The evolution of genomic organization through chromosomal rearrangements in Arctic charr (Salvelinus alpinus)

Chromosomal rearrangements (CR) can play an important role in evolutionary diversification by preserving linkage among favourable alleles through reduced recombination and/or by reducing hybrid fitness due to genomic incompatibilities.  Our goal was to determine to what extent CR contribute to patterns of genetic variation in Arctic charr (Salvelinus alpinus).  To address this goal, we compared genetic linkage maps to identify whole arm CR and smaller structural variants (translocations, inversions) found in groups of populations that reflect the temporal sequence of geographic isolation events.  If CR contribute to genetic differentiation, we expected that CR would be specific to glacial lineages, geographic clusters of populations within lineages and sympatric morphs.  We detected CR involving fusions and fissions of whole chromosome arms, translocations/transpositions of the sex-determining gene (sdY) and inversions.  Several CR were shared across populations from the Arctic and Atlantic glacial lineages, Canadian and Icelandic populations within the Atlantic lineage, between two Icelandic populations and sympatric morphs within Icelandic populations, suggesting that their origin predate geographic isolation in glacial refugia.  The detection of other CR specific to single populations suggests a more recent origin in refugia and/or in contemporary populations.  Thus, CR contribute mostly to genetic variation within populations and represent a pool of standing variation for evolution.   The current database provides the raw accession IDs of various genotype-by-sequencing (GBS) reads of Arctic charr SNP markers and their alignments to the Salvelinus sp. genome assembly (https://www.ncbi.nlm.nih.gov/assembly/GCF_002910315.2).  Assignments of markers to both male- and female-specific genetic linkage maps are provided.