Statistical properties of the site-frequency spectrum associated with Lambda-coalescents
Statistical properties of the site frequency spectrum associated with Lambda-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estima...
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ftdatacite:10.48550/arxiv.1305.6043 2023-05-15T15:27:36+02:00 Statistical properties of the site-frequency spectrum associated with Lambda-coalescents Birkner, Matthias Blath, Jochen Eldon, Bjarki 2013 https://dx.doi.org/10.48550/arxiv.1305.6043 https://arxiv.org/abs/1305.6043 unknown arXiv arXiv.org perpetual, non-exclusive license http://arxiv.org/licenses/nonexclusive-distrib/1.0/ Populations and Evolution q-bio.PE FOS Biological sciences 92D15 Preprint Article article CreativeWork 2013 ftdatacite https://doi.org/10.48550/arxiv.1305.6043 2022-04-01T13:38:24Z Statistical properties of the site frequency spectrum associated with Lambda-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Lambda-coalescents for datasets too large for full likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values which give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a given number of leaves (DNA sequences), allowing us to apply a pseudo-likelihood inference to estimate coalescence parameters associated with certain subclasses of Lambda coalescents. The properties of the pseudo-likelihood approach are investigated on simulated as well as real mtDNA datasets for the high fecundity Atlantic cod (\emph{Gadus morhua}). Our results for two subclasses of Lambda coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Lambda-subclasses, even for moderate sample sizes. : 45 pages, 14 figures, 4 tables, Appendix, supporting information Report atlantic cod Gadus morhua DataCite Metadata Store (German National Library of Science and Technology) Lambda ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
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collection |
DataCite Metadata Store (German National Library of Science and Technology) |
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ftdatacite |
language |
unknown |
topic |
Populations and Evolution q-bio.PE FOS Biological sciences 92D15 |
spellingShingle |
Populations and Evolution q-bio.PE FOS Biological sciences 92D15 Birkner, Matthias Blath, Jochen Eldon, Bjarki Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
topic_facet |
Populations and Evolution q-bio.PE FOS Biological sciences 92D15 |
description |
Statistical properties of the site frequency spectrum associated with Lambda-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Lambda-coalescents for datasets too large for full likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values which give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a given number of leaves (DNA sequences), allowing us to apply a pseudo-likelihood inference to estimate coalescence parameters associated with certain subclasses of Lambda coalescents. The properties of the pseudo-likelihood approach are investigated on simulated as well as real mtDNA datasets for the high fecundity Atlantic cod (\emph{Gadus morhua}). Our results for two subclasses of Lambda coalescents show that one can distinguish these subclasses from the Kingman coalescent, as well as between the Lambda-subclasses, even for moderate sample sizes. : 45 pages, 14 figures, 4 tables, Appendix, supporting information |
format |
Report |
author |
Birkner, Matthias Blath, Jochen Eldon, Bjarki |
author_facet |
Birkner, Matthias Blath, Jochen Eldon, Bjarki |
author_sort |
Birkner, Matthias |
title |
Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
title_short |
Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
title_full |
Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
title_fullStr |
Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
title_full_unstemmed |
Statistical properties of the site-frequency spectrum associated with Lambda-coalescents |
title_sort |
statistical properties of the site-frequency spectrum associated with lambda-coalescents |
publisher |
arXiv |
publishDate |
2013 |
url |
https://dx.doi.org/10.48550/arxiv.1305.6043 https://arxiv.org/abs/1305.6043 |
long_lat |
ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
geographic |
Lambda |
geographic_facet |
Lambda |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_rights |
arXiv.org perpetual, non-exclusive license http://arxiv.org/licenses/nonexclusive-distrib/1.0/ |
op_doi |
https://doi.org/10.48550/arxiv.1305.6043 |
_version_ |
1766358015021154304 |