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

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.

How Many Kinds of Birds Are There and Why Does It Matter?

“…Thus, there may be a bias towards a higher phylogenetic to traditional species ratio for molecular studies. Secondly, molecular studies have shown that tropical species tend to show greater levels of differentiation than those of temperate species [22,23], and therefore estimates of the total number of taxa/species worldwide will be biased if the distribution of sampled species does not coincide with the geographic distribution of species diversity. We investigated this by plotting the distribution of phylogroups, generally recognized as reciprocally monophyletic populations on a mtDNA gene tree, as a function of latitude.…”

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

“…First, we performed species tree phylogenetic analyses using SNAPP (Bryant et al, 2012). Because the computational demands of SNAPP depend on the number of individuals included in the analysis (Bryant et al, 2012), we used a subsampling approach similar to that used by Harvey and Brumfield (2015) in which we randomly selected three individuals (six chromosomes) to represent each of the groups Figure 1 Map of sampling locations for S. catenatus samples (darker shading) and S. tergeminus samples (lighter shading). Populations are indicated with smaller bold font, and state or province names are indicated with larger bold font.…”

Reticulation, divergence, and the phylogeography–phylogenetics continuum

“…By the early 2000s, phylogeographic surveys of nonmodel species typically included a handful of loci, mostly using methods that facilitated a locus-by-locus phylogeographic analysis (5,6). There are now a growing number of studies realizing a distant goal of phylogeography, geographically informed whole-genome resequencing (7,8), as well many more sampling subgenomes through varied approaches (9)(10)(11)(12). With the expansion to genome-wide analyses afforded by NGS, phylogeographic analysis has necessarily expanded its analytical toolkit.…”