Phylogenomics Supports Island Contribution to Metapopulation Dynamics in a Predominantly Continental Bird Species

ABSTRACT Aim Islands have recently been recognised as potential sources of biodiversity, challenging the traditional view that their small population sizes and low genetic diversity limit such a role. This raises the question of how insular genetic variation becomes incorporated into continental populations, contrary to expectations of unidirectional colonisation. Here, we investigate whether and how island‐derived genetic variation has influenced a continental population through population establishment and gene flow in a bird species where frequent trans‐ocean dispersal is expected. Location Continental East Asia (Russian Far East), Japanese Archipelago. Taxon Swinhoe's rail ( Coturnicops exquisitus ). Materials and Methods We apply integrative phylogenomics to reconstruct the spatiotemporal history of the species. Colonisation sequences and gene flow are inferred by comparing four different phylogenetic reconstruction methods, using mitochondrial sequences obtained by Sanger sequencing and genome‐wide data obtained by genotyping by sequencing (MIG‐seq). A spatiotemporally explicit history of colonisation and gene flow is reconstructed based on summary statistics, demographic trajectory inference by Stairway Plot2, demographic modelling by fastsimcoal2 and species distribution modelling. Results Analyses collectively supported asymmetric gene flow from the island to the continental population, following divergence around the Middle Pleistocene. Post‐divergence, the island maintained a large and stable population, while the continental population underwent a severe bottleneck, suggesting a significant evolutionary role of the island for the continental population. Additionally, evidence of recent re‐establishment on the island by continental individuals indicates dynamic exchange and persistence within a continent–island metapopulation. Main Conclusions The maintenance of insular genetic variation within a dynamic continent‐island metapopulation may have enabled the island to act as a genetic and demographic reservoir for the continental population. Thus, continent‐island metapopulation dynamics may be a key evolutionary pathway through which island populations contribute to continental genetic diversity.