Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

TL;DR

This study uses genomic SNP data to explore the demographic history and phylogeography of Xenops minutus, revealing landscape barriers, population growth, and gene flow, advancing understanding of Neotropical bird diversification.

Contribution

It applies genomic SNP analysis to elucidate the demographic and phylogeographic history of a widespread Neotropical bird, highlighting landscape barriers and gene flow.

Findings

Landscape features like rivers and mountains are linked to deep phylogeographic breaks.

Most populations show signs of positive growth.

Historical gene flow occurred between isolated populations.

Abstract

Elucidating the demographic and phylogeographic histories of species provides insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of histories and demographic parameters with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Even with genomic estimates of historical demographic parameters, we found the prominent diversification hypotheses to be untestable. We conclude that investigations into the multifarious processes shaping species histories, aided by genomic datasets, will provide greater resolution of diversification in the Neotropics, but that future efforts should focus on understanding the processes shaping the histories of lineages rather than trying to reconcile these histories with landscape and climatic events in Earth history.