Spatial patterns of intraspecific variation are shaped by geographical distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographical variation in body size across its range. We combined a comprehensive single nucleotide polymorphism and phenotypic data set to test whether genome‐wide genetic and phenotypic differentiation are best explained by (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. We find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow, phenotypic diversity can be best predicted by contemporary environmental heterogeneity. Our genomic analyses reveal strong phylogeographical structure coinciding with the Chivela Pass at the Isthmus of Tehuantepec that was formed during the Pleistocene, when populations were isolated in north–south refugia. In contrast, we found a strong association between body size and environmental variables, such as temperature and precipitation. The relationship between body size and local climate is consistent with a pattern produced by either natural selection or environmental plasticity. Overall, these results provide empirical evidence for why phenotypic and genomic data are often in conflict in taxonomic and phylogeographical studies.

中文翻译：

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在低地中美洲鸟类（Icterus gularis）中，基因组和表型变异的空间预测因子有所不同。

种内变异的空间格局由种群之间的地理距离，基因流的历史变化以及与当地环境的相互作用所决定。尽管这些因素不是互斥的，并且在基因组和表型变异上都起作用，但尚不清楚它们如何影响这两个变异轴。我们通过探索Igterus gularis的基因组和表型差异的预测因子来解决这个问题，一种分布广泛的中美洲鸟类，在其整个范围内的体型都有明显的地理差异。我们结合了全面的单核苷酸多态性和表型数据集，以测试通过（i）按距离隔离，（ii）按历史隔离或（iii）按环境隔离来最好地解释全基因组遗传和表型分化。我们发现在I. gularis中明显的遗传和表型变异只是部分相关，并且在空间预测变量方面有所不同。尽管基因组变异很大程度上是由基因流动的历史障碍所解释，但表型多样性可以通过当代环境异质性最好地预测。我们的基因组分析表明，强健的地理结构与更新世期间在特胡安特佩克地峡形成的Chivela Pass相吻合，当时该种群在南北避难所被隔离。相反，我们发现人体大小与环境变量（例如温度和降水）之间有很强的联系。体型与当地气候之间的关系与自然选择或环境可塑性产生的模式一致。总体，