Character-based phylogenetic analysis

An overall biogenetic scheme for the 3-alkylpiperidine alkaloids isolated from sponges in the order Haplosclerida. The numbers indicate molecular structures used as character states in the phylogenetic analysis based on molecule types presented in section 4.3. 

The third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

In what way can the phylogenetic history of the group best be reconstructed This question can tn asked for its own scientific value but also in order to use the answer in the classification (see p. 7 under nr. 4). Phylogenetical research can be done on different taxon uni cal levels and with different means. The factual data on which to base the phylogenetical hypothesis are the same as those emerging from the character analysis that is used in classification. 

FIGURE 4.1 Phylogenetic tree based on De Weerdt s [88] morphological character analysis. Black squares represent (syn)apomorphic characters of clades and terminal taxa. The tree is the result of a reanalysis of De Weerdt s data using PAUP 3.1.1 [87] (single most parsimonious tree). The taxon-character matrix is given in Table 4.2. 

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