Data from: A comparison of SNP and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird

The development of genetic markers has revolutionized molecular studies within and among populations. Although poly-allelic microsatellites are the most commonly used genetic marker for within-population studies of free-living animals, bi-allelic single nucleotide polymorphisms, or SNPs, have also emerged as a viable option for use in non-model systems. We describe a robust method of SNP discovery from the transcriptome of a non-model organism that resulted in more than 99% of the markers working successfully during genotyping. We then compare the use of 102 novel SNPs with 15 previously-developed microsatellites for studies of parentage and kinship in cooperatively breeding superb starlings (Lamprotornis superbus) that live in highly kin-structured groups. For 95% offspring surveyed, SNPs and microsatellites identified the same genetic father, but only when behavioral information about the likely parents at a nest was included to aid in assignment. Moreover, when such behavioral information was available, the number of SNPs necessary for successful parentage assignment was reduced by half. Despite high variation between individual pairwise relatedness values, microsatellites and SNPs performed equally well in kinship analyses. This study is the first to compare SNPs and microsatellites for analyses of parentage and relatedness in a species that lives in groups with a complex social and genetic structure. It should also prove informative for those interested in developing SNP loci from transcriptome data when published genomes are unavailable.