Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

Abstract

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

Sociality and migration predict hybridization across birds

“…Longer periods of pair formation may allow individuals to more accurately assess potential partners, and consequently reduce the likelihood of hybridization. Indeed, a recent genomic study [36] dovetails with the results presented here; specifically, among eight trans-Beringian lineages, species with low levels of migration showed especially low admixture. Consequently, our results suggest the results of McLaughlin et al [36] may be relevant across the avian phylogeny.…”

“…Indeed, a recent genomic study [36] dovetails with the results presented here; specifically, among eight trans-Beringian lineages, species with low levels of migration showed especially low admixture. Consequently, our results suggest the results of McLaughlin et al [36] may be relevant across the avian phylogeny.…”

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China

“…Compared to their wild ancestors, domestic animals have great variation in behavior, morphology and physiology in response to domestication, and this variation is the result of genetic changes across many generations. The genetic differentiation among domestic animals and their wild ancestors is influenced by multiple mechanisms, including selection, mutation, drift and gene flow [ 2 ]. Detecting selective signatures associated with domestication is important for understanding the genetic basis of both adaptations to new environments and rapid phenotype change.…”

An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data

“…These datasets consist of one single nucleotide polymorphism (SNP) per locus from over 1,500 UCE loci per lineage (each lineage is a pairwise, two-population sample of diverging populations, subspecies, or species). For bioinformatics methods, see Winker et al (2019) and McLaughlin et al (2020); a summary of our pipeline is given here: https://github.com/jfmclaughlin92/beringia_scripts. Each dataset consists of 100% coverage for all individuals (all individuals have phased, high-quality SNPs called at both alleles for all loci).…”

“…Each dataset consists of 100% coverage for all individuals (all individuals have phased, high-quality SNPs called at both alleles for all loci). Z-linked loci were removed because they have a different inheritance scalar from autosomal loci (Winker et al, 2019;McLaughlin et al, 2020). Original sequence data are deposited in the NCBI Sequence Read Archive (SRA; PRJNA393740).…”