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The site-frequency spectrum associated with Ξ-coalescents

Jochen Blath, Mathias Christensen Cronjäger, Bjarki Eldon, Matthias Hammer
doi: https://doi.org/10.1101/025684
Jochen Blath
1TU Berlin, Institut für Mathematik, 10623 Berlin, Germany
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Mathias Christensen Cronjäger
2University of Oxford, OX1 2DL Oxford, UK
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Bjarki Eldon
1TU Berlin, Institut für Mathematik, 10623 Berlin, Germany
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Matthias Hammer
1TU Berlin, Institut für Mathematik, 10623 Berlin, Germany
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Abstract

We give recursions for the expected site-frequency spectrum associated with 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 diploidv, recurrent advantageous mutations, or strong bottlenecks. In contrast, 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-coalescent models are applied to data obtained from Lambda-coalescents, and vice versa. In general, Xi-coalescents predict fewer singletons than corresponding Lambda-coalescents, but higher count of mutations of ‘size’ larger than singletons. We analyse unfolded site-frequency spectra obtained for nuclear loci of the diploid Atlantic cod, and obtain different coalescent parameter estimates than previously obtained with Lambda-coalescents. Our results provide new inference tools, and suggest that for nuclear 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.

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Posted August 28, 2015.
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The site-frequency spectrum associated with Ξ-coalescents
Jochen Blath, Mathias Christensen Cronjäger, Bjarki Eldon, Matthias Hammer
bioRxiv 025684; doi: https://doi.org/10.1101/025684
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The site-frequency spectrum associated with Ξ-coalescents
Jochen Blath, Mathias Christensen Cronjäger, Bjarki Eldon, Matthias Hammer
bioRxiv 025684; doi: https://doi.org/10.1101/025684

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