Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Abstract

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated 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 compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28-1622)] 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 positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation 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 (16% vs. 11-18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion-contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.

Genetic diversity, genetic structure and demographic history of Cycas simplicipinna(Cycadaceae) assessed by DNA sequences and SSR markers

“…The influence of Quaternary climate change on present patterns of genetic variation of some species has been studied [5,6]. Gugger [7] verified that late Quaternary glacial cycles played an important role in shaping the genetic structure and diversity of the present population of Quercus lobata Nee. The results showed that Quercus lobata maintained a stable distribution with local migration from the last interglacial period (~120 ka) through the Last Glacial Maximum (~21 ka, LGM) to the present.…”

“…The results showed that Quercus lobata maintained a stable distribution with local migration from the last interglacial period (~120 ka) through the Last Glacial Maximum (~21 ka, LGM) to the present. This contrasts with large-scale range shifts in Quercus alba L [7]. More recent climatic oscillations have had profound effects on the dynamics of population expansion and contraction, causing populations to contract into glacial refugia, become extinct and possibly to adapt locally [8,9].…”

Multiple glacial refugia lead to genetic structuring and the potential for reproductive isolation in a herbaceous plant

“…One of the primary historical processes that infl uence genetic structure is climate change, in particular glacial cycles, which have caused cyclic expansions and contractions of many species' ranges ( Hewitt, 2000( Hewitt, , 2004Tollefsrud et al, 2008 ;Gugger et al, 2013 ;Roberts and Hamann, 2015 ). Phylogeography ( Avise et al, 1987 ) is oft en used to understand the eff ects of glacial cycles on current genetic structure, including the number and location of glacial refugia as well as the recolonization routes from those refugia to current locations ( Hewitt, 1996 ;Taberlet et al, 1998 ;Hewitt, 2000 ).…”

First Draft Assembly and Annotation of the Genome of a California Endemic OakQuercus lobataNée (Fagaceae)

“…Quercus ), but they differ markedly in recent evolutionary history. The European oaks experienced severe bottlenecks during Pleistocene glaciations, with most populations surviving in southern refugia (Petit et al 2003; Petit et al 2002), while the California endemic oaks have not experienced serious bottlenecks in at least 150,000 yr or more, with evidence of relatively stable species distributions during the last few interglacial cycles (Gugger et al 2013). Many oak studies have utilized genomic approaches, but without the benefit of a reference genome ( e.g.…”