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Genetic demographic networks: Mathematical model and applications

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  • Kimmel, Marek
  • WojdyÅ‚a, Tomasz

Abstract

Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O’Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs–Balts–Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters–gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans.

Suggested Citation

  • Kimmel, Marek & WojdyÅ‚a, Tomasz, 2016. "Genetic demographic networks: Mathematical model and applications," Theoretical Population Biology, Elsevier, vol. 111(C), pages 75-86.
    • Handle: RePEc:eee:thpobi:v:111:y:2016:i:c:p:75-86
    DOI: 10.1016/j.tpb.2016.06.004
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    1. Unknown, 2005. "Forward," 2005 Conference: Slovenia in the EU - Challenges for Agriculture, Food Science and Rural Affairs, November 10-11, 2005, Moravske Toplice, Slovenia 183804, Slovenian Association of Agricultural Economists (DAES).
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    3. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
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