Conifer convergence

Convergent local adaptation is typically studied within a species or between closely related species. In these cases, it is perhaps not unexpected to observe parallel evolution due to common genetic variation, constraints, etc. Convergence between species is somewhat less studied, especially when complex polygenic traits are considered. Are similar genes required for different species to adapt to similar environments? That is, is adaptation genetically constrained?
To address this question (link to paper), Sam Yeaman and colleagues involved with the AdapTree project focused on two tree species from western North America, lodgepole pine and interior spruce. These species are about 140 million years diverged but occupy similar environmental clines and consist of locally adapted populations throughout their ranges.
It is known that these species show local adaptation to their environment, but are the underlying genetic adaptations convergent? To address this, the authors grew > 1100 individuals from 250 populations across the range of both species in a greenhouse. These individuals were phenotyped for 17 climate related traits. They were genotyped for > 1 million SNPs in 23,000 genes and genotype-phenotype and genotype-environment associations (for 22 environmental variables) were conducted. These associations identified outliers, and the authors looked at specific genes, identifying which had the highest proportion of their total SNPs as outliers. They then looked for signals of adaptation in the orthologs of these outliers in the other species.
For a false discovery rate (FDR) of 0.05, 47 genes showed evidence for convergence. That is, about 10-18% of locally adapted genes are evolving convergently (depending on the FDR used). I really don’t have a sense about whether this is high or low… if anyone has thoughts, please weigh in. Another interesting finding is that duplicated genes were more likely to show convergence than unduplicated genes (see figure). This pattern may be explained by a relaxation of selective constraint following duplication.


Candidate genes with signatures of convergent local adaptation. From Yeaman et al., 2016

I like this study for a number of reasons. First, the authors are explicitly looking for convergence in distantly related species. This allows them to address the degree of convergence in adaptive evolution in species that should share no standing genetic variation. Second, they asked this question in regard to complex physiological traits. This is nice because many previous examples of convergence between species have been found in relatively simple traits (I’m looking at you, MC1R). Now, we just need other people to perform similar studies so we can figure out if these rates of convergence are consistent across taxa and phenotypes.
Yeaman, Sam, Kathryn A. Hodgins, Katie E. Lotterhos, Haktan Suren, Simon Nadeau, Jon C. Degner, Kristin A. Nurkowski et al. “Convergent local adaptation to climate in distantly related conifers.” Science 353, no. 6306 (2016): 1431-1433. DOI: 10.1126/science.aaf7812

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