Applyingf4-statistics and admixture graphs: Theory and examples

被引：31
作者：
Lipson, Mark [1 ,2 ]
机构：
[1] Harvard Med Sch, Dept Genet, Boston, MA 02115 USA
[2] Harvard Univ, Dept Human Evolutionary Biol, Cambridge, MA 02138 USA
来源：
MOLECULAR ECOLOGY RESOURCES | 2020年 / 20卷 / 06期
关键词：
admixture; admixture graphs; f-statistics; parameter estimation; ANCIENT; INFERENCE; ANCESTRY; HISTORY;
D O I：
10.1111/1755-0998.13230
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
A popular approach to learning about admixture from population genetic data is by computing the allele-sharing summary statistics known asf-statistics. Compared to some methods in population genetics,f-statistics are relatively simple, but interpreting them can still be complicated at times. In addition,f-statistics can be used to build admixture graphs (multi-population trees allowing for admixture events), which provide more explicit and thorough modelling capabilities but are correspondingly more complex to work with. Here, I discuss some of these issues to provide users of these tools with a basic guide for protocols and procedures. My focus is on the kinds of conclusions that can or cannot be drawn from the results off(4)-statistics and admixture graphs, illustrated with real-world examples involving human populations.
引用
收藏
页码：1658 / 1667
页数：10
相关论文
共 25 条
  • [1] Robust Demographic Inference from Genomic and SNP Data
    Excoffier, Laurent
    Dupanloup, Isabelle
    Huerta-Sanchez, Emilia
    Sousa, Vitor C.
    Foll, Matthieu
    [J]. PLOS GENETICS, 2013, 9 (10):
  • [2] African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations
    Fan, Shaohua
    Kelly, Derek E.
    Beltrame, Marcia H.
    Hansen, Matthew E. B.
    Mallick, Swapan
    Ranciaro, Alessia
    Hirbo, Jibril
    Thompson, Simon
    Beggs, William
    Nyambo, Thomas
    Omar, Sabah A.
    Meskel, Dawit Wolde
    Belay, Gurja
    Froment, Alain
    Patterson, Nick
    Reich, David
    Tishkoff, Sarah A.
    [J]. GENOME BIOLOGY, 2019, 20 (1)
  • [3] Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America
    Flegontov, Pavel
    Altinisik, N. Ezgi
    Changmai, Piya
    Rohland, Nadin
    Mallick, Swapan
    Adamski, Nicole
    Bolnick, Deborah A.
    Broomandkhoshbacht, Nasreen
    Candilio, Francesca
    Culleton, Brendan J.
    Flegontova, Olga
    Friesen, T. Max
    Jeong, Choongwon
    Harper, Thomas K.
    Keating, Denise
    Kennett, Douglas J.
    Kim, Alexander M.
    Lamnidis, Thiseas C.
    Lawson, Ann Marie
    Olalde, Inigo
    Oppenheimer, Jonas
    Potter, Ben A.
    Raff, Jennifer
    Sattler, Robert A.
    Skoglund, Pontus
    Stewardson, Kristin
    Vajda, Edward J.
    Vasilyev, Sergey
    Veselovskaya, Elizaveta
    Hayes, M. Geoffrey
    O'Rourke, Dennis H.
    Krause, Johannes
    Pinhasi, Ron
    Reich, David
    Schiffels, Stephan
    [J]. NATURE, 2019, 570 (7760) : 236 - +
  • [4] Bayesian inference of ancient human demography from individual genome sequences
    Gronau, Ilan
    Hubisz, Melissa J.
    Gulko, Brad
    Danko, Charles G.
    Siepel, Adam
    [J]. NATURE GENETICS, 2011, 43 (10) : 1031 - U151
  • [5] The presence and impact of reference bias on population genomic studies of prehistoric human populations
    Gunther, Torsten
    Nettelblad, Carl
    [J]. PLOS GENETICS, 2019, 15 (07):
  • [6] Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
    Gutenkunst, Ryan N.
    Hernandez, Ryan D.
    Williamson, Scott H.
    Bustamante, Carlos D.
    [J]. PLOS GENETICS, 2009, 5 (10):
  • [7] DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
    Hofreiter, M
    Jaenicke, V
    Serre, D
    von Haeseler, A
    Pääbo, S
    [J]. NUCLEIC ACIDS RESEARCH, 2001, 29 (23) : 4793 - 4799
  • [8] Efficiently Inferring the Demographic History of Many Populations With Allele Count Data
    Kamm, Jack
    Terhorst, Jonathan
    Durbin, Richard
    Song, Yun S.
    [J]. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2020, 115 (531) : 1472 - 1487
  • [9] admixturegraph: an R package for admixture graph manipulation and fitting
    Leppala, Kalle
    Nielsen, Svend V.
    Mailund, Thomas
    [J]. BIOINFORMATICS, 2017, 33 (11) : 1738 - 1740
  • [10] Ancient West African foragers in the context of African population history
    Lipson, Mark
    Ribot, Isabelle
    Mallick, Swapan
    Rohland, Nadin
    Olalde, Inigo
    Adamski, Nicole
    Broomandkhoshbacht, Nasreen
    Lawson, Ann Marie
    Lopez, Saioa
    Oppenheimer, Jonas
    Stewardson, Kristin
    Asombang, Raymond Neba'ane
    Bocherens, Herve
    Bradman, Neil
    Culleton, Brendan J.
    Cornelissen, Els
    Crevecoeur, Isabelle
    de Maret, Pierre
    Fomine, Forka Leypey Mathew
    Lavachery, Philippe
    Mindzie, Christophe Mbida
    Orban, Rosine
    Sawchuk, Elizabeth
    Semal, Patrick
    Thomas, Mark G.
    Van Neer, Wim
    Veeramah, Krishna R.
    Kennett, Douglas J.
    Patterson, Nick
    Hellenthal, Garrett
    Lalueza-Fox, Carles
    MacEachern, Scott
    Prendergast, Mary E.
    Reich, David
    [J]. NATURE, 2020, 577 (7792) : 665 - +
123