Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs 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 SNPs and six previously described microsatellites for assigning paternity in the black-throated blue warbler, Setophaga caerulescens. We show that the full panel of 97 SNPs (mean Ho = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (mean Ho = 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 SNPs by a 75% call rate maximized the number of offspring assigned with 95% confidence using SNPs. We also found that the 40 most heterozygous SNPs (mean Ho = 0.37) had similar power to assign paternity as the full panel of 97 SNPs. These findings demonstrate that a relatively small number of variable SNPs 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.
2011 genotypes msat 50
Microsatellite genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >50%.
2011 genotypes snps 50
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >50%.
2012 genotypes msats 50
Microsatellite genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >50%.
2012 genotypes snps 50
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >50%.
2011 genotypes snps 75
SNPs genotypes of offspring and adult black-throated blue warblers. Loci call rate >75%.
2012 genotypes snps 75
SNPs genotypes of offspring and adult black-throated blue warblers. Loci call rate >75%.
2011 genotypes snps 90
SNPs genotypes of offspring and adult black-throated blue warblers. Loci call rate >90%.
2012 genotypes snps 90
SNPs genotypes of offspring and adult black-throated blue warblers. Loci call rate >90%.
2011 genotypes ind 75
SNPs genotypes of offspring and adult black-throated blue warblers. Sample call rate >75%.
2012 genotypes ind 75
SNPs genotypes of offspring and adult black-throated blue warblers. Sample call rate >75%.
2011 genotypes ind 90
SNPs genotypes of offspring and adult black-throated blue warblers. Sample call rate >90%.
2012 genotypes ind 90
SNPs genotypes of offspring and adult black-throated blue warblers. Sample call rate >90%.
2011 genotypes ind snps 75
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >75%.
2012 genotypes ind snps 75
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >75%.
2011 genotypes ind snps 90
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >90%.
2012 genotypes ind snps 90
SNPs genotypes of offspring and adult black-throated blue warblers. Loci and sample call rate >90%.
2011 genotypes 77 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 77 Loci with the highest call rates.
2012 genotypes 77 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 77 Loci with the highest call rates.
2011 genotypes 57 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 57 Loci with the highest call rates.
2012 genotypes 57 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 57 Loci with the highest call rates.
2011 genotypes 37 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 37 Loci with the highest call rates.
2012 genotypes 37 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 37 Loci with the highest call rates.
2011 genotypes 27 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 27 Loci with the highest call rates.
2012 genotypes 27 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 27 Loci with the highest call rates.
2011 genotypes 17 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 17 Loci with the highest call rates.
2012 genotypes 17 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 17 Loci with the highest call rates.
2011 genotypes 7 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 7 Loci with the highest call rates.
2012 genotypes 7 snps
SNPs genotypes of offspring and adult black-throated blue warblers. 7 Loci with the highest call rates.
2011 genotypes 77H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 77 most heterozygous loci.
2012 genotypes 77H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 77 most heterozygous loci.
2011 genotypes 57H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 57 most heterozygous loci.
2012 genotypes 57H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 57 most heterozygous loci.
2011 genotypes 37H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 37 most heterozygous loci.
2012 genotypes 37H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 37 most heterozygous loci.
2011 genotypes 27H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 27 most heterozygous loci.
2012 genotypes 27H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 27 most heterozygous loci.
2011 genotypes 17H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 17 most heterozygous loci.
2012 genotypes 17H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 17 most heterozygous loci.
2011 genotypes 7H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 7 most heterozygous loci.
2012 genotypes 7H snps
SNPs genotypes of offspring and adult black-throated blue warblers. 7 most heterozygous loci.