POPTREEW constructs phylogenetic trees from allele frequency data by using the neighbor-joining method (Saitou and Nei 1987) and the unweighted pair-group method with arithmetic mean (UPGMA) (Sneath and Sokal 1973). Bootstrap test can be performed for phylogenetic trees. POPTREEW also computes heterozygosities and GST, the measures of the extent of genetic variation in a population and genetic differentiation among subdivided populations.
(δμ)2 distance and DSW distance can be used only for microsatellite DNA data, in which alleles are represented by the number of repeats. By contrast, DA, DST, and FST* can be used for any kind of allele frequency data. DST and FST* are computed by the original method without sample size bias correction as well as with the bias correction (Nei 1978, 1987).
- DA distance (Nei et al. 1983)
- Nei's standard genetic distance (DST) (Nei 1972)
- FST* distance (Latter 1972)
- (δμ)2 distance (Goldstein et al. 1995)
- DSW distance (Shriver et al. 1995)
- Average heterozygosities (H) and its standard error for each population
- Number of alleles for each population
- Measures of genetic differentiation among subdivided populations and their standard errors
Values of distance measures 1-5
Heterozygosities and GST, standardized GST, and Jost's D are computed without sample size bias correction (Nei 1973) or with bias correction (Nei and Roychoudhury 1974, Nei 1987).
The web-interface of POPTREEW has an intuituve and simple design, as the Windows-interface of POPTREE2. All the results of the analyses can be obtained by clicking icons and choosing options under pull-down menus. The displayed tree can be printed and changed interactively using icons on the window. The image file in EMF format or the tree file in Newick format can be downloaded.
- GST (Nei 1973),
- Standardized GST (Hedrick 2005)
- Jost's (2008) D
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- Jost L. 2008. GST and its relatives do not measure differentiation. Mol Ecol 17: 4015-4026.
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- Nei M. 1972. Genetic distance between populations. Am Nat 106:283-291.
- Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321-3323.
- Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
- Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
- Nei M, Roychoudhury A. 1974. Sampling variances of heterozygosity and genetic distance. Genetics 76:379-390.
- Nei M, Tajima F, Tateno Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19: 153-170.
- Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
- Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R. 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol 12:914-920.
- Sneath PHA, Sokal RR. 1973. Numerical Taxonomy. W. H. Freeman, San Francisco.
Koichiro Tamura is Professor of Tokyo Metropolitan University, and a primary author of MEGA 6 (Molecular Evolutionary Genetics Analysis), software for evolutionary analyses of DNA and protein sequences.
Masatoshi Nei is Evan Pugh Professor of the Department of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics.
Life Science Research Center, Kagawa University
Ikenobe 1750-1, Mikicho, Kitagun, Kagawa 760-0793
takezaki at med.kagawa-u.ac.jp
December 26, 2013