Tree Genetics & Genomes

, Volume 9, Issue 3, pp 707–722 | Cite as

Genetic structure of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill populations at gene-based EST-SSR and nuclear SSR markers

  • Jennifer F. Lind
  • Oliver GailingEmail author
Original Paper


Sympatric hybridizing oak species provide a model system for studying local adaptation. Disjunct populations of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill at the northern edge of their distribution may harbor important reservoirs of adaptive genetic variation. Genic (expressed sequence tag- simple sequence repeat = EST-SSR) and non-genic nuclear microsatellite (nuclear SSR = nSSR) markers were used to estimate neutral and potentially adaptive genetic variation in these two supposedly interfertile oak species showing different adaptations to drought. Eleven populations of putative Q. rubra and Q. ellipsoidalis located in the Western Upper Peninsula of Michigan were characterized using seven EST-SSRs and eight nSSRs. Bayesian cluster analysis revealed two distinct groups corresponding to each species with evidence of low levels of potential introgression. A comparison of the genetic structure of adult trees and seedlings revealed no evidence for selection against hybrids. Overall, similar levels of genetic variation and differentiation between populations and species were found at both EST-SSRs and nSSRs indicating that most EST-SSRs chosen reflect neutral variation. Two loci, 3A05 (nSSR) and GOT021 (EST-SSR, putative histidine kinase 4-like), were identified as putative outlier loci between species showing largely reduced variation in Q. ellipsoidalis. Future analyses of an increased number of EST-SSRs located in functional genes will allow the identification of genes involved in the reproductive isolation between both species.


EST-SSRs Nuclear SSRs Oaks Genetic assignment 



We would like to thank James Schmierer for his help in sample collection in the Baraga Plains and Dr. Kerry Woods for his help in the identification of populations in the Huron Mountain Wildlife Reserve. Q. rubra and Q. ellipsoidalis reference samples were provided by Jeanne Romero-Severson and Andrew Hipp. Additionally, we would like to thank Jonathan Riehl for invaluable advice and guidance on the construction of many of the graphics. We also thank two anonymous reviewers for their very helpful comments on earlier drafts. Funding for the study came from Michigan Technological University start-up funds to Oliver Gailing, the Michigan Technological University Research Excellence fund, the USDA McIntire Stennis fund, the Huron Mountain Wildlife Foundation, the Hanes Trust and the NSF Plant Genome Research program (NSF 1025974).

Supplementary material

11295_2012_586_MOESM1_ESM.doc (307 kb)
ESM 1 (DOC 307 kb)


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© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Michigan Technological UniversityHoughtonUSA

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