A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales

A diverse range of high-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are amenable to phylogenomic analyses but the integration of such mixed data types into a single phylogenomic dataset requires a number of bioinformatic tools and significant computational resources. Here, we present a novel pipeline, CAPTUS, to analyze mixed data in a fast and efficient way. CAPTUS assembles these data types, allows searching of the assemblies for loci of interest, and finally produces alignments that have been filtered for paralogs. Compared to other software, CAPTUS allows the recovery of a greater number of more complete loci across a larger number of species. We apply CAPTUS to assemble a comprehensive mixed dataset, comprising the four types of sequencing data for the angiosperm order Cucurbitales, a clade of about 3,100 species in eight mainly tropical plant families, including begonias (Begoniaceae) and gourds (Cucurbitaceae). Our phylogenomic results support the currently accepted circumscription of Cucurbitales except for the position of the holoparasitic Apodanthaceae. Within Cucurbitaceae, we confirm the monophyly of all currently accepted tribes. However, we also reveal deep reticulation patterns both in Cucurbitales and within Cucurbitaceae. We show that conflicting results of earlier phylogenetic studies in Cucurbitales can be reconciled when accounting for gene tree conflict. ### Competing Interest Statement The authors have declared no competing interest.