Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.

Genome Research
Ines HellmannRasmus Nielsen

Abstract

We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show that the elevated diversity in telomeric regions is mainly due to elevated mutation rates and not due to decreased levels of background selection. However, we find indications that telomeres as well as centromeres experience greater impact from natural selection than intrachromosomal regions. Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate.

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Jun 20, 1991·Nature·J H McDonald, M Kreitman
May 1, 1987·Genetics·R R HudsonM Aguadé
Aug 1, 1993·Genetics·B CharlesworthD Charlesworth
Jan 1, 1995·Annual Review of Genetics·P Donnelly, S Tavaré
Feb 22, 2001·Science·J C VenterX Zhu
Dec 26, 2001·Cytokine & Growth Factor Reviews·Nikki ChengJin Chen
Mar 29, 2002·Nature Genetics·Scott D Briggs, Brian D Strahl
Jun 8, 2002·Nature Genetics·Augustine KongKari Stefansson
Jul 20, 2002·Trends in Genetics : TIG·Martin J Lercher, Laurence D Hurst
Oct 26, 2002·Genetics·Gilean A T McVean
Dec 25, 2002·Critical Reviews in Oral Biology and Medicine : an Official Publication of the American Association of Oral Biologists·D P Dickinson
May 13, 2003·American Journal of Human Genetics·Ines HellmannMolly Przeworski
Aug 9, 2003·American Journal of Human Genetics·Yoav GiladSvante Pääbo
Dec 13, 2003·Science·Andrew G ClarkMichele Cargill
Jan 6, 2004·Genetics·Hideki Innan, Wolfgang Stephan
Jan 7, 2004·Genome Research·Arek KasprzykEwan Birney
Mar 11, 2004·Journal of Molecular Evolution·Stanley A SawyerDaniel L Hartl
May 5, 2005·PLoS Biology·Rasmus NielsenMichele Cargill
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Sep 1, 2005·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·H RiethmanS Paul
Sep 2, 2005·Nature·UNKNOWN Chimpanzee Sequencing and Analysis Consortium
Sep 6, 2005·Genome Research·Ines HellmannSusan E Ptak
Oct 21, 2005·Nature·Peter Andolfatto
Oct 21, 2005·Nature·Carlos D BustamanteAndrew G Clark
Dec 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Benjamin F VoightAnna Di Rienzo
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Feb 28, 2006·Bioinformatics·Fan HsuDavid Haussler
Sep 7, 2006·Genome Research·Philip L F Johnson, Montgomery Slatkin
Sep 9, 2006·Journal of Mathematical Biology·Carsten Wiuf

❮ Previous
Next ❯

Citations

May 19, 2011·Nature Reviews. Genetics·Rasmus NielsenYun S Song
Sep 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Antoine BrancaPeter Tiffin
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wei-Chun Kao, Yun S Song
Dec 16, 2010·Bioinformatics·Bernhard HauboldPeter Pfaffelhuber
Jan 11, 2013·The Journal of Heredity·Brian Charlesworth
Jan 5, 2011·Molecular Biology and Evolution·Asher D Cutter, Alan M Moses
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Oct 6, 2009·Genome Research·Adam Siepel
Apr 13, 2011·Genome Research·Wei-Chun KaoYun S Song
Dec 8, 2009·Science·Michael A GoreEdward S Buckler
Jul 10, 2013·Annual Review of Genomics and Human Genetics·Wenqing Fu, Joshua M Akey
Mar 24, 2012·BMC Genomics·Tamara HoferLaurent Excoffier
Mar 19, 2013·BMC Genomics·Anna Esteve-CodinaMiguel Pérez-Enciso
Jan 17, 2009·PLoS Genetics·James J CaiDmitri A Petrov
May 9, 2009·PLoS Genetics·Graham McVickerPhil Green
Jun 9, 2009·PLoS Genetics·Guy SellaPeter Andolfatto
Feb 9, 2010·PLoS Genetics·David EnardHugues Roest Crollius
Nov 6, 2008·Genetics·Rong JiangPaul Marjoram
Jun 5, 2012·Genetics·Luca FerrettiSebastian Ramos-Onsins
Jun 21, 2012·Genetics·Graham Coop, Peter Ralph
Jun 8, 2012·Genetics·Charles H LangleyDavid J Begun
Feb 5, 2014·Nature Reviews. Genetics·Krishna R Veeramah, Michael F Hammer
Feb 19, 2011·Science·Ryan D HernandezMolly Przeworski
Jul 9, 2014·Annual Review of Genomics and Human Genetics·Laure SégurelMolly Przeworski
Oct 4, 2013·BMC Bioinformatics·Thorfinn Sand KorneliussenRasmus Nielsen
Dec 27, 2011·Molecular Phylogenetics and Evolution·John E McCormackRobb T Brumfield
Oct 10, 2013·Molecular Ecology·Luca FerrettiMiguel Pérez-Enciso

❮ 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.