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Yushchenko PV, Lee JL, Neang T, Seiha H, Tan NV, Vogel G, Poyarkov Jr NA. A taxonomic re-assessment of Oligodon cinereus (Günther, 1864) (Squamata, Serpentes, Colubridae) populations from southern Indochina. VERTEBRATE ZOOLOGY 2023. [DOI: 10.3897/vz.73.e91230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ashy kukri snake Oligodon cinereus (Günther, 1864) is a widely distributed and morphologically variable species found throughout mainland Southeast Asia. In this paper, we re-assessed the taxonomic status of O. cinereus populations found in southern Indochina (southern Vietnam, Cambodia, and southern Laos), including the recently described Cat Tien kukri snake Oligodon cattienensisVassilieva et al., 2013, which was previously confused with this species. Phylogenetic analyses using mitochondrial DNA from the 12S–16S ribosomal subunit and cytochrome b gene revealed that O. cattienensis is embedded in a mixed clade containing samples of the subspecies O. cinereus pallidocinctus, which bears a dorsal color pattern with white crossbars and black edges. This clade forms a strongly supported sister group with a topotypic sample of O. cinereus cinereus, representing populations bearing a uniform dorsal color pattern and slight reticulate markings, however the genetic divergence between the two clades is very low. The morphological characters used to distinguish O. cattienensis from O. cinereus sensu lato broadly overlap and supposed differences in hemipenial morphology between the two taxa are due to outdated terminologies used to describe the organ. We relegate both O. cattienensis and O. cinereus pallidocinctus to the junior synonymy of O. cinereus and consider all color patterns of this species found near the type locality in Cambodia, southern Laos, and southern Vietnam to represent O. cinereus sensu stricto. Future integrative investigations across the range of O. cinereus sensu lato are needed to resolve the status of the remaining subspecies and synonyms associated with this taxon. Problems associated with hemipenial morphology and Oligodon systematics are also discussed.
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Wood DA, Richmond JQ, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Westphal M, Fisher RN, Vandergast AG, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern. J Hered 2022; 113:632-640. [PMID: 35939354 PMCID: PMC9923794 DOI: 10.1093/jhered/esac040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California's coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
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Affiliation(s)
- Dustin A Wood
- Address correspondence to D.A. Wood at the address above, or e-mail:
| | - Jonathan Q Richmond
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael Westphal
- U.S. Bureau of Land Management—Central Coast Field Office, Marina, CA 93933, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Amy G Vandergast
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Ian J Wang
- 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
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
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Nguyen HN, Tran BV, Nguyen LH, Neang T, Yushchenko PV, Poyarkov NA. A new species of Oligodon Fitzinger, 1826 from the Langbian Plateau, southern Vietnam, with additional information on Oligodon annamensis Leviton, 1953 (Squamata: Colubridae). PeerJ 2020; 8:e8332. [PMID: 31934510 PMCID: PMC6951295 DOI: 10.7717/peerj.8332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/02/2019] [Indexed: 11/20/2022] Open
Abstract
We describe a new species of Oligodon from the highlands of the Langbian Plateau, southern Truong Son Mountains, Vietnam, based on morphological and molecular phylogenetic analyses. The new species, Oligodon rostralissp. nov is distinguished from its congeners by the following morphological characters: medium size in adults (male TL = 582 mm); small and broad head with long protruding snout; dorsal scale row formula 15-15-13; 167 ventrals, 47 subcaudals; single preocular, single postocular; loreal and presubocular absent; six supralabials, third and fourth entering orbit; six infralabials, anterior four contacting first pair of chin shields; internasals separate from prefrontals; nasal divided; single anterior and two posterior temporals; cloacal plate undivided; hemipenes short, bilobed, bifurcating in anterior one third of their length, extending to 8th subcaudal, lacking spines and papillae, with a prominent transverse flounces and distal calyces; six maxillary teeth, the posterior three enlarged; dorsal pattern consisting of 14+4 large dark-brown blotches and a bright-orange vertebral stripe on tail and dorsum; and ventral surfaces in life cream laterally with dark quadrangular spots; dark temporal streak present, edged with white. We also provide additional information on O. annamensis, including a morphological dataset of all specimens known from natural history collections and confirmation of an earlier record of O. annamensis from Cambodia. We also provide the first record of O. annamensis for Dak Lak Province. Phylogenetic analyses of mtDNA genes (3,131 bp of 12S rRNA, 16S rRNA and cyt b) suggest sister relationships of Oligodon rostralissp. nov. and O. annamensis and place them in one clade with the O. cyclurus and O. taeniatus species groups, which is concordant with previous studies on the phylogenetic relationships of Oligodon. Our study demonstrates high level of herpetofaunal diversity and endemism of Langbian Plateau and further supports the importance of this area for conservation herpetofaunal diversity in Indochina.
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Affiliation(s)
- Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam.,School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Bang Van Tran
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Thy Neang
- Wild Earth Allies, Phnom Penh, Cambodia
| | - Platon V Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Nikolay A Poyarkov
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia.,Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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