Glossary of terms used in Phylogeny Reconstruction.
N
Nearest
Neighbor Interchange (NNI) This is a heuristic algorithm for
searching through treespace. It proceeds by juxtaposing the positions
of neighbors on a phylogenetic tree. If the resulting tree is better,
then it is retained. This algorithm is quite a gentle perturbation
of the tree and is inferior to either SPR
or TBR in terms of completeness of the searsh. On average it will
be quicker than SPR or TBR.
Nexus-format
This is a format that has been published in: Maddison,
D.R., D.L. Swofford, and W.P. Maddison. Nexus: An extensible file format
for systematic information. Systematic Biology 46(4) 1997: 590-621.
Neighbor-Joining (NJ) This is
an algorithm for inferring a branching tree diagram from a distance
matrix. It works by successively clustering pairs of taxa together.
It is related to the UPGMA method of inferring a branching diagram from
a distance matrix. Unlike the UPGMA method, NJ can facilitate contemporary
tips of uneven length. This makes it a more appropriate tree reconstruction
method than UPGMA in thos instances when evolution has not proceeded in
a strictly clock-like fashion.
Newick format
This is a method of representing trees using nested parentheses. Two sister
taxa are enclosed in a pair of parentheses, separated by a comma.
If the closest relative of these two taxa is another single taxon, then
all three taxa will be enclosed within another pair of parentheses.
In this way, a complete tree description may be built. This format
is also called the New Hampshirt format. Apparently it is named after
a restaurant in New Hampshire, USA.
NNI see Nearest Neighbor
Interchange.
Non-synonymous substitutions
Substitutions
that occur in protein-coding genes that result in a change at the amino
acid level. The ratio of non-synonymous to synonymous substitutions
is sometimes used to detect positive
Darwinian selection.
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