Gasterosteus aculeatus Variation. Gasterosteus aculeatus

ABSTRACT:Advances in sequencing technologies are providing unprecedented views into patterns of genetic variation in nature. The field of population genomics, which aims to understand population genetic patterns and processes at a genome-wide scale, has advanced particularly quickly through new technologies such as RAD-seq. Although genomically more broad, short sequence reads limit the depth of information at any one locus, often to a single biallelic SNP, limiting analysis of genealogical structure of genomic regions. Thus, methods developed to infer more complete histories of individual loci, principally those rooted in coalescent theory, have been difficult to apply at a genome-wide scale. This limitation is acute in natural systems with limited genomic resources. Here we extend RAD-seq to generate phased haplotypes amenable to coalescent analysis at thousands of genomic loci. By simulating sequence evolution, we show that estimation of TMRCA required sequences greater than 300 bp per locus but only limited population sampling. Using a pair of threespine stickleback populations (Gasterosteus aculeatus) as a case study, we show that adaptive divergence in a freshwater pond occurred primarily from standing genetic variation that evolved long before the population was founded and that a chromosomal inversion harbors a pair of anciently-evolved haplotypes. These results demonstrate the feasibility of extending RAD-seq for high-throughput coalescent analysis to better understand genealogical histories in a population genomic context.