The genomic landscapes of desert birds form over multiple time scales

Spatial models show that genetic differentiation between populations can
be explained by factors ranging from geographic distance to environmental
resistance across the landscape. However, genomes exhibit a landscape of
differentiation, which could indicate that multiple spatial models better
explain divergence in different portions of the genome. We test whether
alternative geographic predictors of intraspecific differentiation vary
across the genome in ten bird species that co-occur in Sonoran and
Chihuahuan Deserts of North America. Using population-level genomic data,
we characterized the genomic landscapes across species and modeled five
predictors that represented historical and contemporary mechanisms. The
characteristics of genomic landscapes differed across the ten species,
influenced by varying levels of population structuring and admixture
between deserts. General dissimilarity matrix modeling indicated that the
best-fit models differed from the whole genome and partitions along the
genome. Almost all of the historical and contemporary mechanisms were
important in explaining genetic distance, particularly historical and
contemporary environment, while contemporary abundance, position of the
barrier to gene flow, and distance explained relatively less. Individual
species have significantly different patterns of genomic variation. These
results illustrate that the genomic landscape of differentiation was
influenced by alternative geographic factors operating on different
portions of the genome.