Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence

Abstract

Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified Amborella, followed by Nymphaea (water lilies) or Amborella plus Nymphaea, in the ANITA clade (Amborella, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by Nymphaea, suggesting that Amborella, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This evolution-development discordance is possibly caused by erroneous inference based on phylogenetic signals with low neutrality and/or high saturation. Here we show that the 3 rd codon transversion (P 3 Tv), with high neutrality and low saturation, is a robust high-resolution phylogenetic signal for such divergences and that the P 3 Tvbased land plant phylogeny cautiously identifies Nymphaea, followed by Amborella, as the most basal among the angiosperm species examined in this study. This P 3 Tv-based phylogeny contributes insights to the origin of angiosperms with concordance to fossil and stomata development evidence.

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

“…Moreover, several investigations reported incongruence between phylogenetic reconstructions based on the signal of only the third codon position compared to reconstructions on the first and second codon position [39,44]. The removal of third codon position data from the alignment of protein-coding genes is, thus, a commonly employed strategy in phylogenetic investigations of early-diverging plant lineages ( [45][46][47], but see [48]). The first and second codon positions are subject to functional constraints of the resulting amino acids and typically display lower rates of substitution and, by extension, homoplasy [42,49].…”