Tree Genetics & Genomes

, 12:15 | Cite as

Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

  • Paul F. Gugger
  • Shawn J. Cokus
  • Victoria L. Sork
Original Article
Part of the following topical collections:
  1. Adaptation


A fundamental goal of evolutionary biology is to understand how environment shapes genetic variation through its effect on demographic processes and through natural selection. In non-model species, transcriptome sequencing generates large single nucleotide polymorphism (SNP) panels to disentangle these influences. Quercus lobata (valley oak) offers an excellent system for such analyses because it has stably occupied a climatically heterogeneous landscape throughout California. We used 220,427 diallelic SNPs from 22 individuals identified against a recently assembled reference transcriptome to (1) quantify transcriptome-wide associations of SNPs with climate indicative of demographic responses to climate, (2) identify SNPs especially associated with climate and thus potential targets of natural selection, and (3) test the hypothesis that genetic diversity is high in climate-adaptive candidate genes. Constrained ordinations (redundancy analysis) and variance partitioning showed that genetic structure in Q. lobata was explained by spatial location (49 %) and climate (24 %), especially minimum temperature and summer/spring precipitation balance, suggesting that climate influences neutral demographic processes and gene flow. After accounting for underlying structure, individual-based environmental association analyses identified 79 SNPs from 49 transcripts as candidates under natural selection by climate. These candidate genes had significantly higher SNP rates per base pair per locus (θ W), nucleotide diversity (π), and gene diversity (G) than non-candidate genes. These results provide preliminary support for the hypothesis that balancing selection maintains diversity in climate-adaptive genes. Climate has likely shaped both population demography and local adaptation in valley oak.


Climate Natural selection Quercus lobata Single nucleotide polymorphism Transcriptome 



We thank E. Eskin, K. Lohmueller, M. Pellegrini, and A. Platt for helpful discussion. This project was funded by seed money from UCLA to VLS.

Supplementary material

11295_2016_975_MOESM1_ESM.pdf (15 kb)
ESM 1 (PDF 15 kb)


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© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesUSA
  2. 2.Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgUSA
  3. 3.Molecular, Cell, and Developmental BiologyUniversity of CaliforniaLos AngelesUSA
  4. 4.Institute of the Environment and SustainabilityUniversity of CaliforniaLos AngelesUSA

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