Inferring admixture histories of human populations using linkage disequilibrium

Po-Ru LohBonnie Berger


Long-range migrations and the resulting admixtures between populations have been important forces shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We define an LD-based three-population test for admixture and identify scenarios in which it can detect admixture events that previous formal tests cannot. We further show that we can uncover phylogenetic relationships among populations by comparing weighted LD curves obtained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the calculations. We implement all of these advanc...Continue Reading


May 28, 2013·Molecular Biology and Evolution·Mark LipsonBonnie Berger
Jun 13, 2014·PLoS Genetics·Jason A HodgsonRyan L Raaum
Jun 19, 2013·PloS One·Claudia MoreauDamian Labuda
May 23, 2014·PloS One·Alexia CardonaToomas Kivisild
Dec 19, 2013·TheScientificWorldJournal·Abhishek Bohra
Feb 12, 2014·Nature Communications·Choongwon JeongAnna Di Rienzo
Feb 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Joseph K PickrellDavid Reich
Feb 18, 2014·Science·Garrett HellenthalSimon Myers
Aug 20, 2014·Nature Communications·Mark LipsonDavid Reich
Feb 6, 2016·American Journal of Human Genetics·Garrett HellenthalNick Patterson
Feb 6, 2016·American Journal of Human Genetics·Qasim AyubChris Tyler-Smith
Feb 5, 2016·Biology Letters·L Y RutledgeB N White
Nov 25, 2015·Theoretical Population Biology·Nicolas Duforet-Frebourg, Montgomery Slatkin
Jan 14, 2016·Scientific Reports·Gyaneshwer ChaubeyKumarasamy Thangaraj
Dec 6, 2014·BMC Genetics·Massimo MezzavillaVincenza Colonna
Dec 2, 2014·Forensic Science International. Genetics·Massimo MezzavillaYali Xue
Nov 25, 2015·Nature·Iain MathiesonDavid Reich
Dec 17, 2015·European Journal of Human Genetics : EJHG·Guangju ZhaiRoger C Green
Jun 2, 2015·American Journal of Human Genetics·Luca PaganiChris Tyler-Smith
Oct 10, 2013·Molecular Ecology·Zachariah Gompert, C Alex Buerkle
Aug 30, 2014·Current Opinion in Genetics & Development·Ana T Duggan, Mark Stoneking
May 6, 2015·American Journal of Human Genetics·Qasim AyubChris Tyler-Smith
Apr 3, 2015·Investigative Genetics·Irina Pugach, Mark Stoneking
Aug 30, 2014·Trends in Genetics : TIG·Joseph K Pickrell, David Reich
Aug 13, 2013·American Journal of Human Genetics·Priya MoorjaniLalji Singh
May 4, 2016·Proceedings of the National Academy of Sciences of the United States of America·Priya MoorjaniDavid Reich
Oct 22, 2015·European Journal of Human Genetics : EJHG·Marc HaberChris Tyler-Smith
Jun 16, 2016·European Journal of Human Genetics : EJHG·Alexander MörseburgToomas Kivisild
Jun 22, 2016·ELife·George Bj BusbyMalaria Genomic Epidemiology Network
Jul 6, 2016·Human Genetics·Yedael Y WaldmanAlon Keinan
Apr 22, 2015·PLoS Genetics·Bayazit YunusbayevRichard Villems
Jul 7, 2016·Molecular Biology and Evolution·Nicolas BrucatoFrançois-Xavier Ricaut
Sep 24, 2016·Current Opinion in Genetics & Development·John Novembre, Benjamin M Peter
Oct 5, 2016·Nature·Pontus SkoglundDavid Reich


Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R Chakraborty, K M Weiss
May 11, 2001·Nature·David ReichEric S Lander
Dec 21, 2002·Science·Noah A RosenbergMarcus Feldman
Mar 27, 2004·Molecular Biology and Evolution·Isabelle DupanloupGuido Barbujani
Dec 6, 2005·Journal of Human Genetics·Michael HammerSatoshi Horai
Jun 15, 2006·American Journal of Human Genetics·Hua TangNeil Risch
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Oct 19, 2007·Nature·International HapMap ConsortiumJohn Stewart
Jan 25, 2008·Proceedings of the National Academy of Sciences of the United States of America·Lluís Quintana-MurciDoron M Behar
Feb 7, 2008·American Journal of Human Genetics·Sriram SankararamanEran Halperin
Jul 9, 2008·American Journal of Human Genetics·Alkes L PriceDavid Reich
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
Feb 10, 2009·Current Biology : CB·Paul VerduEvelyne Heyer
May 8, 2009·Molecular Biology and Evolution·Jeffrey D WallVincent Plagnol
May 9, 2009·Journal of Human Genetics·Rita Rasteiro, Lounès Chikhi
Sep 26, 2009·Nature·David ReichLalji Singh
Feb 25, 2010·Current Biology : CB·Pedro SoaresMartin B Richards
May 8, 2010·Science·Richard E GreenSvante Pääbo
Sep 3, 2010·Nature·International HapMap 3 ConsortiumJean E McEwen
Mar 1, 2011·Genome Biology·Irina PugachMark Stoneking
May 3, 2011·PLoS Genetics·Priya MoorjaniDavid Reich
Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Simon GravelCarlos D Bustamante
Feb 1, 2012·PLoS Genetics·Daniel J LawsonDaniel Falush
Apr 12, 2012·Genetics·Simon Gravel
Aug 15, 2012·Trends in Genetics : TIG·Ron PinhasiJoachim Burger
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Oct 18, 2012·Nature Communications·Joseph K PickrellBrigitte Pakendorf
Nov 21, 2012·PLoS Genetics·Joseph K Pickrell, Jonathan K Pritchard
Mar 22, 2013·PloS One·Priya MoorjaniBéla Melegh
May 28, 2013·Molecular Biology and Evolution·Mark LipsonBonnie Berger

Related Concepts

Human Genetics
Dysequilibrium Syndrome
Allergy Testing Alder
Human Migration
Computer Programs and Programming
School Age Population
Linkage Disequilibrium

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.

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.

Synapse Loss as Therapeutic Target in MS

As we age, the number of synapses present in the human brain starts to decline, but in neurodegenerative diseases this occurs at an accelerated rate. In MS, it has been shown that there is a reduction in synaptic density, which presents a potential target for treatment. Here is the latest research on synapse loss as a therapeutic target in MS.

Artificial Intelligence in Cardiac Imaging

Artificial intelligence (ai) techniques are increasingly applied to cardiovascular (cv) medicine in cardiac imaging analysis. 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.

Social Learning

Social learning involves learning new behaviors through observation, imitation and modeling. Follow this feed to stay up to date on the latest research.

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.

Single Cell Chromatin Profiling

Techniques like ATAC-seq and CUT&Tag have the potential to allow single cell profiling of chromatin accessibility, histones, and TFs. This will provide novel insight into cellular heterogeneity and cell states. Discover the latest research on single cell chromatin profiling here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

© 2020 Meta ULC. All rights reserved