Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)

Spatial patterns of intraspecific variation are shaped by factors such as
geographic 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 geographic variation in body size across its range. We
combined a comprehensive SNP and phenotypic dataset to test whether
genome-wide genetic and phenotypic differentiation are best explained by
(a) isolation by distance, (b) isolation by history, or (c) 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 phylogeographic structure coinciding with the Chivela Pass at the
Isthmus of Tehuantepec and was formed in 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 phylogeographic studies.