The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data

Abstract

The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for Eriospermum as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + Theropogon is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

“…The monophyly of Aspidistra was well supported with 100% BS (Figure 6). In our results, the sister genus of Aspidistra was Tupistra, a finding similar to those of previous studies based on the plastid genome (containing four Aspidistra species) [29] and transcriptome data (with one Aspidistra species) [47]. Within the Aspidistra, the first branching clade was A. erecta, representing a group with distinguishable vegetative morphology (erect stem) [10,48].…”

Transcriptome-based phylogenomic analysis reveals evidence of ancient hybridization events in the Mepraia genus (Hemiptera: Reduviidae: Triatominae)

“…Our results suggest that there are only a small number of concordant trees, indicating that several alternative topologies are being supported. This pattern is expected, as gene trees are rarely entirely concordant with species trees (Vargas et al, 2019;Meng et al, 2021;Xiao et al, 2022), especially in recently diverged taxa. Incongruence in the phylogenetic signal across distinct parts of the genome can be the result of various evolutionary phenomena, including incomplete lineage sorting, gene flow, hybridization, lateral gene transfer, recent divergence, convergent evolution, different evolutionary rates, or loss of information during evolution (Betancur et al, 2019).…”