POPTREE2 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 tests can be performed for phylogenetic trees. POPTREE2 also computes heterozygosities and GST, the measures of the extent of genetic variation in a population and genetic differentiation among subdivided populations.
- 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)
δμ2 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).
- 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
- GST (Nei 1973),
- Standardized GST (Hedrick 2005)
- Jost's (2008) D
- 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).
Windows-interface of POPTREE2 has an intuituve and simple design. All the results of the analyses can be obtained by clicking icons and choosing options under pull-down menus. The phylogenetic trees are displayed in a readily publishable quality. The displayed tree can be printed, copied to other applications, and changed interactively using icons on the window.
- Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW. 1995. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92:6723-6727.
- Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59: 1633-1638.
- Jost L. 2008. GST and its relatives do not measure differentiation. Mol Ecol 17: 4015-4026.
- Latter BDH. 1972. Selection in finite populations with multiple alleles. III. Genetic divergence with centripetal selection and mutation. Genetics 70:475-490.
- 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.
Naoko Takezaki
Life Science Research Center, Kagawa University
Ikenobe 1750-1, Mikicho, Kitagun, Kagawa 760-0793
Japan
takezaki at med.kagawa-u.ac.jp
December 26, 2013
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