Abstract
Advances in high-throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high-throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD-Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large-scale initiatives such as collaborative global marine turtle genetic databases.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Molecular Ecology Resources |
| Vol/bind | 19 |
| Udgave nummer | 2 |
| Sider (fra-til) | 497-511 |
| Antal sider | 15 |
| ISSN | 1755-098X |
| DOI | |
| Status | Udgivet - mar. 2019 |
| Udgivet eksternt | Ja |
Bibliografisk note
Funding Information:We would like to thank members of the Marine Mammal and Turtle Division for assistance in the laboratory, logistics and project design suggestions, especially A. Frey, P. Morin, V. Pease, E. LaCasella, A. Lanci, G. Serra‐Valente and S. Roden. Funding was provided by the National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, the National Research Council of the National Academies of Science, Engineering and Medicine to LMK, through a Lenfest Ocean Program grant to KRS (the views expressed are those of the authors and do not necessarily reflect the views of the Len-fest Ocean Program or The Pew Charitable Trusts) and The Sea Turtle Census Initiative at The Ocean Foundation. We would like to thank T. Summers, D. Graff, A. Tagarino, N. Fitzsimmons, A. Gaos, M. Liles, K. Dodge, H. Guzman, N. Marcovaldi, J. Thome, B. Bowen, J. Mortimer, E. Harrison and G. Balazs, Centro Tamar/ICMbio and Projeto Tamar/Fundação Pro Tamar, The Sea Turtle Conservancy, American Samoa Department of Marine and Wildlife Resources, CNMI Division of Fish and Wildlife & Department of Lands & Natural Resources and NOAA‐Fisheries Pacific Islands Science Center, for sample contributions. We appreciate the constructive feedback from Brant Faircloth and two anonymous reviewers that improved the quality of our manuscript.
Funding Information:
Lenfest Ocean Program; National Research Council of the National Academies of Science, Engineering and Medicine; National Oceanic and Atmospheric Administration; The Ocean Foundation; Southwest Fisheries Science Center
Publisher Copyright:
© 2019 John Wiley & Sons Ltd