Genome-Wide Phylogenetic Incongruence Indicates Ancient Introgression in Ancestors of Arabidopsis, Capsella, Camelina, and Boechera (Brassicaceae)

Organismal phylogenies are typically inferred from either a single molecular marker or concatenated sequences from a small number of loci. However, loci with in a genome can have different histories due to processes such as gene duplication and loss, incomplete lineage sorting, and introgressive hybridization. These processes can cause phylogenetic incongruence within and between nuclear and organelle genomes. More explicitly, a gene tree inferred from a locus that has undergone any of these processes may differ 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. Such analyses can inform our understanding of genome evolution by indicating regions of the genome with alternative histories. Here, we 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. We apply the pipeline to whole genome sequences from Arabidopsis and its close relatives to identify a significant signature of ancient introgression, which led to nuclear mosaicism, chloroplast capture, and cytonuclear discordance. Our findings serve as a valuable resource to dissect the impact of historical processes on genome content and architecture within the agriculturally and scientifically important Brassicaceae.