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Westeen EP, Escalona M, Beraut E, Marimuthu MPA, Nguyen O, Fisher RN, Toffelmier E, Shaffer HB, Wang IJ. A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus. J Hered 2023; 114:690-697. [PMID: 37688363 PMCID: PMC10650948 DOI: 10.1093/jhered/esad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023] Open
Abstract
Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, 92101, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
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Cox CL, Chung AK, Blackwell C, Davis MM, Gulsby M, Islam H, Miller N, Lambert C, Lewis O, Rector IV, Walsh M, Yamamoto AD, Davis Rabosky AR. Tactile stimuli induce deimatic antipredator displays in ringneck snakes. Ethology 2021. [DOI: 10.1111/eth.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biological Sciences Florida International University Miami FL USA
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Albert K. Chung
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA
| | | | - Maura M. Davis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Miranda Gulsby
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Biology Kennesaw State University Kennesaw GA USA
| | - Hasib Islam
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Nathan Miller
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- James Madison University Harrisonburg VA USA
| | - Carson Lambert
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Olivia Lewis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Ian V. Rector
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Marleigh Walsh
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Alannah D. Yamamoto
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- University of Maryland College Park MD USA
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Fry BG, Casewell NR, Wüster W, Vidal N, Young B, Jackson TNW. The structural and functional diversification of the Toxicofera reptile venom system. Toxicon 2012; 60:434-48. [PMID: 22446061 DOI: 10.1016/j.toxicon.2012.02.013] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/23/2012] [Accepted: 02/28/2012] [Indexed: 11/25/2022]
Abstract
The evolutionary origin and diversification of the reptilian venom system is described. The resolution of higher-order molecular phylogenetics has clearly established that a venom system is ancestral to snakes. The diversification of the venom system within lizards is discussed, as is the role of venom delivery in the behavioural ecology of these taxa (particularly Varanus komodoensis). The more extensive diversification of the venom system in snakes is summarised, including its loss in some clades. Finally, we discuss the contentious issue of a definition for "venom", supporting an evolutionary definition that recognises the homology of both the venom delivery systems and the toxins themselves.
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Affiliation(s)
- Bryan G Fry
- Venom Evolution Research Laboratory, School of Biological Sciences, University of Queensland, St Lucia, Queensland 4072, Australia.
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