Data from: Parallel evolution of gene classes, but not genes: evidence from Hawai’ian honeycreeper populations exposed to avian malaria

Adaptation in nature is ubiquitous, yet characterizing its genomic basis
is difficult because population demographics cause correlations with
non-adaptive loci. Introduction events provide opportunities to observe
adaptation over known spatial and temporal scales, facilitating the
identification of genes involved in adaptation. The pathogen causing avian
malaria, Plasmodium relictum, was introduced to Hawai’i in the 1930s and
elicited extinctions and precipitous population declines in native
honeycreepers. After a sharp initial population decline, the Hawai’i
‘amakihi (Chlorodrepanis virens) has evolved tolerance to the parasite at
low elevations where P. relictum exists, and can sustain infection without
major fitness consequences. High-elevation, unexposed populations of
‘amakihi display little to no tolerance. To explore the genomic basis of
adaptation to P. relictum in low-elevation ‘amakihi, we genotyped 125
‘amakihi from the island of Hawai’i via hybridization capture to 40,000
oligonucleotide baits containing SNPs, and used the reference ‘amakihi
genome to identify genes potentially under selection from malaria. We
tested for outlier loci between low- and high-elevation population pairs
and identified loci with signatures of selection within low-elevation
populations. In some cases, genes commonly involved in the immune response
(e.g., major histocompatibility complex) were associated with malaria
presence in the population. We also detected several novel candidate loci
that may be implicated in surviving malaria infection (e.g., beta
defensin, glycoproteins, and interleukin-related genes). Our results
suggest that rapid adaptation to pathogens may occur through changes in
different immune genes, but in the same classes of genes, across
populations.