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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A resolution for the coiling direction paradox in Neogloboquadrina pachyderma.
TL;DR: The genetic evidence demonstrates that coiling direction in N. pachyderma is a genetic trait, heritable through time, and is not a morphological feature reflecting ecophenotypic variation, meaning that the two opposite coiling morphotypes appear to have diverged during the late Miocene and should be considered different species.
Journal ArticleDOI
The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission
Rita Tewari,Ursula Straschil,Ursula Straschil,Alex Bateman,Ulrike Böhme,Inna Cherevach,Peng Gong,Arnab Pain,Arnab Pain,Oliver Billker,Oliver Billker +10 more
TL;DR: A systematic functional analysis of ePKs in the genetically tractable rodent parasite Plasmodium berghei found that 23 e PKs are redundant for asexual erythrocytic parasite development in mice and identifies functional clusters of kinases required for sexual development and sporogony.
Journal ArticleDOI
Detection of toxigenicity by a probe for the microcystin synthetase A gene (mcyA) of the cyanobacterial genus Microcystis: comparison of toxicities with 16S rRNA and phycocyanin operon (Phycocyanin Intergenic Spacer) phylogenies.
TL;DR: The consistent linkage ofmcyC touma1 suggests that mcyC has not been frequently transferred into nontoxic strains via any mechanism involving insertion at random chromosomal locations, which could explain the patchy distribution of toxigenicity among the various Microcystis clades.
of genomic regions associated with phenotypic variation between dog breeds using selection mapping.
Amaury Vaysse,Abhirami Ratnakumar,Thomas Derrien,Erik Axelsson,Gerli Pielberg,Snaevar Sigurdsson,Cindy Lawley +6 more
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Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin.
Alban Ramette,Michele Frapolli,Marion Fischer-Le Saux,Christelle Gruffaz,Jean-Marie Meyer,Geneviève Défago,Laurent Sutra,Yvan Moënne-Loccoz,Yvan Moënne-Loccoz +8 more
TL;DR: In this article, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl(+) Plt(+) strains isolated from tobacco, cotton or wheat on different continents.
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.