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

ABSTRACT Calligonum is the only C4 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 inter- and intra- specific taxonomic sampling, may prove to be cost-effective methods for further investigation of the evolutionary history of this genus.

摘要：沙拐枣属（Calligonum）是蓼科（Polygonaceae）中唯一的C4光合途径属。本研究利用细胞核核糖体内部转录间隔区（nrITS）序列以及5个质体基因组区域（psbA-trnH、ycf6-psbM、trnL-F、rpl32-trnL和rbcL），对沙拐枣属的系统发育关系进行重建。研究分别对nrITS序列与合并的质体DNA序列矩阵开展系统发育分析。基于5个质体基因组区域构建的系统发育树支持将蒙古沙拐枣复合群处理为具有种内地理结构的单一物种；结合nrITS系统发育树的比较分析结果，表明多倍体物种美杜莎沙拐枣（C. caput-medusae）和木本沙拐枣（C. arborescens）为独立起源的杂交类群。本研究检测到nrITS序列与质体DNA序列构建的系统发育树之间存在系统发育冲突，并据此推测沙拐枣属存在网状进化或杂交物种形成事件。基于nrITS序列的分化时间估算显示，沙拐枣属物种的最近共同祖先于346万年前（mya；95%高概率密度区间[HPD]：187万-571万年前）开始发生分化，而中亚与中国演化支的分化起始时间约为268万年前（mya；95% HPD：128万-459万年前）。本研究认为，未来结合限制性位点关联DNA测序（RAD-seq）等下一代测序技术与更密集的种间和种内分类群采样策略，将可为该属演化历史的深入研究提供经济高效的研究方案。