PgmNr P2130: Genome-wide RAD genealogical analyses highlight the role of ancient genomic variation during rapid adaptation in threespine stickleback.

Authors:
T. Nelson; W. Cresko


Institutes
Institute of Ecology and Evolution, University of Oregon, Eugene, OR.


Abstract:

Present genetic diversity, from the level of individual genes to genomic regions and entire chromosomes, is the product of the entire evolutionary history of a species. This deep history influences future adaptive potential. Recent advances in sequencing technologies have provided unprecedented views into patterns of genetic variation and spurred the field of population genomics, which aims to understand the distribution of genetic variation throughout genomes. While short sequence reads have greatly facilitated our understanding of genomic patterns of SNP variation, inference of deeper patterns of sequence evolution has been elusive. To facilitate genomic studies of haplotype evolution, we have use restriction site-associated DNA sequencing (RAD-seq) to generate phased sequence of length and quality comparable to Sanger reads — and thus amenable to genealogical analysis — at thousands of genomic loci. By comparing two populations of threespine stickleback (Gasterosteus aculeatus) to a sister species, the ninespine stickleback (Pungitius pungitius), we show that adaptive divergence in a freshwater pond population occurred primarily from standing genetic variation that originated long before that population was founded. Furthermore, we demonstrate that a chromosomal inversion under divergent selection is harboring a pair of anciently-evolved adaptive haplotypes. These data highlight the ability of RAD-seq to sample haplotypic variation at a genomic scale and help advance the field of populations genomics towards a deeper understanding of the genealogical structure of standing genetic variation and its importance for adaptation in the wild.