Genomic variation, population history and within-archipelago adaptation between island bird populations

Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.

This work was supported by Natural Environment Research Council (NERC) studentships to C.A.M. and C.A. (NE/L002582/1), a Norwich Research Park Science Links grant to D.S.R., M.C. and L.G.S., and a BBSRC fellowship (BB/N011759/1) and British Ecological Society Large Research Grant to L.G.S.We thank two anonymous reviewers whose insight and helpful suggestions have improved this manuscript. We thank Matthew Clark and Lawrence Percival-Alwyn for assistance generating the Berthelot's pipit genome, and Helen Hipperson, Clemens Küpper and Terry Burke (NERC Biomolecular Analysis Facility—Sheffield) for assistance with RAD sequencing. We also thank the Spanish Environment Ministry, the Canary government and the Natural Park of Madeira who gave permission for us to perform the sampling work, local governments in the Canary Islands and Madeira who provided accommodation, and the Portuguese Navy who provided transport. The research presented in this paper was carried out on the High Performance Computing Cluster supported by the Research and Specialist Computing Support service at the University of East Anglia.

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