In article nd2 at nntp3.u.washington.edu, dmt at u.washington.edu (John Blankenship) writes:
> I'm currently using GCG 8.1, and the Distances program does a very nice
> job of calculating distances by several methods. My question concerns the
> methods it uses, none of which I am familiar with. They include the
> following:
>> *Kimura's two parameter method
> *Tajima-Nei's method
> *Jin-Nei's gamma distance method
> *Jukes-Cantor method
>> I've found the 1990 paper by Tajima and Nei, but it doesn't shed much
> light on what techniques are most appropriate/valid for a certain type of
> sequence. If someone could point me to a site, or journal discussing the
> pros and cons of each (or some of them), or pass along any pointers, I'd
> *really* appreciate it.
>> John Blankenship
These distance computation methods differ in the evolutionary model they
assume to correct for multiple substitutions. Attempts to compare the
assumed models and to choose the best one for a given data set were made
only recently (Works of Zarkikh, Yang and Goldman, Rhzetsky and Nei), and no
standard answer can currently be given.
Roughly :
Jukes-Cantor's method assumes all kinds of substitutions (A->C, A->G, ... T->G)
equivalent.
Kimura's method allows for unequal transition/transversion and no other difference.
Tajima-Nei's method allows for unequal base composition WITHIN sequences.
Jin-Nei's method allows for unequal substitution rates between sites.
By the way, the commonly called Tajima-Nei's method is that of Tajima and Nei 1984,
not 1990.
Some references :
Kimura (1980) A simple method for estimating evolutionary rates of base substitution
through comparative studies of nucleotide sequences. Journal of Molecular
Evolution 16:111-120
Tajima and Nei (1984) Estimation of evolutionary distance between nucleotide sequences.
Molecular Biology and Evolution 1:269-285
Jin and Nei (1990) Limitations of the evolutionary parsimony method of phylogenetic
analysis. Molecular Biology and Evolution
Gojobori et al. (1990) Statistical methods for estimating sequence
divergence, Methods in Enzymology 183: 531-550
Zharkikh (1994) Estimation of evolutionary distances between nucleotide
sequences, Journal of Molecular Evolution 39: 315-329
Rzhetsky and Nei (1995) Tests of applicability of several substitution
models for DNA sequence data, Molecular Biology and Evolution 12: 131-151
Yang, Goldman, Friday (1994) Comparison of models for nucleotide substitution
used in maximum likelihood phylogenetic estimation. Molecular Biology and Evolution
11: 316-324
Hope this helps.
