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Analysis of DNA sequence variation within marine species using Beta-coalescents

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  • Steinrücken, Matthias
  • Birkner, Matthias
  • Blath, Jochen

Abstract

We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock’s “reproduction sweepstakes†. Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta-coalescents (as opposed to Kingman’s coalescent), allowing multiple mergers of genealogies.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:thpobi:v:87:y:2013:i:c:p:15-24
    DOI: 10.1016/j.tpb.2013.01.007
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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. Eldon, Bjarki, 2011. "Estimation of parameters in large offspring number models and ratios of coalescence times," Theoretical Population Biology, Elsevier, vol. 80(1), pages 16-28.
    3. 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.
    4. Schweinsberg, Jason, 2003. "Coalescent processes obtained from supercritical Galton-Watson processes," Stochastic Processes and their Applications, Elsevier, vol. 106(1), pages 107-139, July.
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    Cited by:

    1. Eldon, Bjarki & Stephan, Wolfgang, 2018. "Evolution of highly fecund haploid populations," Theoretical Population Biology, Elsevier, vol. 119(C), pages 48-56.
    2. Paul F. Slade, 2018. "Linearization of the Kingman Coalescent," Mathematics, MDPI, vol. 6(5), pages 1-27, May.
    3. 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.
    4. Freund, Fabian & Siri-Jégousse, Arno, 2021. "The impact of genetic diversity statistics on model selection between coalescents," Computational Statistics & Data Analysis, Elsevier, vol. 156(C).
    5. Blath, Jochen & Buzzoni, Eugenio & Koskela, Jere & Wilke Berenguer, Maite, 2020. "Statistical tools for seed bank detection," Theoretical Population Biology, Elsevier, vol. 132(C), pages 1-15.

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