Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs
Khimoun, Aurélie; Ollivier, Anthony; Faivre, Bruno; Garnier, Stéphane (2016), Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs, Dryad, Dataset, https://doi.org/10.5061/dryad.0p3j8
Microsatellites, also called simple sequence repeats (SSRs) are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers and highly conserved SSRs have recently been developed from Expressed Sequence Tags (EST) to improve SRR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multi-species approach on passerine birds. We tested whether patterns and levels of genetic diversity within- and between-populations assessed from EST- and from genomic SSRs are congruent and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SRRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.