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Westeen EP, Escalona M, Holding ML, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Perri R, Fisher RN, Toffelmier E, Shaffer HB, Wang IJ. A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex. J Hered 2023; 114:681-689. [PMID: 37493092 PMCID: PMC10650947 DOI: 10.1093/jhered/esad045] [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: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Matthew L Holding
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Colin Fairbairn
- 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, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Ralph Perri
- 1001 Foothill Drive, Fillmore, CA, 93015, 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, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
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Bishop AP, Westeen EP, Yuan ML, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Chumchim N, Toffelmier E, Fisher RN, Shaffer HB, Wang IJ. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis. J Hered 2023; 114:521-528. [PMID: 37335574 PMCID: PMC10445515 DOI: 10.1093/jhered/esad037] [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: 04/10/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023] Open
Abstract
Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.
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Affiliation(s)
- Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Michael L Yuan
- Center for Population Biology, University of California, Davis, Davis, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert N Fisher
- U.S. Geological Survey Western Ecological Research Center, San Diego, CA, United States
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
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Prieto‐Ramírez AM. Effects of landscape structure and patch characteristics on the density of central populations of the eastern green lizard Lacerta viridis. Ecol Evol 2023; 13:e10419. [PMID: 37600491 PMCID: PMC10433115 DOI: 10.1002/ece3.10419] [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: 04/26/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
A better understanding of the impact of habitat loss on population density can be achieved by evaluating effects of both parameters within remnant habitat patches and parameters of the landscape surrounding those patches. The integration of predictors at the patch and landscape level is scarce in animal ecological studies, especially for reptiles. In this study, a patch-landscape approach was applied to evaluate the combined effects of within-patch habitat quality, patch geometry and landscape configuration and composition on the density of remnant populations of the eastern green lizard, Lacerta viridis, in a highly modified landscape in Bulgaria. Landscape composition variables (proportion of different land covers) were measured at different spatial scales surrounding patches. Single-scale models were built to evaluate combined effects of all predictors on density, when including all landscape composition variables at a specific spatial scale. Multi-scale models were applied to analyze combined effects when including landscape composition variables at the scale of their strongest effect (scale of effect, SoE). Results showed that the SoE of proportion of cropland and urban areas was small (50 m), while for proportion of habitat was large (1.5 km). The overall effect of habitat loss was better explained by the multi-scale model. Population density increased with patch area and decreased with patch shape irregularity and with the proportion of three land cover types surrounding patches-cropland, urban areas, and habitat. Combining patch and landscape parameters is important to identify ecological processes that occur simultaneously at different spatial levels and landscape scales, which would imply the application of multi-scale approaches for the protection of wild animal populations. Results are contrasted with what is known about occupancy patterns of the species in the same region and approaches to integrate both occupancy and density, in the field design of animal ecological studies are suggested.
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Wenner SM, Murphy MA, Delaney KS, Pauly GB, Richmond JQ, Fisher RN, Robertson JM. Natural and anthropogenic landscape factors shape functional connectivity of an ecological specialist in urban Southern California. Mol Ecol 2022; 31:5214-5230. [PMID: 35962747 PMCID: PMC9826396 DOI: 10.1111/mec.16656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 01/11/2023]
Abstract
Identifying how natural (i.e., unaltered by human activity) and anthropogenic landscape variables influence contemporary functional connectivity in terrestrial organisms can elucidate the genetic consequences of environmental change. We examine population genetic structure and functional connectivity among populations of a declining species, the Blainville's horned lizard (Phrynosoma blainvillii), in the urbanized landscape of the Greater Los Angeles Area in Southern California, USA. Using single nucleotide polymorphism data, we assessed genetic structure among populations occurring at the interface of two abutting evolutionary lineages, and at a fine scale among habitat fragments within the heavily urbanized area. Based on the ecology of P. blainvillii, we predicted which environmental variables influence population structure and gene flow and used gravity models to distinguish among hypotheses to best explain population connectivity. Our results show evidence of admixture between two evolutionary lineages and strong population genetic structure across small habitat fragments. We also show that topography, microclimate, and soil and vegetation types are important predictors of functional connectivity, and that anthropogenic disturbance, including recent fire history and urban development, are key factors impacting contemporary population dynamics. Examining how natural and anthropogenic sources of landscape variation affect contemporary population genetics is critical to understanding how to best manage sensitive species in a rapidly changing landscape.
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Affiliation(s)
- Sarah M. Wenner
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA
| | - Melanie A. Murphy
- Department of Ecosystem Science and Management, Program in EcologyUniversity of WyomingLaramieWyomingUSA
| | | | - Gregory B. Pauly
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA,Natural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | | | - Robert N. Fisher
- US Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Jeanne M. Robertson
- Department of BiologyCalifornia State UniversityNorthridgeCaliforniaUSA,Natural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
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