ORCID Profile
0000-0002-9413-5074
Current Organisation
Princeton University
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Publisher: Cold Spring Harbor Laboratory
Date: 12-09-2017
DOI: 10.1101/187534
Abstract: High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few in iduals are s led. Still, s ling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of s ling 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 non-model organisms. Using ,000 genome-wide SNPs from 30 in iduals 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 in iduals, or hundreds of SNPs and 10 in iduals, 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 in iduals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few s les per population, and underscores the importance of s ling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions. “Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.” - Fred Allendorf (2017, p. 420)
Publisher: Wiley
Date: 23-10-2017
DOI: 10.1111/EVA.12551
Abstract: High‐throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms ( SNP s) 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 in iduals are s led. Still, s ling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of s ling 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 SNP s, thereby questioning decades of studies in nonmodel organisms. Using ,000 genomewide SNP s from 30 in iduals 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 SNP s and 2–5 in iduals, or hundreds of SNP s and 10 in iduals, 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 in iduals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few s les per population, and underscores the importance of s ling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
Publisher: Wiley
Date: 25-09-2021
DOI: 10.1111/MEC.16176
Abstract: Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of ersity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three in iduals of the 12 extant lineages of Galapagos giant tortoise and estimate ersity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within in iduals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
No related grants have been discovered for Stephen Gaughran.