Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study

dc.contributor.author Gaughran, Stephen J
dc.contributor.author Quinzin, Maud C
dc.contributor.author Miller, Joshua M
dc.contributor.author Garrick, Ryan C
dc.contributor.author Edwards, Danielle L
dc.contributor.author Russello, Michael A
dc.contributor.author Poulakakis, Nikos
dc.contributor.author Ciofi, Claudio
dc.contributor.author Beheregaray, Luciano Bellagamba
dc.contributor.author Caccone, Adalgisa
dc.date.accessioned 2018-09-28T05:41:37Z
dc.date.available 2018-09-28T05:41:37Z
dc.date.issued 2017-08-31
dc.description This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. en_US
dc.description.abstract High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2–5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions. en_US
dc.description.sponsorship This work was enabled by substantial logistical and personnel support of the Galápagos National Park Directorate in conjunction with the Galapagos Conservancy. Expedition expenses and laboratory analyses were also supported by grants from the Galapagos Conservancy, the Mohamed bin Zayed Species Conservation Fund, National Geographic Society, and the Oak Foundation to AC, the Belgian American Educational Foundation to MCQ, and the Yale Institute for Biospheric Studies. en_US
dc.identifier.citation Gaughran, S. J., Quinzin, M. C., Miller, J. M., (2017). Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evolutionary Applications, 11:1084–1093. en_US
dc.identifier.doi https://doi.org/10.1111/eva.12551 en_US
dc.identifier.issn 1752-4571
dc.identifier.uri http://hdl.handle.net/2328/38349
dc.language.iso en en_US
dc.publisher Wiley en_US
dc.rights This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd en_US
dc.rights.holder © 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd en_US
dc.rights.license CC-BY
dc.subject single nucleotide polymorphism en_US
dc.subject sampling design en_US
dc.subject population structure en_US
dc.subject genomics en_US
dc.subject conservation en_US
dc.subject Chelonoidis en_US
dc.title Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study en_US
dc.type Article en
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