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
Citations
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Quantification of biofilm structures by the novel computer program COMSTAT.
Arne Heydorn,Alex Toftgaard Nielsen,Morten Hentzer,Claus Sternberg,Michael Givskov,Bjarne Kjær Ersbøll,Søren Molin +6 more
TL;DR: Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration, whereas surface to volume ratio increased with higher citrate concentrations.
Journal ArticleDOI
Autoantibodies against type I IFNs in patients with life-threatening COVID-19.
Paul Bastard,Paul Bastard,Paul Bastard,Lindsey B. Rosen,Qian Zhang,Eleftherios Michailidis,Hans-Heinrich Hoffmann,Yu Zhang,Karim Dorgham,Quentin Philippot,Quentin Philippot,Jérémie Rosain,Jérémie Rosain,Vivien Béziat,Vivien Béziat,Vivien Béziat,Jeremy Manry,Jeremy Manry,Elana Shaw,Liis Haljasmägi,Pärt Peterson,Lazaro Lorenzo,Lazaro Lorenzo,Lucy Bizien,Lucy Bizien,Sophie Trouillet-Assant,Kerry Dobbs,Adriana Almeida de Jesus,Alexandre Belot,Anne Kallaste,Emilie Catherinot,Yacine Tandjaoui-Lambiotte,Jérémie Le Pen,Gaspard Kerner,Gaspard Kerner,Benedetta Bigio,Yoann Seeleuthner,Yoann Seeleuthner,Rui Yang,Alexandre Bolze,András N Spaan,András N Spaan,Ottavia M. Delmonte,Michael S. Abers,Alessandro Aiuti,Giorgio Casari,Vito Lampasona,Lorenzo Piemonti,Fabio Ciceri,Kaya Bilguvar,Richard P. Lifton,Richard P. Lifton,Marc Vasse,David M. Smadja,Mélanie Migaud,Mélanie Migaud,Jérôme Hadjadj,Benjamin Terrier,Darragh Duffy,Lluis Quintana-Murci,Lluis Quintana-Murci,Diederik van de Beek,Lucie Roussel,Donald C. Vinh,Stuart G. Tangye,Stuart G. Tangye,Filomeen Haerynck,David Dalmau,Javier Martinez-Picado,Javier Martinez-Picado,Petter Brodin,Petter Brodin,Michel C. Nussenzweig,Michel C. Nussenzweig,Stéphanie Boisson-Dupuis,Stéphanie Boisson-Dupuis,Stéphanie Boisson-Dupuis,Carlos Rodríguez-Gallego,Guillaume Vogt,Trine H. Mogensen,Trine H. Mogensen,Andrew J. Oler,Jingwen Gu,Peter D. Burbelo,Jeffrey I. Cohen,Andrea Biondi,Laura Rachele Bettini,Mariella D'Angiò,Paolo Bonfanti,Patrick Rossignol,Julien Mayaux,Frédéric Rieux-Laucat,Eystein S. Husebye,Eystein S. Husebye,Eystein S. Husebye,Francesca Fusco,Matilde Valeria Ursini,Luisa Imberti,Alessandra Sottini,Simone Paghera,Eugenia Quiros-Roldan,Camillo Rossi,Riccardo Castagnoli,Daniela Montagna,Amelia Licari,Gian Luigi Marseglia,Xavier Duval,Jade Ghosn,Hgid Lab,Covid Clinicians,Covid-Storm Clinicians§,CoV-Contact Cohort§,Amsterdam Umc Covid Biobank,Amsterdam Umc Covid Biobank,Amsterdam Umc Covid Biobank,Covid Human Genetic Effort,John S. Tsang,Raphaela Goldbach-Mansky,Kai Kisand,Michail S. Lionakis,Anne Puel,Anne Puel,Anne Puel,Shen-Ying Zhang,Shen-Ying Zhang,Shen-Ying Zhang,Steven M. Holland,Guy Gorochov,Emmanuelle Jouanguy,Emmanuelle Jouanguy,Emmanuelle Jouanguy,Charles M. Rice,Aurélie Cobat,Aurélie Cobat,Aurélie Cobat,Luigi D. Notarangelo,Laurent Abel,Laurent Abel,Laurent Abel,Helen C. Su,Jean-Laurent Casanova +140 more
TL;DR: A means by which individuals at highest risk of life-threatening COVID-19 can be identified is identified, and the hypothesis that neutralizing auto-Abs against type I IFNs may underlie critical CO VID-19 is tested.
Journal ArticleDOI
Bacterial Diversity in Human Subgingival Plaque
Bruce J. Paster,Bruce J. Paster,Susan K. Boches,Jamie L. Galvin,Rebecca E. Ericson,C. N. Lau,Valerie A. Levanos,Ashish Sahasrabudhe,Floyd E. Dewhirst,Floyd E. Dewhirst +9 more
TL;DR: The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria.
Journal ArticleDOI
Mash: fast genome and metagenome distance estimation using MinHash.
Brian D. Ondov,Todd J. Treangen,Páll Melsted,Adam B. Mallonee,Nicholas H. Bergman,Sergey Koren,Adam M. Phillippy +6 more
TL;DR: Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections.
Journal ArticleDOI
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
TL;DR: A statistical model for inferring the patterns of population splits and mixtures in multiple populations and it is shown that a simple bifurcating tree does not fully describe the data; in contrast, many migration events are inferred.
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.