Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pgen.1000695
Download full text from publisher
References listed on IDEAS
- Joshua M Akey & Michael A Eberle & Mark J Rieder & Christopher S Carlson & Mark D Shriver & Deborah A Nickerson & Leonid Kruglyak, 2004. "Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes," PLOS Biology, Public Library of Science, vol. 2(10), pages 1-1, September.
- Myers, Simon & Fefferman, Charles & Patterson, Nick, 2008. "Can one learn history from the allelic spectrum?," Theoretical Population Biology, Elsevier, vol. 73(3), pages 342-348.
- Jody Hey, 2005. "On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas," PLOS Biology, Public Library of Science, vol. 3(6), pages 1-1, May.
- Mattias Jakobsson & Sonja W. Scholz & Paul Scheet & J. Raphael Gibbs & Jenna M. VanLiere & Hon-Chung Fung & Zachary A. Szpiech & James H. Degnan & Kai Wang & Rita Guerreiro & Jose M. Bras & Jennifer C, 2008. "Genotype, haplotype and copy-number variation in worldwide human populations," Nature, Nature, vol. 451(7181), pages 998-1003, February.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Krystyna Nadachowska-Brzyska & Reto Burri & Pall I Olason & Takeshi Kawakami & Linnéa Smeds & Hans Ellegren, 2013. "Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data," PLOS Genetics, Public Library of Science, vol. 9(11), pages 1-14, November.
- Kirk E Lohmueller & Anders Albrechtsen & Yingrui Li & Su Yeon Kim & Thorfinn Korneliussen & Nicolas Vinckenbosch & Geng Tian & Emilia Huerta-Sanchez & Alison F Feder & Niels Grarup & Torben Jørgensen , 2011. "Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome," PLOS Genetics, Public Library of Science, vol. 7(10), pages 1-15, October.
- Raul Torres & Zachary A Szpiech & Ryan D Hernandez, 2018. "Human demographic history has amplified the effects of background selection across the genome," PLOS Genetics, Public Library of Science, vol. 14(6), pages 1-27, June.
- Melissa J Hubisz & Amy L Williams & Adam Siepel, 2020. "Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph," PLOS Genetics, Public Library of Science, vol. 16(8), pages 1-24, August.
- Dominic Nelson & Jerome Kelleher & Aaron P Ragsdale & Claudia Moreau & Gil McVean & Simon Gravel, 2020. "Accounting for long-range correlations in genome-wide simulations of large cohorts," PLOS Genetics, Public Library of Science, vol. 16(5), pages 1-12, May.
- Felix M Key & Benjamin Peter & Megan Y Dennis & Emilia Huerta-Sánchez & Wei Tang & Ludmila Prokunina-Olsson & Rasmus Nielsen & Aida M Andrés, 2014. "Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)," PLOS Genetics, Public Library of Science, vol. 10(10), pages 1-12, October.
- Kelley Harris & Rasmus Nielsen, 2013. "Inferring Demographic History from a Spectrum of Shared Haplotype Lengths," PLOS Genetics, Public Library of Science, vol. 9(6), pages 1-20, June.
- Laurent Excoffier & Isabelle Dupanloup & Emilia Huerta-Sánchez & Vitor C Sousa & Matthieu Foll, 2013. "Robust Demographic Inference from Genomic and SNP Data," PLOS Genetics, Public Library of Science, vol. 9(10), pages 1-17, October.
- Aurélien Tellier & Peter Pfaffelhuber & Bernhard Haubold & Lisha Naduvilezhath & Laura E Rose & Thomas Städler & Wolfgang Stephan & Dirk Metzler, 2011. "Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-13, May.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Rafajlović, M. & Klassmann, A. & Eriksson, A. & Wiehe, T. & Mehlig, B., 2014. "Demography-adjusted tests of neutrality based on genome-wide SNP data," Theoretical Population Biology, Elsevier, vol. 95(C), pages 1-12.
- Baharian, Soheil & Gravel, Simon, 2018. "On the decidability of population size histories from finite allele frequency spectra," Theoretical Population Biology, Elsevier, vol. 120(C), pages 42-51.
- Mikula, Lynette Caitlin & Vogl, Claus, 2024. "The expected sample allele frequencies from populations of changing size via orthogonal polynomials," Theoretical Population Biology, Elsevier, vol. 157(C), pages 55-85.
- Costa, Rui J. & Wilkinson-Herbots, Hilde M., 2021. "Inference of gene flow in the process of speciation: Efficient maximum-likelihood implementation of a generalised isolation-with-migration model," Theoretical Population Biology, Elsevier, vol. 140(C), pages 1-15.
- Garrett Hellenthal & Adam Auton & Daniel Falush, 2008. "Inferring Human Colonization History Using a Copying Model," PLOS Genetics, Public Library of Science, vol. 4(5), pages 1-11, May.
- Kirk E Lohmueller & Anders Albrechtsen & Yingrui Li & Su Yeon Kim & Thorfinn Korneliussen & Nicolas Vinckenbosch & Geng Tian & Emilia Huerta-Sanchez & Alison F Feder & Niels Grarup & Torben Jørgensen , 2011. "Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome," PLOS Genetics, Public Library of Science, vol. 7(10), pages 1-15, October.
- Sol Katzman & Andrew D Kern & Katherine S Pollard & Sofie R Salama & David Haussler, 2010. "GC-Biased Evolution Near Human Accelerated Regions," PLOS Genetics, Public Library of Science, vol. 6(5), pages 1-13, May.
- Pei-Kuan Cong & Wei-Yang Bai & Jin-Chen Li & Meng-Yuan Yang & Saber Khederzadeh & Si-Rui Gai & Nan Li & Yu-Heng Liu & Shi-Hui Yu & Wei-Wei Zhao & Jun-Quan Liu & Yi Sun & Xiao-Wei Zhu & Pian-Pian Zhao , 2022. "Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
- Magnus Nordborg & Tina T Hu & Yoko Ishino & Jinal Jhaveri & Christopher Toomajian & Honggang Zheng & Erica Bakker & Peter Calabrese & Jean Gladstone & Rana Goyal & Mattias Jakobsson & Sung Kim & Yuri , 2005. "The Pattern of Polymorphism in Arabidopsis thaliana," PLOS Biology, Public Library of Science, vol. 3(7), pages 1-1, May.
- Xuchao Li & Shengpei Chen & Weiwei Xie & Ida Vogel & Kwong Wai Choy & Fang Chen & Rikke Christensen & Chunlei Zhang & Huijuan Ge & Haojun Jiang & Chang Yu & Fang Huang & Wei Wang & Hui Jiang & Xiuqing, 2014. "PSCC: Sensitive and Reliable Population-Scale Copy Number Variation Detection Method Based on Low Coverage Sequencing," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-9, January.
- Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
- Benjamin F Voight & Sridhar Kudaravalli & Xiaoquan Wen & Jonathan K Pritchard, 2006. "A Map of Recent Positive Selection in the Human Genome," PLOS Biology, Public Library of Science, vol. 4(3), pages 1-1, March.
- Wilkinson-Herbots, Hilde M., 2012. "The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow," Theoretical Population Biology, Elsevier, vol. 82(2), pages 92-108.
- Eric R Londin & Margaret A Keller & Cathleen Maista & Gretchen Smith & Laura A Mamounas & Ran Zhang & Steven J Madore & Katrina Gwinn & Roderick A Corriveau, 2010. "CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-12, October.
- Živković, Daniel & Stephan, Wolfgang, 2011. "Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory," Theoretical Population Biology, Elsevier, vol. 79(4), pages 184-191.
- Ryosuke Kimura & Akihiro Fujimoto & Katsushi Tokunaga & Jun Ohashi, 2007. "A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation," PLOS ONE, Public Library of Science, vol. 2(3), pages 1-10, March.
- Jason G. Matheny, 2007. "Reducing the Risk of Human Extinction," Risk Analysis, John Wiley & Sons, vol. 27(5), pages 1335-1344, October.
- Chaolong Wang & Sebastian Zöllner & Noah A Rosenberg, 2012. "A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations," PLOS Genetics, Public Library of Science, vol. 8(8), pages 1-16, August.
- Terence C. Burnham & Aimee Dunlap & David W. Stephens, 2015. "Experimental Evolution and Economics," SAGE Open, , vol. 5(4), pages 21582440156, November.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pgen00:1000695. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosgenetics (email available below). General contact details of provider: https://journals.plos.org/plosgenetics/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.