Marked genetic differentiation of the UCSD juncos
Our results confirmed the striking differentiation of the urban
population of Oregon juncos inhabiting the UCSD campus. Even when time
of divergence was allowed to vary between 20 and 60 generations,
parameter estimates, and bootstrap procedures recovered a time of
divergence highly consistent with the time at which the juncos where
first observed to breed at UCSD in the 1980s, with a narrow 95% CI of
20 to 32 generations, lending support to the recent founder event
hypothesis. Recovered levels of divergence for the UCSD residents that
were comparable to those of long-established, geographically isolated
forms like townsendi and pontilis from Baja California sky
islands, and in sharp contrast with the low genetic structure found
among more northern forms. Both the PCA and the STRUCTURE analyses based
on selectively neutral or near-neutral SNPs, revealed that the UCSD
juncos represent a genetically differentiated population, although some
degree of recent admixture with northern forms was detected. Juncos have
become established in other suburban and natural areas of southern
California in recent years (including the campus at UCLA in 2007, pers.
obs.), and the degree to which the UCSD population is genetically
isolated from these will require more extensive sampling in the region.
At first sight, the pattern of divergence of UCSD juncos is comparable
to that of other dark-eyed junco forms, known to have originated several
thousand years ago (Friis et al. 2016). However, demographic
inference analyses yielded results that are consistent with a very
recent origin of the urban population. The inferred number of founders
was as low as two to three individuals, just below the seven to 70
individuals previously estimated using microsatellite markers (Rasner et
al. 2004). The analysis also favored a scenario of isolation with
migration over a strict isolation model.
The migration rate from pinosus to UCSD was estimated at 6.02%
with fastSIMCOAL2. This estimate is consistent with results from Yeh and
Price (2004), who reported an immigration rate of 7% (95% CI:
4%-10%) based on observed ratios of banded to unbanded birds over a
four-year period, although immigrants from other populations besidespinosus may be included in that estimate (see below). In any
case, our results suggest that some degree of gene flow occurred during
the differentiation of the urban population of juncos. In contrast, the
inferred migration rate from UCSD to pinosus was negligible.
Our analyses also recovered a strong correlation between δD in feathers
and population assignment likelihoods in UCSD individuals sampled during
the non-breeding season, confirming the presence of both local residents
and genetically distinct individuals from northern latitudes that do not
represent recent immigrants but rather wintering visitors. These
visitors were also genetically distinct from the juncos from Laguna
Mountains and more similar to northern Oregon juncos.