Abstract
Chromosomal fusions are hypothesized to facilitate evolutionary adaptation, but empirical evidence has been scarce. Here, we analyze chromosome-level genome sequences of three clades within the copepod Eurytemora affinis species complex, known for its remarkable ability to rapidly colonize novel habitats. Among three genetically distinct clades, we discover remarkable patterns of chromosomal evolution, with independent fusions in two different clades. Genomes of this species complex show expansions of ion transport-related gene families, likely related to adaptation to varied salinity habitats. Notably, for the highly invasive Atlantic clade (E. carolleeae), chromosomal fusion sites, especially the centromeres, are significantly enriched with signatures of selection between saline and freshwater populations. These chromosomal fusions join functionally related ion transporter genes, forming “supergenes” at the centromeres, where recombination is low. This study uncovers novel patterns of genome architecture evolution with potentially important implications for mechanisms of adaptive evolution in response to radical environmental change.