Data and code from: Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data

Phylogenomic datasets comprising hundreds of genes have become the
standard for plant systematics and phylogenetics. However, large-scale
phylogenomic studies often exclude polyploids and hybrids due to the
challenges in assessing the origin of duplicated loci and incorporating
them into tree reconstruction methods. Using a newly generated target
enrichment dataset of 1081 genes from 452 samples from the Brassicaceae
tribe Arabideae, including many hybrid and high ploidy taxa, we developed
a novel approach to disentangle the evolutionary history of this
phylogenetically and taxonomically challenging clade. Our approach extends
beyond commonly used gene tree-species tree reconciliation techniques by
using phylogenetic placement, a method adopted from metagenomics, of gene
copies into a diploid tree. We show how it allows for the simultaneous
assessment of the origins of ancient and recent hybrids and
autopolyploids, and the detection of nested polyploidization events.
Additionally, we demonstrate how synonymous substitution rates provide
further evidence for the mode of polyploidization, specifically to
distinguish between allo- and autopolyploidization, and to identify
hybridization events involving a ghost lineage. Our approach can serve as
an exploratory tool for large and complex phylogenomic datasets and can
aid in identifying polyploid and hybrid clades for further analysis with
specialized methods.