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Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri


Fischer, Martin C; Rellstab, Christian; Leuzinger, Marianne; Roumet, Marie; Gugerli, Felix; Shimizu, Kentaro K; Holderegger, Rolf; Widmer, Alex (2017). Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. BMC Genomics, 18(1):69.

Abstract

Background: Microsatellite markers are widely used for estimating genetic diversity within and differentiation
among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide
patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single
nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).
Results: Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and
species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-He) was not significantly correlated with genome-wide SNP diversity estimates (SNP-He and θWatterson) in A. halleri. Instead, microsatellite allelic richness (Ar) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (FST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high varianc microsatellite-derived estimates. In contrast, genomewide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.
Conclusions: We recommend that future analyses of genetic diversity within and differentiation among populations
use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity
patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.

Abstract

Background: Microsatellite markers are widely used for estimating genetic diversity within and differentiation
among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide
patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single
nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).
Results: Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and
species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-He) was not significantly correlated with genome-wide SNP diversity estimates (SNP-He and θWatterson) in A. halleri. Instead, microsatellite allelic richness (Ar) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (FST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high varianc microsatellite-derived estimates. In contrast, genomewide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.
Conclusions: We recommend that future analyses of genetic diversity within and differentiation among populations
use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity
patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Uncontrolled Keywords:Microsatellites, SSR, Arabidopsis halleri, Genetic diversity, Expected heterozygosity, SNPs, Population genomics, Whole-genome re-sequencing, Pool-Seq, Conservation units
Language:English
Date:11 January 2017
Deposited On:10 Feb 2017 13:47
Last Modified:06 Aug 2017 07:02
Publisher:BioMed Central
ISSN:1471-2164
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/s12864-016-3459-7
PubMed ID:28077077

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