POPTREEW: Web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities

Molecular Biology and Evolution

Volumn 31, Issue 6, 2014, Pages 1622-1624

  Takezaki, Naoko ^a   Nei, Masatoshi ^b   Tamura, Koichiro ^c  

^a KAGAWA UNIVERSITY   (Japan)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

allele frequency data; genetic differentiation; genetic diversity; microsatellite DNA; population tree; web interface

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ARTICLE; COMPUTER PROGRAM; GENE FREQUENCY; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; HETEROZYGOSITY; MUTATION RATE; PHYLOGENETIC TREE; PHYLOGENY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; EVOLUTION; GENETIC DRIFT; INTERNET;

BIOLOGICAL EVOLUTION; GENE FREQUENCY; GENETIC DRIFT; GENETIC VARIATION; GENETICS, POPULATION; INTERNET; MODELS, GENETIC; PHYLOGENY; SOFTWARE;

EID: 84901435187     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu093     Document Type: Article

References (21)

1. Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nat Rev Genet. 11:697-709.
2. Brito PH, Edwards SV. 2009. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439-455.
3. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
4. Goldstein DB, Ruiz Linares A, Cavalli-Sforza LL, Feldman MW. 1995. Genetic absolute dating based on microsatellites and the origin and modern humans. Proc Natl Acad Sci USA. 92: 6723-6727.
5. Hedrick PW. 2005. A standardized genetic differentiation measure. Evolution 59:1633-1638.
6. Jost L. 2008. GST and its relatives do not measure differentiation. Mol Ecol. 17:4015-4026.
7. Latter BDH. 1972. Selection in finite populations with multiple alleles. III. Genetic divergence with centripetal selection and mutation. Genetics 70:475-490.
8. Meirmans PG, Hedrick PW. 2011. Assessing population structure: FST and related measures. Mol Ecol Resour. 11:5-18.
9. Nei M. 1972. Genetic distance between populations. Am Nat. 106: 283-291.
10. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA. 70:3321-3323.
11. Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Ann Hum Genet. 47:253-259.
12. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
13. NeiM, Roychoudhury A. 1974. Sampling variances of heterozygosity and genetic distance. Genetics 76:379-390.
14. Nei M, Tajima F, Tateno Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol. 19:153-170.
15. Rousset F. 2008. GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour. 8: 103-106.
16. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4: 406-425.
17. Schlötterer C. 2004. The evolution and molecular markers-just a matter of fashion? Nat Rev Genet. 5:63-69.
18. 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.
19. Sneath PHA, Sokal RR. 1973. Numerical taxonomy. San Francisco (CA): W.H. Freeman.
20. Takezaki N, Nei M, Tamura K. 2010. POPTREE2: software for constructing population trees from allele frequency data and computing some other population statistics with Windows interface. Mol Biol Evol. 27:747-752.
21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0.Mol Biol Evol. 30:2725-2729.