Question

How can phylogenies be used to test a hypothesis? provide an example.

Answer 1

Probabilistic method of phylogeny reconstruction relies on explicit models of evolution, and provides a powerful framework for testing evolutionary hypotheses.

The likelihood principle provide a direct approach to hypothesis testing in terms of probability.

The likelihood ratio test is a powerful tool for comparing two alternative hypotheses.

Molecular dating analyses, by converting evolutionary distances into absolute ages, allow comparing alternative scenarios of temporal divergence on phylogenetic trees.

The effects of natural selection can be detected by measuring the relative rates of synonymous and nonsynonymous substitutions in multiple nucleotide sequence alignments of protein‐coding genes.

Explicit model of trait evolution supports probabilistic reconstruction of ancestral character state at internal nodes on phylogeny and testing of hypotheses regarding the process of trait evolution.

Phylogenetic comparative method aims to identify adaptation through correlation between species traits and other variables, while accounting for phylogenetic nonindependence of data.

For example, in trees with several species‐rich clades separated by long internal branches (trees that are stemmy), species within each clade will be connected by short branches and, hence, tend to share similar trait values, but the larger distances separating clades will translate into large differences among their trait means, resulting in an overall uneven trait distribution.

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