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The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a highquality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ~1.03Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation. [ABSTRACT FROM AUTHOR]

The relative roles of natural and sexual selection in promoting evolutionary lineage divergence remains controversial and difficult to assess in natural systems. Local adaptation through natural selection is known to play a central role in promoting evolutionary divergence, yet secondary sexual traits can vary widely among species in recent radiations, suggesting that sexual selection may also be important in the early stages of speciation. Here, we compare rates of divergence in ecologically relevant traits (morphology) and sexually selected signalling traits (coloration) relative to neutral structure in genome‐wide molecular markers and examine patterns of variation in sexual dichromatism to explore the roles of natural and sexual selection in the diversification of the songbird genus Junco (Aves: Passerellidae). Juncos include divergent lineages in Central America and several dark‐eyed junco (J. hyemalis) lineages that diversified recently as the group recolonized North America following the last glacial maximum (ca. 18,000 years ago). We found an accelerated rate of divergence in sexually selected characters relative to ecologically relevant traits. Moreover, sexual dichromatism measurements suggested a positive relationship between the degree of colour divergence and the strength of sexual selection when controlling for neutral genetic distance. We also found a positive correlation between dichromatism and latitude, which coincides with the geographic axis of decreasing lineage age in juncos but also with a steep ecological gradient. Finally, we found significant associations between genome‐wide variants linked to functional genes and proxies of both sexual and natural selection. These results suggest that the joint effects of sexual and ecological selection have played a prominent role in the junco radiation. [ABSTRACT FROM AUTHOR]

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., (© 2018 John Wiley & Sons Ltd.)