Principal component analysis under population genetic models of range expansion and admixture

Molecular Biology and Evolution
Olivier FrançoisJohn Novembre

Abstract

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East approximately 10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the "allele surfing" phenomen...Continue Reading

References

Sep 1, 1978·Science·P MenozziL Cavalli-Sforza
Oct 1, 1992·Genetics·R R HudsonW P Maddison
Nov 1, 1989·American Journal of Physical Anthropology·R R SokalN L Oden
Jan 1, 1982·Analytical Biochemistry·H HughesR A Sutton
Feb 1, 1995·American Journal of Physical Anthropology·G BarbujaniN L Oden
Jan 29, 1993·Science·L L Cavalli-SforzaA Piazza
May 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·G Barbujani, A Pilastro
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·L ChikhiG Barbujani
Jun 3, 2000·Genetics·J K PritchardP Donnelly
Aug 9, 2002·Proceedings of the National Academy of Sciences of the United States of America·Lounes ChikhiMark A Beaumont
Apr 26, 2003·Science·Jared Diamond, Peter Bellwood
Jan 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·Christopher A EdmondsL Luca Cavalli-Sforza
Mar 27, 2004·Molecular Biology and Evolution·Isabelle DupanloupGuido Barbujani
May 8, 2004·Nature Reviews. Genetics·Mark A Beaumont, Bruce Rannala
Oct 16, 2004·Annual Review of Genomics and Human Genetics·Guido Barbujani, David B Goldstein
May 5, 2005·Proceedings. Biological Sciences·Mathias Currat, Laurent Excoffier
Nov 11, 2005·Molecular Biology and Evolution·Seraina KlopfsteinLaurent Excoffier
Nov 19, 2005·PLoS Biology·Ron PinhasiAlbert J Ammerman
Jan 26, 2006·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Kana WuEdward Giovannucci
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Apr 17, 2007·American Journal of Human Genetics·Marc BauchetMark D Shriver
Oct 30, 2007·Theoretical Population Biology·Oskar Hallatschek, David R Nelson
Dec 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Oskar HallatschekDavid R Nelson
Feb 22, 2008·Nature·Mattias JakobssonAndrew B Singleton
Apr 22, 2008·Nature Genetics·John Novembre, Matthew Stephens
May 27, 2008·Trends in Ecology & Evolution·Laurent Excoffier, Nicolas Ray
Aug 12, 2008·Current Biology : CB·Oscar LaoManfred Kayser
Sep 2, 2008·Nature·John NovembreCarlos D Bustamante
Nov 21, 2008·European Journal of Human Genetics : EJHG·Simon C HeathMark Lathrop
May 23, 2009·Molecular Biology and Evolution·Eric DurandOlivier François
Nov 6, 2009·Current Biology : CB·Peter Rowley-Conwy
Nov 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jacques ChiaroniLuca L Cavalli-Sforza
Feb 1, 1993·Evolution; International Journal of Organic Evolution·Montgomery Slatkin

❮ Previous
Next ❯

Citations

Mar 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Emily Jane McTavishDavid M Hillis
Aug 28, 2012·Molecular Biology and Evolution·Miguel ArenasLaurent Excoffier
Oct 12, 2012·Molecular Biology and Evolution·Michael DeGiorgio, Noah A Rosenberg
Nov 23, 2012·Molecular Biology and Evolution·Flora JayMichael G B Blum
Feb 16, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Pascale GerbaultMark G Thomas
Jun 14, 2012·PLoS Computational Biology·Miguel Arenas
Nov 21, 2012·PLoS Genetics·Joseph K Pickrell, Jonathan K Pritchard
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Pascale GerbaultMark G Thomas
Aug 2, 2011·Annual Review of Genomics and Human Genetics·John Novembre, Sohini Ramachandran
Oct 25, 2013·Evolution; International Journal of Organic Evolution·Benjamin M Peter, Montgomery Slatkin
Nov 13, 2015·Molecular Ecology·J SwaegersR Stoks
Aug 15, 2012·Trends in Genetics : TIG·Ron PinhasiJoachim Burger
Apr 23, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Raphaël LebloisThierry Wirth
Nov 22, 2013·The Journal of Animal Ecology·Regula Schmid-HempelPaul Schmid-Hempel
May 7, 2011·Journal of Evolutionary Biology·L-M Chevin, R Lande
Sep 14, 2011·American Journal of Physical Anthropology·Sohini Ramachandran, Noah A Rosenberg
May 14, 2011·Molecular Ecology Resources·Olivier François, Eric Durand
Jul 7, 2011·American Journal of Physical Anthropology·Patrik GaletaJaroslav Bruzek
Jul 12, 2013·Molecular Ecology·Amanda M V BrownJohn P McCutcheon
Nov 20, 2010·American Journal of Physical Anthropology·Eugene E Harris
Aug 21, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ming-Chi TsaiRussell Schwartz
Nov 11, 2015·Nature Reviews. Genetics·Joshua G Schraiber, Joshua M Akey
Jun 26, 2015·BMC Genomics·Konstantin KozlovTatiana V Tatarinova
May 6, 2015·Investigative Genetics·Andreas Wollstein, Oscar Lao
Sep 14, 2011·Progress in Neuro-psychopharmacology & Biological Psychiatry·Paolo OlgiatiAlessandro Serretti
Mar 19, 2014·Trends in Ecology & Evolution·Marc Rius, John A Darling
Aug 9, 2016·American Journal of Physical Anthropology·Robert Carreras-TorresPedro Moral
Sep 2, 2016·Current Opinion in Genetics & Development·Stephan PeischlLaurent Excoffier
Jan 16, 2016·PLoS Genetics·Gideon S BradburdGraham M Coop
Oct 14, 2017·Molecular Biology and Evolution·João PimentaMiguel Arenas
Jan 4, 2018·BMC Genetics·Petr TriskaEgor Prokhortchouk
Dec 28, 2018·Molecular Ecology·James W DemastesTheresa A Spradling
Oct 16, 2012·Animal Genetics·A FrkonjaJ Sölkner

❮ 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.