Discovery and preliminary multi-species evaluation of single nucleotide polymorphism resources for genus Buteo developed
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METHODS AND RESOUrCES ArTICLE
Discovery and preliminary multi-species evaluation of single nucleotide polymorphism resources for genus Buteo developed from restriction site-associated DNA paired-end data Megan A. Mayo1 · Joshua M. Hull1
Received: 1 September 2016 / Accepted: 8 September 2016 © Springer Science+Business Media Dordrecht 2016
Abstract J ust a few years ago, genomic studies of nonmodel organisms were extremely time and cost prohibitive, but recent advances in next-generation sequencing have made it possible to generate hundreds to thousands of informative single nucleotide polymorphisms (SNPs) for non-model organisms. We generated a SNP panel using restriction site-associated DNA (RAD) sequencing for species of the genus Buteo (Falconiformes: Accipitridae) with the aim of creating genomic resources in the absence of a reference genome. Using blood and feather samples from three different Buteo species, we used HiSeq Illumina sequencing to generate raw reads. We built 29 162 contigs and discovered 89 921 SNPs using paired-end single-digest RAD data. Using Bayesian clustering and principal componenets analysis, this SNP panel successfully assigned individuals of three Buteo (B. swainsoni, B. jamaicensis, B. lagopus) species correctly to species. We then scanned the SNPs for association with variation in coloration within the three species. This de novo reference will have broad application to the study of Buteo genomic diversity, analysis of population structure within species, identification of hybrids, and other applied studies of the avian genome. Keywords Buteo · RAD seq · Population genetics · Genomics · Raptor · Accipitridae
Megan A. Mayo [email protected] 1
Department of Animal Science, University of California, Davis, CA 95616, USA
Introduction Species of the genus Buteo are recently radiated and almost globally distributed raptors (Riesling et al. 2003). They are a genus of interest for many reasons, including their extreme degree of plumage polymorphism (Roulin and Wink 2004), patterns of recent sub-speciation and secondary contact (Hull et al. 2008a, b, 2010), hybridization among wild populations (Hull et al. 2007), and a variety of conservation concerns around the globe (Kjellén and Roos 2000; Fisher et al. 2015). Despite the plethora of studies directed towards Buteos, we lack genomic resources with which to analyze fine-scale population differentiation, selection, drift, and genotypic associations with phenotypic characteristics. Restriction-site associated DNA sequencing (RADseq; Miller et al. 2007) has shown promise in genomic studies of organisms because (1) it can be used to study organisms without a reference genome, (2) shrinking costs make the technology more readily available, and (3) many opensource analysis software packages are currently available for downstream analyses (e.g., angsd, Korneliussen et al. 2014). This opens up the possibilities of population studies for non-model species and allows for an increase in the breadth of questions possible for researchers
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