The site-frequency spectrum associated with Ξ-coalescents

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

Theoretical Population Biology, 2016, vol. 110, issue C, 36-50

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.

Keywords: Site-frequency spectrum; Xi-coalescents; Diploidy; Atlantic cod; Simultaneous mergers (search for similar items in EconPapers)
Date: 2016
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0040580916300053
Full text for ScienceDirect subscribers only

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:110:y:2016:i:c:p:36-50

DOI: 10.1016/j.tpb.2016.04.002

Access Statistics for this article

Theoretical Population Biology is currently edited by Jeremy Van Cleve

More articles in Theoretical Population Biology from Elsevier
Bibliographic data for series maintained by Catherine Liu ().