Demographic inference
Eight different models were compared to identify the most likely
scenario under which UCSD juncos diverged from its closest relative, thepinosus form, using fastSIMCOAL2. AIC revealed that the most
likely scenario was the one consistent with a recent population split
due to a founder event (Fig. 2A) under a model of isolation with
migration, and clearly rejected alternative models (Table 3). Parameter
estimates revealed a very recent colonization time of the urban
environment (TDIV = 44 years, 95% CI = [30 - 47]) by a very small
number of effective founders, from two to three individuals
(Ne = 2 individuals; 95% CI = [2 - 3]). The
estimate for the current effective population size of UCSD was
Ne = 252 individuals, 95% CI = [215 - 274]). The
best estimate for UCSD population growth rate since colonization was
estimated at r = 0.159, 95% CI = [0.150 – 0.244]). The estimate
for pinosus effective population size was high, at
Ne = 5.86x106 individuals, 95% CI =
[5.86x106 - 5.87x106]. The
analysis also recovered a narrow, limited rate of gene migration frompinosus to UCSD (MIG pin →UCSD = 6.02x10-2, 95% CI =
[5.87x10-2 – 8.03x10-2]). The
migration rate range from UCSD to pinosus varied by several
orders of magnitude and was close to zero, revealing little impact of
the parameter in the SFS (MIG UCSD →pin = 2.01x10-6, 95% CI =
[9.38x10-10 - 2.57x10-5]) (Table
3).
Despite the marked difference in AIC scores supporting a recent
population split due to a founder event, it should be noted that none of
the next best-fitting models included a recent population split, and
that the model including a recent population split due to a founder
event in strict isolation was not among those at the top (Table 3). This
may be due to the effect of gene flow during the establishment and
genetic differentiation of the UCSD population, resulting in highly
different site frequency spectra when comparing scenarios of recent
colonization with and without migration. However, it could also reflect
a lack of resolution of the analysis in discriminating the historical
factors shaping the current patterns of genetic variability in the UCSD
population of juncos, so that these results should be interpreted with
caution.
Genotype association analysis In the RDA, four explanatory environmental variables accounted for
7.65% (R2 = 0.0765) of the variability in the SNP
dataset, and the model was highly significant (P = 0.001). Both mean
temperature of the warmest quarter and temperature seasonality showed
large contributions to the RDA2 axis, while variability in NDVI and
elevation was more evenly captured by both RDA1 and RDA2 axes (Fig. 6).
RDA association scores revealed a strong positive correlation of mean
temperature of the warmest quarter with genetic differences of UCSD
residents, and negative correlations with the remaining explanatory
variables. Correlation patterns were less conspicuous in other junco
forms, mostly differentiated along RDA1. Forms townsendi andpontilis showed negative correlations with vegetation greenness,
with the former also loading heavily on elevation. The formpinosus presented general associations of the same sign as UCSD,
yet much less pronounced. The remaining, more boreal forms presented
moderate and positive correlations with vegetation greenness and
temperature seasonality, while loading negatively on mean temperature of
the warmest quarter, an inverse pattern with respect to UCSD juncos
(Fig. 6).