title: A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird.
abstract: 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.
authors.affiliation: Macaulay Library, Cornell Lab of Ornithology, 159 Sapsucker Woods Rd, Ithaca, NY, 14850, USA.|Migratory Bird Center, Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC, 20013, USA.
authors.forename: Sara A
authors.initials: SA
authors.lastname: Kaiser
authors.affiliation: Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Rd, Ithaca, NY, 14850, USA.|Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Taylor
authors.affiliation: Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Rd, Ithaca, NY, 14850, USA.|Department of Ecology and Evolutionary Biology, Cornell University, E145 Corson Hall, 215 Tower Road, Ithaca, NY, 14853, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Chen
authors.affiliation: Migratory Bird Center, Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC, 20013, USA.
authors.forename: T Scott
authors.initials: TS
authors.lastname: Sillett
authors.affiliation: Department of Ecology and Evolutionary Biology, Cornell University, E145 Corson Hall, 215 Tower Road, Ithaca, NY, 14853, USA.
authors.forename: Eliana R
authors.initials: ER
authors.lastname: Bondra
authors.affiliation: Macaulay Library, Cornell Lab of Ornithology, 159 Sapsucker Woods Rd, Ithaca, NY, 14850, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Webster
mesh_terms: D000818:Animals; D060005:Genotyping Techniques / Q000379:methods*; D018895:Microsatellite Repeats; D046109:Passeriformes / Q000145:classification* / Q000235:genetics*; D010334:Paternity; D020641:Polymorphism, Single Nucleotide
keywords: RNA-seq; microsatellite; paternity; single-nucleotide polymorphism; social monogamy; transcriptome