Evidence map›Paper›PMID 31024760›Full record

ArticlePeerJ2019

The synergistic effect of concatenation in phylogenomics: the case in

Marike Palmer, Stephanus N Venter, Alistair R McTaggart, Martin P A Coetzee, Stephanie Van Wyk, Juanita R Avontuur, Chrizelle W Beukes, Gerda Fourie, Quentin C Santana, Magriet A Van Der Nest and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PeerJ, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.8field-weighted citation impact, top 29% of its field
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

5 citing papers in PubMed, 12 citations in OpenAlex.

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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

12 authors at 3 institutions in 3 countries.

Marike PalmerDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Stephanus N VenterDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Alistair R McTaggartDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Martin P A CoetzeeDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Stephanie Van WykDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Juanita R AvontuurDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Chrizelle W BeukesDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Gerda FourieDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Quentin C SantanaDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Magriet A Van Der NestDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
Jochen BlomBioinformatics and Systems Biology, Justus Liebig Universität Gießen, Giessen, Germany.
Emma T SteenkampDepartment of Biochemistry, Genetics and Microbiology, DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa.
University of Pretoria · ZAUniversity of Giessen · DEUniversity of Queensland · AU

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for

Indexed as

ConcatenatePhylogenetic conflictPhylogeneticsPhylogenetic signalPhylogenomicsSuper trees

Identifiers

PMID31024760
PMCPMC6474361
OpenAlexW2937451309

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.