Parallel evolution and the extent to which genes are reused across different populations continues to represent important research questions. In this paper by Anne-Laure Ferchaud and I, we analyzed lateral plate morphology and genomic footprints of selection in three-spine stickleback populations using RAD sequencing (a total of 28,888 SNPs). There are by now several studies that have shown distinct patterns of parallel evolution between marine and freshwater populations, at morphological traits (lateral plate morphs) and at the genomic level, using both SNP chips, RAD sequencing and whole genome sequencing. We wanted to assess if this pattern also applies across freshwater environments that differ significantly from each other, ranging from small lakes with no fish predators and sticklebacks being the dominant species, to large lakes with many fish predators and stickleback being just one among several fish species.
Long story short: we saw surprisingly little parallel evolution across freshwater lakes, and definitely not to the extent that have been reported in other studies. A complicating factor was the finding of signatures of bottlenecks in all freshwater populations (based on analysis of allele frequency spectra), particularly in the two smallest populations. We nevertheless argue that the very low parallelism observed is a genuine finding and not induced by bottlenecks. Among others, the two smallest and most bottlenecked populations were at the same time those that showed the highest degree of parallelism and conformed the most to patterns observed in other studies.
In total, our results suggest that patterns of parallelism depend on heterogeneity across environments. In itself perhaps not such a big surprise, but it stresses the need for considering a wide range of environments before making strong conclusions, for instance about the generality of patterns of parallelism between freshwater-marine stickleback population pairs. It will be interesting to make a direct comparison of these results to RAD data obtained from Greenland sticklebacks. They represent the completely opposite type of environments; simple and species-poor ecosystems that are highly similar across different lakes. So, the prediction there should certainly be lots of parallelism at phenotypic and genomic levels.
Ferchaud AL, Hansen MM (2016) The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments. Molecular Ecology 25, in press. DOI: http://dx.doi.org/10.1111/mec.13399
This study was funded by the Villum Foundation (grant no. VKR022523 to MMH).