Originally published as Genetics Published Articles Ahead of Print on July 13, 2009.

Genetics, Vol. 183, 289-298, September 2009, Copyright © 2009
doi:10.1534/genetics.109.103895

Multilocus Patterns of Nucleotide Diversity and Divergence Reveal Positive Selection at Candidate Genes Related to Cold Hardiness in Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii)

Andrew J. Eckert^*,, Jill L. Wegrzyn, Barnaly Pande, Kathleen D. Jermstad, Jennifer M. Lee^*, John D. Liechty^*, Brandon R. Tearse, Konstantin V. Krutovsky^** and David B. Neale^*,,1

^* Section of Evolution and Ecology, Center for Population Biology and Department of Plant Sciences, University of California, Davis, California 95616, Institute of Forest Genetics, Pacific Southwest Research Station, U.S. Department of Agriculture Forest Service, Placerville, California 95667 and ^** Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843

¹ Corresponding author: Department of Plant Sciences, Mail Stop 6, University of California, Davis, CA 95616.
E-mail: dbneale{at}ucdavis.edu

Forest trees exhibit remarkable adaptations to their environments. The genetic basis for phenotypic adaptation to climatic gradients has been established through a long history of common garden, provenance, and genecological studies. The identities of genes underlying these traits, however, have remained elusive and thus so have the patterns of adaptive molecular diversity in forest tree genomes. Here, we report an analysis of diversity and divergence for a set of 121 cold-hardiness candidate genes in coastal Douglas fir (Pseudotsuga menziesii var. menziesii). Application of several different tests for neutrality, including those that incorporated demographic models, revealed signatures of selection consistent with selective sweeps at three to eight loci, depending upon the severity of a bottleneck event and the method used to detect selection. Given the high levels of recombination, these candidate genes are likely to be closely linked to the target of selection if not the genes themselves. Putative homologs in Arabidopsis act primarily to stabilize the plasma membrane and protect against denaturation of proteins at freezing temperatures. These results indicate that surveys of nucleotide diversity and divergence, when framed within the context of further association mapping experiments, will come full circle with respect to their utility in the dissection of complex phenotypic traits into their genetic components.

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Online ISSN: 1943-2361  Print ISSN: 0016-6731
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