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The site-frequency spectrum associated with Ξ-coalescents

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  • Blath, Jochen
  • Cronjäger, Mathias Christensen
  • Eldon, Bjarki
  • Hammer, Matthias

Abstract

We give recursions for the expected site-frequency spectrum associated with so-called Xi-coalescents, that is exchangeable coalescents which admit simultaneous multiple mergers of ancestral lineages. Xi-coalescents arise, for example, in association with population models of skewed offspring distributions with diploidy, recurrent advantageous mutations, or strong bottlenecks. In contrast, the simpler Lambda-coalescents admit multiple mergers of lineages, but at most one such merger each time. Xi-coalescents, as well as Lambda-coalescents, can predict an excess of singletons, compared to the Kingman coalescent. We compare estimates of coalescent parameters when Xi-coalescents are applied to data generated by Lambda-coalescents, and vice versa. In general, Xi-coalescents predict fewer singletons than corresponding Lambda-coalescents, but a higher count of mutations of size larger than singletons. We fit examples of Xi-coalescents to unfolded site-frequency spectra obtained for autosomal loci of the diploid Atlantic cod, and obtain different coalescent parameter estimates than obtained with corresponding Lambda-coalescents. Our results provide new inference tools, and suggest that for autosomal population genetic data from diploid or polyploid highly fecund populations who may have skewed offspring distributions, one should not apply Lambda-coalescents, but Xi-coalescents.

Suggested Citation

  • Blath, Jochen & Cronjäger, Mathias Christensen & Eldon, Bjarki & Hammer, Matthias, 2016. "The site-frequency spectrum associated with Ξ-coalescents," Theoretical Population Biology, Elsevier, vol. 110(C), pages 36-50.
    • Handle: RePEc:eee:thpobi:v:110:y:2016:i:c:p:36-50
    DOI: 10.1016/j.tpb.2016.04.002
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    References listed on IDEAS

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    1. Durrett, Rick & Schweinsberg, Jason, 2005. "A coalescent model for the effect of advantageous mutations on the genealogy of a population," Stochastic Processes and their Applications, Elsevier, vol. 115(10), pages 1628-1657, October.
    2. Schweinsberg, Jason, 2003. "Coalescent processes obtained from supercritical Galton-Watson processes," Stochastic Processes and their Applications, Elsevier, vol. 106(1), pages 107-139, July.
    3. Steinrücken, Matthias & Birkner, Matthias & Blath, Jochen, 2013. "Analysis of DNA sequence variation within marine species using Beta-coalescents," Theoretical Population Biology, Elsevier, vol. 87(C), pages 15-24.
    4. Birkner, Matthias & Blath, Jochen & Steinrücken, Matthias, 2011. "Importance sampling for Lambda-coalescents in the infinitely many sites model," Theoretical Population Biology, Elsevier, vol. 79(4), pages 155-173.
    5. Eldon, Bjarki, 2009. "Structured coalescent processes from a modified Moran model with large offspring numbers," Theoretical Population Biology, Elsevier, vol. 76(2), pages 92-104.
    6. Sargsyan, Ori & Wakeley, John, 2008. "A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms," Theoretical Population Biology, Elsevier, vol. 74(1), pages 104-114.
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    3. Eldon, Bjarki & Stephan, Wolfgang, 2018. "Evolution of highly fecund haploid populations," Theoretical Population Biology, Elsevier, vol. 119(C), pages 48-56.

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