So, what about the molecular clock hypothesis
PPT – Molecular Clock Hypothesis PowerPoint …
(The Molecular Clock Hypothesis means that all tips of the tree are equidistant from the root of the tree.) two log-likelihood values are calculated and displayed, one with and one without the clock hypothesis.
Molecular clock hypothesis - Revolvy
The molecular clock hypothesis originally rested on the assumption of rate constancy across lineages of a phylogeny, which would produce an approximately steady rate of accumulation of deoxyribonucleic acid or amino acid changes through time. This assumption has been questioned on the basis of increasingly large data sets, which have shown significant variability of rates in evolutionary lineages. To address this issue, tests have been developed to examine whether rates of molecular evolution vary significantly among taxonomic groups or phylogenetic lineages. Two major types of tests exist: those based on comparisons of genetic distances and those based on likelihood ratios. The first ones compare genetic distances between two species (or groups of species) relative to an outgroup; the latter ones compare maximum likelihood values for the same phylogeny calculated with and without the constant rate assumption. In those cases where the rate constancy assumption is violated, modern molecular clocks (relaxed clocks) are now being applied to implement the rate heterogeneity in the time estimation process.
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Takezaki N, Rzhetsky A and Nei M (1995) Phylogenetic test of the molecular clock and linearized tree. Molecular Biology and Evolution 12: 823–833.