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Exact coalescent likelihoods for unlinked markers in finite-sites mutation models

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David Bryant, Arindam RoyChoudhury, Remco Bouckaert, Joseph Felsenstein, Noah Rosenberg

Populations and Evolution · Submitted 16 Sep 2011

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past.

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arXiv ID1109.3525 (version 1)
Pith IDBXH2XYC5, Pith's permanent record of this paper and its review
CitationArindam RoyChoudhury, David Bryant, Joseph Felsenstein, Noah Rosenberg, Remco Bouckaert. "Exact coalescent likelihoods for unlinked markers in finite-sites mutation models." arXiv:1109.3525 (2011). https://pith.science/paper/BXH2XYC5
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Compiled by classifier-1.13-20260917 via OpenRouter, question bank abstract-p1-20260923, 2026-09-23: 1 request, 3,562 input tokens, $0.0001 reported.

What the abstract itself states, as probabilities: claims first 0.06 · states limitation 0.09 · human participants 0.04 · controlled comparison 0.02 · randomized assignment 0.01 · states quantitative result 0.10 · compares with prior results 0.12 · mentions code or data availability 0.03.

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arXiv listing abstract v1. Results and the main claim are underlined; .

We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or infinite sites, model. This work extends the coalescent theory of unlinked biallelic markers, enabling fast computations of allele frequency spectra in multiple populations. Our results have applications to demographic inference, species tree inference, and the analysis of genetic variation in closely related species more generally.

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#sentencerolethe authors' own workstates the main conclusionstrength
s0 We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. contribution 0.76 0.97 0.47 asserted 1.00
s1 We consider unlinked biallelic markers mutating according to a finite sites, or infinite sites, model. method 0.92 0.55 0.06 asserted 0.97
s2 This work extends the coalescent theory of unlinked biallelic markers, enabling fast computations of allele frequency spectra in multiple populations. contribution 0.90 0.85 0.47 asserted 1.00
s3 Our results have applications to demographic inference, species tree inference, and the analysis of genetic variation in closely related species more generally. interpretation 0.98 0.38 0.13 asserted 0.96

What kind of paper the classifier reports this is: theoretical result 0.99 · evidence from proof or derivation 1.00.

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Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

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Original abstract

We derive exact formulae for the allele frequency spectrum under the coalescent with mutation, conditioned on allele counts at some fixed time in the past. We consider unlinked biallelic markers mutating according to a finite sites, or infinite sites, model. This work extends the coalescent theory of unlinked biallelic markers, enabling fast computations of allele frequency spectra in multiple populations. Our results have applications to demographic inference, species tree inference, and the analysis of genetic variation in closely related species more generally.

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