Soft sweeps II--molecular population genetics of adaptation from recurrent mutation or migration

Molecular Biology and Evolution
Pleuni S Pennings, Joachim Hermisson

Abstract

In the classical model of molecular adaptation, a favored allele derives from a single mutational origin. This ignores that beneficial alleles can enter a population recurrently, either by mutation or migration, during the selective phase. In this case, descendants of several of these independent origins may contribute to the fixation. As a consequence, all ancestral haplotypes that are linked to any of these copies will be retained in the population, affecting the pattern of a selective sweep on linked neutral variation. In this study, we use analytical calculations based on coalescent theory and computer simulations to analyze molecular adaptation from recurrent mutation or migration. Under the assumption of complete linkage, we derive a robust analytical approximation for the number of ancestral haplotypes and their distribution in a sample from the population. We find that so-called "soft sweeps," where multiple ancestral haplotypes appear in a sample, are likely for biologically realistic values of mutation or migration rates.

References

Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Nov 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·S E AntonarakisA Chakravarti
Jun 1, 1995·Genetics·N H Barton
Apr 14, 2000·American Journal of Human Genetics·M T Hamblin, A Di Rienzo
Sep 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bettina HarrChristian Schlötterer
Jun 18, 2004·Molecular Biology and Evolution·Jay F StorzMichael W Nachman
Jul 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Hideki Innan, Yuseob Kim
Aug 11, 2004·Theoretical Population Biology·Richard Durrett, Jason Schweinsberg
Aug 25, 2004·Science·Cally RoperTim Anderson
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
Mar 15, 1955·Proceedings of the National Academy of Sciences of the United States of America·M Kimura

❮ Previous
Next ❯

Citations

Nov 16, 2010·Journal of Mathematical Biology·G EwingJ Rudolf
Mar 2, 2011·Journal of Mathematical Biology·Cornelia Pokalyuk
May 31, 2012·Bulletin of Mathematical Biology·Sivan Leviyang
Oct 1, 2013·Trends in Ecology & Evolution·Philipp W Messer, Dmitri A Petrov
Sep 18, 2010·Nature Reviews. Genetics·Fred W AllendorfGordon Luikart
Nov 17, 2012·Nature Reviews. Genetics·Carrie F Olson-ManningThomas Mitchell-Olds
Dec 26, 2008·Briefings in Bioinformatics·Yuseob Kim, Thomas Wiehe
Sep 19, 2008·Molecular Biology and Evolution·John Wakeley
Aug 31, 2010·Molecular Biology and Evolution·Angela M HancockAnna Di Rienzo
Oct 30, 2012·Molecular Biology and Evolution·Ryan J Haasl, Bret A Payseur
Jul 21, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Angela M HancockAnna Di Rienzo
Feb 16, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Pascale GerbaultMark G Thomas
Dec 28, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Michael W Nachman, Bret A Payseur
Dec 28, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jeffrey L FederPatrik Nosil
Feb 9, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·John Novembre, Eunjung Han
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Apr 24, 2010·Cold Spring Harbor Symposia on Quantitative Biology·C R Linnen, H E Hoekstra
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Apr 28, 2010·Annual Review of Nutrition·F LucaA Di Rienzo
Jan 1, 2008·Annual Review of Anthropology·Angela M Hancock, Anna Di Rienzo
Mar 24, 2012·Malaria Journal·Andrea M McCollumAnanias A Escalante
Dec 19, 2006·PLoS Genetics·Pleuni S Pennings, Joachim Hermisson
Mar 21, 2009·PLoS Genetics·Nathan A BoggsMikhail E Nasrallah
Jun 9, 2009·PLoS Genetics·Graham CoopJonathan K Pritchard
Jun 30, 2010·PLoS Genetics·Talia KarasovDmitri A Petrov
Jun 30, 2010·PLoS Genetics·Nick Barton
Nov 17, 2010·PLoS Genetics·Anna M JohanssonOrjan Carlborg
Jul 26, 2012·PLoS Genetics·Isabel AlvesLaurent Excoffier
Jan 28, 2014·PLoS Genetics·Pleuni S PenningsJohn Wakeley
Oct 10, 2006·Genetics·Juliette de MeauxT Mitchell-Olds
Jun 21, 2012·Genetics·Graham Coop, Peter Ralph
Aug 2, 2012·Genetics·Natalja Strelkowa, Michael Lässig
Oct 28, 2014·Nature Communications·Jeffrey D Jensen
Mar 1, 2015·Theoretical Population Biology·Guillaume Martin, Amaury Lambert

❮ 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

Evolution; International Journal of Organic Evolution
Molly PrzeworskiJeffrey D Wall
Proceedings of the National Academy of Sciences of the United States of America
Hideki Innan, Yuseob Kim
© 2021 Meta ULC. All rights reserved