Wynns Justin T, Lange Conny B Asmussen
Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 21, DK-1958 Frederiksberg, Denmark.
Am J Bot. 2014 Apr;101(4):652-69. doi: 10.3732/ajb.1300269. Epub 2014 Apr 3.
Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps.
For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given.
Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics.
Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.
在Hypnales（侧蒴藓类中进化程度最高且物种最丰富的目）内，科级及科级以下的系统发育树通常分辨率较低。在准备绘制斜蒴藓属（Plagiothecium）的系统发育树时，我们希望确定最适合用于该类Hypnales侧蒴藓进化重建的DNA标记。
对25个斜蒴藓及相关类群的样本，测序了16个DNA区域：核ITS和26S，以及质体rps4、rps4-trnL、trnL-F、trnK(matK)-psbA、psbA-trnH、trnM-V、trnD-T、rbcL、atpB-rbcL、psbT-H、rpoC1外显子2（部分）、trnG内含子、rpl16内含子和质体核糖体间隔DNA（cpITS）。根据每个区域解析分支的能力、数据集中存在的同塑性程度以及获取数据的相对难易程度对其进行评估。给出了每个区域的描述性统计数据。
诸如trnK-psbA、rps4-trnL和trnD-T等未充分利用的苔藓植物质体标记比trnL-F和rps4等更传统的标记表现更好。单个质体拓扑结构相似，这表明只需有限的质体数据就能恢复主干系统发育树。在大量质体矩阵中添加少量核糖体数据会重构恢复的拓扑结构，强调了在苔藓植物系统学中对多个基因组进行采样的重要性以及对新的低拷贝核标记的需求。
未来侧蒴藓属的科级系统发育研究应针对trnK-psbA和rps-4trnL等未充分利用的质体标记，并结合低拷贝核标记。
