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Prado NA, Armstrong EE, Brown JL, Goldenberg SZ, Leimgruber P, Pearson VR, Maldonado JE, Campana MG. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research. J Hered 2023; 114:529-538. [PMID: 37246890 DOI: 10.1093/jhered/esad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.
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Affiliation(s)
- Natalia A Prado
- Biology Department, College of Arts and Sciences, Adelphi University, Garden City, NY, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA, United States
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janine L Brown
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Shifra Z Goldenberg
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Peter Leimgruber
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Virginia R Pearson
- Glenn Rall Laboratory, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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White LC. Shallow sequencing can mislead when evaluating hybridization capture methods. CONSERV GENET RESOUR 2023. [DOI: 10.1007/s12686-023-01298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Parker LD, Quinta JD, Rivera I, Cypher BL, Kelly EC, Campana MG, Fleischer RC, Boarman R, Boarman WI, Maldonado JE. Genetic analyses are more sensitive than morphological inspection at detecting the presence of threatened Mojave desert tortoise (
Gopherus agassizii
) remains in canid scat and raven pellets. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Lillian D. Parker
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
| | - Jessica D. Quinta
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Isabel Rivera
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Brian L. Cypher
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Erica C. Kelly
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Michael G. Campana
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
| | - Robert C. Fleischer
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Ryan Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - William I. Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
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