Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China.
Mol Phylogenet Evol. 2019 Apr;133:142-151. doi: 10.1016/j.ympev.2019.01.002. Epub 2019 Jan 11.
Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g., whole chloroplast genomes) can identify species with higher resolution than a few loci, e.g., partial chloroplast or nuclear gene fragments. In this study, we tested this hypothesis by sampling population genetics samples of the endangered herb genus Notopterygium. We sequenced the complete plastomes, five nuclear gene regions, three chloroplast DNA fragments, and a nuclear internal transcribed spacer (nrITS) region for 18 populations sampled throughout most of the geographic ranges of all six Notopterygium species. Species identification analysis showed that four DNA barcodes (matK, rbcL, trnS-trnG, and nrITS) and/or combinations of these markers achieved Notopterygium species discrimination at higher resolution than the general plastomes and nuclear gene sequences. In particular, nrITS had the highest discriminatory power among all of the individual markers. Molecular data sets and morphological evidence indicated that all six Notopterygium species could be reclassified unambiguously to four putative species clades. N. oviforme and N. franchetii had the closest relationship. Molecular dating showed that the origin and divergence of Notopterygium species was significantly associated with geological and climatic fluctuations during the middle of the Pliocene. In conclusion, our results suggest that a few nucleotide variations can achieve species discrimination with higher resolution than numerous plastomes and general nuclear gene fragments when discerning related Notopterygium species.
物种鉴定和区分是生物多样性研究的基础。一般认为，与少数基因座（如部分叶绿体或核基因片段）相比，大量核苷酸变异（如整个叶绿体基因组）可以提高物种鉴定的分辨率。在这项研究中，我们通过对濒危草本植物羌活属的种群遗传学样本进行抽样，来检验这一假设。我们对 18 个种群的完整叶绿体基因组、5 个核基因区域、3 个叶绿体 DNA 片段和 1 个核内转录间隔区（nrITS）区域进行了测序，这些种群分布在六个羌活属物种的地理分布范围的大部分地区。物种鉴定分析表明，四个 DNA 条形码（matK、rbcL、trnS-trnG 和 nrITS）和/或这些标记物的组合，在更高的分辨率上实现了羌活属物种的区分，优于一般的叶绿体基因组和核基因序列。特别是，nrITS 在所有单个标记物中具有最高的区分能力。分子数据集和形态学证据表明，所有六个羌活属物种都可以明确地重新归类为四个假定的种系群。鹅绒藤和羌活的亲缘关系最近。分子定年表明，羌活属物种的起源和分化与上新世中期的地质和气候波动有显著关联。总之，我们的研究结果表明，在鉴别相关羌活属物种时，少数核苷酸变异可以比大量叶绿体基因组和一般核基因片段实现更高分辨率的物种区分。
