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.

空间模型表明，种群间的遗传分化（genetic differentiation）可由多种因素解释，范围涵盖地理距离至跨景观的环境阻力。然而，基因组呈现分化景观（genomic landscape），这提示多种空间模型可更好地解释基因组不同区域的分化情况。本研究针对北美索诺兰沙漠（Sonoran Desert）与奇瓦瓦沙漠（Chihuahuan Desert）中共域分布的10种鸟类，检验种内分化的不同地理预测因子是否在基因组中存在差异。本研究利用种群水平的基因组数据，对各物种的基因组景观进行了表征，并构建了代表历史与现代机制的5个预测因子模型。10个物种的基因组景观特征存在差异，这受种群结构水平及沙漠间基因混杂（admixture）程度的不同影响。广义不相似性矩阵模型结果显示，最优拟合模型在全基因组及基因组分区中存在差异。几乎所有历史与现代机制均对遗传距离（genetic distance）的解释具有重要作用，其中尤以历史与现代环境因子最为显著；而当代种群丰度、基因流障碍（barrier to gene flow）位置及地理距离的解释力相对较弱。不同物种的基因组变异模式存在显著差异。本研究结果表明，基因组分化景观受作用于基因组不同区域的差异化地理因子影响。