Genomic associations with poxvirus across divergent island populations in Berthelot’s pipit

Understanding the mechanisms and genes that enable animal populations to
adapt to pathogens is important from an evolutionary, health and
conservation perspective. Berthelot’s pipit (Anthus berthelotii)
experiences extensive and consistent spatial heterogeneity
in avian pox infection pressure across its range of island
populations, thus providing an excellent system with which to examine how
pathogen-mediated selection drives spatial variation in immunogenetic
diversity. Here we test for evidence of genetic variation associated with
avian pox at both an individual and population-level. At the individual
level, we find no evidence that variation in MHC class I and TLR4 (both
known to be important in recognising viral infection) was associated with
pox infection within two separate populations. However, using
genotype-environment association (Bayenv) in conjunction with genome-wide
(ddRAD-seq) data, we detected strong associations
between population-level avian pox prevalence and allele
frequencies of single nucleotide polymorphisms (SNPs) at a number of sites
across the genome. These sites were located within genes involved
in cellular stress signalling and immune responses, many of which
have previously been associated with responses to viral infection in
humans and other animals. Consequently, our analyses indicates that
pathogen-mediated selection may play a role in shaping genomic variation
among relatively recently colonised island bird populations and highlights
the utility of genotype-environment associations for identifying candidate
genes potentially involved in host-pathogen interactions.