Epsilon Archive for Student Projects

Abstract

From a subset of P. tremula samples taken from across Europe and China, principal component analysis of genetic variation indicated population structure in the Scottish population compared with the rest of Eurasia. In light of this, the Scottish population was subjected to a genome-wide scan for differential regions by calculating FST and scanning for selective sweeps, using iSAFE and Tajima's D. Two possible selective sweeps located on chromosomes 4 and 14 were identified. Further analysis of these sweep regions, using identity-by-state calculations, indicated particular clusters within the Scottish population, associated to distinct geographic locations within Scotland. This indicated local adaptation was acting upon particular individuals in particular regions of Scotland, as opposed to all Scottish populations. The use of identity-by-state and iSAFE together outlines a method by which unfixed selective sweeps can be detected. A number of genes located near the selective sweep region were identified, including the WRKY3 transcription factor, which has been shown to affect radial stem growth in Populus tomentosa. These selection for these genes and its effect on neighbouring regions of the genome may be contributing to local adaptation within the Scottish P. tremula population. WRKY3 was also present in a region of chromosome 17, yet signatures of the selective sweep on chromosome 4 were not shared with chromosome 17. This is an example differential evolutionary processes affecting paralogous genes within the same genome, providing a unique insight into the evolutionary history of the P. tremula genome.