Phylogenetic hypotheses, testing

Fig. 2. Schematic representation of phenetic or phylogenetic hypotheses tested immuno-logically. The immunological evidence indicated that the proteins from taxa B and C resemble one another more than they do the protein from taxon A (left-hand side of figure), whereas earlier hypotheses, based on nonmolecular evidence, had suggested the organismal relationships shown on the right-hand side, with C being the outgroup taxon. See Table III and text for examples.

Cartmill, M., Hypothesis testing and phylogenetic reconstruction, Z. Zoo/. Syst. EvoL, 19, 73-96, 1981. 

Phylogenetic analysis provides an evolutionary framework with which we can map the evolution of characters, including those pertinent to parasitism, that define the diversity and biology of extant flatworms, and from which ancestral conditions may be inferred. Alternative scenarios can be tested in terms of how parsimoniously they may map on to the evolutionary hypothesis to hand and through these... 

Belle E.M.S., Smith N., Eyre-Walker A. (2002). Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J. Mol. Evol. 55 356-363. 

Having said all of this, it is important to remember, however (Popper, 1976 Appendix IX), ... that non-statistical theories have as a rule a form totally different from that of the h here described, that is, they are of the form of a universal proposition. The question thus becomes whether systematics, or phylogeny reconstruction, can be construed in terms of a statistical theory that satisfies the rejection criteria formulated by Popper (see footnote 1) and that, in case of favorable evidence, allows the comparison of degree of corroboration versus Fisher s likelihood function. As far as phylogenetic analysis is concerned, I found no indication in Popper s writing that history is subject to the same logic as the test of random samples of statistical data. As far as a metric for degree of corroboration relative to a nonstatistical hypothesis is concerned. Popper (1973 58-59 see also footnote 1) clarified. 

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