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Neighbor-Joining Method. Advantages Fast and thus suited for large datasets and for bootstrap analysis Permits lineages with largely different branch lengths Permits correction for multiple substitutions Disadvantages Sequence information is reduced Gives only one possible tree
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Neighbor-Joining Method • Advantages • Fast and thus suited for large datasets and for bootstrap analysis • Permits lineages with largely different branch lengths • Permits correction for multiple substitutions • Disadvantages • Sequence information is reduced • Gives only one possible tree • Strongly dependent on the model of evolution used • Principle • find pairs of operational taxonomic units (neighbors) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree • Keeps track of nodes on a tree • Constructed by linking the least-distant pair of nodes in the distance matrix • When two nodes are linked, their common ancestral node is added to the tree and the terminal nodes are removed • Pruning converts the newly added common ancestor into a terminal node on a tree of reduced size • At each stage, two terminal nodes are replaced by one new node • Process is complete when two nodes remain, separated by a single branch. • Does not require that all lineages have diverged by equal amounts • Suited for datasets comprising lineages with largely varying rates of evolution. (Saitou and Nei, 1987)
