title: Testing morphological concepts of orders of pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on TRNL-TRNF and RPS4 sequences.
abstract: The ordinal classification of pleurocarpous mosses rests on characters such as branching mode and architecture of the peristome teeth that line the mouth of the capsule. The Leucodontales comprise mainly epiphytic taxa, characterized by sympodial branching and reduced peristomes, whereas the Hypnales are primarily terricolous and monopodially branching. The third order, the Hookeriales, is defined by a unique architecture of the endostome. We sampled 78 exemplar taxa representing most families of these orders and sequenced two chloroplast loci, the trnL-trnF region and the rps4 gene, to test the monophyly and relationships of these orders of pleurocarpous mosses. Estimates of levels of saturation suggest that the trnL-trnF spacer and the third codon position of the rps4 gene have reached saturation, in at least the transitions. Analyses of the combined data set were performed under three optimality criteria with different sets of assumptions, such as excluding hypervariable positions, downweighting the most likely transformations, and indirect weighting of rps4 codon positions by including amino acid translations. Multiple parallelism in nonsynonymous mutations led to little or no improvement in various indices upon inclusion of amino acid sequences. Trees obtained under likelihood were significantly better under likelihood than the trees derived from the same matrix under parsimony. Our phylogenetic analyses suggest that (1) the pleurocarpous mosses, with the exception of the Cyrtopodaceae, form a monophyletic group which is here given formal recognition as the Hypnidae; (2) the Leucodontales are at least paraphyletic; and (3) the Hypnales form, with most members of the Leucodontalean grade, a monophyletic group sister to a Hookerialean lineage. The Hypopterygiaceae, Hookeriales, and a clade composed of Neorutenbergia, Pseudocryphaea, and Trachyloma likely represent a basal clade or grade within the Hypnidae. These results suggest that mode of branching and reduced peristomes are homoplastic at the ordinal level in pleurocarpous mosses.
authors.affiliation: Institute of Systematic Botany, New York Botanical Garden, Bronx, New York 10458-5126, USA.
authors.forename: W R
authors.initials: WR
authors.lastname: Buck
authors.forename: B
authors.initials: B
authors.lastname: Goffinet
authors.forename: A J
authors.initials: AJ
authors.lastname: Shaw
mesh_terms: D001483:Base Sequence; D019068:Bryopsida / Q000145:classification* / Q000235:genetics*; D002736:Chloroplasts / Q000378:metabolism; D002965:Classification; D003062:Codon; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003062:Codon; D010940:Plant Proteins; C097421:rps4 protein, plant