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

Abstract

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.

The ecological, genetic and genomic architecture of local adaptation and population differentiation inBoechera stricta

“…By contrast, the survival fitness component is important in the drier NOR habitats, with local NOR accessions possessing more succulent leaves. In contrast to research systems where the key environmental factors, selection forces and traits for isolation by adaptation could only be inferred [47][48][49], our empirical field experiments demonstrate how environmental differences facilitate trait divergence due to ecological factors, a much-needed approach to validate isolation by environment [9]. Similar examples exist not only in plants.…”

Color and morphological differentiation in the Sinaloa Wren (Thryophilus sinaloa) in the tropical dry forests of Mexico: The role of environment and geographic isolation

“…The inclusion of genetic data is necessary in order to distinguish between these two mechanisms that could promote phenotypic variation (e.g. [ 8 , 21 , 126 , 127 ]). Moreover, the use of neutral and under selection molecular markers (such as single nucleotide polymorphisms: SNPs) could help to separate the effect of drift and local adaptation in phenotypic variation.…”

A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical savannas

“…Even though it is postulated that open‐habitat organisms have high dispersal capacity (Sheard et al, 2020), landscape elements such as rivers, mountains or regions with unsuitable habitat conditions (e.g., rainforest patches) are expected to modulate gene flow and influence population genetic structure (Cabanne et al, 2016; Moreira et al, 2020; Vasconcellos et al, 2019). Furthermore, geomorphological and climatic conditions within biomes are not homogeneous, resulting in a mosaic with different levels of habitat integration, limiting gene flow between populations (McRae, 2006; Taylor et al, 1993).…”