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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Detecting individual sites subject to episodic diversifying selection
PLoS Genetics, Volume 8, No. 7, Article e1002764, Year 2012
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Description
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. © 2012 Murrell et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s001.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s002.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s003.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s004.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s005.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s006.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s007.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s008.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s009.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s010.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s011.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s012.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s013.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s014.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s015.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s016.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s017.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s018.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s019.pdf
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https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s022.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s023.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s024.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3395634/bin/pgen.1002764.s025.pdf
Authors & Co-Authors
Murrell, Ben
South Africa, Tygerberg
South African Medical Research Council
South Africa, Stellenbosch
Stellenbosch University
Wertheim, Joel O.
United States, La Jolla
University of California, San Diego
Moola, Sasha
South Africa, Stellenbosch
Stellenbosch University
Weighill, Thomas
South Africa, Stellenbosch
Stellenbosch University
Scheffler, Konrad
South Africa, Stellenbosch
Stellenbosch University
United States, La Jolla
University of California, San Diego
Pond, Sergei L.Kosakovsky
United States, La Jolla
University of California, San Diego
Statistics
Citations: 1,349
Authors: 6
Affiliations: 3
Identifiers
Doi:
10.1371/journal.pgen.1002764
e-ISSN:
15537404