Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs

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.