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.