Genome‐wide signals of drift and local adaptation during rapid lineage divergence in a songbird

Abstract

The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic‐environment association analyses (GEA) while controlling for population structure. Analysis of genome‐wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation‐by‐adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.

Testing for Hardy–Weinberg equilibrium in structured populations using genotype or low‐depth next generation sequencing data

“…As a limitation of PCA, it can be sensitive to batch effects that reflect other confounding factors as well, which will be a problem if they are captured contrary to population structure by the top eigenvectors. Even with these potential limitations, PCAngsd seems robust in its inference of population structure as seen in the results of the low-coverage 1000 Genomes Project dataset as well as another application of PCAngsd in a recent songbird study (Friis et al, 2018). Here PCAngsd was used to remove paralogous loci with an excess of heterozygotes based on our HWE test.…”

Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm

“…This diversity is thought to have arisen since the most recent glacial maxima when the J. hyemalis ancestor diverged from J. phaeonotus fulvescens of southern Mexico and subsequently expanded its range across North America 30,31 . While environmental factors have been shown to partition genetic variation within a subset of J. hyemalis taxa 32 , the major J. hyemalis morphotypes do not exhibit strong population genetic differentiation 31 suggesting that considerable phenotypic diversity persists in the face of high rates of gene flow. The role that environmental conditions play in driving the diversification of this lineage thus remain unclear.…”

Dorsal color variation among subspecies of the “Oregon” Dark-eyed Junco complex

“…For example, many subspecies exhibit substantial overlap in morphological characters, such as tail length, wing length, and the extent of white on rectrices (Ferree 2013). Furthermore, four out of five of the Oregon Dark-eyed Junco subspecies included in this study ( thurberi , shufeldti , montanus , and oreganus ) exhibit little to no genetic population structure based on genomic analyses involving thousands of loci (Friis et al 2018). Pinosus , however, exhibits pronounced genomic differentiation (Friis et al 2018), is non-migratory, and has the shortest wings of all Oregon Dark-eyed Junco subspecies (Ferree 2013), and is therefore a valid subspecies.…”

“…Furthermore, four out of five of the Oregon Dark-eyed Junco subspecies included in this study ( thurberi , shufeldti , montanus , and oreganus ) exhibit little to no genetic population structure based on genomic analyses involving thousands of loci (Friis et al 2018). Pinosus , however, exhibits pronounced genomic differentiation (Friis et al 2018), is non-migratory, and has the shortest wings of all Oregon Dark-eyed Junco subspecies (Ferree 2013), and is therefore a valid subspecies. Although oreganus exhibits less genomic differentiation than pinosus , oreganus is also distinct in its darker plumage and partially geographically isolated range, suggesting it too may be a valid subspecies.…”