What are some limitations of phylogenetic trees

Testing and comparing: models, trees and methods

Genes and Family Trees pp 277-304 | Cite as

abstract

How do you actually know which of the reconstruction methods presented in the book to use? Not at all (at least not without further ado). Otherwise we would only present “the” best method here and recommend ignoring the rest. But the whole thing is not that simple, and there are a number of publications on this question, not infrequently more of a philosophical nature. We give an overview in this chapter. If you choose distance and Likelihood-based analyzes, then the question is which of the numerous models from the previous chapters should actually be used? There are various tests for this, which we present here - or you can leave the choice of the model to the analysis itself is at least as important as the reconstruction of the tree itself, because otherwise extremely shaky hypotheses that cannot withstand any test could not be distinguished from the really almost certain core findings of a phylogenetic study. Bayesian methods provide this estimation of the node reliability at the same time, other methods do not - this chapter introduces the common methods.

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© Spectrum Academic Publishing Heidelberg 2009