Late Quaternary demography and selection shape modern genetic structure of California valley oak: Insights from phylogeography, ecological niche modeling, and multivariate statistics

Background/Question/Methods

Phylogeographic and ecological niche modeling (ENM) studies suggest a prominent role for neutral, historical demographic processes in shaping modern genetic structure, but have largely ignored the role of past natural selection.  We used multilocus phylogeographic inference, climate-based ENMs, and multivariate statistical approaches to determine the effects of both past demography and selection associated with late Quaternary climate change on contemporary genetic structure of valley oak (Quercus lobata Née), a California endemic found in the Central Valley and surrounding foothills.

Results/Conclusions

ENMs revealed that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present.  Coast Range foothill and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time.  In accordance with neutral expectations for stable populations, nuclear microsatellite diversity was positively correlated with niche stability from the LGM to present.  Most strikingly, we found that nuclear and chloroplast microsatellite variation was significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses.  Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (22-26% v. 18-27%) and substantially more than geography (12%).  These results highlight that past and present selection, not just neutral processes, are important in shaping modern genetic variation for species with stable distributions.  Past signatures of selection in modern genetic structure could suggest long lag times for adaptive evolution to changing climates, implying that climate refugia, local migration in the variable topoclimate of California’s mountains, or perhaps non-genetic adaptation will be more important for the future response of valley oak to projected climate change.