Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

作者：Paul A. Hohenlohe, Susan Bassham, Paul D. Etter, Nicholas Stiffler, Eric A. Johnson, William A. Cresko · 发表于：PLoS Genetics · 年份：2010 · DOI：10.1371/journal.pgen.1000862 · 被引用次数：1486 · 研究领域：Genetic diversity and population structure、Genetic and phenotypic traits in livestock、Genetic Mapping and Diversity in Plants and Animals

Next-generation sequencing technology provides novel opportunities for gathering genome-scale sequence data in natural populations, laying the empirical foundation for the evolving field of population genomics. Here we conducted a genome scan of nucleotide diversity and differentiation in natural populations of threespine stickleback (Gasterosteus aculeatus). We used Illumina-sequenced RAD tags to identify and type over 45,000 single nucleotide polymorphisms (SNPs) in each of 100 individuals from two oceanic and three freshwater populations. Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations. Genomic regions exhibiting signatures of both balancing and divergent selection were remarkably consistent across multiple, independently derived populations, indicating that replicate parallel phenotypic evolution in stickleback may be occurring through extensive, parallel genetic evolution at a genome-wide scale. Some of these genomic regions co-localize with previously identified QTL for stickleback phenotypic variation identified using laboratory mapping crosses. In addition, we have identified several novel regions showing parallel differentiation across independent populations. Annotation of these regions revealed numerous genes that are candidates for stickleback phenotypic evolution and will form the ...