Geographic origin of the UCSD juncos
Phylogenetic and co-ancestry analyses strongly supported the formpinosus as the sister group of the UCSD juncos, and not the
population at the nearby Laguna Mountains as reported in previous
studies. Phylogenetic, co-ancestry or population structure analyses
failed to detect any significant admixture or clustering of birds
breeding or wintering at UCSD with the thurberi individuals from
Laguna Mountains. One UCSD breeder did present an intermediate
assignment probability to the Laguna Mountains population, while one of
the likely residents detected among the UCSD wintering birds showed some
admixture with pinosus , which is consistent with the migration
rates estimated in fastSIMCOAL2 analyses. These two birds also occupy
intermediate positions between the pinosus -northern Oregon juncos
and the UCSD clusters in the PCA, suggesting these two individuals are
likely the result of recent introgression.
The population genomics analyses presented here thus support a recent
colonization of urban San Diego by a few individuals from thepinosus population up the coast, followed by limited gene flow
from other Oregon junco forms over the last ca. 40 years. Although gene
flow between divergent populations could have acted as a homogenizing
force, eroding population differentiation (Slatkin 1987; Wright 1931),
there is theoretical and empirical evidence showing that under
conditions of rapid population growth following a founder event,
divergence of allele frequencies established during colonization may be
resistant to decay by gene exchange (Boileau et al. 1992; Lombalet al. 2020). Moreover, moderate admixture can also contribute to
colonization success by minimizing deleterious effects of reduced
intra-population diversity or by introducing favorable alleles and
enhancing evolutionary potential (Keller & Taylor 2010). That
introgression between taxa contributes to adaptation and sorting of
genes has become increasingly recognized as a major contributor to
population divergence and speciation (Abbott et al. 2013;
Lamichhaney et al. 2015; Wegener et al. 2019). Based on
our genomic analyses and on the migration rates reported here and in Yeh
and Price (2004), as well as in the phenotypic studies in Yeh (2004), it
seems that several over-wintering birds on the UCSD campus came from
populations other than pinosus , and some of these may have
remained to breed on campus. It thus appears likely that there has been
introgression into the UCSD population from forms other thanpinosus , and its relevance remains to be determined.
The form pinosus , from which the UCSD population originated, is a
non-migratory form found along the coastal ranges of central California
and occurs in a range of Mediterranean habitats, displaying a tolerance
for low zonal conditions not found in thurberi (Miller 1941).
Individuals from the pinosus population would generally be
expected to produce higher fitness progeny at UCSD than thurberiindividuals. The amount of white on the tail feathers of pinosusis reduced relative to thurberi (Miller 1941), and more similar
to UCSD individuals. Indeed, Price et al. (2008) inferred strong
selection on juvenile juncos carrying excess white in their tail, which
they attributed to both direct selection on white, and correlated
responses to greater dispersal propensity, both of which would be most
prominent in offspring from thurberi immigrants, and lead to
lower rates of introgression. Nevertheless, some alleles may
successfully introgress from other subspecies, and the large pool from
which immigrants appear to be drawn from increases chances of adaptive
alleles such as the ones we have inferred from entering into the UCSD
population.