Volume 5 Supplement 7
Population and conservation genomics of forest trees: seeing the forest for the trees
© Eckert; licensee BioMed Central Ltd. 2011
Published: 13 September 2011
Forest trees exhibit striking adaptations to the environments in which they grow. A long history of quantitative genetic experimentation has established the genetic basis for many traits, which are likely adaptive since many of them are also correlated with environmental heterogeneity. The genes underlying these traits, however, have largely remained elusive. Recent applications of high-throughput sequencing and genotyping technologies to natural populations of forest trees have identified several promising candidates for genes underlying complex and adaptive traits (reviewed by ). The diversity of analytical approaches employed in those studies, however, begs the question of the generality of reported results. Here, I exploited the diversity of analytical approaches used previously to identify genes underlying adaptive traits for two conifer species to assess the logical consistency among results generated from different conceptual frameworks.
Materials and methods
Many of the genes associated to phenotypes for both species were also correlated to environmental variables and exhibited patterns of non-neutral evolution. Thus, associated genes are prime targets for conservation efforts. The questions posed here, however, make the strong assumption that genes associated to phenotypes or environmental variables should also show non-neutral patterns of evolution. This is not always expected to be the case [3, 4], yet the lack of consistency is often interpreted as such and is one explanation for those genes or sets of genes reported here as lacking non-neutral signals. The search for logical consistency among analytical approaches, however, often focuses on uninformative patterns. To illustrate this point, I employed a novel environmental association approach that correlates genetic divergence to environmental change and show that most of the site-frequency spectrum based outliers for coastal Douglas-fir  are correlated to change in climate variables but not to extant climate patterns. Taken together these results illustrate that non-neutral genes are often identified during association analyses, that departures from neutrality for genes driving associations are not only those due to recent directional selection, and that further work is needed to understand the population genetic processes underlying associations between genotypes, phenotypes and the environment.
I would like to thank J. L. Liechty, B. N. Figueroa G. Rosa, and J. L. Wegrzyn for bioinformatics and computational support. I would like to thank all of the collaborators on the ADEPT2 project (http://dendrome.ucdavis.edu/NealeLab/adept2/). This work was funded by the National Science Foundation (IOS-PGRP-0501763, IOS-PGRP 0638502) and the United States Department of Agriculture (NRI Plant Genome 04-712-0084).
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