Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome

Molecular Biology and Evolution
Daniel R Schrider, Andrew D Kern


The degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is in part due to the limited evidence in humans for classic "hard selective sweeps", wherein a novel beneficial mutation rapidly sweeps through a population to fixation. However, positive selection may often proceed via "soft sweeps" acting on mutations already present within a population. Here, we examine recent positive selection across six human populations using a powerful machine learning approach that is sensitive to both hard and soft sweeps. We found evidence that soft sweeps are widespread and account for the vast majority of recent human adaptation. Surprisingly, our results also suggest that linked positive selection affects patterns of variation across much of the genome, and may increase the frequencies of deleterious mutations. Our results also reveal insights into the role of sexual selection, cancer risk, and central nervous system development in recent human evolution.


Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Apr 1, 1975·Theoretical Population Biology·G A Watterson
Jan 1, 1991·Journal of Molecular Evolution·M Long, J H Gillespie
Sep 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·C W Birky, J B Walsh
Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Mar 10, 2001·Nature·Eric S LanderInternational Human Genome Sequencing Consortium
Mar 30, 2001·Nature Genetics·Masami KuramochiY Murakami
Feb 12, 2002·Nature Reviews. Genetics·Willie J Swanson, Victor D Vacquier
Apr 5, 2002·Genome Research·W James Kent
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jun 25, 2002·Japanese Journal of Cancer Research : Gann·Hiroshi FukuharaYoshinori Murakami
Feb 8, 2003·Brain Research. Molecular Brain Research·Kazuhisa KohdaMichisuke Yuzaki
Dec 19, 2003·Nucleic Acids Research·Donna KarolchikW James Kent
Jul 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Hideki Innan, Yuseob Kim
Jul 29, 2004·Genetics·Yuseob Kim, Rasmus Nielsen
Dec 14, 2004·Neuroscience·R LujánG López-Bendito
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
May 5, 2005·PLoS Biology·Rasmus NielsenMichele Cargill
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos D Bustamante
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Mar 8, 2006·Molecular Biology and Evolution·Pleuni S Pennings, Joachim Hermisson
Apr 14, 2006·Molecular and Cellular Biology·Louise van der WeydenAllan Bradley
Dec 13, 2006·Nature Genetics·Sarah A TishkoffPanos Deloukas
Dec 19, 2006·PLoS Genetics·Pleuni S Pennings, Joachim Hermisson
Jan 9, 2007·Nature Genetics·Agnar HelgasonKari Stefansson
Jun 5, 2007·PLoS Genetics·Scott H WilliamsonRasmus Nielsen
Nov 6, 2007·Proceedings of the National Academy of Sciences of the United States of America·Nelson J R FagundesLaurent Excoffier
Nov 17, 2007·Nucleic Acids Research·Obi L GriffithOpen Regulatory Annotation Consortium
Jun 3, 2008·PLoS Genetics·Adam R BoykoCarlos D Bustamante
Sep 20, 2008·PLoS Genetics·Jeffrey D JensenPeter Andolfatto
Oct 30, 2008·Biochemical and Biophysical Research Communications·Y ZhilingMariko Y Momoi
Mar 25, 2009·Genome Research·Joseph K PickrellJonathan K Pritchard
Aug 4, 2009·Genome Research·David H AlexanderKenneth Lange
Jun 30, 2010·PLoS Genetics·Talia KarasovDmitri A Petrov
Feb 19, 2011·Science·Ryan D HernandezMolly Przeworski
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Simon GravelCarlos D Bustamante
Aug 6, 2011·Molecular Biology and Evolution·Chad D HuffStephen L Guthery
Sep 3, 2011·Evolution; International Journal of Organic Evolution·Matthew Hartfield, Sarah P Otto
Sep 9, 2011·PLoS Genetics·Sung Chun, Justin C Fay
Jun 8, 2012·Genetics·Charles H LangleyDavid J Begun
Aug 24, 2012·Nature·Augustine KongKari Stefansson
Sep 7, 2012·Genome Biology·Baikang PeiMark B Gerstein
Sep 8, 2012·Nature·ENCODE Project Consortium
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
May 30, 2013·Nature Genetics·GTEx Consortium
Jun 19, 2013·Genetics·Roy RonenVineet Bafna
Nov 7, 2013·Nucleic Acids Research·Mulin Jun LiJunwen Wang
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Jan 1, 2014·Proceedings of the National Academy of Sciences of the United States of America·Elodie GazaveAlon Keinan
Mar 13, 2014·Genome Research·David EnardDmitri A Petrov
Jul 22, 2014·Nature·Emilia Huerta-SánchezRasmus Nielsen
Jul 26, 2014·Genetics·Benjamin A WilsonPhilipp W Messer
Aug 8, 2014·PLoS Genetics·Jeremy J Berg, Graham Coop
Aug 15, 2014·PLoS Genetics·H Allen Orr, Robert L Unckless
Oct 31, 2014·Nucleic Acids Research·Simon A ForbesPeter J Campbell
Nov 27, 2014·Database : the Journal of Biological Databases and Curation·Peng ZhangDa-Wei Huang
Nov 28, 2014·Nucleic Acids Research·Andrew Chatr-AryamontriMike Tyers
Dec 24, 2014·Genome Biology and Evolution·Wei QianKun Tang
May 2, 2015·Molecular Reproduction and Development·Yuan-Yi WuHua-Liang Yu
Jun 10, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·L Nunney, B Muir
Aug 28, 2015·Genetics·Jeremy J Berg, Graham Coop
Sep 15, 2015·Nature·UK10K ConsortiumNicole Soranzo
Sep 24, 2015·Molecular Ecology·Gregory B Ewing, Jeffrey D Jensen
Oct 4, 2015·Nature·1000 Genomes Project ConsortiumGonçalo R Abecasis
Oct 18, 2015·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Nov 20, 2015·Nucleic Acids Research·Melissa J LandrumDonna R Maglott
Nov 22, 2015·Genome Biology and Evolution·Daniel R Schrider, Andrew D Kern
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek
Dec 25, 2015·Proceedings of the National Academy of Sciences of the United States of America·Clare D MarsdenKirk E Lohmueller
Mar 16, 2016·PLoS Genetics·Daniel R Schrider, Andrew D Kern
Mar 29, 2016·PLoS Computational Biology·Sara Sheehan, Yun S Song
May 18, 2016·ELife·David EnardDmitri A Petrov
Aug 26, 2016·Bioinformatics·Andrew D Kern, Daniel R Schrider
Sep 9, 2016·Genetics·Daniel R SchriderAndrew D Kern
Oct 16, 2016·Science·Yair FieldJonathan K Pritchard
Nov 16, 2016·Science·Shaohua FanSarah A Tishkoff


May 4, 2018·Molecular Biology and Evolution·Andrew D Kern, Matthew W Hahn
Nov 1, 2017·BMC Biology·Tom R BookerPeter D Keightley
May 31, 2018·Molecular Biology and Evolution·Ravi PatelSudhir Kumar
Jul 17, 2018·Genome Biology and Evolution·Jeremy D Lange, John E Pool
Oct 2, 2018·Genes & Genetic Systems·Naoko T FujitoNaoyuki Takahata
Nov 22, 2018·Evolution; International Journal of Organic Evolution·Jeffrey D JensenBrian Charlesworth
Nov 7, 2018·Molecular Biology and Evolution·Mehreen R Mughal, Michael DeGiorgio
Dec 6, 2018·Molecular Biology and Evolution·Lex FlagelDaniel R Schrider
Feb 21, 2018·Nature Communications·Lauren Alpert SugdenSohini Ramachandran
May 8, 2019·Nature Ecology & Evolution·Lawrence H UricchioDavid Enard
Apr 8, 2018·G3 : Genes - Genomes - Genetics·Andrew D Kern, Daniel R Schrider
Nov 26, 2019·PLoS Genetics·Joshua M SchmidtAida M Andrés
Dec 6, 2019·G3 : Genes - Genomes - Genetics·Jared GallowayPeter Ralph
Jan 25, 2020·G3 : Genes - Genomes - Genetics·Matthew Hartfield, Thomas Bataillon
Mar 11, 2020·Genetics·Alexandre M Harris, Michael DeGiorgio
Apr 15, 2020·Annual Review of Genomics and Human Genetics·Natalie Niepoth, Andres Bendesky
May 12, 2020·Molecular Biology and Evolution·Alexandre M Harris, Michael DeGiorgio
Aug 28, 2020·PLoS Genetics·Mehreen R MughalMichael DeGiorgio
Nov 8, 2017·Molecular Ecology·Xiaoheng ChengMichael DeGiorgio
Aug 17, 2018·Molecular Biology and Evolution·August E WoernerMichael F Hammer
Feb 23, 2019·Evolution Letters·Lawrence H UricchioNoah A Zaitlen
May 7, 2019·Annual Review of Genomics and Human Genetics·Marc J WilliamsTrevor A Graham
Dec 13, 2019·PloS One·Nick KinneyHarold R Garner
Nov 12, 2019·PLoS Computational Biology·Yichen Zheng, Thomas Wiehe
Jul 28, 2018·Briefings in Bioinformatics·Clare HorscroftAndrew Collins
Oct 6, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David Enard, Dmitri A Petrov
Dec 10, 2020·Hereditas·Ziqing Pan, Shuhua Xu
Mar 18, 2020·Computational and Structural Biotechnology Journal·Federico Scossa, Alisdair R Fernie
Oct 7, 2020·Molecular Biology and Evolution·Alexander T XueAg1000G Consortium

Related Concepts

Machine Learning
Biological Adaptation
Adaptation, Physiological
Genetics, Population
Selection, Genetic
Variation (Genetics)
Genome, Human
Evolution, Molecular

Trending Feeds


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.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

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.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms 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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Zoe June AssafJamie R Blundell
Cellular and Molecular Life Sciences : CMLS
D I Nurminsky
© 2021 Meta ULC. All rights reserved