Cladograms nodes

Fig. 1.7 Evolution of alkaloids in the phylogeny of plants. Using nucleotide sequences of the chloroplast gene rbcL a phylogenetic tree was computed with Maximum Parsimony. A bootstrap cladogram is shown with bootstrap values shown at the nodes. Branches leading to taxa that accumulate alkaloids are shown in bold.

FIGURE 10.11 Pruned consensus tree for Heterandria and Xiphophorus, showing four nodes of agreement obtained by removing unique and conflicting area positions from the two reduced area cladograms shown in Figure 10.9. 

Because many named brachiopod orders appear to be paraphyletic (Fig. 26.1), many suborders (whose exemplars are the terminal taxa here) are likely to be paraphyletic as well, and could thus be ancestral to other higher taxa. PAUP does not allow taxa to occupy internal nodes, because it constructs patterns of character distribution among taxa (cladograms), rather than patterns of evolution over time (evolutionary trees), so it cannot represent these types of relationships directly. ANOP requires that internal nodes be occupied by included taxa, allowing them to function as ancestors, and thus provides an alternative to standard cladistic methods in yet another sense. 

Explaining the result of a PACT analysis begins a two-part process. First, we must distinguish general from unique nodes in an area cladogram. Unique nodes are those produced by an evolutionary event affecting only a single clade. At present, all... 

Ambiguous results in placement of particular taxa in a GAC produced by PACT may arise from such things as polytomies in a taxon-area cladogram, which may indicate that the phylogenetic hypothesis is not well supported or that speciation at the poly-tomous node(s) did not leave a clear temporal and spatial signal, or from differential patterns of dispersal and differentiation amongst multiple clades in response to the same episode of biotic expansion (see Halas et al., 2005 for a discussion). 

One way to assess the placement of ambiguous taxa on the GAC is to attempt to date each event in each taxon-area cladogram and then place ambiguous nodes and taxa in accordance with those estimated ages. At this point, we begin to enter a new level of consilience studies, one in which we look to minimise the difference between data and model, between reason and experience, and between what is and what ought to be. This is because our means of dating evolutionary events rely on inference, models of reason, rather than direct experience. 

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