Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)
Cite this dataset
Rocha Moreira, Lucas; Hernandez-Baños, Blanca E.; Smith, Brian T. (2023). Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis) [Dataset]. Dryad. https://doi.org/10.5061/dryad.931zcrjh8
Abstract
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.
Usage notes
icterus_ingroup_6xcov_090diff_min5.vcf
SNP dataset assembled using iPyRAD (90% sequence identity, min coverage 6x, max missing data 50%)
Icterus_gularis_ND2.fasta
Alignment of ND2 sequences
Measurements-TOTAL_DATASET.csv
Phenotypic measurements of museum-vouchered specimens
Maxent_model_LQHP_05_full_data.asc
Ecological niche model (ENM) for the current climate
MidHolocene_average.asc
Ecological niche model (ENM) for the Mid-Holocene averaged across climate models
LGM_average.asc
Ecological niche model (ENM) for the Last Glacial Maximum averaged across climate models