Fifty mosses on five trees: comparing phylogenetic information in three types of non-coding mitochondrial DNA and two chloroplast loci
- 227 Downloads
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.
KeywordsBryophytes Group I intron Group II intron Indels Intergenic region Mitochondrial DNA Mosses Phylogeny RNA editing
The authors are very grateful to Drs. Jan-Peter Frahm, Bonn; Bernard Goffinet, Storrs CT; Hermann Muhle, Ulm; Yin-Long Qiu, Ann Arbor MI and Dietmar Quandt, Dresden, who made biological material or DNA samples, respectively, available. Financial support through the Deutsche Forschungsgemeinschaft (DFG) is gratefully acknowledged. The last author is grateful to the Deutsche Bahn for continuous, reliable and comfortable ICE transportation commuting between Bonn and Ulm on a weekly basis also in preparation of the present manuscript.
- Crandall-Stotler B, Forrest LL, Stotler RE (2005) Evolutionary trends in the simple thalloid liverworts (Marchantiophyta, Jungermanniopsida subclass Metzgeriidae). Taxon 54:299–316Google Scholar
- Davis EC (2004) A molecular phylogeny of leafy liverworts (Jungermanniidae: Marchantiophyta). In: Goffinet B, Hollowell V, Magill R (eds) Molecular systematics of bryophytes. Missouri Botanical Garden Press, St Louis, pp 61–86Google Scholar
- Forrest LL, Crandall-Stotler BJ (2005) Progress towards a robust phylogeny for the liverworts, with particular focus on the simple thalloids. J Hattori Bot Lab 97:127–159Google Scholar
- Goffinet B, Buck WR (2004) Systematics of the bryophyta (mosses): from molecules to a revised classification. In: Goffinet B, Hollowell V, Magill R (eds) Molecular systematics of bryophytes. Missouri Botanical Garden Press, St Louis, pp 205–239Google Scholar
- Goffinet B, Wickett NJ, Shaw AJ, Cox CJ (2005) Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses. Taxon 54:353–360Google Scholar
- La Farge C, Shaw AJ, Vitt DH (2002) The circumscription of the Dicranaceae (Bryopsida) based on the chloroplast regions trnL-trnF and rps4. Syst Bot 27:435–452Google Scholar
- Maddison WP, Maddison DR (2003) Mesquite: a modular system for evolutionary analysis. [1.0]Google Scholar
- Magombo ZLK (2003) The phylogeny of basal peristomate mosses: evidence from cpDNA, and implications for peristome evolution. Syst Bot 28:24–38Google Scholar
- Quandt D, Bell N, Stech M (2007) Unravelling the knot: the Pulchrinodaceae fam. nov (Bryales). Nova Hedwigia 21–39Google Scholar
- Sugita M, Sugiura C, Arikawa T, Higuchi M (2004) Molecular evidence of an rpoA gene in the basal moss chloroplast genomes: rpoA is a useful molecular marker for phylogenetic analysis of mosses. Hikobia 14:171–175Google Scholar
- Swofford DL (2003) PAUP* Phylogenetic analysis using parsimony (* and Other Methods). Version 4. Sinauer Assoc., Sunderland, MA. . Sunderland, MA, Sinauer AssociatesGoogle Scholar