trees of the superfamily Typhlopoidea. We also carried out divergence time analysis and biogeographic analysis to understand the time and modes of dispersal and diversification of these species. The results show Indotyphlops sensu lato to be polyphyletic, with the clade consisting of I. porrectus and I. exiguus sister to a clade consisting of the southeast Asian typhlopid genera Ramphotyphlops, Anilios, Malayotyphlops, Acutotyphlops, Sundatyphlops, and Indotyphlops sensu stricto. The other clade consists of I. pammeces and I. braminus from the Indian subcontinent and I. albiceps from Southeast Asia. Biogeographical analysis suggests two dispersals from Asia to the Indian landmass-an earlier dispersal from Eurasia into India led to the lineage consisting of I. porrectus and I. exiguus, followed by a later dispersal that evolved into I. pammeces and I. braminus. These results necessitate a taxonomic revision. We propose the genus Pseudoindotyphlops gen. nov. for the clade currently consisting of the most recent common ancestor (MRCA) of I. porrectus and I. exiguus, and all descendants thereof.
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Affiliation(s)
- Chinta Sidharthan
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560 012, India,
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7
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Saha A, Bellucci A, Fratini S, Cannicci S, Ciofi C, Iannucci A. Ecological factors and parity mode correlate with genome size variation in squamate reptiles. BMC Ecol Evol 2023; 23:69. [PMID: 38053023 PMCID: PMC10696768 DOI: 10.1186/s12862-023-02180-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles. RESULTS The best-fitting model showed that the interaction between microhabitat use and parity mode mainly accounted for genome size variation. Larger genome sizes were found in live-bearing species that live in rock/sand ecosystems and in egg-laying arboreal taxa. On the other hand, smaller genomes were found in fossorial live-bearing species. CONCLUSIONS Environmental factors and species parity mode appear to be among the main parameters explaining genome size variation in squamates. Our results suggest that genome size may favour adaptation of some species to certain environments or could otherwise result from the interaction between environmental factors and parity mode. Integration of genome size and genome sequencing data could help understand the role of differential genome content in the evolutionary process of genome size variation in squamates.
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Affiliation(s)
- Anik Saha
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Arianna Bellucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
- National Biodiversity Future Center, 90133, Palermo, Italy.
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Liu Q, Lyu B, Xie X, Zeng Y, Guo P. Genomic evidence sheds new light on phylogeny of Rhabdophis nuchalis (sensu lato) complex (Serpentes: Natricidae). Mol Phylogenet Evol 2023; 189:107893. [PMID: 37536649 DOI: 10.1016/j.ympev.2023.107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Stable taxonomy and robust phylogeny are essential for the evolution and conservation of organisms. The Rhabdophis nuchalis (sensu lato) complex presently contains three species (R. nuchalis, R. chiwen, R. pentasupralabialis). Although several studies have explored the diversity and phylogeography of this group, certain issues related to systematics and taxonomy remain unresolved. Here, based on genome-wide data, including single nucleotide polymorphisms (SNPs) generated from ddRAD-seq and mitochondrial DNA (mtDNA), we re-evaluated the phylogenetic relationships and cryptic diversity of this species group. Our results are generally consistent with previous studies but provide some new insights. Phylogenetic relationship reconstruction based on SNPs and mtDNA revealed that three species in the R. nuchalis (sensu lato) complex did not form a monophyly but each species is well supported as monophyletic lineage in SNP-based analyses. Population structure analyses showed genetic admixture between several species pairs. Additionally, the population in eastern Yunnan, China, was identified as a potential cryptic species and thus described as a new species based on morphological data. From our results and previous studies, we redefined the distribution boundary for each species in the R. nuchalis (sensu lato) species complex.
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Affiliation(s)
- Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Sichuan 644000, China
| | - Bing Lyu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Sichuan 644000, China
| | - Xinhong Xie
- Agricultural and Rural Bureau, Yuechi County, Sichuan 638300, China
| | - Yangmei Zeng
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Sichuan 644000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Sichuan 644000, China.
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Sitthivong S, Brakels P, Xayyasith S, Maury N, Idiiatullina S, Pawangkhanant P, Wang K, Nguyen TV, Poyarkov NA. Hiding on jagged karst pinnacles: A new microendemic genus and species of a limestone-dwelling agamid lizard (Squamata: Agamidae: Draconinae) from Khammouan Province, Laos. Zool Res 2023; 44:1039-1051. [PMID: 37872005 PMCID: PMC10802101 DOI: 10.24272/j.issn.2095-8137.2023.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
We describe a unique new species and genus of agamid lizard from the karstic massifs of Khammouan Province, central Laos. Laodracon carsticola Gen. et sp. nov. is an elusive medium-sized lizard (maximum snout-vent length 101 mm) specifically adapted to life on limestone rocks and pinnacles. To assess the phylogenetic position of the new genus amongst other agamids, we generated DNA sequences from two mitochondrial gene fragments (16S rRNA and ND2) and three nuclear loci ( BDNF, RAG1 and c-mos), with a final alignment comprising 7 418 base pairs for 64 agamid species. Phylogenetic analyses unambiguously place the new genus in the mainland Asia subfamily Draconinae, where it forms a clade sister to the genus Diploderma from East Asia and the northern part of Southeast Asia. Morphologically, the new genus is distinguished from all other genera in Draconinae by possessing a notably swollen tail base with enlarged scales on its dorsal and ventral surfaces. Our work provides further evidence that limestone regions of Indochina represent unique "arks of biodiversity" and harbor numerous relict lineages. To date, Laodracon carsticola Gen. et sp. nov. is known from only two adult male specimens and its distribution seems to be restricted to a narrow limestone massif on the border of Khammouan and Bolikhamxai provinces of Laos. Additional studies are required to understand its life history, distribution, and conservation status.
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Affiliation(s)
- Saly Sitthivong
- Faculty of Forestry, National University of Laos, Vientiane 01170, Lao PDR
| | | | - Santi Xayyasith
- Faculty of Environmental Sciences, National University of Laos, Vientiane 01170, Lao PDR
| | - Nathanaël Maury
- Chelonian Conservation Center Laos, World Encyclopedia of Herpetofauna, Vientiane 01000, Lao PDR
| | - Sabira Idiiatullina
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin , Nay Pyi Taw 05282, Myanmar. E-mail:
| | - Tan Van Nguyen
- Institute for Research and Training in Medicine, Biology and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- College of Medicine & Pharmacy, Duy Tan University, Da Nang 550000, Vietnam. E-mail:
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi 122000, Vietnam. E-mail:
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10
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Koludarov I, Senoner T, Jackson TNW, Dashevsky D, Heinzinger M, Aird SD, Rost B. Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily. Nat Commun 2023; 14:4861. [PMID: 37567881 PMCID: PMC10421932 DOI: 10.1038/s41467-023-40550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.
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Affiliation(s)
- Ivan Koludarov
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany.
| | - Tobias Senoner
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel Dashevsky
- Australian National Insect Collection, Commonwealth Scientific & Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Heinzinger
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Steven D Aird
- 7744-23 Hotaka Ariake, 399-8301, Azumino-shi, Nagano-ken, Japan
| | - Burkhard Rost
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
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11
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Peng C, Wu DD, Ren JL, Peng ZL, Ma Z, Wu W, Lv Y, Wang Z, Deng C, Jiang K, Parkinson CL, Qi Y, Zhang ZY, Li JT. Large-scale snake genome analyses provide insights into vertebrate development. Cell 2023; 186:2959-2976.e22. [PMID: 37339633 DOI: 10.1016/j.cell.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 04/06/2023] [Accepted: 05/19/2023] [Indexed: 06/22/2023]
Abstract
Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of limb loss, an elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations in snakes. We identified some of the genes and regulatory elements that might have shaped the evolution of vision, the skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides insights into the evolution and development of snakes and vertebrates.
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Affiliation(s)
- Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhong-Liang Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhifei Ma
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; College of Life Science, Neijiang Normal University, Neijiang, Sichuan 641100, China
| | - Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cao Deng
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China
| | - Ke Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | | | - Yin Qi
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhi-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar.
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12
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Tang CY, Zhang X, Xu X, Sun S, Peng C, Song MH, Yan C, Sun H, Liu M, Xie L, Luo SJ, Li JT. Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 2023; 24:46. [PMID: 36895044 PMCID: PMC9999515 DOI: 10.1186/s13059-023-02887-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved. RESULTS We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77-Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in SMARCE1, which may be involved in the regulation of chromatophore development initiated from neural crest cells. SMARCE1 knockdown in zebrafish and immunofluorescence verify the interactions among SMARCE1, iridophores, and tfec, which may determine color variations in the Asian vine snake. CONCLUSIONS This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.
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Affiliation(s)
- Chen-Yang Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaohu Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Shijie Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Mingfeng Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Sichuan University-The Chinese University of Hong Kong Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Liang Xie
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin Nay Pyi Taw, 05282, Myanmar.
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13
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Choquette JD, Litzgus JD, Gui JXY, Pitcher TE. A systematic review of snake translocations to identify potential tactics for reducing postrelease effects. Conserv Biol 2023; 37:e14016. [PMID: 36436192 PMCID: PMC10100070 DOI: 10.1111/cobi.14016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 05/30/2023]
Abstract
Advancements in the field of reintroduction biology are needed, but understanding of how to effectively conduct translocations, particularly with snakes, is lacking. We conducted a systematic review of snake translocation studies to identify potential tactics for reducing postrelease effects. We included studies on intentional, human-mediated, wild-wild, or captive-wild translocations to any location, regardless of motive or number of snakes translocated. Only studies that presented results for at least 1 of 4 outcomes (movement behavior, site fidelity, survival, or population establishment) were included. We systematically searched 4 databases for published studies and used 5 methods to search the gray literature. Our search and screening criteria yielded 121 data sources, representing 130 translocation cases. We quantified the association between 15 translocation tactics and short-term translocation outcomes by calculating odds ratios and used forest plots to display results. Snake translocations involved 47 species (from mainly 2 families), and most were motivated by research, were monitored for at least 6 months, occurred in North America, and took place from the 1990s onward. The odds of a positive snake translocation outcome were highest with release of captive reared or juvenile snakes, release of social groups together, delayed release, provision of environmental enrichment or social housing before release, or minimization of distance translocated. The odds of a positive outcome were lowest when snakes were released early in their active season. Our results do not demonstrate causation, but outcomes of snake translocation were associated with 8 tactics (4 of which were strongly correlated). In addition to targeted comparative studies, we recommend practitioners consider the possible influence of these tactics when planning snake translocations.
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Affiliation(s)
- Jonathan D. Choquette
- School of Natural SciencesLaurentian UniversitySudburyOntarioCanada
- Wildlife Preservation CanadaGuelphOntarioCanada
| | | | | | - Trevor E. Pitcher
- Great Lakes Institute for Environmental Research & Department of Integrative BiologyUniversity of WindsorWindsorOntarioCanada
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14
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Pereira AG, Grizante MB, Kohlsdorf T. What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda. Proc Biol Sci 2022; 289:20220841. [PMID: 35975445 PMCID: PMC9382212 DOI: 10.1098/rspb.2022.0841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022] Open
Abstract
Developmental pathways encompass transcription factors and cis-regulatory elements that interact as transcription factor-regulatory element (TF-RE) units. Independent origins of similar phenotypes likely involve changes in different parts of these units, a hypothesis promisingly tested addressing the evolution of the rib-associated lumbar (RAL) morphotype that characterizes emblematic animals such as snakes and elephants. Previous investigation in these lineages identified a polymorphism in the Homology region 1 [H1] enhancer of the Myogenic factor-5 [Myf5], which interacts with HOX10 proteins to modulate rib development. Here we address the evolution of TF-RE units focusing on independent origins of RAL morphotypes. We compiled an extensive database for H1-Myf5 and HOX10 sequences with two goals: (i) evaluate if the enhancer polymorphism is present in amphibians exhibiting the RAL morphotype and (ii) test a hypothesis of enhanced evolutionary flexibility mediated by TF-RE units, according to which independent origins of the RAL morphotype might involve changes in either component of the interaction unit. We identified the H1-Myf5 polymorphism in lineages that diverged around 340 Ma, including Lissamphibia. Independent origins of the RAL morphotype in Tetrapoda involved sequence variation in either component of the TF-RE unit, confirming that different changes may similarly affect the phenotypic outcome of a given developmental pathway.
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Affiliation(s)
- Anieli G. Pereira
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mariana B. Grizante
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Dante Pazzanese Institute of Cardiology, Sao Paulo, Brazil
| | - Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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15
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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16
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Hallas JM, Parchman TL, Feldman CR. Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution. Mol Phylogenet Evol 2021; 167:107374. [PMID: 34896619 DOI: 10.1016/j.ympev.2021.107374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Garter snakes (Thamnophis) are a successful group of natricines endemic to North America. They have become important natural models for ecological and evolutionary research, yet prior efforts to resolve phylogenetic relationships have resulted in conflicting topologies and weak support for certain relationships. Here, we use genomic data generated with a reduced representation double-digest RADseq approach to reassess evolutionary relationships across Thamnophis. We then use the resulting phylogeny to better understand how biogeography and feeding ecology have influenced lineage diversification and morphological evolution. We recovered highly congruent and strongly supported topologies from maximum likelihood and Bayesian analyses, but some discordance with a multispecies coalescent approach. All phylogenomic estimates split Thamnophis into two clades largely defined by northern and southern North American species. Divergence time estimates and biogeographic analyses indicate a mid-Miocene origin of Thamnophis in Mexico. In addition, historic vicariant events thought to explain biogeographic patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns of diversification in Thamnophis as well. Analyses of morphological traits associated with feeding ecology showed moderate to strong phylogenetic signal. Nevertheless, phylogenetic ANOVA suggested significant differences in certain cranial morphologies between aquatic specialists and garter snakes that are terrestrial-aquatic generalists, independent of evolutionary history. Our new estimate of Thamnophis phylogeny yields an improved understanding of the biogeographic history and morphological evolution of garter snakes, and provides a robust framework for future research on these snakes.
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Affiliation(s)
- Joshua M Hallas
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA.
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
| | - Chris R Feldman
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA; Graduate Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557-0314, USA
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17
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Torres-Carvajal O, Terán C. Molecular phylogeny of Neotropical Parrot Snakes (Serpentes: Colubrinae: Leptophis) supports underestimated species richness. Mol Phylogenet Evol 2021; 164:107267. [PMID: 34293395 DOI: 10.1016/j.ympev.2021.107267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022]
Abstract
Tetrapod taxa with broad geographic distributions across the Neotropics are often composed of multiple evolutionary lineages. In this paper, we present the most complete phylogeny of Leptophis to date and assess morphology-based species limits within the broadly distributed green parrot snake Leptophis ahaetulla sensu lato, which occurs from Mexico to Argentina. Although L. ahaetulla sensu stricto, L. nigromarginatus and L. occidentalis were recovered as paraphyletic, tree topology tests failed to reject their monophyly. Monophyly of L. bocourti, L. coeruleodorsus, L. cupreus, L. depressirostris, L. marginatus, L. riveti and L. sp. nov. was strongly supported. Our phylogenetic trees support recognition of multiple species within Leptophis ahaetulla sensu lato and suggest that color evolution and the uplift of the Andes played an important role in the diversification of parrot snakes.
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Affiliation(s)
- Omar Torres-Carvajal
- Museo de Zoología, Departamento de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador.
| | - Claudia Terán
- Museo de Zoología, Departamento de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
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18
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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19
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Nachtigall PG, Rautsaw RM, Ellsworth SA, Mason AJ, Rokyta DR, Parkinson CL, Junqueira-de-Azevedo ILM. ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. Brief Bioinform 2021; 22:6235957. [PMID: 33866357 DOI: 10.1093/bib/bbab095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide. RESULTS Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time ($>20x$ faster), coding sequence prediction ($>3x$ more accurate) and the number of toxins predicted (generating $>4x$ less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
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20
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Bayona-Serrano JD, Viala VL, Rautsaw RM, Schramer TD, Barros-Carvalho GA, Nishiyama MY, Freitas-de-Sousa LA, Moura-da-Silva AM, Parkinson CL, Grazziotin FG, Junqueira-de-Azevedo ILM. Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes. Mol Biol Evol 2020; 37:3563-3575. [PMID: 32722789 PMCID: PMC8525196 DOI: 10.1093/molbev/msaa192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an "SVMP-like" function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.
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Affiliation(s)
| | - Vincent Louis Viala
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC
| | | | | | - Milton Yutaka Nishiyama
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | | | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
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21
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Singchat W, Ahmad SF, Laopichienpong N, Suntronpong A, Panthum T, Griffin DK, Srikulnath K. Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome. Cells 2020; 9:cells9112386. [PMID: 33142713 PMCID: PMC7692289 DOI: 10.3390/cells9112386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.
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Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.S.); (S.F.A.); (N.L.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
- Correspondence: ; Tel.: +66-2562-5644
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22
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Ullate-Agote A, Burgelin I, Debry A, Langrez C, Montange F, Peraldi R, Daraspe J, Kaessmann H, Milinkovitch MC, Tzika AC. Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. Proc Natl Acad Sci U S A 2020; 117:26307-26317. [PMID: 33020272 PMCID: PMC7584913 DOI: 10.1073/pnas.2003724117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Reptiles exhibit a spectacular diversity of skin colors and patterns brought about by the interactions among three chromatophore types: black melanophores with melanin-packed melanosomes, red and yellow xanthophores with pteridine- and/or carotenoid-containing vesicles, and iridophores filled with light-reflecting platelets generating structural colors. Whereas the melanosome, the only color-producing endosome in mammals and birds, has been documented as a lysosome-related organelle, the maturation paths of xanthosomes and iridosomes are unknown. Here, we first use 10x Genomics linked-reads and optical mapping to assemble and annotate a nearly chromosome-quality genome of the corn snake Pantherophis guttatus The assembly is 1.71 Gb long, with an N50 of 16.8 Mb and L50 of 24. Second, we perform mapping-by-sequencing analyses and identify a 3.9-Mb genomic interval where the lavender variant resides. The lavender color morph in corn snakes is characterized by gray, rather than red, blotches on a pink, instead of orange, background. Third, our sequencing analyses reveal a single nucleotide polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene (LYST) that shortens the corresponding protein by 603 amino acids and removes evolutionary-conserved domains. Fourth, we use light and transmission electron microscopy comparative analyses of wild type versus lavender corn snakes and show that the color-producing endosomes of all chromatophores are substantially affected in the LYST mutant. Our work provides evidence characterizing xanthosomes in xanthophores and iridosomes in iridophores as lysosome-related organelles.
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Affiliation(s)
- Asier Ullate-Agote
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ingrid Burgelin
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Adrien Debry
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Carine Langrez
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Florent Montange
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Rodrigue Peraldi
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Jean Daraspe
- Faculté de Biologie et de Médecine, Electron Microscopy Facility, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), D-69120 Heidelberg, Germany
| | - Michel C Milinkovitch
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland;
- SIB Swiss Institute of Bioinformatics, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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23
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Mahtani-Williams S, Fulton W, Desvars-Larrive A, Lado S, Elbers JP, Halpern B, Herczeg D, Babocsay G, Lauš B, Nagy ZT, Jablonski D, Kukushkin O, Orozco-terWengel P, Vörös J, Burger PA. Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia. Genes (Basel) 2020; 11:genes11101218. [PMID: 33080926 PMCID: PMC7603136 DOI: 10.3390/genes11101218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.
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Affiliation(s)
- Sarita Mahtani-Williams
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
- Fundación Charles Darwin, Avenida Charles Darwin s/n, Casilla 200144, Puerto Ayora EC-200350, Ecuador
| | - William Fulton
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Amelie Desvars-Larrive
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Institute of Food Safety, Food Technology and Veterinary Public Health, Vetmeduni Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
- Complexity Science Hub Vienna, Josefstädter Straße 39, A-1080 Vienna, Austria
| | - Sara Lado
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Jean Pierre Elbers
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Bálint Halpern
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
| | - Dávid Herczeg
- Lendület Evolutionary Ecology Research Group, Centre for Agricultural Research, Plant Protection Institute, Herman Ottó út 15., H-1022 Budapest, Hungary;
| | - Gergely Babocsay
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
- Mátra Museum of the Hungarian Natural History Museum, Kossuth Lajos utca 40., H-3200 Gyöngyös, Hungary
| | - Boris Lauš
- Association HYLA, Lipocac I., No. 7, C-10000 Zagreb, Croatia;
| | - Zoltán Tamás Nagy
- Independent Researcher, Hielscherstraße 25, D-13158 Berlin, Germany;
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská Dolina, S-84215 Bratislava, Slovakia;
| | - Oleg Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring, T. I. Vyazemsky Karadag Scientific Station–Nature Reserve–Branch of Institute of Biology of the Southern Seas of the Russian Academy of Sciences, Nauki Street 24, R-298188 Theodosia, Crimea;
- Department of Herpetology, Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, R-199034 Saint Petersburg, Russia
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13., H-1088 Budapest, Hungary
- Molecular Taxonomy Laboratory, Hungarian Natural History Museum, Ludovika tér 2-6., H-1083 Budapest, Hungary
- Correspondence: (J.V.); (P.A.B.)
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Correspondence: (J.V.); (P.A.B.)
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24
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Viana PF, Ezaz T, Cioffi MDB, Liehr T, Al-Rikabi A, Tavares-Pinheiro R, Bertollo LAC, Feldberg E. Revisiting the Karyotype Evolution of Neotropical Boid Snakes: A Puzzle Mediated by Chromosomal Fissions. Cells 2020; 9:cells9102268. [PMID: 33050432 PMCID: PMC7601083 DOI: 10.3390/cells9102268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 11/16/2022] Open
Abstract
The Boidae family is an ancient group of snakes widely distributed across the Neotropical region, where several biogeographic events contributed towards shaping their evolution and diversification. Most species of this family have a diploid number composed of 2n = 36; however, among Booidea families, the Boidae stands out by presenting the greatest chromosomal diversity, with 2n ranging between 36 and 44 chromosomes and an undifferentiated XY sex chromosome system. Here, we applied a comparative chromosome analysis using cross-species chromosome paintings in five species representing four Boidae genera, to decipher the evolutionary dynamics of some chromosomes in these Neotropical snakes. Our study included all diploid numbers (2n = 36, 40, and 44) known for this family and our comparative chromosomal mappings point to a strong evolutionary relationship among the genera Boa, Corallus, Eunectes, and Epicrates. The results also allowed us to propose the cytogenomic diversification that had occurred in this family: a process mediated by centric fissions, including fission events of the putative and undifferentiated XY sex chromosome system in the 2n = 44 karyotype, which is critical in solving the puzzle of the karyotype evolution of boid snakes.
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Affiliation(s)
- Patrik F. Viana
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra 12 2616, ACT, Australia;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
- Correspondence: ; Tel.: +49-3641-9396850
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Rodrigo Tavares-Pinheiro
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Herpetologia, Universidade Federal do Amapá, Macapá 68903-419, AP, Brazil;
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (L.A.C.B.)
| | - Eliana Feldberg
- Laboratory of Animal Genetics, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil; (P.F.V.); (E.F.)
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25
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Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C. The tuatara genome reveals ancient features of amniote evolution. Nature 2020; 584:403-409. [PMID: 32760000 PMCID: PMC7116210 DOI: 10.1038/s41586-020-2561-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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Affiliation(s)
- Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - David L Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - José H Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen, Berlin, Germany
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chris Organ
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Paul P Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Thomas R Buckley
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Melissa D Jordan
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Richard D Newcomb
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - José Ignacio Arroyo
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Tim A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Jaime Renart
- Instituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid, Spain
| | - Valentina Peona
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Claire R Peart
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Vera M Warmuth
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Lu Zeng
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joy M Raison
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Victoria G Twort
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Helen Taylor
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - James M Paterson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Stephan Pabinger
- Austrian Institute of Technology (AIT), Center for Health and Bioresources, Molecular Diagnostics, Vienna, Austria
| | | | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Oliver Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Anderson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clive Stone
- Ngatiwai Trust Board, Whangarei, New Zealand
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Clemente L, Mazzoleni S, Pensabene Bellavia E, Augstenová B, Auer M, Praschag P, Protiva T, Velenský P, Wagner P, Fritz U, Kratochvíl L, Rovatsos M. Interstitial Telomeric Repeats Are Rare in Turtles. Genes (Basel) 2020; 11:genes11060657. [PMID: 32560114 PMCID: PMC7348932 DOI: 10.3390/genes11060657] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/18/2023] Open
Abstract
Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG)n repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.
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Affiliation(s)
- Lorenzo Clemente
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Eleonora Pensabene Bellavia
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Markus Auer
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | | | | | - Petr Velenský
- Prague Zoological Garden, 17100 Prague, Czech Republic;
| | | | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, 01109 Dresden, Germany; (M.A.); (U.F.)
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic; (L.C.); (S.M.); (E.P.B.); (B.A.); (L.K.)
- Correspondence:
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27
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Wood DA, Rose JP, Halstead BJ, Stoelting RE, Swaim KE, Vandergast AG. Combining genetic and demographic monitoring better informs conservation of an endangered urban snake. PLoS One 2020; 15:e0231744. [PMID: 32369486 PMCID: PMC7200000 DOI: 10.1371/journal.pone.0231744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 11/24/2022] Open
Abstract
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T. s. tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T. s. tetrataenia populations could promote persistence of this endangered snake.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Jonathan P. Rose
- U.S. Geological Survey, Western Ecological Research Center, Santa Cruz Field Station, Santa Cruz, California, United States of America
| | - Brian J. Halstead
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, United States of America
| | - Ricka E. Stoelting
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Karen E. Swaim
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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28
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Simard J, Marschang RE, Leineweber C, Hellebuyck T. Prevalence of inclusion body disease and associated comorbidity in captive collections of boid and pythonid snakes in Belgium. PLoS One 2020; 15:e0229667. [PMID: 32119716 PMCID: PMC7051093 DOI: 10.1371/journal.pone.0229667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/11/2020] [Indexed: 12/30/2022] Open
Abstract
Inclusion body disease (IBD) is caused by reptarenaviruses and constitutes one of the most notorious viral diseases in snakes. Although central nervous system disease and various other clinical signs have been attributed to IBD in boid and pythonid snakes, studies that unambiguously reveal the clinical course of natural IBD and reptarenavirus infection are scarce. In the present study, the prevalence of IBD and reptarenaviruses in captive snake collections and the correlation of IBD and reptarenavirus infection with the clinical status of the sampled snakes were investigated. In three IBD positive collections, long-term follow-up during a three- to seven-year period was performed. A total of 292 snakes (178 boas and 114 pythons) from 40 collections in Belgium were sampled. In each snake, blood and buffy coat smears were evaluated for the presence of IBD inclusion bodies (IB) and whole blood was tested for reptarenavirus RNA by RT-PCR. Of all tested snakes, 16.5% (48/292) were positive for IBD of which all were boa constrictors (34.0%; 48/141) and 17.1% (50/292) were reptarenavirus RT-PCR positive. The presence of IB could not be demonstrated in any of the tested pythons, while 5.3% (6/114) were reptarenavirus positive. In contrast to pythons, the presence of IB in peripheral blood cells in boa constrictors is strongly correlated with reptarenavirus detection by RT-PCR (P<0.0001). Although boa constrictors often show persistent subclinical infection, long-term follow-up indicated that a considerable number (22.2%; 6/27) of IBD/reptarenavirus positive boas eventually develop IBD associated comorbidities.
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Affiliation(s)
- Jules Simard
- Division of Poultry, Department of Pathology, Bacteriology and Avian Diseases, Exotic Companion Animals, Wildlife and Experimental Animals, Ghent University, Merelbeke, Belgium
| | | | | | - Tom Hellebuyck
- Division of Poultry, Department of Pathology, Bacteriology and Avian Diseases, Exotic Companion Animals, Wildlife and Experimental Animals, Ghent University, Merelbeke, Belgium
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29
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Mallik AK, Achyuthan NS, Ganesh SR, Pal SP, Vijayakumar SP, Shanker K. Discovery of a deeply divergent new lineage of vine snake (Colubridae: Ahaetuliinae: Proahaetulla gen. nov.) from the southern Western Ghats of Peninsular India with a revised key for Ahaetuliinae. PLoS One 2019; 14:e0218851. [PMID: 31314800 PMCID: PMC6636718 DOI: 10.1371/journal.pone.0218851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 06/11/2019] [Indexed: 11/18/2022] Open
Abstract
The Western Ghats are well known as a biodiversity hotspot, but the full extent of its snake diversity is yet to be uncovered. Here, we describe a new genus and species of vine snake Proahaetulla antiqua gen. et sp. nov., from the Agasthyamalai hills in the southern Western Ghats. It was found to be a member of the Ahaetuliinae clade, which currently comprises the arboreal snake genera Ahaetulla, Dryophiops, Dendrelaphis and Chrysopelea, distributed in South and Southeast Asia. Proahaetulla shows a sister relationship with all currently known taxa belonging to the genus Ahaetulla, and shares ancestry with Dryophiops. In addition to its phylogenetic position and significant genetic divergence, this new taxon is also different in morphology from members of Ahaetuliinae in a combination of characters, having 12-13 partially serrated keels on the dorsal scale rows, 20 maxillary teeth and 3 postocular scales. Divergence dating reveals that the new genus is ancient, dating back to the Mid-Oligocene, and is one of the oldest persisting monotypic lineages of snakes in the Western Ghats. This discovery adds to the growing list of ancient lineages endemic to the Agasthyamalai hills and underscores the biogeographic significance of this isolated massif in the southern Western Ghats.
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Affiliation(s)
- Ashok Kumar Mallik
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | | | | | - Saunak P. Pal
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- Bombay Natural History Society, Hornbill House, Opposite Lion Gate, Fort, Mumbai, India
| | - S. P. Vijayakumar
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- Department of Biological Sciences, The George Washington University, Washington, DC, United States of America
| | - Kartik Shanker
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
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Folt B, Bauder J, Spear S, Stevenson D, Hoffman M, Oaks JR, Wood PL, Jenkins C, Steen DA, Guyer C. Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, Drymarchon couperi. PLoS One 2019; 14:e0214439. [PMID: 30913266 PMCID: PMC6435180 DOI: 10.1371/journal.pone.0214439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.
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Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
| | - Javan Bauder
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, United States of America
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Stephen Spear
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- The Wilds, Cumberland, Ohio United States of America
| | - Dirk Stevenson
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Altamaha Environmental Consulting, Hinesville, Georgia, United States of America
| | - Michelle Hoffman
- The Orianne Center for Indigo Conservation, Central Florida Zoo and Botanical Gardens, Sanford, Florida, United States of America
| | - Jamie R. Oaks
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Perry L. Wood
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Christopher Jenkins
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
| | - David A. Steen
- Georgia Sea Turtle Center, Jekyll Island Authority, Jekyll Island, Georgia, United States of America
| | - Craig Guyer
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
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Matsubara K, Kumazawa Y, Ota H, Nishida C, Matsuda Y. Karyotype Analysis of Four Blind Snake Species (Reptilia: Squamata: Scolecophidia) and Karyotypic Changes in Serpentes. Cytogenet Genome Res 2019; 157:98-106. [PMID: 30754040 DOI: 10.1159/000496554] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The suborder Serpentes is divided into 2 infraorders, Scolecophidia and Alethinophidia, which diverged at an early stage of snake diversification. In this study, we examined karyotypes of 4 scolecophidian species (Letheobia simonii, Xerotyphlops vermicularis, Indotyphlops braminus, and Myriopholis macrorhyncha) and performed FISH with 18S-28S rDNA as well as microchromosomal and Z chromosome-linked genes of Elaphe quadrivirgata (Alethinophidia) to investigate the karyotype evolution in the scolecophidian lineage. Diploid chromosome numbers of X. vermicularis and L. simonii were 30 (16 macrochromosomes and 14 microchromosomes) and 32 (16 macrochromosomes and 16 microchromosomes), respectively. The karyotype of a female M. macrorhyncha consisted of 15 macrochromosomes and 19 microchromosomes, including a heterochromatic microchromosome, indicating the presence of a heteromorphic chromosome pair. E. quadrivirgata Z-linked genes mapped to chromosome 4 of M. macrorhyncha, not to the heteromorphic pair. Therefore, M. macrorhyncha may have differentiated ZW sex chromosomes which are not homologous to those of E. quadrivirgata. One of the E. quadrivirgata microchromosomal genes mapped to the terminal region of chromosome 4q in X. vermicularis, suggesting that fusions between microchromosomes and macrochromosomes occurred in this species. rDNA was localized in different macrochromosomal pairs in the 2 diploid scolecophidian snakes examined here, whereas the gene location in a microchromosomal pair was conserved in 5 alethinophidian species examined. These results might imply the occurrence of chromosome fusions in the scolecophidian lineages. In I. braminus, a unique parthenogenetic snake with a triploid karyotype (21 macrochromosomes and 21 microchromosomes), morphological heteromorphisms were identified in chromosomes 1 and 7. Such heteromorphisms in 2 chromosomes were also observed in individuals from distant locations in the broad distribution range of this species, suggesting that the heteromorphisms were fixed in the genome at an early stage of its speciation.
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van den Hurk P, Kerkkamp HMI. Phylogenetic origins for severe acetaminophen toxicity in snake species compared to other vertebrate taxa. Comp Biochem Physiol C Toxicol Pharmacol 2019; 215:18-24. [PMID: 30268769 DOI: 10.1016/j.cbpc.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/24/2022]
Abstract
While it has been known for a while that some snake species are extremely sensitive to acetaminophen, the underlying mechanism for this toxicity has not been reported. To investigate if essential detoxification enzymes are missing in snake species that are responsible for biotransformation of acetaminophen in other vertebrate species, livers were collected from a variety of snake species, together with samples from alligator, snapping turtle, cat, rat, and cattle. Subcellular fractions were analyzed for enzymatic activities of phenol-type sulfotransferase and UDP‑glucuronosyltransferase, total glutathione S‑transferase, and N‑acetyltransferase. The results showed that none of the snake species, together with the cat samples, had any phenol-type glucuronidation activity, and that this activity was much lower in alligator and turtle samples than in the mammalian species. Combined with the lack of N‑acetyltransferase activity in snakes and cats, this would explain the accumulation of the aminophenol metabolite, which induces methemoglobinemia and subsequent suffocation of snakes and cats after acetaminophen exposure. While previous investigations have concluded that in cats the gene for the phenol-type glucuronosyltransferase isoform has turned into a pseudogene because of several point mutations, evaluation of genomic information for snake species revealed that they have only 2 genes that may code for glucuronosyltransferase isoforms. Similarity of these genes with mammalian genes is <50%, and suggests that the expressed enzymes may act on other types of substrates than aromatic amines. This indicates that the extreme sensitivity for acetaminophen in snakes is based on a different phylogenetic origin than the sensitivity observed in cats.
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Affiliation(s)
- Peter van den Hurk
- Department of Biological Sciences, Clemson University, Clemson, SC 20624, USA.
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33
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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34
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Murray-Dickson G, Ghazali M, Ogden R, Brown R, Auliya M. Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species. PLoS One 2017; 12:e0182049. [PMID: 28817588 PMCID: PMC5560690 DOI: 10.1371/journal.pone.0182049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.
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Affiliation(s)
- Gillian Murray-Dickson
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
- * E-mail:
| | - Muhammad Ghazali
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
| | - Rob Ogden
- Trace Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Rafe Brown
- KU Biodiversity Institute, 1345 Jayhawk Blvd, Dyche, Lawrence, KS, United States of America
| | - Mark Auliya
- Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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35
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Abstract
Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.
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Affiliation(s)
- Asier Ullate-Agote
- Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - Athanasia C Tzika
- Laboratory of Artificial and Natural Evolution (LANE), Department of Genetics and Evolution, University of Geneva, Sciences III, 30, Quai Ernest-Ansermet, 1211, Geneva, Switzerland.
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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Jackson TNW, Fry BG. A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology. Toxins (Basel) 2016; 8:E263. [PMID: 27618098 PMCID: PMC5037489 DOI: 10.3390/toxins8090263] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 11/16/2022] Open
Abstract
The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.
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Affiliation(s)
- Timothy N W Jackson
- Venom Evolution Lab, School of Bioloigical Sciences, University of Queensland, St Lucia QLD, 4072 Brisbane, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia QLD, 4072 Brisbane, Australia.
| | - Bryan G Fry
- Venom Evolution Lab, School of Bioloigical Sciences, University of Queensland, St Lucia QLD, 4072 Brisbane, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia QLD, 4072 Brisbane, Australia.
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Figueroa A, McKelvy AD, Grismer LL, Bell CD, Lailvaux SP. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus. PLoS One 2016; 11:e0161070. [PMID: 27603205 PMCID: PMC5014348 DOI: 10.1371/journal.pone.0161070] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/28/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). RESULTS Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. CONCLUSION Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.
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Affiliation(s)
- Alex Figueroa
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Alexander D. McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, United States of America
- Department of Biology, 6S-143, College of Staten Island, 2800 Victory Boulevard, Staten Island, NY, United States of America
| | - L. Lee Grismer
- Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, United States of America
| | - Charles D. Bell
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Simon P. Lailvaux
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
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Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA. Coral snakes predict the evolution of mimicry across New World snakes. Nat Commun 2016; 7:11484. [PMID: 27146100 PMCID: PMC4858746 DOI: 10.1038/ncomms11484] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World snake species to demonstrate that shifts to mimetic coloration in nonvenomous snakes are highly correlated with coral snakes in both space and time, providing overwhelming support for Batesian mimicry. We also find that bidirectional transitions between mimetic and cryptic coloration are unexpectedly frequent over both long- and short-time scales, challenging traditional views of mimicry as a stable evolutionary 'end point' and suggesting that insect and snake mimicry may have different evolutionary dynamics.
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Affiliation(s)
- Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, 3101 Valley Life Sciences, Berkeley, California 94720, USA
| | - Christian L. Cox
- Department of Biology, Georgia Southern University, PO Box 8042, Statesboro, Georgia 30460, USA
- Department of Biology, The University of Texas, Arlington, Texas 76019, USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Pascal O. Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Anat Feldman
- Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, 3101 Valley Life Sciences, Berkeley, California 94720, USA
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Krysko KL, Nuñez LP, Lippi CA, Smith DJ, Granatosky MC. Pliocene-Pleistocene lineage diversifications in the Eastern Indigo Snake (Drymarchon couperi) in the Southeastern United States. Mol Phylogenet Evol 2016; 98:111-22. [PMID: 26778258 DOI: 10.1016/j.ympev.2015.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
Indigo Snakes (Drymarchon; with five currently recognized species) occur from northern Argentina, northward to the United States in southern Texas and eastward in disjunct populations in Florida and Georgia. Based on this known allopatry and a difference in supralabial morphology the two United States taxa previously considered as subspecies within D. corais (Boie 1827), the Western Indigo Snake, D. melanurus erebennus (Cope 1860), and Eastern Indigo Snake, D. couperi (Holbrook 1842), are currently recognized as separate species. Drymarchon couperi is a Federally-designated Threatened species by the United States Fish and Wildlife Service under the Endangered Species Act, and currently being incorporated into a translocation program. This, combined with its disjunct distribution makes it a prime candidate for studying speciation and genetic divergence. In this study, we (1) test the hypothesis that D. m. erebennus and D. couperi are distinct lineages by analyzing 2411 base pairs (bp) of two mitochondrial (mtDNA) loci and one single copy nuclear (scnDNA) locus; (2) estimate the timing of speciation using a relaxed phylogenetics method to determine if Milankovitch cycles during the Pleistocene might have had an influence on lineage diversifications; (3) examine historical population demography to determine if identified lineages have undergone population declines, expansions, or remained stable during the most recent Milankovitch cycles; and (4) use this information to assist in an effective and scientifically sound translocation program. Our molecular data support the initial hypothesis that D. melanurus and D. couperi should be recognized as distinct species, but further illustrate that D. couperi is split into two distinct genetic lineages that correspond to historical biogeography and sea level changes in peninsular Florida. These two well-supported genetic lineages (herein termed Atlantic and Gulf lineages) illustrate a common biogeographic distributional break previously identified for other plants and animals, suggesting that these organisms might have shared a common evolutionary history related to historic sea level changes caused by Milankovitch cycles. Our estimated divergence times suggest that the most recent common ancestor (MRCA) between D. melanurus and southeastern United States Drymarchon occurred ca. 5.9Ma (95% HPD=2.5-9.8Ma; during the late Blancan of the Pleistocene through the Hemphillian of the Miocene), whereas the MRCA between the Atlantic and Gulf lineages in the southeastern United States occurred ca. 2.0Ma (95% HPD=0.7-3.7Ma; during the Irvingtonian of the Pleistocene through the Blancan of the Pliocene). During one or more glacial intervals within these times, these two lineages must have become separated and evolved independently. Despite numerous Milankovitch cycles along with associated forming of physical barriers (i.e., sea level fluctuations, high elevation sand ridges, clayey soils, and/or insufficient habitats) since their initial lineage diversification, these two lineages have likely come in and out of contact with each other many times, yet today they still illustrate near discrete geographic distributions. Although the Atlantic and Gulf lineages appear to be cryptic, a thorough study examining morphological characters should be conducted. We believe that our molecular data is crucial and should be incorporated in making conscious decisions in the management of a translocation program. We suggest that source populations for translocations include maintaining the integrity of the known genetic lineages found herein, as well as those coming from the closest areas that currently support sizable Drymarchon populations.
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Affiliation(s)
- Kenneth L Krysko
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Leroy P Nuñez
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA; School of Natural Resources and Environment, 103 Black Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Catherine A Lippi
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, 13201 Bruce B Downs, MDC56, Tampa, FL 33612, USA.
| | - Daniel J Smith
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Michael C Granatosky
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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Ruane S, Raxworthy CJ, Lemmon AR, Lemmon EM, Burbrink FT. Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes. BMC Evol Biol 2015; 15:221. [PMID: 26459325 PMCID: PMC4603904 DOI: 10.1186/s12862-015-0503-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/01/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar's serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. METHODS Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. RESULTS Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. CONCLUSIONS Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees.
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Affiliation(s)
- Sara Ruane
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
| | - Alan R Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA.
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Biology Department, College of Staten Island/CUNY, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.
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Aubret F. Island colonisation and the evolutionary rates of body size in insular neonate snakes. Heredity (Edinb) 2015; 115:349-56. [PMID: 25074570 PMCID: PMC4815452 DOI: 10.1038/hdy.2014.65] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/27/2014] [Accepted: 06/04/2014] [Indexed: 11/09/2022] Open
Abstract
Island colonisation by animal populations is often associated with dramatic shifts in body size. However, little is known about the rates at which these evolutionary shifts occur, under what precise selective pressures and the putative role played by adaptive plasticity on driving such changes. Isolation time played a significant role in the evolution of body size in island Tiger snake populations, where adaptive phenotypic plasticity followed by genetic assimilation fine-tuned neonate body and head size (hence swallowing performance) to prey size. Here I show that in long isolated islands (>6000 years old) and mainland populations, neonate body mass and snout-vent length are tightly correlated with the average prey body mass available at each site. Regression line equations were used to calculate body size values to match prey size in four recently isolated populations of Tiger snakes. Rates of evolution in body mass and snout-vent length, calculated for seven island snake populations, were significantly correlated with isolation time. Finally, rates of evolution in body mass per generation were significantly correlated with levels of plasticity in head growth rates. This study shows that body size evolution occurs at a faster pace in recently isolated populations and suggests that the level of adaptive plasticity for swallowing abilities may correlate with rates of body mass evolution. I hypothesise that, in the early stages of colonisation, adaptive plasticity and directional selection may combine and generate accelerated evolution towards an 'optimal' phenotype.
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Affiliation(s)
- F Aubret
- Station d'Ecologie Expérimentale du CNRS à Moulis, Saint-Girons, France
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Cavalheri H, Both C, Martins M. The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities. PLoS One 2015; 10:e0127959. [PMID: 26061038 PMCID: PMC4465701 DOI: 10.1371/journal.pone.0127959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community were also related to habitat type, showing that communities from non-forest areas tend to be more clustered. Our study showed that both environmental filtering and spatial gradients play important roles in shaping the composition of Neotropical snake communities.
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Affiliation(s)
- Hamanda Cavalheri
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, 05508–090, São Paulo, SP, Brazil
- * E-mail:
| | - Camila Both
- Programa de Pós-graduação em Biodiversidade animal, Universidade Federal de Santa Maria, 97105–900, Santa Maria, RS, Brazil
| | - Marcio Martins
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, 05508–090, São Paulo, SP, Brazil
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Bellini GP, Giraudo AR, Arzamendia V, Etchepare EG. Temperate snake community in South America: is diet determined by phylogeny or ecology? PLoS One 2015; 10:e0123237. [PMID: 25945501 PMCID: PMC4422434 DOI: 10.1371/journal.pone.0123237] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/28/2015] [Indexed: 11/18/2022] Open
Abstract
Communities are complex and dynamic systems that change with time. The first attempts to explain how they were structured involve contemporary phenomena like ecological interactions between species (e.g., competition and predation) and led to the competition-predation hypothesis. Recently, the deep history hypothesis has emerged, which suggests that profound differences in the evolutionary history of organisms resulted in a number of ecological features that remain largely on species that are part of existing communities. Nevertheless, both phylogenetic structure and ecological interactions can act together to determine the structure of a community. Because diet is one of the main niche axes, in this study we evaluated, for the first time, the impact of ecological and phylogenetic factors on the diet of Neotropical snakes from the subtropical-temperate region of South America. Additionally, we studied their relationship with morphological and environmental aspects to understand the natural history and ecology of this community. A canonical phylogenetical ordination analysis showed that phylogeny explained most of the variation in diet, whereas ecological characters explained very little of this variation. Furthermore, some snakes that shared the habitat showed some degree of diet convergence, in accordance with the competition-predation hypothesis, although phylogeny remained the major determinant in structuring this community. The clade with the greatest variability was the subfamily Dipsadinae, whose members had a very different type of diet, based on soft-bodied invertebrates. Our results are consistent with the deep history hypothesis, and we suggest that the community under study has a deep phylogenetic effect that explains most of the variation in the diet.
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Affiliation(s)
| | - Alejandro R. Giraudo
- Instituto Nacional de Limnología (CONICET-UNL), Santa Fe, Argentina
- Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Vanesa Arzamendia
- Instituto Nacional de Limnología (CONICET-UNL), Santa Fe, Argentina
- Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Eduardo G. Etchepare
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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Reeder TW, Townsend TM, Mulcahy DG, Noonan BP, Wood PL, Sites JW, Wiens JJ. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa. PLoS One 2015; 10:e0118199. [PMID: 25803280 PMCID: PMC4372529 DOI: 10.1371/journal.pone.0118199] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/08/2015] [Indexed: 11/18/2022] Open
Abstract
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
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Affiliation(s)
- Tod W. Reeder
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Ted M. Townsend
- Department of Biology, San Diego State University, San Diego, California, 92182, United States of America
| | - Daniel G. Mulcahy
- Laboratories of Analytical Biology, Smithsonian Institution, 10th & Constitution Aves. NW, Washington, D.C., 20560, United States of America
| | - Brice P. Noonan
- Department of Biology, University of Mississippi, Box 1848, Mississippi, 38677, United States of America
| | - Perry L. Wood
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, United States of America
- * E-mail:
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Huang Y, Zhang YY, Zhao CJ, Xu YL, Gu YL, Huang WQ, Lin K, Li L. [DNA barcoding and its utility in commonly-used medicinal snakes]. Zhongguo Zhong Yao Za Zhi 2015; 40:868-874. [PMID: 26087547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Identification accuracy of traditional Chinese medicine is crucial for the traditional Chinese medicine research, production and application. DNA barcoding based on the mitochondrial gene coding for cytochrome c oxidase subunit I (COI), are more and more used for identification of traditional Chinese medicine. Using universal barcoding primers to sequence, we discussed the feasibility of DNA barcoding method for identification commonly-used medicinal snakes (a total of 109 samples belonging to 19 species 15 genera 6 families). The phylogenetic trees using Neighbor-joining were constructed. The results indicated that the mean content of G + C(46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the mean intraspecies genetic distance of Trimeresurus albolabris, Ptyas dhumnades and Lycodon rufozonatus was greater than 2%. Further phylogenetic relationship results suggested that identification of one sample of T. albolabris was erroneous. The identification of some samples of P. dhumnades was also not correct, namely originally P. korros was identified as P. dhumnades. Factors influence on intraspecific genetic distance difference of L. rufozonatus need to be studied further. Therefore, DNA barcoding for identification of medicinal snakes is feasible, and greatly complements the morphological classification method. It is necessary to further study in identification of traditional Chinese medicine.
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van Soldt BJ, Metscher BD, Poelmann RE, Vervust B, Vonk FJ, Müller GB, Richardson MK. Heterochrony and early left-right asymmetry in the development of the cardiorespiratory system of snakes. PLoS One 2015; 10:e116416. [PMID: 25555231 PMCID: PMC4282204 DOI: 10.1371/journal.pone.0116416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 11/21/2014] [Indexed: 01/19/2023] Open
Abstract
Snake lungs show a remarkable diversity of organ asymmetries. The right lung is always fully developed, while the left lung is either absent, vestigial, or well-developed (but smaller than the right). A 'tracheal lung' is present in some taxa. These asymmetries are reflected in the pulmonary arteries. Lung asymmetry is known to appear at early stages of development in Thamnophis radix and Natrix natrix. Unfortunately, there is no developmental data on snakes with a well-developed or absent left lung. We examine the adult and developmental morphology of the lung and pulmonary arteries in the snakes Python curtus breitensteini, Pantherophis guttata guttata, Elaphe obsoleta spiloides, Calloselasma rhodostoma and Causus rhombeatus using gross dissection, MicroCT scanning and 3D reconstruction. We find that the right and tracheal lung develop similarly in these species. By contrast, the left lung either: (1) fails to develop; (2) elongates more slowly and aborts early without (2a) or with (2b) subsequent development of faveoli; (3) or develops normally. A right pulmonary artery always develops, but the left develops only if the left lung develops. No pulmonary artery develops in relation to the tracheal lung. We conclude that heterochrony in lung bud development contributes to lung asymmetry in several snake taxa. Secondly, the development of the pulmonary arteries is asymmetric at early stages, possibly because the splanchnic plexus fails to develop when the left lung is reduced. Finally, some changes in the topography of the pulmonary arteries are consequent on ontogenetic displacement of the heart down the body. Our findings show that the left-right asymmetry in the cardiorespiratory system of snakes is expressed early in development and may become phenotypically expressed through heterochronic shifts in growth, and changes in axial relations of organs and vessels. We propose a step-wise model for reduction of the left lung during snake evolution.
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Affiliation(s)
| | - Brian D. Metscher
- Department of Theoretical Biology, University of Vienna, Vienna, Austria
| | - Robert E. Poelmann
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Bart Vervust
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Freek J. Vonk
- Institute of Biology, University of Leiden, Leiden, the Netherlands
- NCB Naturalis, Leiden, the Netherlands
| | - Gerd B. Müller
- Department of Theoretical Biology, University of Vienna, Vienna, Austria
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Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H. Early mesozoic coexistence of amniotes and hepadnaviridae. PLoS Genet 2014; 10:e1004559. [PMID: 25501991 PMCID: PMC4263362 DOI: 10.1371/journal.pgen.1004559] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/24/2014] [Indexed: 12/16/2022] Open
Abstract
Hepadnaviridae are double-stranded DNA viruses that infect some species of birds and mammals. This includes humans, where hepatitis B viruses (HBVs) are prevalent pathogens in considerable parts of the global population. Recently, endogenized sequences of HBVs (eHBVs) have been discovered in bird genomes where they constitute direct evidence for the coexistence of these viruses and their hosts from the late Mesozoic until present. Nevertheless, virtually nothing is known about the ancient host range of this virus family in other animals. Here we report the first eHBVs from crocodilian, snake, and turtle genomes, including a turtle eHBV that endogenized >207 million years ago. This genomic “fossil” is >125 million years older than the oldest avian eHBV and provides the first direct evidence that Hepadnaviridae already existed during the Early Mesozoic. This implies that the Mesozoic fossil record of HBV infection spans three of the five major groups of land vertebrates, namely birds, crocodilians, and turtles. We show that the deep phylogenetic relationships of HBVs are largely congruent with the deep phylogeny of their amniote hosts, which suggests an ancient amniote–HBV coexistence and codivergence, at least since the Early Mesozoic. Notably, the organization of overlapping genes as well as the structure of elements involved in viral replication has remained highly conserved among HBVs along that time span, except for the presence of the X gene. We provide multiple lines of evidence that the tumor-promoting X protein of mammalian HBVs lacks a homolog in all other hepadnaviruses and propose a novel scenario for the emergence of X via segmental duplication and overprinting of pre-existing reading frames in the ancestor of mammalian HBVs. Our study reveals an unforeseen host range of prehistoric HBVs and provides novel insights into the genome evolution of hepadnaviruses throughout their long-lasting association with amniote hosts. Viruses are not known to leave physical fossil traces, which makes our understanding of their evolutionary prehistory crucially dependent on the detection of endogenous viruses. Ancient endogenous viruses, also known as paleoviruses, are relics of viral genomes or fragments thereof that once infiltrated their host's germline and then remained as molecular “fossils” within the host genome. The massive genome sequencing of recent years has unearthed vast numbers of paleoviruses from various animal genomes, including the first endogenous hepatitis B viruses (eHBVs) in bird genomes. We screened genomes of land vertebrates (amniotes) for the presence of paleoviruses and identified ancient eHBVs in the recently sequenced genomes of crocodilians, snakes, and turtles. We report an eHBV that is >207 million years old, making it the oldest endogenous virus currently known. Furthermore, our results provide direct evidence that the Hepadnaviridae virus family infected birds, crocodilians and turtles during the Mesozoic Era, and suggest a long-lasting coexistence of these viruses and their amniote hosts at least since the Early Mesozoic. We challenge previous views on the origin of the oncogenic X gene and provide an evolutionary explanation as to why only mammalian hepatitis B infection leads to hepatocellular carcinoma.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Claudia C. Weber
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - Christian Kehlmaier
- Museum of Zoology, Senckenberg Research Institute and Natural History Museum, Dresden, Germany
| | - Edward L. Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Research Institute and Natural History Museum, Dresden, Germany
| | - David A. Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Hans Ellegren
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
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Chen K, Jiang C, Yuan Y, Huang LQ, Li M. [Application of rapid PCR to authenticate medicinal snakes]. Zhongguo Zhong Yao Za Zhi 2014; 39:3673-3677. [PMID: 25612419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To obtained an accurate, rapid and efficient method for authenticate medicinal snakes listed in Chinese Pharmacopoeia (Zaocysd humnades, Bungarus multicinctus, Agkistrodon acutus), a rapid PCR method for authenticate snakes and its adulterants was established based on the classic molecular authentication methods. DNA was extracted by alkaline lysis and the specific primers were amplified by two-steps PCR amplification method. The denatured and annealing temperature and cycle numbers were optimized. When 100 x SYBR Green I was added in the PCR product, strong green fluorescence was visualized under 365 nm UV whereas adulterants without. The whole process can complete in 30-45 minutes. The established method provides the technical support for authentication of the snakes on field.
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Mulcahy DG, Martínez-Gómez JE, Aguirre-León G, Cervantes-Pasqualli JA, Zug GR. Rediscovery of an endemic vertebrate from the remote Islas Revillagigedo in the eastern Pacific Ocean: the Clarión nightsnake lost and found. PLoS One 2014; 9:e97682. [PMID: 24837300 PMCID: PMC4023976 DOI: 10.1371/journal.pone.0097682] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/22/2014] [Indexed: 11/18/2022] Open
Abstract
Vertebrates are currently going extinct at an alarming rate, largely because of habitat loss, global warming, infectious diseases, and human introductions. Island ecosystems are particularly vulnerable to invasive species and other ecological disturbances. Properly documenting historic and current species distributions is critical for quantifying extinction events. Museum specimens, field notes, and other archived materials from historical expeditions are essential for documenting recent changes in biodiversity. The Islas Revillagigedo are a remote group of four islands, 700–1100 km off the western coast of mainland México. The islands are home to many endemic plants and animals recognized at the specific- and subspecific-levels, several of which are currently threatened or have already gone extinct. Here, we recount the initial discovery of an endemic snake Hypsiglena ochrorhyncha unaocularus Tanner on Isla Clarión, the later dismissal of its existence, its absence from decades of field surveys, our recent rediscovery, and recognition of it as a distinct species. We collected two novel complete mitochondrial (mt) DNA genomes and up to 2800 base-pairs of mtDNA from several other individuals, aligned these with previously published mt-genome data from samples throughout the range of Hypsiglena, and conducted phylogenetic analyses to infer the biogeographic origin and taxonomic status of this population. We found the Isla Clarión population to be most closely related to populations in the Sonora–Sinaloa state border area of mainland México and Isla Santa Catalina, in the Gulf of California. Based on genetics, morphology, and geographic distributions, we also recognize these two other lineages as distinct species. Our study shows the importance of museum specimens, field notes, and careful surveys to accurately document biodiversity and brings these island endemics (Clarión and Santa Catalina nightsnakes) and mainland population near the Sonora–Sinaloa state border to the attention of conservation biologists currently monitoring biodiversity in these fragile subtropical ecosystems.
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Affiliation(s)
- Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
- * E-mail:
| | - Juan E. Martínez-Gómez
- Instituto de Ecología, Asociación Civil, Red de Interacciones Multitróficas, Xalapa, Veracruz, México
| | - Gustavo Aguirre-León
- Instituto de Ecología, Asociación Civil, Red de Interacciones Multitróficas, Xalapa, Veracruz, México
| | | | - George R. Zug
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
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Liao J, Chao Z, Zhang L. [Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence]. Zhong Yao Cai 2013; 36:1740-1742. [PMID: 24956810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility. METHODS The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0. RESULTS The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%. CONCLUSION DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.
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