Leaf-labelled trees are widely used to describe evolutionary relationships, particularly in biology. In this setting, extant species label the leaves of the tree, while the internal vertices correspond to ancestral species. Various techniques exist for reconstructing these evolutionary trees from data, and an important problem is to determine how "far apart" two such reconstructed trees are from each other, or indeed from the true historical tree. To investigate this question requires tree metrics, and these can be induced by operations that rearrange trees locally. Here we investigate three such operations: nearest neighbour interchange (NNI), subtree prune and regraft (SPR), and tree bisection and reconnection (TBR). The SPR operation is of particular interest as it can be used to model biological processes such as horizontal gene transfer and recombination. We count the number of unrooted binary trees one SPR from any given unrooted binary tree, as well as providing new upper and lower bounds for the diameter of the adjacency graph of trees under SPR and TBR. We also show that the problem of computing the minimum number of TBR operations required to transform one tree to another can be reduced to a problem whose size is a function just of the distance between the trees (and not of the size of the two trees), and thereby establish that the problem is fixed-parameter tractable.
The most common permutation operation is Tree Bisection and Reconnection (TBR) REF .
Subtree Transfer Operations and their Induced Metrics on Evolutionary Trees
Annals of Combinatorics
Mathematics