Fifty mosses on five trees: comparing phylogenetic information in three types of non-coding mitochondrial DNA and two chloroplast loci

Abstract

Given the frequent genomic recombinations in plant mitochondrial DNA, intergenic regions of this organelle genome had so far not been considered as loci of potential phylogenetic information. Based on the recent evidence that an evolutionary ancient mitochondrial nad5-nad4 gene continuum is conserved in bryophytes we have compiled a dataset for a phylogenetically wide sampling of 50 mosses covering this intergenic region. The length of the intergenic region was generally in the range of 585 (Diphyscium) to 646 bp (Tomentypnum) with rare exceptions, for example all Polytrichales taxa showing a 200 bp deletion as an apparent synapomorphy of this order. Phylogenetic information in the novel marker sequence was compared with that of a nad5 gene region containing a group I intron and a nad2 gene region containing a group II intron as well as with two widely sampled chloroplast data sets, rbcL and rps4. Indel evolution in the three types of non-coding mitochondrial sequences is obviously more taxon-dependent than locus-dependent, indicating lineage-specific insertion/deletion rates. For example, larger sequence deletions are a general feature in Schistostega and Tetraphis. Although confidence for particular nodes in the phylogeny was found to vary among data sets, gene trees were essentially without conflict with respect to well-supported ones and add up in information towards a reasonably well-resolved moss phylogeny. However, while a consensus on the latter is clearly emerging, sufficient confidence is still lacking for the first dichotomies among the arthrodontous mosses leading into subclasses Bryidae, Dicranidae and Funariidae and the relative placement of nematodontous mosses (Polytrichales and Tetraphidales) on the backbone of early moss phylogeny.