Population Genomic Analysis of Model and Nonmodel Organisms Using Sequenced RAD Tags

摘要: The evolutionary processes of mutation, migration, genetic drift, and natural selection shape patterns variation among individuals, populations, species, they can do so differentially across genomes. field population genomics provides a comprehensive genome-scale view these processes, even beyond traditional model organisms. Until recently, genome-wide studies have been prohibitively expensive. However, next-generation sequencing (NGS) technologies are revolutionizing the genomics, allowing for analysis at scales not previously possible in organisms which few genomic resources presently exist. To speed this revolution genetics, we colleagues developed Restriction site Associated DNA (RAD) sequencing, method that uses Illumina NGS to simultaneously type score tens hundreds thousands single nucleotide polymorphism (SNP) markers individuals minimal investment resources. core molecular protocol is described elsewhere volume, be modified suit diversity questions. In chapter, outline conceptual framework relate discuss how RAD used study genomics. addition, bioinformatic considerations arise from unique aspects data as compared marker based approaches, some general analytical approaches RAD-seq similar data, including computational pipeline called Stacks. This software with without reference genome. Nonetheless, development tools remains its infancy, further work needed fully quantify sampling variance biases types. As data-gathering technology continues advance, our ability understand evolution populations will limited more by weaknesses than amount data.