POY alignment

Once the main clades within the Brachytheciaceae had become more or less stabilized, our main goal was to elucidate the position of taxa not included or not well represented in the previous analyses, and also to find additional arguments for generic and subfamilial placement of some particular taxa. Three methods are involved here (1) evaluation of the molecular synapomorphies in POY alignment, i.e., characteristic indel events and substitutions (2) analysis of the secondary structure of the tmL intron and (3) phylogenetic analysis of a reduced dataset from previous analyses, with some additional taxa. 

Part of POY Alignment, Including Parts of trnL Intron (Positions 112-170), ps6T-H Region (Positions 706-792) and ITS2 (Positions 1280-1453)... 

Positions in the POY Alignment that Support the Placement of Eurhynchiastrum in the Homalothecioideae (HOM), Helicodontioideae (HEL), or in the Brachythecioideae (BRA)... 

FIGURE 6.3 The secondary structure of the tmL intron of Brachythecium cirmsum and secondary structures of P8 regions of Oxyrrhynchium Mans and Donrichardsia macroneuron. Numbers indicate positions in POY alignment where substitutions/indels occur (see supplemental CD). 

Results of POY analysis are especially interesting for comparison because they are produced without the subjective stage of manual aligning. The details of POY analysis are described in Gardiner et al. (2005). 

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