title: SNP discovery and genotyping for evolutionary genetics using RAD sequencing.
abstract: Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative genomics, and phylogeography that was unthinkable even a few years ago is now possible. More importantly, these next-generation sequencing studies can be performed in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we have developed Restriction site Associated DNA (RAD) genotyping, a method that uses Illumina next-generation sequencing to simultaneously discover and score tens to hundreds of thousands of single-nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. In this chapter, we describe the core RAD-seq protocol, which can be modified to suit a diversity of evolutionary genetic questions. In addition, we discuss bioinformatic considerations that arise from unique aspects of next-generation sequencing data as compared to traditional marker-based approaches, and we outline some general analytical approaches for RAD-seq and similar data. Despite considerable progress, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types.
authors: Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
authors: Paul D
authors: PD
authors: Etter
authors: Susan
authors: S
authors: Bassham
authors: Paul A
authors: PA
authors: Hohenlohe
authors: Eric A
authors: EA
authors: Johnson
authors: William A
authors: WA
authors: Cresko
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000302:isolation & purification; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004587:Electrophoresis, Agar Gel; D019143:Evolution, Molecular; D015723:Gene Library; D005828:Genetics, Population; D016678:Genome / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015183:Restriction Mapping / Q000379:methods*; D012260:Ribonucleases / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA; D012260:Ribonucleases; D004262:DNA Restriction Enzymes