A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird

Single‐nucleotide polymorphisms ( SNP s) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNP s and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA ‐sequencing of a songbird with the most common avian mating system—social monogamy. We compared the effectiveness of 97 novel SNP s and six previously described microsatellites for assigning paternity in the black‐throated blue warbler, Setophaga caerulescens . We show that the full panel of 97 SNP s (mean H o  = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (mean H o  = 0.86). Paternity assignments using the two marker types were in agreement for 92% of the offspring. Filtering individual samples by a 50% call rate and SNP s by a 75% call rate maximized the number of offspring assigned with 95% confidence using SNP s. We also found that the 40 most heterozygous SNP s (mean H o  = 0.37) had similar power to assign paternity as the full panel of 97 SNP s. These findings demonstrate that a relatively small number of variable SNP s can be effective for parentage analyses in a socially monogamous species. We suggest that the development of SNP markers is advantageous for studies that require high‐throughput genotyping or that plan to address a range of ecological and evolutionary questions.