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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.

The second method often involves placing a time constraint on a particular node of the tree based on prior information about the biogeography of the species (for example, we might know one species likely diverged from another after a mountain range formed: the age of the mountain range would be our constraints).Alternatively, we might include a fossil in the phylogeny which has been radiocarbon dated and place an absolute age on that instead.In regards to the former method, mutation rates describe how fast genetic differentiation accumulates as evolution occurs along the branch.Although mutations gradually accumulate over time, the rate at which they occur can depend on a variety of factors (even including the of the organism).Note that the tips are all in the same positions in these two trees.

Typically, it’s easier to read a tree from within the phylogenetic tree.A phylogeny describes the relationships of tips (i.e.which are more closely related than others; referred to as the topology), how different these tips are (the length of the branches) and the order they separated in time (separations shown by the nodes).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).We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data.