Data from: A comparison of single nucleotide polymorphism 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, biallelic single nucleotide polymorphisms, or SNPs,
have also emerged as a viable option for use in nonmodel systems. We
describe a robust method of SNP discovery from the transcriptome of a
nonmodel 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% of the offspring
surveyed, SNPs and microsatellites identified the same genetic father, but
only when behavioural information about the likely parents at a nest was
included to aid in assignment. Moreover, when such behavioural information
was available, the number of SNPs necessary for successful parentage
assignment was reduced by half. However, in a few cases where candidate
fathers were highly related, SNPs did a better job at assigning fathers
than microsatellites. 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 kin structure. It should
also prove informative for those interested in developing SNP loci from
transcriptome data when published genomes are unavailable.