Phylogenetics and dating with

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We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.

One of these limitations we often want to explore in better detail is the estimation of the divergence times within the phylogeny; we want to know exactly two evolutionary lineages (be they genera, species or populations) separated from one another.Even two phylogenetic trees with identical topology can give very different results if they vary in their branch lengths (see the above Figure).The second category determines how likely mutations are between one particular type of nucleotide and another.Different trees can share some traits but not others: the red box shows two phylogenetic trees with similar branch lengths (all of the branches are roughly the same) but different topology (the tips connect differently: A and B are together on the left but not on the right, for example).Conversely, two trees can have the same topology, but show differing lengths in the branches of the same tree (blue box).

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