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Preprint 4-2011

Analysis of DNA Sequence Variation within Marine Species Using Beta-Coalescents

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Author(s) : Matthias Birkner , Jochen Blath , Matthias Steinrücken

Preprint series of the Institute of Mathematics, Technische Universität Berlin
Preprint 4-2011

MSC 2000

62F99 None of the above, but in this section
62P10 Applications to biology and medical sciences
92D10 Genetics
92D20 Protein sequences, DNA sequences

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 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 brie y address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman coalescents), allowing multiple mergers of genealogies. The choice of the underlying coalescent model for the genealogy has drastic implications for the estimation of the above quantities, in particular the real-time embedding of the genealogy.

Keywords : Beta-coalescents, inference of mutation rates, time to the most recent common ancestor, hedgecock sweepstakes, population genetics

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