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# Nei M, Tajima F, Tateno Y.. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 19: 153-170

(Impact Factor: 1.68). 02/1983; 19(2):153-70. DOI: 10.1007/BF02300753
Source: PubMed

ABSTRACT

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

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• "Phylogenetic relationships between populations were quantified using D A genetic distance (Nei et al. 1983), while individual distances were based on the proportion of shared alleles (Bowcock et al. 1994). The allele sharing distances (D PS ) were also used as the average for all animal pairs within and between subpopulations ( D PS ). "
##### Article: The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection
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ABSTRACT: The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north-western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of various phylogenetic parameters offer a reasonable explanation for underlying evolutionary forces working in the investigated island and mainland sheep breeds under variable natural and artificial selection. More than 60% of total genetic, diversity was allocated to virtually unselected Pramenka strains, and an additional 25% to native moderately selected Graue Gehoernte Heidschnucke and intensively selected Ostfriesische Milchschafe. Some economically very important breeds and strains did not contribute to a pool with maximal genetic diversity, while they play an important role in the cultural heritage of respective countries. © 2015 Blackwell Verlag GmbH.
Full-text · Article · Jan 2016 · Journal of Animal Breeding and Genetics
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• "Genetic affinities among collections were examined with an unrooted neighbor-joining (NJ) analysis of Nei's D A distance (Nei et al. 1983) bootstrapped over all loci (10,000 replications) using POPTREE2 (Takezaki et al. 2010). Genetic relationships among locations were assessed with a Principal Coordinate Analysis (PCoA) of pairwise F ST values generated by FSTAT, using GenAlEx (v.6.41; "
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Full-text · Article · Oct 2015 · Conservation Genetics
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• "The genotyping results were employed to perform a cluster analysis using the PowerMarker software (Liu and Muse, 2005). Nei's genetic distance (Nei et al., 1983) was used, and the support values for the degree of confidence at the nodes of the dendrogram were analyzed by bootstrap re-sampling 1000 times. Phylip 3.69 software (Felsenstein, 1997) was employed to construct the consensus tree and TreeView32 (Page, 1996) to visualize it. "
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