TY - JOUR
T1 - A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales)
AU - Wynns, Justin Thomas
AU - Lange, Conny Bruun Asmussen
PY - 2014/4
Y1 - 2014/4
N2 - • Premise of the study: 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. • Methods: 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. • Key results: 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. • Conclusions: 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.
AB - • Premise of the study: 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. • Methods: 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. • Key results: 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. • Conclusions: 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.
U2 - 10.3732/ajb.1300269
DO - 10.3732/ajb.1300269
M3 - Journal article
SN - 0002-9122
VL - 101
SP - 652
EP - 669
JO - American Journal of Botany
JF - American Journal of Botany
IS - 4
ER -