The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TLDR
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.Abstract:
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.read more
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Hot L1s account for the bulk of retrotransposition in the human population
Brook Brouha,Joshua Schustak,Richard M. Badge,Richard M. Badge,Sheila Lutz-Prigge,Alexander H. Farley,John V. Moran,Haig H. Kazazian +7 more
TL;DR: The data indicate that most L1 retrotransposition in the human population stems from hot L1s, with the remaining elements playing a lesser role in genome plasticity.
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Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Yong Wang,Jill Waters,Marco L. Leung,Anna K. Unruh,Whijae Roh,Xiuqing Shi,Ken Chen,Paul Scheet,Selina Vattathil,Han Liang,Asha S. Multani,Hong Zhang,Rui Zhao,Franziska Michor,Funda Meric-Bernstam,Nicholas Navin +15 more
TL;DR: The data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded, which has important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
Journal ArticleDOI
Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake Grevelingen
Yvonne A. Lipsewers,Ellen C. Hopmans,Filip J. R. Meysman,Jaap S. Sinninghe Damsté,Laura Villanueva +4 more
TL;DR: The simultaneous presence and activity of organoheterotrophic Denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.
Journal ArticleDOI
Subtilases: the superfamily of subtilisin-like serine proteases.
TL;DR: Details of more than 100 new subtilases discovered in the past five years are summarized, and amino acid sequences of their catalytic domains are compared in a multiple sequence alignment.
Journal ArticleDOI
Selecting the best-fit model of nucleotide substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: It is shown here that a best-fit model can be readily identified and should be routine in any phylogenetic analysis that uses models of evolution.
References
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Book
Molecular Evolutionary Genetics
TL;DR: 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.
Book
Principles of numerical taxonomy
Robert R. Sokal,P.H.A. Sneath +1 more
TL;DR: The authors continued the story of psychology with added research and enhanced content from the most dynamic areas of the field, such as cognition, gender and diversity studies, neuroscience and more, while at the same time using the most effective teaching approaches and learning tools.