A Novel Phylogenomics Pipeline Reveals Extensive Topological Conflict in the Evolution of the Angiosperm Order Cucurbitales
5 affiliations
- 1Technical University of Munich (TUM), Emil-Ramann-Str. 2 Plant Biodiversity, Department Life Science Systems, , D-85354 Freising ,
- 2Faculty of Life and Environmental Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8572 ,
- 3Botanic Garden Meise, Nieuwedaan38, B-1860 Meise ,
- 4Royal Botanic Gardens, Kew, Richmond , Surrey, TW9 3AE ,
- 5Aarhus University Department of Biology, , 8000 Aarhus ,
Abstract
High-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are used for phylogenomic analyses. Integrating these mixed data types into a single phylogenomic dataset requires several bioinformatic tools and significant computational resources. Here, we present Captus, a novel pipeline to analyze mixed data efficiently. Captus assembles these data types, searches for loci of interest, and produces paralog-filtered alignments. If reference target loci are not available for the studied taxon, Captus can also be used to discover new putative homologs via sequence clustering. Compared to other software, Captus allows the recovery of a greater number of more complete loci across more species. We apply Captus to assemble a comprehensive 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, which group with Rafflesiaceae in Malpighiales. A subset of mitochondrial gene regions supports the earlier divergence of Apodanthaceae in Cucurbitales. However, the nuclear regions and majority of mitochondrial regions place Apodanthaceae in Malpighiales. Within Cucurbitaceae, we confirm the monophyly of all currently accepted tribes but also reveal hybridization and incomplete lineage sorting both in Cucurbitales and within Cucurbitaceae. We show that contradicting results among earlier phylogenetic studies in Cucurbitales can be reconciled when accounting for gene tree conflict and demonstrate the efficiency of Captus for complex datasets.
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BibTeX
@article{ortiz2026novel,
title = {{A Novel Phylogenomics Pipeline Reveals Extensive Topological Conflict in the Evolution of the Angiosperm Order Cucurbitales}},
author = {Edgardo M. Ortiz and Alina Höwener and Gentaro Shigita and Mustafa Raza and Olivier Maurin and Alexandre Rizzo Zuntini and Félix Forest and William J. Baker and Hanno Schaefer},
journal = {Systematic Biology},
year = {2026},
month = jul,
doi = {10.1093/sysbio/syag046},
url = {https://doi.org/10.1093/sysbio/syag046},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - A Novel Phylogenomics Pipeline Reveals Extensive Topological Conflict in the Evolution of the Angiosperm Order Cucurbitales
AU - Edgardo M. Ortiz
AU - Alina Höwener
AU - Gentaro Shigita
AU - Mustafa Raza
AU - Olivier Maurin
AU - Alexandre Rizzo Zuntini
AU - Félix Forest
AU - William J. Baker
AU - Hanno Schaefer
PY - 2026
DA - 2026/07/07
JO - Systematic Biology
DO - 10.1093/sysbio/syag046
UR - https://doi.org/10.1093/sysbio/syag046
AB - High-throughput sequencing data, such as target capture, RNA-Seq, genome skimming, and high-depth whole genome sequencing, are used for phylogenomic analyses. Integrating these mixed data types into a single phylogenomic dataset requires several bioinformatic tools and significant computational resources. Here, we present Captus, a novel pipeline to analyze mixed data efficiently. Captus assembles these data types, searches for loci of interest, and produces paralog-filtered alignments. If reference target loci are not available for the studied taxon, Captus can also be used to discover new putative homologs via sequence clustering. Compared to other software, Captus allows the recovery of a greater number of more complete loci across more species. We apply Captus to assemble a comprehensive 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, which group with Rafflesiaceae in Malpighiales. A subset of mitochondrial gene regions supports the earlier divergence of Apodanthaceae in Cucurbitales. However, the nuclear regions and majority of mitochondrial regions place Apodanthaceae in Malpighiales. Within Cucurbitaceae, we confirm the monophyly of all currently accepted tribes but also reveal hybridization and incomplete lineage sorting both in Cucurbitales and within Cucurbitaceae. We show that contradicting results among earlier phylogenetic studies in Cucurbitales can be reconciled when accounting for gene tree conflict and demonstrate the efficiency of Captus for complex datasets.
SN - 1063-5157
SN - 1076-836X
ER -