Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Joseph F. Walker, Ya Yang, Michael J. Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F. Brockington, Stephen A. Smith

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events. KEY RESULTS: Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68–83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods. C ONCLUSIONS: Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.

Original languageEnglish (US)
Pages (from-to)858-867
Number of pages10
JournalAmerican journal of botany
Issue number6
StatePublished - 2017

Bibliographical note

Funding Information:
We thank Edwige Moyroud, Joseph Brown, and Oscar Vargas for thoughtful comments on the manuscript; Ning Wang, Sonia Ahluwalia, Jordan Shore, Lijun Zhao, Alex Taylor and Drew Larson for helpful discussion on the manuscript; M. Raquel Marchán Rivadeneira for help with laboratory work; and Deborah Lalumondier and Justin Lee at the Missouri Botanical Garden for access to their living collections. We also thank Cambridge University Botanic Gardens for help with growing material and access to living collections. We also thank the Associate Editor and two anonymous reviewers for comments that helped improve the manuscript. The molecular work of this study was conducted in the Genomic Diversity Laboratory of the Department of Ecology and Evolutionary Biology, University of Michigan. This work was supported by NSF DEB awards 1352907 and 1354048.

Publisher Copyright:
© 2017 Botanical Society of America.


  • Caryophyllales
  • Gene tree conflict
  • Paleopolyploidy
  • Phylogenomics
  • Plant carnivory


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