Exploring Phylogenetic Incongruence on a Genome-wide Scale in Brassicaceae

Molecular phylogeneticists traditionally use a small number of genetic marker loci to infer the organismal phylogeny of a group of species. However, the evolutionary history of loci can vary due to processes such as gene duplication and loss, incomplete lineage sorting, and horizontal gene transfer (i.e. hybridization). Thus, a gene tree inferred from a locus that has undergone any of these processes may deviate from trees of genes that have not. The number of publicly available whole genome sequences is rapidly increasing, allowing for phylogenetic analysis of numerous markers across the genome, an approach known as phylogenomics. Here, I introduce a pipeline for performing high-throughput phylogenomic analyses. Alternative topologies uncovered by these analyses are displayed on interactive chromosome maps to identify genomic regions with alternative evolutionary histories. I apply the pipeline to whole genome sequences from Arabidopsis and its close relatives to identify regions that may have experienced hybridization and/or incomplete lineage sorting.