A coalescent-based method for detecting and estimating recombination from gene sequences.

Genetics
Gil McVeanPaul Fearnhead

Abstract

Determining the amount of recombination in the genealogical history of a sample of genes is important to both evolutionary biology and medical population genetics. However, recurrent mutation can produce patterns of genetic diversity similar to those generated by recombination and can bias estimates of the population recombination rate. Hudson 2001 has suggested an approximate-likelihood method based on coalescent theory to estimate the population recombination rate, 4N(e)r, under an infinite-sites model of sequence evolution. Here we extend the method to the estimation of the recombination rate in genomes, such as those of many viruses and bacteria, where the rate of recurrent mutation is high. In addition, we develop a powerful permutation-based method for detecting recombination that is both more powerful than other permutation-based methods and robust to misspecification of the model of sequence evolution. We apply the method to sequence data from viruses, bacteria, and human mitochondrial DNA. The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data.

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jan 1, 1996·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R C Griffiths, P Marjoram
Mar 1, 1997·Molecular Biology and Evolution·N C Grassly, E C Holmes
May 15, 1998·Molecular Biology and Evolution·J Maynard Smith, N H Smith
Oct 15, 1998·Proceedings of the National Academy of Sciences of the United States of America·S SuerbaumM Achtman
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·D J ConwayB M Greenwood
Jun 23, 1999·Proceedings of the National Academy of Sciences of the United States of America·M WorobeyE C Holmes
Feb 10, 2000·Molecular Biology and Evolution·J D Wall
Apr 27, 2000·Trends in Ecology & Evolution·J Hey
Jul 13, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·G McGuireM J Prentice
Dec 29, 2000·Nature·M IngmanU Gyllensten
Jun 19, 2001·American Journal of Human Genetics·J K Pritchard, M Przeworski
Jun 23, 2001·Molecular Biology and Evolution·C J BrownP Joyce
Sep 20, 2001·The Journal of General Virology·C H WoelkD W Brown
Oct 19, 2001·Genetics·C Wiuf
Dec 1, 2001·Genetics·P Fearnhead, P Donnelly
May 1, 1964·Mutation Research·H J MULLER

❮ Previous
Next ❯

Citations

Aug 6, 2008·Immunogenetics·Elise HuchardLeslie A Knapp
Sep 6, 2008·PLoS Pathogens·Marie RagonSylvain Brisse
Apr 10, 2003·Evolution; International Journal of Organic Evolution·Peter AndolfattoBrian Charlesworth
Mar 9, 2017·Genetics·Sònia Casillas, Antonio Barbadilla
Aug 25, 2007·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Naiel BisharatRosalind M Harding
Oct 20, 2006·Current Opinion in Genetics & Development·Garrett Hellenthal, Matthew Stephens
Jun 27, 2008·The ISME Journal·Konstantinos T Konstantinidis, Edward F DeLong
Jan 13, 2006·Journal of Evolutionary Biology·I SchaeferM Maraun
Jan 13, 2006·Journal of Molecular Evolution·Francis M Jiggins
Oct 25, 2006·Bioinformatics·Paul Fearnhead
Sep 7, 2007·Environmental Microbiology·Kevin L VerginStephen J Giovannoni
Jul 10, 2008·PloS One·Leonardo de Oliveira MartinsHirohisa Kishino
Jul 15, 2004·American Journal of Human Genetics·Brian C Verrelli, Sarah A Tishkoff
Apr 29, 2005·Molecular Biology and Evolution·Jianbing MuXin-zhuan Su
Feb 14, 2006·Journal of Molecular Evolution·Stéphane De MitaThomas Bataillon
Jul 29, 2004·Genetics·Philippe LemeyAnne-Mieke Vandamme
Dec 8, 2006·Genetics·Xavier Didelot, Daniel Falush
Mar 1, 2006·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaKeith A Crandall
Dec 16, 2006·FEMS Microbiology Reviews·Carina BrehonyMartin C J Maiden

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
D Posada, Keith A Crandall
Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Jesse E Taylor, Bette T Korber
© 2022 Meta ULC. All rights reserved