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Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics


The monophyly of Nymphaeaceae (water lilies) represents an important, but controversial aspect in the effort to understand the evolutionary history of early-diverging angiosperms. Resolving the phylogenetic position of the genus Nuphar appears to be a key to this understanding. A recent plastid phylogenomic investigation claimed new evidence for the monophyly of Nymphaeaceae. However, a preliminary gene-wise re-analysis of the same dataset provides partial support for the paraphyly of the family. The present investigation re-assesses the previous conclusion of monophyly of Nymphaeaceae under the same dataset and determines the congruence of phylogenetic signal across different plastome genes and data partition strategies. Phylogenetic tree inference is conducted on each of 78 protein-coding plastome genes, both individually and upon concatenation, and under four data partitioning schemes. The results of this re-analysis indicate considerable phylogenetic incongruence among different gene trees as well as data partitioning schemes. Hence, the monophyly of Nymphaeaceae remains indeterminate. The importance of archiving all data of an investigation in publicly accessible data repositories, along with sufficient details to replicate the published results, is discussed.

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The author wishes to thank Thomas Borsch of the Freie Universität Berlin and the Botanischer Garten und Botanisches Museum Berlin, and Robert K. Jansen of the University of Texas at Austin for valuable discussions. The author also wishes to thank two anonymous reviewers for valuable feedback on a previous version of this manuscript. Furthermore, the author acknowledges the high-performance computing service of the ZEDAT of the Freie Universität Berlin for providing allocations of computing time.


This investigation was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project Number 418670221—and by a start-up grant of the Freie Universität Berlin (Initiativmittel der Forschungskommission), both to MG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Correspondence to Michael Gruenstaeudl.

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All datasets generated and analyzed during the present investigation are available on Zenodo (

Online Resource 1. A list of the best-fitting nucleotide substitution models identified for each of the 78 protein-coding plastome genes under study.

Online Resource 2. Results of gene-wise phylogenetic tree inference via ML on each of the 78 protein-coding plastome genes under study. Bootstrap support values are given above the branches. For easier viewing, all taxa of Nymphaeaceae are indicated by a red bar to the right of their taxon names.

Online Resource 3. Results of phylogenetic tree inference via BI on the multi-gene alignment under four different data partitioning schemes. The layout and settings are as in Fig. 2. Posterior probabilities greater than 0.5 are given above the branches of each cladogram.

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Gruenstaeudl, M. Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics. Plant Syst Evol 305, 827–836 (2019).

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  • Gene-wise analysis
  • Monophyly
  • Nymphaeaceae
  • Nymphaeales
  • Plastid genome
  • Re-assessment