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General theory for stochastic admixture graphs and F-statistics

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  • Soraggi, Samuele
  • Wiuf, Carsten

Abstract

We provide a general mathematical framework based on the theory of graphical models to study admixture graphs. Admixture graphs are used to describe the ancestral relationships between past and present populations, allowing for population merges and migration events, by means of gene flow. We give various mathematical properties of admixture graphs with particular focus on properties of the so-called F-statistics. Also the Wright–Fisher model is studied and a general expression for the loss of heterozygosity is derived.

Suggested Citation

  • Soraggi, Samuele & Wiuf, Carsten, 2019. "General theory for stochastic admixture graphs and F-statistics," Theoretical Population Biology, Elsevier, vol. 125(C), pages 56-66.
  • Handle: RePEc:eee:thpobi:v:125:y:2019:i:c:p:56-66
    DOI: 10.1016/j.tpb.2018.12.002
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    1. Steffen L. Lauritzen & Thomas S. Richardson, 2002. "Chain graph models and their causal interpretations," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 321-348, August.
    2. George Nicholson & Albert V. Smith & Frosti Jónsson & Ómar Gústafsson & Kári Stefánsson & Peter Donnelly, 2002. "Assessing population differentiation and isolation from single‐nucleotide polymorphism data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(4), pages 695-715, October.
    3. Joseph K Pickrell & Jonathan K Pritchard, 2012. "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data," PLOS Genetics, Public Library of Science, vol. 8(11), pages 1-17, November.
    4. Mathieu Gautier & Toby Dylan Hocking & Jean-Louis Foulley, 2010. "A Bayesian Outlier Criterion to Detect SNPs under Selection in Large Data Sets," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-16, August.
    5. David Reich & Kumarasamy Thangaraj & Nick Patterson & Alkes L. Price & Lalji Singh, 2009. "Reconstructing Indian population history," Nature, Nature, vol. 461(7263), pages 489-494, September.
    6. Pontus Skoglund & Swapan Mallick & Maria Cátira Bortolini & Niru Chennagiri & Tábita Hünemeier & Maria Luiza Petzl-Erler & Francisco Mauro Salzano & Nick Patterson & David Reich, 2015. "Genetic evidence for two founding populations of the Americas," Nature, Nature, vol. 525(7567), pages 104-108, September.
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