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

Mol Phylogenet Evol. 2015 Feb;83:305-16. doi: 10.1016/j.ympev.2014.10.023. Epub 2014 Nov 13.


The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories 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. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.

Keywords: Coalescent models; Demography; Genotyping by sequencing; Next-generation sequencing; SNPs; Selection.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animal Distribution
  • Animals
  • Bayes Theorem
  • Central America
  • DNA, Mitochondrial / genetics
  • Evolution, Molecular
  • Gene Flow*
  • Genetics, Population*
  • Models, Genetic
  • Passeriformes / classification*
  • Passeriformes / genetics
  • Phylogeny*
  • Phylogeography
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • South America


  • DNA, Mitochondrial

Associated data

  • Dryad/10.5061/dryad.3J0B1