Evidence map›Paper›PMID 28185570›Full record

ArticleBMC bioinformatics2016

An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees.

Lawrence H Uricchio, Tandy Warnow, Noah A Rosenberg

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In one paragraph

Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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0cells of the map it votes in
1citing papers in PubMed
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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Lawrence H UricchioDepartment of Biology, Stanford University, Stanford, CA, USA.
Tandy WarnowDepartments of Computer Science & Bioengineering, University of Illinois, Urbana-Champaign, IL, USA.
Noah A RosenbergDepartment of Biology, Stanford University, Stanford, CA, USA. noahr@stanford.edu.

Funding

A Stanford - SJSU Postdoctoral Training Program to Enhance URM TeachingK12GM088033 · NIGMS · STANFORD UNIVERSITY · PI BOOTHROYD, JOHN C · 2010 to 2016
$4.1M
Mathematical and computational analysis for species tree inferenceR01GM117590 · NIGMS · UNIVERSITY OF ALASKA FAIRBANKS · PI RHODES, JOHN · 2015 to 2018
$1.5M
NIGMS NIH HHS K12 GM088033NIGMS NIH HHS R01 GM117590
6 · The paper itself

Abstract

backgroundMany methods for species tree inference require data from a sufficiently large sample of genomic loci in order to produce accurate estimates. However, few studies have attempted to use analytical theory to quantify "sufficiently large".

resultsUsing the multispecies coalescent model, we report a general analytical upper bound on the number of gene trees n required such that with probability q, each bipartition of a species tree is represented at least once in a set of n random gene trees. This bound employs a formula that is straightforward to compute, depends only on the minimum internal branch length of the species tree and the number of taxa, and applies irrespective of the species tree topology. Using simulations, we investigate numerical properties of the bound as well as its accuracy under the multispecies coalescent.

conclusionsOur results are helpful for conservatively bounding the number of gene trees required by the ASTRAL inference method, and the approach has potential to be extended to bound other properties of gene tree sets under the model.

Indexed as

GenomicsModels, GeneticProbabilityBipartitionsCoalescentGene treesSpecies trees

Identifiers

PMID28185570
PMCPMC5123308

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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.