Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

Abstract

The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is sister to all other angiosperms across different nucleotide rate partitions. Our results also show that commonly applied concatenation methods produce strongly supported, but incongruent placements of Amborella: slow-evolving nucleotide sites corroborate results from coalescent analyses, whereas fast-evolving sites place Amborella alone as the first lineage of extant angiosperms. We further explored the performance of coalescent versus concatenation methods using nucleotide sequences simulated on (i) the two alternate placements of Amborella with branch lengths and substitution model parameters estimated from each of the 310 nuclear genes and (ii) three hypothetical species trees that are topologically identical except with respect to the degree of deep coalescence and branch lengths. Our results collectively suggest that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites. This appears to be exacerbated by the combination of long branches in stem group angiosperms, Amborella, and Nymphaeales with the short internal branch separating Amborella and Nymphaeales. In contrast, coalescent methods appear to be more robust to elevated substitution rates.

Ancestral traits and specializations in the flowers of the basal grade of living angiosperms

“…alone (Qiu & al., 1999;, followed by Nymphaeales, or of Amborella plus Nymphaeales (Barkman & al., 2000;Qiu & al., 2010). Both scenarios are still discussed today based on extended sampling and techniques (Drew & al., 2014;Xi & al., 2014;Goremykin & al., 2015). The next clade in the grade, which is the sister group of mesangiosperms in virtually all analyses, is Austrobaileyales.…”

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

“…Successfully identifying different sources of discord Lould alloL us partition a large dataset into homogenous subsets that can be adequately modeled by existing methods (e.g., Chen et al, 2015;Xi et al, 2014). In this sense, CLASSIPHY analysis frameLork Lould be complementary to various data filtering tools that have been proposed to address the negative impact of data heterogeneity on phylogenomic estimates.…”

“…Or reflect biases in data processing steps and tree reconstruction methods (e.g., Dell'Ampio et al, 2014;Fernández-Mazuecos et al, 2017)? Or are driven by strong signals in small number of genes or sites (Lhich could be outliers; e.g., Shen et al, 2017;Xi et al, 2014)? Many data filtering strategies Lere proposed based on "interrogating" large empirical datasets, from rate of evolution to gene functional categories (e.g., Betancur et al, 2014;Doyle et al, 2015;Klopfstein et al, 2017;Romiguier et al, 2013;Salichos and Rokas, 2013).…”

“…As a consequence, empirical studies have difficulty in judging Lhether their chosen phylogenetic methods adequately model the sources of discord in the data, and Lhat effect this model mis-specification might have on the accuracy of the phylogenetic estimates. For example, several studies have observed that slight changes to dataset assembly and/or phylogenetic reconstruction methods often generate different species trees (Betancur et al, 2014;Jarvis et al, 2014;Wickett et al, 2014;Xi et al, 2014).…”

Water from the rock: Ancient aquatic angiosperms flow from the fossil record

“…However, more critical evaluation of DNA characters has reduced confidence in the basal placement of Amborella (9) and has demonstrated that the incorporation of highly Fossils such as those reported for Monteschia can only help to unravel the evolutionary and ecological events that accompanied the rise of flowering plants to global prominence. saturated sites can alter the position of Amborella and Ceratophyllum in phylogenetic analyses (10,11). The following inconsistencies are particularly noteworthy.…”