Using high-throughput sequencing data to tackle complex taxonomic issues The Artemisia genus as a case study

Abstract

Speciation in plants may not always be the outcome of a gene flow barrier followed by gradual mutations, selection, and drift; instead hybridization and polyploidization events can play a significant role. Consequently, species delimitation can be difficult, as morphological assessments or genotyping assays using standard molecular markers (e.g. Sanger sequencing) may lack sufficient resolution to infer complex evolutionary histories. The use of high-throughput sequencing data enables us to clarify taxonomic issues that could not be resolved based on morphological data or a limited amount of DNA sequence information. The cosmopolitan genus Artemisia (Asteraceae) is known for its complex evolutionary history, marked by multiple polyploidy and hybridization events. In addition, Artemisia taxa have been introduced to other regions where they became invasive and possibly hybridized with local Artemisia species. Here, we present a workflow for the inference of evolutionary patterns based on genetic distances and phylogenetic trees in complex taxonomic groups using a genome-wide set of DArTseq markers. Next, we applied our workflow on a dataset consisting of accessions of A. verlotiorum, A. vulgaris, A. princeps, and other members of the A. vulgaris complex to unravel hybrid taxa and potential new species in the Artemisia genus.