A phylogeny of Calligonum L. (Polygonaceae) yields challenges to current taxonomic classifications

Abstract

Calligonum is the only C 4 genus within Polygonaceae. We applied DNA sequences from the nuclear ribosomal internal transcribed spacer (nrITS) and five plastid genome regions (psbA-trnH, ycf6-psbM, trnL-F, rpl32-trnL and rbcL) to reconstruct the phylogeny of Calligonum. The nrITS and the combined plastid DNA regions were analysed separately. The phylogeny of the five plastid genome regions supports the treatment of the Calligonum mongolicum complex as a single species with intra-specific geographic structure, and suggests independent hybrid origins for the polyploid species C. caput-medusae and C. arborescens through comparisons with the nrITS tree. We detected phylogenetic incongruence between the nrITS and plastid DNA trees and hypothesized reticulate evolution or hybrid speciation in the genus. Divergence time dating based on nrITS determined that the most recent common ancestor of Calligonum species began diversification 3.46 million years ago [mya; 95 % high probability density (HPD): 1.87-5.71 mya], and diversification began in the Central Asia and China clade ca. 2.68 mya (95 % HPD: 1.28-4.59 mya). We expect that future studies employing next generation sequencing methods, such as RAD-seq, coupled with denser interand intra-specific taxonomic sampling, may prove to be cost-effective methods for further investigation of the evolutionary history of this genus.

Phylogenomics, divergence time estimation, and adaptive evolution in the Polygonoideae (Polygonaceae)

“…This finding was in agreement with morphological differentiation: most characters are derived. Short internal branches observed in the Calligonum species suggested rapid divergence (Song et al, 2020; Liu et al, 2021). Many xerophyte groups, such as Gymnocarpos Forssk.…”

“…Complete plastomes contain variants that can provide sufficient phylogenetic information to distinguish closely related species (Wen et al, 2021; Cao et al, 2022; Li et al, 2022), including Polygonaceae species with complex evolutionary histories, such as Atraphaxis and Fagopyrum (Xu & Zhang, 2015; Fan et al, 2021; Wen et al, 2021). In addition to their applicability for phylogenetic studies, complete plastomes can provide insights into other evolutionary processes, such as chloroplast inheritance and adaptive evolution (Liu et al, 2021; Wen et al, 2021; Li et al, 2022). Furthermore, using plastome data to reconstruct phylogenetic relationships and identify ancestral states in a temporal context can provide a better understanding of the evolutionary history (Zhang et al, 2014; Yao et al, 2019).…”

“…However, the ancestral states and evolutionary relationships of Polygonoideae have not been studied on a large scale in the framework of molecular systematics. There have been studies based on phylogenetic analysis in Polygonoideae inferring that some species exhibit different adaptive evolutionary patterns, such as Rheum and Calligonum (Sun et al, 2012; Liu et al, 2021; Zhang et al, 2021). However, within the framework of phylogeny, studies on adaptive evolution of Polygonoideae species in the temporal context have not been reported (Meng et al, 2015; Wen et al, 2015; Liu et al, 2021).…”