Hypothesis testing

The topology of an optimal phylogenetic tree may not necessarily appear as expected. For example, the relationships shown may not agree with traditional taxonomical classifications. The Kishino–Hasegawa (KH) test (Kishino & Hasegawa, 1989) can be used to test the likelihood of alternative phylogenetic hypotheses. The KH test utilised here was based on the resampling estimated log-likelihoods (RELL) method (Kishino et al., 1990) (as implemented in PAUP*) a variant of the non-parametric bootstrap that is computationally less demanding (Schmidt, 2009). In the test, the likelihood score of the optimal tree produced from the original phylogenetic analysis is compared to that of a tree in which the topology has been constrained to fit an alternative hypothesis. For example, certain groups of taxa may fall in independent groups in the optimal phylogenetic tree, but in a large monophyly in taxonomical classifications (see chapter 5). In this case the likelihood scores of the optimal tree, and a tree in which the taxa had been constrained to form a monophyly would be compared. If the likelihood score for the optimal tree is significantly better than for

the alternative topology, the alternative hypothesis can be rejected (see appendix 9.5 for details).

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3 Genotypic variability in the planktonic