Testing glacial refugia and post glacial recolonization
The TMRCA estimation of 96 pairs of populations were used to conduct
ANCOVA for models of K=3 to K=6. In all tested models, the interaction
terms are not significant and thus the type II sum of squares was used
in ANCOVA tests. The K=6 drainage refugia model includes 30 pairs of
populations from the same drainage system and 66 pairs of populations
from different drainage systems. This model has the lowest AIC and BIC,
and explains the data significantly better than either K=3 or K=4
population structure models based on Vuong’s test (Table 1 ).
However, we cannot distinguish the K=5 and K=6 population structure
model, as they possess the same set of paired populations due to the
lack of multiple population samples form the Merced drainage.
In the best fit K=6 model, the result of ANCOVA shows that TMRCA
estimates are significantly older (> 20,000 years ago) for
pairs of populations from different drainages than from the same
drainage (~ 10,000 years ago; p-value <
0.001), regardless of whether geographical distance is included as a
covariant or not (Figure 7A ). However, there are a few of
population pairs from the same drainage that do have older TMRCA,
notably sites in the Kings or Kern drainages. Similarly, there are a few
outliers with recent TMRCA when pairs of different drainages are
compared, including sites from the San Joaquin and Kings drainages. In
contrast, there is no significant difference between the two types of
population pairs when measuring Weir and Cockerham’sF ST (p-value > 0.05). Geographical
distance has a high R2 value (0.35 and 0.55)
when included as a covariate, implying genetic variation is consistent
with isolation by distance (Figure 7 B).