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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Investigation of the bottleneck leading to the domestication of maize
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Diversity of Free-Living and Attached Bacteria in Offshore Western Mediterranean Waters as Depicted by Analysis of Genes Encoding 16S rRNA
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Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci.
TL;DR: It is demonstrated that wolves and coyotes do not show a pattern of genetic differentiation by distance, and gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes.
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Bacterial census of poultry intestinal microbiome
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Journal ArticleDOI
Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779
Astrid Vieler,Guangxi Wu,Chia-Hong Tsai,Blair Bullard,Adam J. Cornish,Christopher M. Harvey,Ida Barbara Reca,Chelsea K. Thornburg,Rujira Achawanantakun,Christopher J. Buehl,Michael S. Campbell,David Cavalier,Kevin L. Childs,Teresa J. Clark,Rahul Deshpande,Erika Erickson,Ann A. Ferguson,Witawas Handee,Que Kong,Xiaobo Li,Bensheng Liu,Steven S. Lundback,Cheng Peng,Rebecca Roston,Sanjaya,Jeffrey P. Simpson,Allan D. TerBush,Jaruswan Warakanont,Simone Zäuner,Eva M. Farré,Eric L. Hegg,Ning Jiang,Min Hao Kuo,Yan Lu,Krishna K. Niyogi,John B. Ohlrogge,Katherine W. Osteryoung,Yair Shachar-Hill,Barbara B. Sears,Yanni Sun,Hideki Takahashi,Mark Yandell,Shin-Han Shiu,Christoph Benning +43 more
TL;DR: The assembly of the 28.7 Mb genome of N. oceanica CCMP1779 is presented and the availability of genomic and transcriptomic data for Nannochloropsis oceanica, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nann Cochloropsis species by a growing academic community focused on this genus.
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.