title: Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs.
abstract: 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 SSR 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 multispecies 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-SSRs 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.
authors.affiliation: Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Khimoun
authors.affiliation: Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Ollivier
authors.affiliation: Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Faivre
authors.affiliation: Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Garnier
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification* / Q000235:genetics*; D020224:Expressed Sequence Tags; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods*; D018895:Microsatellite Repeats
keywords: birds; conservation genetics; genetic diversity; molecular markers; population structure