Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

When populations colonise new environments they may be exposed to novel
selection pressures but also suffer from extensive genetic drift due to
founder effects, small population sizes, and limited interpopulation gene
flow. Genomic approaches enable us to study how these factors drive
divergence, and disentangle neutral effects from differentiation at
specific loci due to selection. Here, we investigate patterns of genetic
diversity and divergence using whole-genome resequencing (> 22X
coverage) in Berthelot’s pipit (Anthus berthelotii), a passerine endemic
to the islands of three north Atlantic archipelagos. Strong environmental
gradients, including in pathogen pressure, across populations in the
species range, make it an excellent system in which to explore traits
important in adaptation and/or incipient speciation. Firstly, we quantify
how genomic divergence accumulates across the speciation continuum, i.e.,
among Berthelot’s pipit populations, between subspecies across
archipelagos, and between Berthelot’s pipit and its mainland ancestor, the
tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1
million – ca. 8,000 years ago), we identify highly differentiated loci
within genomic islands of divergence and conclude that the observed
distributions align with expectations for non-neutral divergence.
Characteristic signatures of selection are identified in loci associated
with craniofacial/bone and eye development, metabolism, and immune
response between population comparisons. Interestingly, we find limited
evidence for repeated divergence of the same loci across the colonisation
range but do identify different loci putatively associated with the same
biological traits in different populations, likely due to parallel
adaptation. Incipient speciation across these island populations, in which
founder effects and selective pressures are strong, may therefore be
repeatedly associated with morphology, metabolism, and immune defence.