Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under
selection via spatial variation in abiotic environmental variables, but
rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus
harrisii) is found only on the environmentally heterogeneous island of
Tasmania and is threatened with extinction by a nearly 100% fatal,
transmissible cancer, devil facial tumor disease (DFTD). Devils persist in
regions of long-term infection despite epidemiological model predictions
of species’ extinction, suggesting possible adaptation to DFTD. Here, we
test the extent to which spatial variation and genetic diversity are
associated with the abiotic environment and/or DFTD. We employ
genetic-environment association analyses using a RAD-capture panel
including 6,886 SNPs from 3,286 individuals sampled pre- and post-disease
arrival. Pre-disease, we find significant correlations of allele
frequencies with environmental variables, including 365 unique loci linked
to 71 genes, suggesting local adaptation to abiotic environment. The
majority of candidate loci detected pre-DFTD were not detected post
disease arrival. Several post-DFTD candidate loci were associated with
disease prevalence and were in linkage disequilibrium with genes involved
in tumor suppression and immune response. Loss of apparent signal of
abiotic local adaptation post-disease suggests swamping by the strong
selection resulting from the rapid onset of DFTD.