title: Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata.
abstract: OBJECTIVE
  The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural populations of valley oak, Quercus lobata, as preliminary indication of local adaptation.
  
  
  METHODS
  Using DNA from 45 individuals from 13 localities across the species' range, we sequenced portions of 40 candidate genes related to budburst/flowering, growth, osmotic stress, and temperature stress. Using 195 single nucleotide polymorphisms (SNPs), we estimated genetic differentiation across populations and correlated allele frequencies with climate gradients using single-locus and multivariate models.
  
  
  RESULTS
  The top 5% of FST estimates ranged from 0.25 to 0.68, yielding loci potentially under spatially divergent selection. Environmental analyses of SNP frequencies with climate gradients revealed three significantly correlated SNPs within budburst/flowering genes and two SNPs within temperature stress genes with mean annual precipitation, after controlling for multiple testing. A redundancy model showed a significant association between SNPs and climate variables and revealed a similar set of SNPs with high loadings on the first axis. In the RDA, climate accounted for 67% of the explained variation, when holding climate constant, in contrast to a putatively neutral SSR data set where climate accounted for only 33%.
  
  
  CONCLUSIONS
  Population differentiation and geographic gradients of allele frequencies in climate-associated functional genes in Q. lobata provide initial evidence of adaptive genetic variation and background for predicting population response to climate change.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California, USA 90095-7239 Institute of Environment and Sustainability, University of California, Box 951767, Los Angeles, California, USA vlsork@ucla.edu.
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Sork
authors.affiliation: Center for High Throughput Biology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Squire
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California, USA 90095-7239.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Gugger
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California, USA 90095-7239.
authors.forename: Stephanie E
authors.initials: SE
authors.lastname: Steele
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, 4140 Terasaki Life Sciences Building, 610 Charles E. Young Drive East, Los Angeles, California, USA 90095-7239.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Levy
authors.affiliation: Department of Biology, Virginia Commonwealth University, Richmond, Virginia 23284 USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Eckert
mesh_terms: D000220:Adaptation, Biological; D002140:California; D002980:Climate; D057231:Climate Change; D017343:Genes, Plant; D020641:Polymorphism, Single Nucleotide; D029963:Quercus / Q000235:genetics*; D012641:Selection, Genetic
keywords: Fagaceae; Quercus; climate change; environmental gradients; landscape genetics; local adaptation; single nucleotide polymorphisms; spatially divergent selection