Population genetics to population genomics: Revisiting multispecies connectivity of the Hawaiian Archipelago using pooled RADseq approaches

Understanding connectivity between populations is key to identifying hotspots of diversity, dispersal sinks and sources, and regions potentially predisposed to resiliency. Restriction site-associated DNA sequencing (RADseq) has become the standard approach for a cost-efficient method for surveying population differentiation, to obtain a high-resolution view of population structure, and determine the scale of gene flow in non-model organisms. Pool-seq combines the DNA from many individuals into a single sample and allows allele frequencies to be calculated for a fraction of the cost of sequencing individuals. Previous work based on one or a handful of mtDNA and microsatellite loci (Toonen ­et al. 2011, Selkoe et al. 2014) identified multi-species boundaries to gene flow across the Hawaiian archipelago shared among a majority of the 35 coral reef species surveyed. Here, we evaluate the value of additional information using pool-seq as a genome-wide SNP approach to assess genetic differentiation among populations. Although pooled sequencing of individuals greatly reduces the cost per sample and is particularly well suited for gathering population genetic information across many individuals and broad geographic areas, methods to analyze pooled data remains computationally challenging and unstandardized. Several programs have been developed specifically to handle pool-seq data, unfortunately most still require heavy formatting or programming skills. Here we report a newly developed and user-friendly pool-seq pipeline (AssessPool) and use it to compare population genomic structure from a subset of six species from the previous studies across eleven islands throughout the Hawaiian Archipelago. Patterns of genetic differentiation defined using thousands of genomic markers are compared to the previous patterns using traditional single-locus genetic markers in terms of cost, ease and consistency of results. A simplified and cost-effective method to quantify patterns of population genomic structure of marine organisms has widespread implications for ecosystem-based management practices.