Conclusions and implications for previous work
Analyses based on genome-wide markers confirmed the marked genetic divergence of the Oregon juncos at UCSD, a population that became established in the early 1980s. Three further, fundamental aspects of the evolutionary history of the UCSD population have also been established here based on genomic data: (i) the UCSD junco population is most closely related to the coastal form pinosus , a group showing ecological and phenotypic similarities; (ii) environmental factors played a role in driving rapid divergence at functional loci, some of which may be involved in adaptations to an anthropogenic habitat; and (iii) demographic inference supports a scenario of contemporary population divergence as a result of a founder event by a very small number of colonizers, consistent with a major role for genetic drift in the process of differentiation. Together these results suggest that a combination of drift and directional selection can result in rapid shifts in both neutral and adaptive loci across the genome, and reveal the Oregon juncos from UCSD as a rare contemporary case of population divergence following the colonization of an anthropogenic environment.
Based on the new evidence regarding the origin of the UCSD juncos presented here, some conclusions from previous studies on this system regarding rates of evolutionary change and phenotypic plasticity may have to be reassessed. Specifically, differences in morphological fitness traits (Rasner et al. 2004), sexual signaling traits (Yeh 2004; Price et al. 2008), and shifts in a range of behavioral and life-history traits (Yeh and Price 2004; Price et al. 2008) were thought to be due to rapid evolutionary change, as were associated differences in hormones and behavior (Atwell et al. 2012; Atwell et al. 2014; Fudickar et al. 2017). Studies comparing individuals from UCSD to those from the nearby mountain thurberi  population attributed differences to a recent transition from a mountain climate to a more benign Mediterranean climate, and from a wild to an anthropogenic urban habitat. These comparative studies remain relevant to understanding phenotypic differences between junco populations adapted to different environments, although assumptions regarding rapid evolution may not be accurate given the new evidence on phylogeny and co-ancestry.
For example, UCSD juncos’ greater phenotypic similarity in tail white to their closest relative pinosus , rather than to the mountainthurberi individuals they were previously compared to, suggests that prior explanations may have overestimated the role of rapid evolutionary change in plumage variation. Further, prior research comparing UCSD and the montane thurberi phenotypes could not distinguish between two potential explanations, adaptation to an anthropogenic environment or to a mild Mediterranean climate. The fact thatpinosus shares some aspects of a mild Mediterranean climate with UCSD suggests that selection reported here is associated more strongly with the anthropogenic environment at UCSD rather than milder climate. Looking forward, our new findings provide the opportunity to develop new comparative studies between UCSD and pinosus individuals that will contribute to effectively addressing the role of urban habitats in driving rapid evolutionary divergence.