# Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?

@article{Eldon2015CanTS, title={Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?}, author={Bjarki Eldon and Matthias C. F. Birkner and Jochen Blath and Fabian Freund}, journal={Genetics}, year={2015}, volume={199}, pages={841 - 856} }

The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood…

## 63 Citations

Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra

- Biology
- 2018

A new method is presented based on the pointwise mutual information of the two-site frequency spectrum for pairs of linked sites that can detect when the genome-wide genetic diversity is inconsistent with the Kingman coalescent, rather than detecting outlier regions, as in selection scan methods.

Multi-locus data distinguishes between population growth and multiple merger coalescents

- Computer ScienceStatistical applications in genetics and molecular biology
- 2018

Abstract We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with…

Non-parametric estimation of population size changes from the site frequency spectrum

- Computer SciencebioRxiv
- 2017

This work presents a new method, CubSFS, for estimating the changes in population size of a panmictic population from an observed SFS, and provides a straightforward proof for the expression of the expected site frequency spectrum depending only on the population size.

The Site Frequency Spectrum for General Coalescents

- Computer ScienceGenetics
- 2016

This work derives a new formula for the expected SFS for general Λ- and Ξ-coalescents, which leads to an efficient algorithm and obtains general theoretical results for the identifiability of the Λ measure when ζ is a constant function, as well as for the identity of the function ζ under a fixed Ξ measure.

The site-frequency spectrum associated with Ξ-coalescents.

- PhysicsTheoretical population biology
- 2016

The site-frequency spectrum associated with Ξ-coalescents

- PhysicsbioRxiv
- 2016

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, are given, and it is suggested that for autosomal population genetic data from diploid or polyploid highly fecund populations who may have skewed offspring distributions, one should not apply Lambda-coaledents, but Xi-cents.

Inference of Super-exponential Human Population Growth via Efficient Computation of the Site Frequency Spectrum for Generalized Models

- MathematicsGenetics
- 2015

Applying the inference framework to data from the NHLBI Exome Sequencing Project, it is found that a model with a generalized growth epoch fits the observed SFS significantly better than the equivalent model with exponential growth (P-value =3.85×10−6).

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- EconomicsMathematical biosciences
- 2019

External branch lengths of Λ-coalescents without a dust component

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- 2019

Λ -coalescents model genealogies of samples of individuals from a large population by means of a family tree. The tree’s leaves represent the individuals, and the lengths of the adjacent edges…

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

- BiologyGenetics
- 2017

An extended Moran model with exponential population growth is developed, and it is demonstrated that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent, and both can be estimated accurately from whole-genome data.

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