Evidence map›Paper›PMID 39233780›Full record

ArticleFrontiers in ecology and evolution2023

Short branch attraction in phylogenomic inference under the multispecies coalescent.

Liang Liu, Lili Yu, Shaoyuan Wu, Jonathan Arnold, Christopher Whalen, Charles Davis, Scott Edwards

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in ecology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Liang LiuDepartment of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States.
Lili YuDepartment of Biostatistics, Georgia Southern University, Statesboro, GA, United States.
Shaoyuan WuJiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China.
Jonathan ArnoldDepartment of Genetics, University of Georgia, Athens, GA, United States.
Christopher WhalenDepartment of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, United States.
Charles DavisDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States.
Scott EdwardsDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States.

Funding

Community Transmission of Tuberculosis Urban AfricaR01AI093856 · NIAID · UNIVERSITY OF GEORGIA · PI WHALEN, CHRISTOPHER C. · 2012 to 2021
$5.7M
NIAID NIH HHS R01 AI093856
6 · The paper itself

Abstract

Accurate reconstruction of species trees often relies on the quality of input gene trees estimated from molecular sequences. Previous studies suggested that if the sequence length is fixed, the maximum likelihood may produce biased gene trees which subsequently mislead inference of species trees. Two key questions need to be answered in this context: what are the scenarios that may result in consistently biased gene trees? and for those scenarios, are there any remedies that may remove or at least reduce the misleading effects of consistently biased gene trees? In this article, we establish a theoretical framework to address these questions. Considering a scenario where the true gene tree is a 4-taxon star tree

Indexed as

coalescent methodsgene treeslong branch attractionmultispecies coalescent modelshort branch attractionspecies trees

Identifiers

PMID39233780
PMCPMC11372852

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

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.