Detecting individual sites subject to episodic diversifying selection.
Ben Murrell,Ben Murrell,Joel O. Wertheim,Sasha Moola,Thomas Weighill,Konrad Scheffler,Konrad Scheffler,Sergei L. Kosakovsky Pond +7 more
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TLDR
It is found that episodic selection is widespread and it is concluded that the number of sites experiencing positive selection may have been vastly underestimated.Abstract:
The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. We present a mixed effects model of evolution (MEME) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. Using empirical and simulated data, we demonstrate the superior performance of MEME over older models under a broad range of scenarios. We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated.read more
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Detection of a SARS-CoV-2 variant of concern in South Africa.
Houriiyah Tegally,Eduan Wilkinson,Marta Giovanetti,Marta Giovanetti,Arash Iranzadeh,Vagner Fonseca,Vagner Fonseca,Jennifer Giandhari,Deelan Doolabh,Sureshnee Pillay,Emmanuel James San,Nokukhanya Msomi,Koleka Mlisana,Anne von Gottberg,Sibongile Walaza,Mushal Allam,Arshad Ismail,Thabo Mohale,Allison J. Glass,Susan Engelbrecht,Gert U. van Zyl,Wolfgang Preiser,Francesco Petruccione,Alex Sigal,Alex Sigal,Diana Hardie,Gert Marais,Nei yuan Hsiao,Stephen N.J. Korsman,Mary-Ann Davies,Lynn Tyers,Innocent Mudau,Denis York,Caroline Maslo,Dominique Goedhals,Shareef Abrahams,Oluwakemi Laguda-Akingba,Arghavan Alisoltani-Dehkordi,Arghavan Alisoltani-Dehkordi,Adam Godzik,Constantinos Kurt Wibmer,B.T. Sewell,José Lourenço,Luiz Carlos Junior Alcantara,Luiz Carlos Junior Alcantara,Sergei L Kosakovsky Pond,Steven Weaver,Darren P. Martin,Richard J Lessells,Richard J Lessells,Jinal N. Bhiman,Carolyn Williamson,Carolyn Williamson,Tulio de Oliveira,Tulio de Oliveira,Tulio de Oliveira +55 more
TL;DR: A newly arisen lineage of SARS-CoV-2 (designated 501Y.V2) was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province.
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Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
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Journal ArticleDOI
FUBAR : A Fast, Unconstrained Bayesian AppRoximation for inferring selection
Ben Murrell,Sasha Moola,Sasha Moola,Amandla Mabona,Amandla Mabona,Thomas Weighill,Daniel J. Sheward,Sergei L. Kosakovsky Pond,Konrad Scheffler,Konrad Scheffler +9 more
TL;DR: This work presents an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes, and leaves the distribution of selection parameters essentially unconstrained.
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