Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects.

Molecular Biology and Evolution
Michael Lynch

Abstract

Recent advances in sequencing strategies have made it feasible to rapidly obtain high-coverage genomic profiles of single individuals, and soon it will be economically feasible to do so with hundreds to thousands of individuals per population. While offering unprecedented power for the acquisition of population-genetic parameters, these new methods also introduce a number of challenges, most notably the need to account for the binomial sampling of parental alleles at individual nucleotide sites and to eliminate bias from various sources of sequence errors. To minimize the effects of both problems, methods are developed for generating nearly unbiased and minimum-sampling-variance estimates of a number of key parameters, including the average nucleotide heterozygosity and its variance among sites, the pattern of decomposition of linkage disequilibrium with physical distance, and the rate and molecular spectrum of spontaneously arising mutations. These methods provide a general platform for the efficient utilization of data from population-genomic surveys, while also providing guidance for the optimal design of such studies.

References

Nov 1, 1989·The Journal of Psychology·A S Luchins
Oct 1, 1993·The Journal of Social Psychology·A Stahelski, M E Patch
Mar 1, 1993·Genetics·Y X Fu, W H Li
May 16, 1998·Genome Research·R Durbin, S Dear
May 16, 1998·Genome Research·P Richterich
Feb 10, 2000·Molecular Biology and Evolution·J D Wall
Nov 25, 2003·Nature Reviews. Genetics·Michael P H Stumpf, Gilean A T McVean
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Oct 24, 2006·Current Opinion in Genetics & Development·David R Bentley
Nov 17, 2006·Nature·Richard E GreenSvante Pääbo
Nov 18, 2006·Science·James P NoonanEdward M Rubin
Jul 31, 2007·Genome Biology·Susan M HuseDavid Mark Welch
Aug 24, 2007·Proceedings of the National Academy of Sciences of the United States of America·Adrian W BriggsSvante Pääbo
Nov 6, 2007·Molecular Biology and Evolution·Philip L F Johnson, Montgomery Slatkin
Feb 12, 2008·Trends in Genetics : TIG·Elaine R Mardis
Apr 5, 2008·Science·M Thomas P GilbertEske Willerslev
Jun 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michael LynchW Kelley Thomas

❮ Previous
Next ❯

Citations

Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Way SungMichael Lynch
Dec 16, 2010·Bioinformatics·Bernhard HauboldPeter Pfaffelhuber
Oct 15, 2011·Molecular Biology and Evolution·Sen XuMelania E Cristescu
Jul 12, 2013·Molecular Biology and Evolution·Iona M MacLeodMike E Goddard
Nov 17, 2011·Nucleic Acids Research·Michael GundryJan Vijg
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Aug 13, 2009·BMC Bioinformatics·Bjarne Knudsen, Michael M Miyamoto
May 20, 2011·BMC Genomics·André GillesJean-François Martin
Jun 5, 2012·Genetics·Luca FerrettiSebastian Ramos-Onsins
Feb 5, 2014·Nature Reviews. Genetics·Krishna R Veeramah, Michael F Hammer
Nov 30, 2013·Molecular Biology and Evolution·Eunjung HanJohn Novembre
Mar 8, 2014·Bioinformatics·Deren A R Eaton
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Dee R DenverCharles F Baer
Dec 25, 2015·Proceedings of the National Academy of Sciences of the United States of America·Clare D MarsdenKirk E Lohmueller
Mar 29, 2011·Trends in Plant Science·Korbinian Schneeberger, Detlef Weigel
Oct 10, 2013·Molecular Ecology·Luca FerrettiMiguel Pérez-Enciso
May 19, 2010·Animal Genetics·M Pérez-Enciso, L Ferretti
Oct 15, 2013·Molecular Ecology·Ke BiCraig Moritz
Sep 18, 2015·BMC Evolutionary Biology·Huateng Huang, Daniel L Rabosky
Jan 18, 2015·Theoretical Population Biology·Luca Ferretti, Sebástian E Ramos-Onsins
Jul 21, 2016·Molecular Biology and Evolution·Mathieu GautierLaurence Flori
Jul 28, 2016·Molecular Ecology Resources·Emmanuel ParadisKlaus Schliep
Sep 13, 2017·Evolutionary Bioinformatics Online·Javier NavarroSebastián E Ramos-Onsins
Apr 27, 2017·Genome Génome / Conseil National De Recherches Canada·Kasey K PhamRichard C Cronn
Apr 10, 2020·PloS One·Mohammed Ali Al AbriSamantha A Brooks

❮ 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.