Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

Genetics
Julien JouganousSimon Gravel

Abstract

Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations. We show that the approach is typically faster, more numerically stable, and more easily generalizable than the state-of-the-art software implementation of the diffusion approximation. We present a number of applications to human sequence data, including demographic inference with a five-population joint frequency spectrum and a discussion of the robustness of the out-of-Africa model inference to the choice of modern population.

References

Mar 21, 2000·American Journal of Human Genetics·M Tremblay, H Vézina
Aug 5, 2006·Theoretical Population Biology·Steven N EvansMontgomery Slatkin
Mar 8, 2011·Theoretical Population Biology·Sergio LukićKevin Chen
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Simon GravelCarlos D Bustamante
Mar 17, 2012·Molecular Biology and Evolution·David BryantArindam RoyChoudhury
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Sep 21, 2013·Nature Reviews. Genetics·Laura B Scheinfeldt, Sarah A Tishkoff
Nov 10, 2013·PLoS Genetics·Laurent ExcoffierMatthieu Foll
Jan 5, 2014·PLoS Genetics·Simon GravelCarlos D Bustamante
Jan 29, 2014·Proceedings of the National Academy of Sciences of the United States of America·Anand BhaskarYun S Song
Mar 19, 2014·Genetics·Simon Gravel, UNKNOWN National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project
Jun 9, 2014·Nature Genetics·Jeremy SchmutzScott A Jackson
Jun 24, 2014·Nature Genetics·Stephan Schiffels, Richard Durbin
Jul 26, 2015·Systematic Biology·Nicola De MaioCarolin Kosiol
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Oct 4, 2015·Nature·Peter H SudmantJan O Korbel
Nov 8, 2015·Molecular Biology and Evolution·Alec J CoffmanRyan N Gutenkunst
Feb 18, 2016·Genetics·Jeffrey P SpenceYun S Song
May 6, 2016·PLoS Computational Biology·Jerome KelleherGilean McVean
Oct 6, 2016·Molecular Biology and Evolution·Benjamin C Haller, Philipp W Messer
Feb 28, 2017·Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America·John A KammYun S Song

❮ Previous
Next ❯

Citations

Apr 1, 2018·Molecular Ecology·Matthias SteinrückenYun S Song
May 31, 2018·Molecular Biology and Evolution·Ravi PatelSudhir Kumar
Jun 14, 2018·Molecular Biology and Evolution·Zafarali Ahmed, Simon Gravel
Jan 22, 2019·Nature Communications·Kaustubh AdhikariAndrés Ruiz-Linares
Jun 11, 2019·PLoS Genetics·Aaron P Ragsdale, Simon Gravel
Nov 24, 2019·BMC Bioinformatics·Luis ToradaMatteo Fumagalli
Feb 19, 2020·Molecular Biology and Evolution·Paul D BlischakRyan N Gutenkunst
Sep 12, 2020·Journal of Evolutionary Biology·Ethan LinckJohn P Dumbacher
Sep 13, 2017·G3 : Genes - Genomes - Genetics·Annabel C BeichmanKirk E Lohmueller
Nov 28, 2018·Nature Ecology & Evolution·Fernando A Villanea, Joshua G Schraiber
Oct 6, 2020·Evolution Letters·Aryn P WilderNina Overgaard Therkildsen
Aug 8, 2019·Proceedings of the National Academy of Sciences of the United States of America·Matthias SteinrückenYun S Song
Oct 6, 2020·Journal of the American Statistical Association·Jack KammYun S Song
Oct 28, 2020·Journal of Evolutionary Biology·Stéphanie ArnouxChristopher Sauvage
Sep 18, 2020·Molecular Biology and Evolution·Simon H Martin, William Amos
Nov 4, 2020·Journal of Evolutionary Biology·Carlos Prada, Michael E Hellberg
Dec 12, 2020·Molecular Ecology·Peiwen XiongPaolo Franchini
Jan 23, 2021·Molecular Biology and Evolution·Ryan N Gutenkunst
Jan 16, 2021·Molecular Ecology Resources·Christelle FraïsseCamille Roux
Oct 24, 2020·BMC Genetics·Sandra WalshJaume Bertranpetit
Feb 12, 2021·Nature·Daniel TaliunGonçalo R Abecasis
Oct 3, 2020·American Journal of Human Genetics·Aaron P RagsdaleJerome Kelleher
Mar 23, 2021·Molecular Ecology Resources·Ulas IsildakMatteo Fumagalli
May 1, 2021·Molecular Biology and Evolution·Alex C McAlvayEve Emshwiller
Jul 28, 2021·Nature Communications·Guohong Albert WuDaniel S Rokhsar
Sep 2, 2021·Molecular Biology and Evolution·Martin KapunAlan O Bergland
Oct 10, 2021·American Journal of Human Genetics·Francesco MontinaroMayukh Mondal
Dec 24, 2021·The Science of the Total Environment·James E FiferSarah W Davies

❮ 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.