The Pleiotropy and Evolutionary Constraint (PLEVOCON) project was a project funded by the Marie Skłodowska-Curie Individual Fellowship (a Horizon 2020 action).
The aims of the project were threefold:
- To identify genomic loci associated with repeated divergence between stickleback adapted to different habitats.
- To estimate levels of pleiotropy across the stickleback genome using novel proxy metrics.
- To test whether pleiotropy explains the repeated use of genetic loci during stickleback adaptation.
To determine which regions of the genome were diverging in parallel among independent population pairs of stickleback we used reduced representation sequencing data (GBS and RADseq) to estimate the pattern of genetic differentiation (Fst). We did this for marine-freshwater ecotype pairs, benthic-limnetic pairs and stream-lake pairs. We found that on average 30-37% of highly differentiated genomic regions were evolving in parallel (Rennison and Peichel, Submitted). Furthermore, we found that many of the regions of the genome repeatedly diverging contained candidate regions for ecologically important traits (e.g. armor and trophic traits), as determined by GWAS (Rennison et al., Phil. Trans. Roy. Soc. B.). Lastly, we were able to associate the magnitude of parallel genomic evolution with levels of ecological similarity and geographic proximity (Rennison et al. 2019 Am. Nat.).
To test whether level of pleiotropy explains patterns of parallel genomic evolution we first estimated the magnitude of pleiotropy for genes or genomic regions, then used these estimates to test whether regions exhibiting parallel evolution had lower levels of pleiotropy than uniquely evolving regions. Previously collected QTL and RNAseq data, were used to estimate the number of mapped traits and gene connectivity for each gene or region – both of which are considered proxies for the overall level of pleiotropy. We found that counter to theoretical predictions, parallel genomic regions contained genes that were more pleiotropic than genomic regions evolving neutrally or diverging between only a single population pair. Other genetic factors, like gene density, mutation rate and recombination rate did not consistently differ between parallel and non-parallel genomic regions, suggesting that intermediate levels of pleiotropy are adaptive.
Rennison, D.J., and Peichel, C.L. Intermediate levels of pleiotropy facilitate parallel adaptation in sticklebacks.
Rennison, D.J., Delmore, K.E., Samuk, K.M., Owens, G.L., and Miller, S.E. Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology. American Naturalist, In Press.
Rennison, D.J., Stuart, Y.E., Bolnick, D.I., and Peichel, C.L. Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback. Philosophical Transactions of the Royal Society B, 374:20180241.