A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales).
OBJECTIVE
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.


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.
Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 21, DK-1958 Frederiksberg, Denmark.
Justin T
JT
Wynns
Conny B Asmussen
CB
Lange
D019068:Bryopsida / Q000235:genetics*; D060365:Chloroplast Proteins / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000235:genetics; D017422:Sequence Analysis, DNA
D060365:Chloroplast Proteins; D021901:DNA, Intergenic; D018744:DNA, Plant; D012335:RNA, Ribosomal; C065096:RNA, ribosomal, 26S
ITS; Plagiothecium; barcoding; bryophytes; intergenic spacer; intron; molecular systematics; rbcL; trnK/matK