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

Evolutionary Applications
Stephen J GaughranAdalgisa Caccone

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 ind...Continue Reading

References

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Citations

Jul 22, 2018·Evolutionary Applications·Margaret E HunterLouis Bernatchez
Apr 13, 2019·Evolutionary Applications·Brenton von Takach DukaiSam C Banks
Aug 29, 2019·Genes·Katharina C Wollenberg ValeroSebastian Steinfartz

Methods Mentioned

BETA
PCA
genotyping
Illumina sequencing

Related Concepts

Biological Markers
Case-Control Studies
Genome
Mitochondria
Testudinidae
Disease Management
Structure
Gene Polymorphism
Simulation
Single Nucleotide Polymorphism

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