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, but 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.

Spatial models show that genetic differentiation 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 factors better explain divergence in different portions of the genome. We test whether the best-predictors of intraspecific differentiation vary across the genome in ten bird species that co-occur in Sonoran and Chihuahuan deserts. Using population-level genomic data, we characterized the genomic landscapes across species and modeled five predictors that represented historical and contemporary mechanisms. The extent 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. The most important predictors of genetic distance were environment and contemporary demography, which each explained 25–38% of observed variation, with paleoclimate and the position of the biogeographic barrier explaining 14–16%, and distance only explaining 9%. In particular, the genome was best explained by the biogeographic barrier in regions where the genome showed high fixation between populations. Similar levels of heterogeneity were observed among species and phenotypic divergence within species. These results illustrate that the genomic landscape of differentiation was influenced by alternative spatial factors operating on different portions of the genome.