The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

Abstract

Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae’s thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family’s complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support, and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevents the confident resolution of these nodes using plastome data alone.

Chronospaces: an R package for the statistical exploration of divergence times reveals extreme dependence on molecular clocks and gene choice

“…Which of these is closer to the truth is beyond the scope of empirical work; nonetheless, those studying the diversification of clades should be aware of the systematic effects that result from using a given subsampling scheme. Surprisingly, the pattern seen here is opposite to that reported in the simulation of Carruthers et al (2022), in which the selection of congruent topologies was tied to an expansion of internal branch lengths and a reduction of terminal ones. This is in fact the expected behavior if topological incongruence is driven by biological factors such as ILS (Mendes & Hahn 2016).…”

“…While some authors have advocated for the selection of clock-like genes in the hopes that reduced lineage-specific rate variation will improve model fit and diminish bias, others have favored loci with less topological conflict, as these are expected to harbor higher phylogenetic signal and be less affected by incomplete lineage sorting (ILS). Simulations have confirmed that both of these subsampling schemes result in more accurate divergence times (Smith et al 2018;Carruthers et al 2020;Carruthers et al 2022). Other sensible options include selecting genes based on phylogenetic usefulness (as estimated using genesortR; Mongiardino Koch 2021), which should balance both aforementioned strategies by discovering loci with increased clock-likeness and decreased topological incongruence; and maximizing occupancy, increasing the amount of information contained within a matrix of a given size.…”

Hiding in plain sight: Phylogenomics reveals a new branch on the Noctuoidea tree of life

“…Incongruence is especially problematic for divergence time estimation (Carruthers et al, 2022) our results (Kitching & Rawlins, 1998). But the interpretation of the tympanal orientation in Noctuoidea systematics (Kitching & Rawlins, 1998;Miller, 1991;Zahiri et al, 2011) to other noctuoids).…”

“…Incongruence is especially problematic for divergence time estimation (Carruthers et al, 2022), and dating three competing topologies illustrates this problem. The stem age of Scranciidae either antedates the K–T boundary or postdates it, depending on the topology, which has major implications for the evolution of the group.…”

Hiding in Plain Sight: Phylogenomics Reveals a New Branch on the Noctuoidea Tree of Life

“…Incongruence is especially problematic for divergence time estimation (Carruthers et al 2022), and we date three competing topologies to illustrate this problem. For example, the stem age of Scranciidae either antedates the K-T boundary or postdates it, depending on topology, which has major implications for the evolution of the group.…”