A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

The premise of this study is to further advance the understanding of the species-rich, economically and ecologically important Myrtales, an angiosperm order in the rosid clade comprising nine families, approximately 400 genera and almost 14000 species occurring on all continents (except Antarctica). The potential of High Throughput Sequencing (HTS) and target enrichment with the Angiosperms353 probe kit is evaluated on a sample of 485 species in 305 genera (76% of all genera in the order). Results provide technical considerations for processing HTS data and the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks such as the relationship of the early diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. HTS and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to enable selection of genes and gene trees that account for incomplete lineage sorting and hybridisation events.