Preprint Article Version 1 This version is not peer-reviewed

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

Version 1 : Received: 29 April 2019 / Approved: 3 May 2019 / Online: 3 May 2019 (14:03:46 CEST)

How to cite: Gruenstaeudl, M. Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics. Preprints 2019, 2019050002 (doi: 10.20944/preprints201905.0002.v1). Gruenstaeudl, M. Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics. Preprints 2019, 2019050002 (doi: 10.20944/preprints201905.0002.v1).

Abstract

The monophyly of Nymphaeaceae (water lilies) represents a critical question in understanding the evolutionary history of early-diverging angiosperms. A recent plastid phylogenomic investigation claimed new evidence for the monophyly of Nymphaeaceae, but its results could not be verified from the available data. Moreover, preliminary gene-wise analyses of the same dataset provided partial support for the paraphyly of the family. The present investigation aims to re-assess the previous conclusion of the monophyly of Nymphaeaceae under the same dataset and to determine the congruence of the phylogenetic signal across different plastome genes and data partition strategies. To that end, phylogenetic tree inference is conducted on each of 78 protein-coding plastome genes, both individually and upon concatenation, and under four data partitioning schemes. Moreover, the possible effects of various sequence variability and homoplasy metrics on the inference of specific phylogenetic relationships are tested using multiple logistic regression. Differences in the variability of polymorphic sites across codon positions are assessed using parametric and non-parametric analysis of variance. The results of the phylogenetic reconstructions indicate considerable incongruence among the different gene trees as well as the data partitioning schemes. The results of the multiple logistic regression tests indicate that the fraction of polymorphic sites of codon position 3 has a significant effect on the recovery of the monophyly of Nymphaeaceae. Taken together, these results indicate that the monophyly of Nymphaeaceae currently remains indeterminate, and that specific phylogenetic conclusions are strongly dependent on the precise plastome gene, data partitioning scheme, and codon position evaluated. In closing, I discuss the importance of archiving all data of an investigation in publicly accessible data repositories, along with sufficient details to replicate the published results, and provide recommendations on future plastid phylogenomic investigations of Nymphaeales.

Supplementary and Associated Material

Subject Areas

codon position; complete chloroplast; early-diverging angiosperms; monophyly; Nymphaeaceae; Nymphaeales; plastid genome; phylogenomics; repeatability

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