Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study
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Date
2017-08-31
Authors
Gaughran, Stephen J
Quinzin, Maud C
Miller, Joshua M
Garrick, Ryan C
Edwards, Danielle L
Russello, Michael A
Poulakakis, Nikos
Ciofi, Claudio
Beheregaray, Luciano Bellagamba
Caccone, Adalgisa
Journal Title
Journal ISSN
Volume Title
Publisher
Wiley
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
Rights Holder
© 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd
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.
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.
Keywords
single nucleotide polymorphism, sampling design, population structure, genomics, conservation, Chelonoidis
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.