Evidence map›Paper›PMID 35951748›Full record

ArticleG3 (Bethesda, Md.)2022

Approximations to the expectations and variances of ratios of tree properties under the coalescent.

Egor Lappo, Noah A Rosenberg

Abstract read
In one paragraph

Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

2 authors.

Egor LappoDepartment of Biology, Stanford University, Stanford, CA 94305, USA.ORCID 0000-0002-0847-4070
Noah A RosenbergDepartment of Biology, Stanford University, Stanford, CA 94305, USA.ORCID 0000-0002-1829-8664

Funding

NTHi LPS: virulence factor and vaccine candidateR01DC005855 · NIDCD · BOSTON UNIVERSITY MEDICAL CAMPUS · PI GOLDSTEIN, RICHARD · 2003 to 2006
$1.5M
Scalable Coalescent Inference for Large Data SetsR01GM131404 · NIGMS · STANFORD UNIVERSITY · PI PALACIOS, JULIA · 2018 to 2021
$1.2M
NIDCD NIH HHS R01 DC005855NIGMS NIH HHS R01 GM131404
6 · The paper itself

Abstract

Properties of gene genealogies such as tree height (H), total branch length (L), total lengths of external (E) and internal (I) branches, mean length of basal branches (B), and the underlying coalescence times (T) can be used to study population-genetic processes and to develop statistical tests of population-genetic models. Uses of tree features in statistical tests often rely on predictions that depend on pairwise relationships among such features. For genealogies under the coalescent, we provide exact expressions for Taylor approximations to expected values and variances of ratios Xn/Yn, for all 15 pairs among the variables {Hn,Ln,En,In,Bn,Tk}, considering n leaves and 2≤k≤n. For expected values of the ratios, the approximations match closely with empirical simulation-based values. The approximations to the variances are not as accurate, but they generally match simulations in their trends as n increases. Although En has expectation 2 and Hn has expectation 2 in the limit as n→∞, the approximation to the limiting expectation for En/Hn is not 1, instead equaling π2/3-2≈1.28987. The new approximations augment fundamental results in coalescent theory on the shapes of genealogical trees.

Indexed as

Models, GeneticMotivationComputer SimulationHumansPhylogenycoalescent theoryexternal branchesinternal branchestime to the most recent common ancestor

Identifiers

PMID35951748
PMCPMC9526068

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.