Leveraging whole genomes, mitochondrial DNA, and haploblocks to decipher complex demographic histories: an example from a broadly admixed arctic fish

The study of phylogeography has transitioned from mitochondrial haplotypes to genome-wide analyses, blurring the line between this field and population genomics. Whole-genome sequencing offers the opportunity to join use both and provides the density of markers necessary to investigate genetic linkage and recombination along the genome. This facilitates the unraveling of complex demographic histories of admixture between divergent lineages, as is often the case in species evolving in recently deglaciated habitats. In this study, we sequenced 1120 Arctic Char genomes from 33 populations across Canada and Western Greenland to characterize patterns of genetic variation and diversity, and how they are shaped by hybridization between the Arctic and Atlantic glacial lineages. Several lines of evidence supported mito-nuclear discordance in lineage distribution, with all Canadian populations under the 66th parallel being characterized by introgression from the Atlantic lineage, leading to higher nuclear genetic diversity. By scanning the genome using local PCAs, we identified putative low-recombining haploblocks as local ancestry tracts from either lineage and described the impacts of recombination on the introgression landscape in admixed populations. Finally, we inferred conflicting origins of recolonization using whole genomes vs. ancestry tracts for the Arctic lineage, suggesting that haplotypes sheltered from introgression by low recombination could enlighten complex post-glacial histories. Overall, we argue that Whole-Genome Sequencing, even at low depths of coverage, provides a versatile approach to the study of phylogeographic dynamics.