A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data

Benjamin Merget,Matthias Wolf

doi:10.1186/1756-0500-3-320

Abstract

BackgroundHypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously.FindingsWe built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs.ConclusionsProfile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes.

Highlights

Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes
Programs 4SALE and ProfDistS were used in this study to generate a large scale phylogenetic analysis of 1,634 complete and correctly annotated hypnalean internal transcribed spacer 2 (ITS2) sequence-structure pairs, which were currently available at the ITS2 Database [11,12,13,14,23,24]
Every single base pair is 90% conserved over the whole alignment. This is evidence for the correctness of the 4SALE [15,16] alignment of over 1,500 sequencestructure pairs. It underlines the strong preservation of the ITS2 secondary structure which allowed us to proceed on this basis

Summary

Background

Pleurocarpous mosses, which are mainly found in tropical forests, account for more than 50% of all moss species [1,2]. The remaining sequences lying in the non-monophyletic rests of the distance tree, were not considered to confine this computation to only the backbone of the Hypnales (see below), and how it is supported regarding the ITS2 sequence-structure alignment (Figure 4). Among the order of Hypnales several families (Hypnaceae, Neckeraceae, Leptodontaceae, Anomodontaceae, Hylocomiaceae, Amblystegiaceae, Brachytheciaceae, Lembophyllaceae, Meteoriaceae and Leskeaceae) were recently revealed as polyphyletic [9,27] Despite the Lepyrodontaceae could successfully be grouped as a monophylum with a bootstrap support of 76%, provided that the Stereophyllaceae were included, the clade shows the same characteristics as in the distance tree (Figure 2). With PNJ 963 of 1,634 sequence-structure pairs could be grouped to 30 monophyla

Conclusion

Material and methods

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