Phylogenomics supports island contribution to metapopulation dynamics in a predominantly continental bird species

Aim:

Islands have recently been recognized as potential sources of biodiversity, challenging the traditional view that their small population sizes and low genetic diversity limit such roles. This raises the question of how insular genetic variation becomes incorporated into continental populations, contrary to expectations of unidirectional colonization. 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. Colonization 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). We assess a history of colonization and gene flow based on summary statistics, demographic trajectory inference by Stairway Plot2, demographic modeling by fastsimcoal2, and species distribution modeling.

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 of 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.

Methods
This dataset is created to conduct bioinformatics and population genomics analyses on MIG-seq data and species distribution modeling. MIG-seq is one of the genotyping-by-sequencing (GBS) techniques to obtain genetic variants on inter-simple sequence repeats (ISSR) across the genome of organisms. We have conducted MIG-seq on Swinhoe's Rail (Coturnicops exquisitus), distributed in continental Asia (Far East Russia) and Japan, whose raw sequence data have been deposited in an external archive, DDBJ DRA. Species distribution modeling was conducted using MaxEnt on occurrence data of the Swinhoe's Rail compiled from previous publications. The raw data, including MIG-seq raw reads, can be downloaded from NCBI, following the main text and supplementary materials. The occurrence data is available only upon request.

This dataset includes several R scripts that can reproduce bioinformatics and analyses, including raw read processing and quality assessment, genotype likelihood analyses, phylogenetic analyses, demographic analyses using site frequency spectrum, and species distribution modeling. However, the analysis environment (mainly conda environment) needs to be prepared separately to run the R scripts.