Different phylogenetic relationships within the genome of European Oxyria digyna (l.) Hill

Abstract

Innovations in genomics are revolutionizing our understanding of biodiversity. Complex phyloge netic relationships can now be represented through graphs and networks, enabling incorporation of for instance gene flow and recombination. This thesis investigates the phylogenetic relationships between ten European populations of the Arctic-alpine plant species Oxyria digyna (L.) Hill (Pol ygonaceae). I explore the phylogenetic differences between core genes (conserved across species) and accessory genes (unique to a species). I hypothesize 1) divergence of the sampled populations will follow the retreat of the glaciers, and 2) core- and accessory genes will show different phylog enies and gene flow, since core genes are under strong purifying selection, accessory genes may be locally adaptive, and with these genes having different locations on the chromosome affecting re combination. Phylogenies for core and accessory genes were compared using two bioinformatic approaches (TreeMix and SplitsTree). Results show 1) southern populations diverge early as ex pected, but not earlier than populations in Greenland, and 2) there are phylogenetic differences between core- and accessory genes. The phylogeny not only following the glacial retreat may be due to different dispersal ways into and across Europe. Contrary to our expectations, core genes needed more migration events and network reticulations to explain the data perhaps due to these genes occurring in regions of high recombination. Accessory genes showed higher variation and fewer total migration events than core genes, perhaps suggesting local adaptation affect these genes more. Core gene phylogenies were more consistent than those from accessory genes, potentially because of higher purifying selection due to their essential cellular functions. For phylogenetic studies of interbreeding populations, evolutionary differences between regions of the genome should be considered, as treating variable sites equally may not show the diverse evolutionary pat terns within the species.