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Molecular Evolutionary Genetics
TLDR
Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.Abstract:
Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.read more
Citations
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Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Arlequin (version 3.0): An integrated software package for population genetics data analysis
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Journal ArticleDOI
Linkage disequilibrium and fingerprinting in sugar beet
T. Kraft,M. Hansen,N.-O. Nilsson +2 more
TL;DR: A low but significant level of linkage disequilibrium was found for unlinked markers and only for very tigthly linked (<3 cM) markers was this level substantially higher, implying that little is gained in utilising the map position of the markers in fingerprinting applications.
Journal ArticleDOI
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
TL;DR: SeaView version 4 combines all the functions of the widely used programs SeaView and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.
Journal ArticleDOI
Population growth makes waves in the distribution of pairwise genetic differences.
Alan R. Rogers,Henry Harpending +1 more
TL;DR: In this article, the authors present histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1,.... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate.
References
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Evidence for higher rates of nucleotide substitution in rodents than in man (molecular clock/generation-time effect/synonymous substitution/nonsynonymous substitution/neutral theory)
Chung-I Wu,Wen-Hsiung Lit +1 more
TL;DR: Rodents evolve significantly faster than humans as discussed by the authors, and the ratio of the number of nucleotide substitutions in the rodent lineage to that in the human lineage since their divergence is 2.0 for synonymous substitutions and 1.3 for nonsynonymous substitutions.
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