Accuracy of estimated phylogenetic trees from molecular data

By Y. Tateno, Masatoshi Nei, F. Tajima. Journal of Molecular Evolution, 2005

1,037 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/07f891a75ea277fce8e2c200710f3e21e596e77a

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Citations in the corpus

Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. (2002, methodology): “The cluster analysis was performed with the distance matrix using the UPGMA method (Nei et al. 1983).”
Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China (2012, methodology): “…of alleles per locus (N A ), observed heterozygosity (H O ), Shannon's information index (I), number of private alleles (N PA ), genetic distance (Nei et al. 1983), and pair-wise F ST among the six geographical populations were all estimated with POPGENE version 1.31 developed by Yeh et al.…”
Reconstructing routes of invasion using genetic data: why, how and so what? (2010, methodology): “…and tree algorithms in the context of invasion biology: microsatellite loci, the genetic distances proposed by Cavalli-Sforza & Edwards (1967) and Nei et al. (1983) and the neighbour-joining algorithm for tree construction (NJ, Saitou & Nei 1987) (see Takezaki & Nei 1996) for a comparative study…”
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. (2010, methodology): “The distance measures computed by POPTREE2 and used for phylogeny construction are 1) D A distance (Nei et al. 1983), 2) Nei’s standard genetic distance ( D ST ) (Nei 1972), 3) F (cid:1) ST distance (Latter 1972) (added in the new version), 4) ( dl ) 2 distance (Goldstein et al. 1995), and 5) D SW…”
Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994 (2001, methodology): “We also estimated pairwise genetic distances among populations using DA (Nei et al. 1983), a nonSMM (stepwise mutation model) estimate of genetic distance with low variance relative to other nonSMM measures (Takezaki and Nei 1996; see also Ruzzante 1998).”
GENECLASS2: a software for genetic assignment and first-generation migrant detection. (2004, methodology): “…distances have been implemented: Nei’s standard genetic distance (Nei 1972), Nei’s minimum genetic distance (Nei 1973 in Nei 1987), Nei’s Da distance (Nei et al. 1983), Chord distance (Cavalli-Sforza and Edwards 1967), and a distance taking into account the allele size of microsatellite markers…”
Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers (2011, neutral): “Nei’s genetic distance (Nei et al. 1983) was calculated and used for construction of unrooted phylogeny based on neighborjoining method.”
Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL (2008, methodology): “Cluster analysis was performed according to the unweighted pair group mean algorithm (UPGMA) with the Nei et al. (1983) similarity index using Power Marker version 3.25 (Liu and Muse, 2005).”
Both geometric morphometric and microsatellite data consistently support the differentiation of the Apis mellifera M evolutionary branch (2011, methodology): “Neighbor-joining tree (bootstrap with 1000 iterations (A7, A28, A113, B124, A24, A88) using DA distance matrix (Nei et al., 1983) based on data from 6 DNA microsatellite loci of populations of A, M, and C evolutionary branches (Estoup et al.”
Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia) (2010, methodology): “…the utility of the microsatellites for tuatara phylogenetic analysis, a minimum evolution tree of individuals as well as populations (not shown) was constructed in MEGA 3.1 (Kumar et al. 2004) using Nei’s Da distance (Nei et al. 1983) calculated with MSA 4.05 (Dieringer and Schlötterer 2003).”
Genetic variability and structure of common carp (Cyprinus carpio) populations throughout the distribution range inferred from allozyme, microsatellite and mitochondrial DNA markers (2003, methodology): “For microsatellite loci, the DA distances (Nei et al., 1983) among pairs of populations were calculated, a NJ dendrogram was constructed and population grouping was tested by bootstrapping analysis (1000 replicates) using the DISPAN program (Ota, 1993).”
Sheep resources of Ethiopia : genetic diversity and breeding strategy (2008, methodology): “Genetic characterization has recently been the method of describing and classifying livestock breeds using measures of genetic distances between populations (Cavalli-Sforza and Edwards, 1967; Nei, 1972; Nei et al., 1983).”