1
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Guo P, Wang P, Lyu B, Liu Q, Zheng J, Fu C, Wu Y, Shu G, Hou S. Molecular phylogeny reveals cryptic diversity in Sibynophis from China (Serpentes: Sibynophiidae). Ecol Evol 2023; 13:e10367. [PMID: 37529581 PMCID: PMC10375455 DOI: 10.1002/ece3.10367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
The elucidation of species diversity and distribution is critical within the fields of evolution, genetics, and conservation. The genus Sibynophis contains rare snakes that have historically received little attention. In this study, we conducted comprehensive sampling and use both mitochondrial and nuclear genetic markers to explore Sibynophis species diversity within China. Our findings revealed that S. c. miyiensis should be considered synonymous with S. c. grahami, and S. c. grahami should be gave a specific rank as S. grahami. In addition, we discovered S. triangularis was new to China and Myanmar. Based on the specimens and molecular phylogeny results, we redefined the species distribution boundaries of each Chinese species.
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Affiliation(s)
- Peng Guo
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Ping Wang
- Sichuan Academy of ForestryChengduChina
| | - Bing Lyu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Jieyu Zheng
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Chunmei Fu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Guocheng Shu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Shaobing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
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2
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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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3
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Bernstein JM, Ruane S. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.Life Science Identifier (Hydrablabes periops)urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.
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4
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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] [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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5
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Deepak V, Cooper N, Poyarkov NA, Kraus F, Burin G, Das A, Narayanan S, Streicher JW, Smith SJ, Gower DJ. Multilocus phylogeny, natural history traits and classification of natricine snakes (Serpentes: Natricinae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likelihood trees form the basis for evaluations of genus-level classification, historical biogeography, lineage diversification, and dietary, habit and reproductive-mode diversity and evolution, although several, mostly deeper, relationships remain poorly resolved. The optimal trees support natricine origins in Asia, with dispersals to Australo-Melanesia, sub-Saharan Africa (including Seychelles Archipelago, excluding Aldabra), Europe and North Africa and into North and Central America. Viviparity appears to have evolved independently three times in Natricinae but was not significantly associated with an aquatic habit. We found limited associations between habit and diet categories. We propose generic reallocations for four natricine species and highlight other points of uncertainty in natricine classification.
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Affiliation(s)
- V Deepak
- Department of Life Sciences, Natural History Museum, London, UK
- Senckenberg Dresden, Königsbrücker Landstraße, Dresden, Germany
| | - Natalie Cooper
- Department of Life Sciences, Natural History Museum, London, UK
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
- Joint Russian–Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Gustavo Burin
- Department of Life Sciences, Natural History Museum, London, UK
| | - Abhijit Das
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Surya Narayanan
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Srirampura, Bangalore, Karnataka, India
| | | | - Sarah-Jane Smith
- Department of Life Sciences, Natural History Museum, London, UK
- Imperial College London, South Kensington, London, UK
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London, UK
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6
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Zhu G, Yang S, Savitzky AH, Cheng Y, Mori A, Ding L, Rao D, Wang Q. Cryptic diversity and phylogeography of the Rhabdophis nuchalis group (Squamata: Colubridae). Mol Phylogenet Evol 2021; 166:107325. [PMID: 34655748 DOI: 10.1016/j.ympev.2021.107325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022]
Abstract
Previous studies, have found that the rapid uplift of the Tibetan plateau accelerated the diversification of species. However, there are few relevant biogeographic data for the Colubridae in this region. We conducted a comprehensive study of the Rhabdophis nuchalis Group, which presently contains four nominal species, R. nuchalis, R. pentasupralabialis, R. leonardi, and R. chiwen. Building upon previous studies with specimens we have recently examined, greater interspecific and intraspecific diversity has been revealed. Here we address three questions: (1) Do the intraspecific differences represent only geographic variation within lineages, or are there cryptic species? (2) What are the interspecific relationships among members of the R. nuchalis Group? (3) What has been the biogeographic history of this species group? To resolve these questions we used four mitochondrial gene sequences and one nuclear sequence to investigate the molecular phylogenetic and geographic relationships among populations. Our molecular analysis reveals cryptic species diversity within the R. nuchalis Group, and seven clades were identified in the analysis. Ancestral area estimation suggests that the R. nuchalis Group originated in the Hengduan Mountains approximately 6.24 Mya and expanded its range northward to the Qinling-Daba Mountains. The Sichuan Basin appears to have been a barrier to migration. Species divergence seems to have been related to the rapid uplift of the Qinghai-Tibet Plateau.
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Affiliation(s)
- Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Alan H Savitzky
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
| | - Yuqi Cheng
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Akira Mori
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Li Ding
- Chengdu Institute of Biology, Chinese Academy of Sciences. Chengdu 610041, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, China.
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7
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Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation. Mol Phylogenet Evol 2021; 160:107109. [PMID: 33609712 DOI: 10.1016/j.ympev.2021.107109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022]
Abstract
Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.
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8
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Camp CD, Wooten JA, Pepper MK, Austin RM, Whitfield Gibbons J. Eye size in North American watersnakes (genus Nerodia) correlates with variation in feeding ecology. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Visual acuity and sensitivity positively correlate to eye size in vertebrates, and eye size relates to the ecology of colubrid snakes. We investigated whether eye morphology of North American colubrids of the genus Nerodia correlates with ecology as well. Although all members of the genus utilize aquatic habits, they differ widely in the proportion of anurans they eat. We specifically tested whether eye size and placement is associated with the proportion of frogs in the diet to determine whether these two aspects of eye morphology relate to feeding ecology. Using phylogenetic comparative methods, we found a significantly positive association between eye size and the proportion of anurans eaten by Nerodia species. Although the evidence is equivocal, the anterior placement of relatively small eyes in one species may also enhance anurophagy. Although eye size may improve a snake’s ability to feed on frogs, eye size must compete with other selective forces on head shape in trade-offs that may also influence eye size.
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Affiliation(s)
- Carlos D Camp
- Department of Biology, Piedmont College, Demorest, GA, USA
| | | | | | | | - J Whitfield Gibbons
- University of Georgia’s Savannah River Ecology Laboratory, Drawer E, Aiken, SC, USA
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9
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Intraspecific dietary variation in niche partitioning within a community of ecologically similar snakes. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10078-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Out of the Hengduan Mountains: Molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae). Mol Phylogenet Evol 2020; 152:106927. [PMID: 32771547 DOI: 10.1016/j.ympev.2020.106927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 06/30/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023]
Abstract
The Asian water snake genus Trimerodytes (formerly Sinonatrix) is endemic to East and Southeast Asia. Although several species have been included in various phylogenetic studies previously, the evolution and relationships among members of this genus as a whole remain unexplored. In this study, we report the sequencing two protein-coding mitochondrial gene fragments (MTCYB and ND2) and three nuclear genes (c-mos, NT3, and Rag1), reconstruct interspecific phylogeny, and explore biogeography for the genus Trimerodytes. Both Bayesian inference and maximum likelihood analyses consistently recover the monophyly of Trimerodytes with strong support, with T. yapingi the sister-group to the remaining species. The divergence date and ancestral area estimation suggest that Trimerodytes likely originated in Hengduan Mountains (eastern Tibetan Plateau) in western China at 23.93 Ma (95% HPD: 17.09-31.30), and intraspecific divergence began at about 4.23 Ma (95% HPD: 2.74-6.10). Analyses support the validity of T. yunnanensis.
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11
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Manjarrez J, Macías Garcia C, Drummond H. Congenital feeding response to a novel prey in a Mexican gartersnake. PeerJ 2020; 8:e8718. [PMID: 32185111 PMCID: PMC7060902 DOI: 10.7717/peerj.8718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/10/2020] [Indexed: 11/20/2022] Open
Abstract
In this study, we explored chemosensory, ingestive and prey-catching responses of neonate Mexican Black-bellied Gartersnakes (Thamnophis melanogaster) to crayfish (Cambarellus montezumae). By comparing snakes from a recently discovered crayfish-eating population and a typical non-crayfish-eating population, we asked which behavioral components change as a species enlarges its feeding niche. In the crayfish-eating population chemosensory responsiveness to crayfish was not enhanced but its heritability was higher. Neonates of both populations showed similar preference for freshly-molted versus unmolted crayfish, and whereas the tendency to ingest both crayfish stages remained stable between ages 15 and 90 days in the non-crayfish-eating population, in the crayfish-eating population it actually decreased. Techniques to catch and manipulate molted crayfish were similar in the two populations. We discuss the possibility that there is no increase in the behavioral response to eat crayfish by the neonates of the crayfish-eating populations, possibly due to the absence of ecological and spatial isolation between the two T. melanogaster populations. The crayfish ingestion in some population of T. melanogaster can be explained by environmental differences between populations, or by recent origin of crayfish ingestion in T. melanogaster.
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Affiliation(s)
- Javier Manjarrez
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Constantino Macías Garcia
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Hugh Drummond
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
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12
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Key KN, Banta JA, Gluesenkamp AG, Hertweck KL, Placyk JS. CONSERVATION BIOLOGY OF A SOUTHWESTERN ENDEMIC, THE TEXAS GARTER SNAKE, THAMNOPHIS SIRTALIS ANNECTENS: AN INTEGRATIVE PERSPECTIVE. SOUTHWEST NAT 2019. [DOI: 10.1894/0038-4909-64-1-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kayla N. Key
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - Joshua A. Banta
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | | | - Kate L. Hertweck
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - John S. Placyk
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
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13
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Perkins MW, Eason PK. The relationship of head morphology and diet among three sympatric watersnake species. AMPHIBIA-REPTILIA 2019. [DOI: 10.1163/15685381-20181042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Investigating dietary resource utilization and head morphology of gape-limited predators can provide a basis for understanding interspecific competition and species coexistence. For sympatric species, convergence of head morphology can indicate similar prey or foraging strategies while divergence can suggest competition, resource partitioning or expansion into new habitats. Sexual dimorphism can further complicate the head morphology-diet relationship by potentially reducing intraspecific competition. To understand the relationship between head morphology and diet, we studied three sympatric species, the plain-bellied (Nerodia erythrogaster), diamondback (N. rhombifer), and northern (N. sipedon) watersnakes in western Kentucky. All three species inhabit similar wetlands and feed on amphibians and fishes. The anurophagous plain-bellied watersnakes had longer, narrower heads that likely allow snakes to capture anuran metamorphs and froglets while facilitating movement through dense vegetation. The piscivorous diamondback watersnake had a wider head, which would enhance contact with prey in this open-mouth forager, and smaller interocular distance, resulting in dorsally placed eyes that facilitate seeing fish prey from below. The mostly piscivorous northern watersnake had an intermediate, generalized head shape, which may reflect the typically wide diet range of this species. Head shape did not differ between snake sexes but diamondback and northern females had larger heads than males and fed more frequently on fishes. The relationship between head morphology and diet highlights potential interspecific and intersexual competition and aids in the understanding of species coexistence patterns.
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Affiliation(s)
- Micah W. Perkins
- 1Owensboro Community and Technical College, Owensboro, KY 42303, USA
| | - Perri K. Eason
- 2University of Louisville, Department of Biology, Louisville, KY 40292, USA
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14
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Takeuchi H, Savitzky AH, Ding L, de Silva A, Das I, Nguyen TT, Tsai T, Jono T, Zhu G, Mahaulpatha D, Tang Y, Mori A. Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny. Ecol Evol 2018; 8:10219-10232. [PMID: 30397460 PMCID: PMC6206205 DOI: 10.1002/ece3.4497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 06/22/2018] [Accepted: 07/24/2018] [Indexed: 01/25/2023] Open
Abstract
A large body of evidence indicates that evolutionary innovations of novel organs have facilitated the subsequent diversification of species. Investigation of the evolutionary history of such organs should provide important clues for understanding the basis for species diversification. An Asian natricine snake, Rhabdophis tigrinus, possesses a series of unusual organs, called nuchal glands, which contain cardiotonic steroid toxins known as bufadienolides. Rhabdophis tigrinus sequesters bufadienolides from its toad prey and stores them in the nuchal glands as a defensive mechanism. Among more than 3,500 species of snakes, only 17 Asian natricine species are known to possess nuchal glands or their homologues. These 17 species belong to three nominal genera, Balanophis, Macropisthodon, and Rhabdophis. In Macropisthodon and Rhabdophis, however, species without nuchal glands also exist. To infer the evolutionary history of the nuchal glands, we investigated the molecular phylogenetic relationships among Asian natricine species with and without nuchal glands, based on variations in partial sequences of Mt-CYB, Cmos, and RAG1 (total 2,767 bp). Results show that all species with nuchal glands belong to a single clade (NGC). Therefore, we infer that the common ancestor of this clade possessed nuchal glands with no independent origins of the glands within the members. Our results also imply that some species have secondarily lost the glands. Given the estimated divergence time of related species, the ancestor of the nuchal gland clade emerged 19.18 mya. Our study shows that nuchal glands are fruitful subjects for exploring the evolution of novel organs. In addition, our analysis indicates that reevaluation of the taxonomic status of the genera Balanophis and Macropisthodon is required. We propose to assign all species belonging to the NGC to the genus Rhabdophis, pending further study.
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Affiliation(s)
- Hirohiko Takeuchi
- Seto Marine Biological LaboratoryField Science Education and Research CenterKyoto UniversityShirahamaJapan
- Present address:
College of Bioresource ScienceNihon UniversityFujisawaKanagawaJapan
| | | | - Li Ding
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | | | - Indraneil Das
- Institute of Biodiversity and Environmental ConservationUniversity Malaysia SarawakSarawakMalaysia
| | - Tao Thien Nguyen
- Vietnam National Museum of NatureVietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHanoiVietnam
| | - Tein‐Shun Tsai
- Department of Biological Science and TechnologyNational Pingtung University of Science and TechnologyNeipu TownshipTaiwan
| | - Teppei Jono
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
- Present address:
Tropical Biosphere Research CenterUniversity of the RyukyusNishiharaOkinawaJapan
| | - Guang‐Xiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | | | - Yezhong Tang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Akira Mori
- Department of ZoologyGraduate School of ScienceKyoto UniversityKyotoJapan
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15
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Manjarrez J, Macías Garcia C, Drummond H. Morphological convergence in a Mexican garter snake associated with the ingestion of a novel prey. Ecol Evol 2017; 7:7178-7186. [PMID: 28944009 PMCID: PMC5606893 DOI: 10.1002/ece3.3265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 11/30/2022] Open
Abstract
Morphological convergence is expected when organisms which differ in phenotype experience similar functional demands, which lead to similar associations between resource utilization and performance. To consume prey with hard exoskeletons, snakes require either specialized head morphology, or to deal with them when they are vulnerable, for example, during molting. Such attributes may in turn reduce the efficiency with which they prey on soft‐bodied, slippery animals such as fish. Snakes which consume a range of prey may present intermediate morphology, such as that of Thamnophiine (Natricinae), which may be classified morphometrically across the soft–hard prey dietary boundary. In this study, we compared the dentition and head structure of populations of Thamnophis melanogaster that have entered the arthropod–crustacean (crayfish)‐eating niche and those that have not, and tested for convergence between the former and two distantly related crayfish specialists of the genus Regina (R. septemvittata and R. grahamii). As a control, we included the congener T. eques. Multivariate analysis of jaw length, head length, head width, and number of maxillary teeth yielded three significant canonical variables that together explained 98.8% of the variance in the size‐corrected morphological data. The first canonical variable significantly discriminated between the three species. The results show that head dimensions and number of teeth of the two Regina species are more similar to those of crayfish‐eating T. melanogaster than to non‐crayfish‐eating snakes or of T. eques. It is unclear how particular head proportions or teeth number facilitates capture of crayfish, but our results and the rarity of soft crayfish ingestion by T. melanogaster may reflect the novelty of this niche expansion, and are consistent with the hypothesis that some populations of T. melanogaster have converged in their head morphology with the two soft crayfish‐eating Regina species, although we cannot rule out the possibility of a morphological pre‐adaptation to ingest crayfish.
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Affiliation(s)
- Javier Manjarrez
- Facultad de Ciencias Universidad Autónoma del Estado de México Toluca State of Mexico Mexico
| | | | - Hugh Drummond
- Instituto de Ecología Universidad Nacional Autónoma de México Mexico DF Mexico
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16
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Blackburn DG, Anderson KE, Lo AR, Marquez EC, Callard IP. Placentation in watersnakes II: Placental ultrastructure in N
erodia erythrogaster
(Colubridae: Natricinae). J Morphol 2017; 278:675-688. [DOI: 10.1002/jmor.20662] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 01/05/2017] [Accepted: 01/11/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Daniel G. Blackburn
- Department of Biology, and Electron Microscopy Facility; Trinity College; Hartford Connecticut 06106
| | - Kristie E. Anderson
- Department of Biology, and Electron Microscopy Facility; Trinity College; Hartford Connecticut 06106
| | - Amy R. Lo
- Department of Biology, and Electron Microscopy Facility; Trinity College; Hartford Connecticut 06106
| | - Emily C. Marquez
- Department of Biology; Boston University; Boston Massachusetts 02215
| | - Ian P. Callard
- Department of Biology; Boston University; Boston Massachusetts 02215
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17
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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] [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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18
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Mitochondrial divergence between slow- and fast-aging garter snakes. Exp Gerontol 2015; 71:135-46. [PMID: 26403677 DOI: 10.1016/j.exger.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/26/2023]
Abstract
Mitochondrial function has long been hypothesized to be intimately involved in aging processes--either directly through declining efficiency of mitochondrial respiration and ATP production with advancing age, or indirectly, e.g., through increased mitochondrial production of damaging free radicals with age. Yet we lack a comprehensive understanding of the evolution of mitochondrial genotypes and phenotypes across diverse animal models, particularly in species that have extremely labile physiology. Here, we measure mitochondrial genome-types and transcription in ecotypes of garter snakes (Thamnophis elegans) that are adapted to disparate habitats and have diverged in aging rates and lifespans despite residing in close proximity. Using two RNA-seq datasets, we (1) reconstruct the garter snake mitochondrial genome sequence and bioinformatically identify regulatory elements, (2) test for divergence of mitochondrial gene expression between the ecotypes and in response to heat stress, and (3) test for sequence divergence in mitochondrial protein-coding regions in these slow-aging (SA) and fast-aging (FA) naturally occurring ecotypes. At the nucleotide sequence level, we confirmed two (duplicated) mitochondrial control regions one of which contains a glucocorticoid response element (GRE). Gene expression of protein-coding genes was higher in FA snakes relative to SA snakes for most genes, but was neither affected by heat stress nor an interaction between heat stress and ecotype. SA and FA ecotypes had unique mitochondrial haplotypes with amino acid substitutions in both CYTB and ND5. The CYTB amino acid change (Isoleucine → Threonine) was highly segregated between ecotypes. This divergence of mitochondrial haplotypes between SA and FA snakes contrasts with nuclear gene-flow estimates, but correlates with previously reported divergence in mitochondrial function (mitochondrial oxygen consumption, ATP production, and reactive oxygen species consequences).
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19
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McVay JD, Flores-Villela O, Carstens B. Diversification of North American natricine snakes. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12558] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John D. McVay
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - Oscar Flores-Villela
- Facultad de Ciencias; Museo de Zoologia; Universidad Nacional Autonoma de Mexico; Circuito Extrior de CU Mexico DF 04510 Mexico
| | - Bryan Carstens
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
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20
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Manjarrez J, San-Roman-Apolonio E. Timing of Birth and Body Condition in Neonates of Two Gartersnake Species from Central México. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-13-00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Siegel DS, Trauth SE, Rheubert JL, Rabe B, Ruopp B, Miralles A, Murray CM, Aldridge RD. Novel Cloacal Glands in Snakes: The Phylogenetic Distribution of Ventral Urodaeal Glands in Thamnophiini. HERPETOLOGICA 2014. [DOI: 10.1655/herpetologica-d-13-00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Dustin S. Siegel
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63103, USA
| | - Stanley E. Trauth
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72467, USA
| | | | - Brian Rabe
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63103, USA
| | - Brenton Ruopp
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63103, USA
| | - Aurélien Miralles
- Centre d'Ecologie Fonctionnelle & Evolutive, Centre National de la Recherche Scientifique, Montpellier, France
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22
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Takeuchi H, Zhu GX, Ding L, Tang Y, Ota H, Mori A, Oh HS, Hikida T. Taxonomic Validity and Phylogeography of the East Eurasian Natricine Snake,Rhabdophis lateralis(Berthold, 1859) (Serpentes: Colubridae), as Inferred from Mitochondrial DNA Sequence Data. CURRENT HERPETOLOGY 2014. [DOI: 10.5358/hsj.33.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Rose JP, Todd BD. Projecting invasion risk of non-native watersnakes (Nerodia fasciata and Nerodia sipedon) in the western United States. PLoS One 2014; 9:e100277. [PMID: 24964204 PMCID: PMC4070932 DOI: 10.1371/journal.pone.0100277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/24/2014] [Indexed: 11/19/2022] Open
Abstract
Species distribution models (SDMs) are increasingly used to project the potential distribution of introduced species outside their native range. Such studies rarely explicitly evaluate potential conflicts with native species should the range of introduced species expand. Two snake species native to eastern North America, Nerodia fasciata and Nerodia sipedon, have been introduced to California where they represent a new stressor to declining native amphibians, fish, and reptiles. To project the potential distributions of these non-native watersnakes in western North America, we built ensemble SDMs using MaxEnt, Boosted Regression Trees, and Random Forests and habitat and climatic variables. We then compared the overlap between the projected distribution of invasive watersnakes and the distributions of imperiled native amphibians, fish, and reptiles that can serve as prey or competitors for the invaders, to estimate the risk to native species posed by non-native watersnakes. Large areas of western North America were projected to be climatically suitable for both species of Nerodia according to our ensemble SDMs, including much of central California. The potential distributions of both N. fasciata and N. sipedon overlap extensively with the federally threatened Giant Gartersnake, Thamnophis gigas, which inhabits a similar ecological niche. N. fasciata also poses risk to the federally threatened California Tiger Salamander, Ambystoma californiense, whereas N. sipedon poses risk to some amphibians of conservation concern, including the Foothill Yellow-legged Frog, Rana boylii. We conclude that non-native watersnakes in California can likely inhabit ranges of several native species of conservation concern that are expected to suffer as prey or competing species for these invaders. Action should be taken now to eradicate or control these invasions before detrimental impacts on native species are widespread. Our methods can be applied broadly to quantify the risk posed by incipient invasions to native biodiversity.
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Affiliation(s)
- Jonathan P. Rose
- Department of Wildlife, Fish & Conservation Biology, University of California Davis, Davis, California, United States of America
- Graduate Group in Ecology, University of California Davis, Davis, California, United States of America
| | - Brian D. Todd
- Department of Wildlife, Fish & Conservation Biology, University of California Davis, Davis, California, United States of America
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24
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Uhrig EJ, LeMaster MP, Mason RT. Species specificity of methyl ketone profiles in the skin lipids of female garter snakes, genus Thamnophis. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Showalter I, Todd BD, Brennan PLR. Intraspecific and interspecific variation of female genitalia in two species of watersnake. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irina Showalter
- Department of Biology; University of Massachusetts Amherst; 611 N. Pleasant Street Amherst MA 01003 USA
| | - Brian D. Todd
- Department of Wildlife, Fish, and Conservation Biology; University of California; Davis, One Shields Avenue Davis CA 95616 USA
| | - Patricia L. R. Brennan
- Department of Biology; University of Massachusetts Amherst; 611 N. Pleasant Street Amherst MA 01003 USA
- Organismal and Evolutionary Biology Program and Department of Psychology; UMASS Amherst; Amherst MA 01003 USA
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26
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McVay JD, Carstens B. Testing monophyly without well-supported gene trees: Evidence from multi-locus nuclear data conflicts with existing taxonomy in the snake tribe Thamnophiini. Mol Phylogenet Evol 2013; 68:425-31. [DOI: 10.1016/j.ympev.2013.04.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 11/28/2022]
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27
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Evidence of Hybridization between Common Gartersnakes (Thamnophis sirtalis) and Butler's Gartersnakes (Thamnophis butleri) in Wisconsin, USA. J HERPETOL 2013. [DOI: 10.1670/12-057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Variation in the Diet of the Mexican Black-bellied GartersnakeThamnophis melanogaster: Importance of Prey Availability and Snake Body Size. J HERPETOL 2013. [DOI: 10.1670/12-174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol 2013; 13:93. [PMID: 23627680 PMCID: PMC3682911 DOI: 10.1186/1471-2148-13-93] [Citation(s) in RCA: 962] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. RESULTS The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. CONCLUSIONS We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA
| | - Frank T Burbrink
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 5th Ave., New York, NY 10016, USA
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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30
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Seasonal, Condition-Dependent, and Individual Variation in Testosterone in a Natricine Snake. J HERPETOL 2013. [DOI: 10.1670/12-001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Guo P, Liu Q, Xu Y, Jiang K, Hou M, Ding L, Alexander Pyron R, Burbrink FT. Out of Asia: Natricine snakes support the Cenozoic Beringian Dispersal Hypothesis. Mol Phylogenet Evol 2012; 63:825-33. [DOI: 10.1016/j.ympev.2012.02.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 02/16/2012] [Accepted: 02/22/2012] [Indexed: 11/15/2022]
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32
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Rodriguez D, Forstner MRJ, McBride DL, Densmore III LD, Dixon JR. Low genetic diversity and evidence of population structure among subspecies of Nerodia harteri, a threatened water snake endemic to Texas. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0346-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Lillywhite HB, Albert JS, Sheehy CM, Seymour RS. Gravity and the evolution of cardiopulmonary morphology in snakes. Comp Biochem Physiol A Mol Integr Physiol 2012; 161:230-42. [PMID: 22079804 PMCID: PMC3242868 DOI: 10.1016/j.cbpa.2011.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 10/28/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
Abstract
Physiological investigations of snakes have established the importance of heart position and pulmonary structure in contexts of gravity effects on blood circulation. Here we investigate morphological correlates of cardiopulmonary physiology in contexts related to ecology, behavior and evolution. We analyze data for heart position and length of vascular lung in 154 species of snakes that exhibit a broad range of characteristic behaviors and habitat associations. We construct a composite phylogeny for these species, and we codify gravitational stress according to species habitat and behavior. We use conventional regression and phylogenetically independent contrasts to evaluate whether trait diversity is correlated with gravitational habitat related to evolutionary transitions within the composite tree topology. We demonstrate that snake species living in arboreal habitats, or which express strongly climbing behaviors, possess relatively short blood columns between the heart and the head, as well as relatively short vascular lungs, compared to terrestrial species. Aquatic species, which experience little or no gravity stress in water, show the reverse - significantly longer heart-head distance and longer vascular lungs. These phylogenetic differences complement the results of physiological studies and are reflected in multiple habitat transitions during the evolutionary histories of these snake lineages, providing strong evidence that heart-to-head distance and length of vascular lung are co-adaptive cardiopulmonary features of snakes.
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Affiliation(s)
| | - James S. Albert
- Department of Biology, University of Louisiana, Lafayette, Louisiana USA,
| | - Coleman M. Sheehy
- Department of Biology, University of Texas, Arlington, Texas 76019 USA,
| | - Roger S. Seymour
- Department of Environmental Biology, University of Adelaide, South Australia 5005 Australia,
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Placyk JS, Fitzpatrick BM, Casper GS, Small RL, Reynolds RG, Noble DWA, Brooks RJ, Burghardt GM. Hybridization between two gartersnake species (Thamnophis) of conservation concern: a threat or an important natural interaction? CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0315-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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TAKEUCHI HIROHIKO, OTA HIDETOSHI, OH HONGSHIK, HIKIDA TSUTOMU. Extensive genetic divergence in the East Asian natricine snake, Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01792.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Tibetan Plateau Relict Snakes of the Genus Thermophis and Their Relationship to New World Relict Snakes. ASIAN HERPETOL RES 2011. [DOI: 10.3724/sp.j.1245.2011.00161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Wood DA, Vandergast AG, Lemos Espinal JA, Fisher RN, Holycross AT. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data. Mol Ecol 2011; 20:3856-78. [PMID: 21851436 DOI: 10.1111/j.1365-294x.2011.05211.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.
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Affiliation(s)
- Dustin A Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101, USA.
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39
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Hampton PM. Comparison of cranial form and function in association with diet in natricine snakes. J Morphol 2011; 272:1435-43. [DOI: 10.1002/jmor.10995] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/20/2011] [Accepted: 04/24/2011] [Indexed: 11/10/2022]
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40
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Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci 2011; 4:257-70. [PMID: 21677863 PMCID: PMC3111982 DOI: 10.4056/sigs.1664145] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonvenomous North American species that has served as a model for diverse studies in evolutionary biology, physiology, genomics, behavior and coevolution. The anole lizard is currently the only genome sequence available for a non-avian reptile. Thus, the garter snake at this time would be the first available snake genome sequence and as such would provide much needed comparative representation of non-avian reptilian genomes, and would also allow critical new insights for vertebrate comparative genomic studies. We outline the major areas of discovery that the availability of the garter snake genome would enable, and describe a plan for whole-genome sequencing.
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Affiliation(s)
- Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
- Corresponding Author: Todd A. Castoe,
| | - Anne M. Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Edmund D. Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | | | | | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - Wesley C. Warren
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO
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Siegel DS, Miralles A, Trauth SE, Aldridge RD. The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes. ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2011.00514.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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42
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43
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Blackburn D, Stewart J. Viviparity and Placentation in Snakes. REPRODUCTIVE BIOLOGY AND PHYLOGENY OF SNAKES 2011. [DOI: 10.1201/b10879-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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Using Mitochondrial DNA to Determine the Identity and Origin of a Gartersnake Found in Alaska. J HERPETOL 2011. [DOI: 10.1670/09-180.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Brandley MC, Guiher TJ, Pyron RA, Winne CT, Burbrink FT. Does dispersal across an aquatic geographic barrier obscure phylogeographic structure in the diamond-backed watersnake (Nerodia rhombifer)? Mol Phylogenet Evol 2010; 57:552-60. [DOI: 10.1016/j.ympev.2010.07.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Revised: 07/22/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
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46
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Makowsky R, Marshall JC, McVay J, Chippindale PT, Rissler LJ. Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake (Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation. Mol Phylogenet Evol 2010; 55:985-95. [PMID: 20302955 DOI: 10.1016/j.ympev.2010.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 02/22/2010] [Accepted: 03/11/2010] [Indexed: 11/25/2022]
Abstract
Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrial genes (NADH-II, Cyt-b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations.
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Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Arlington, TX, USA.
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47
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FONTANELLA FRANK, SIDDALL MARKE. Evaluating hypotheses on the origin and diversification of the ringneck snake Diadophis punctatus (Colubridae: Dipsadinae). Zool J Linn Soc 2009. [DOI: 10.1111/j.1096-3642.2009.00554.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Blackburn DG, Flemming AF. Morphology, development, and evolution of fetal membranes and placentation in squamate reptiles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2009; 312:579-89. [DOI: 10.1002/jez.b.21234] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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49
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Blackburn DG, Anderson KE, Johnson AR, Knight SR, Gavelis GS. Histology and ultrastructure of the placental membranes of the viviparous brown snake,Storeria dekayi(Colubridae: Natricinae). J Morphol 2009; 270:1137-54. [DOI: 10.1002/jmor.10650] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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KING RICHARDB, JADIN ROBERTC, GRUE MICHAEL, WALLEY HARLAND. Behavioural correlates with hemipenis morphology in New World natricine snakes. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01270.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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