Abstract
Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST) and absolute (dXY) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window‐based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.
Highlights
The integration of genomic data into research on population differentiation and speciation has led to the observation that genomic differentiation between closely related populations is often highly variable across the genome, with areas of elevated differentiation interspersed with areas of low differentiation (e.g., Nadeau et al 2013; Renaut et al 2013; Han et al 2017; Vijay et al 2017)
We used genomic data from eight population pairs of birds that span a broad taxonomic scale to study the contribution of local genomic features to variation in genome-wide estimates of differentiation
We rely on the fact genomic features are conserved across birds to draw inferences from our analyses and discuss these findings below, including the potential temporal effect these features can have of genomic differentiation
Summary
The integration of genomic data into research on population differentiation and speciation has led to the observation that genomic differentiation between closely related populations is often highly variable across the genome, with areas of elevated differentiation interspersed with areas of low differentiation (e.g., Nadeau et al 2013; Renaut et al 2013; Han et al 2017; Vijay et al 2017). One of the main conclusions from this observation is that speciation can proceed through a few focal changes and does not require divergence across the entire genome This conclusion conforms to the genic view of speciation proposed by Wu (2001), but there is still considerable controversy concerning the factors that generate variation in estimates of genomic differentiation. REPEATABILITY IN DIFFERENTIATION ACROSS BIRDS both selection and gene flow to explain heterogeneous patterns of differentiation This model holds that divergent selection at loci involved in reproductive isolation protects some regions of the genome from gene flow, elevating an otherwise homogenized landscape of differentiation (Nosil et al 2009; Nosil and Feder 2012). We refer to this model as selection in allopatry and note that there are variants on this model related to when selection acts (Cruickshank and Hahn 2014; Delmore et al 2015; Irwin et al 2016)
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