Evidence map›Paper›PMID 38526019›Full record

ArticleGenome biology and evolution2024

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

David A Duchêne, Sebastián Duchêne, Josefin Stiller, Rasmus Heller, Simon Y W Ho

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. 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

5 authors.

David A DuchêneCenter for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark.ORCID 0000-0002-5479-1974
Sebastián DuchêneDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3010, Australia.ORCID 0000-0002-2863-0907
Josefin StillerVillum Centre for Biodiversity Genomics, University of Copenhagen, 2100 Copenhagen, Denmark.
Rasmus HellerSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.
Simon Y W HoSchool of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0002-0361-2307

Funding

European Research Council H2020-MSCA-IF-2019-883832Medical Research Council APP1157586
6 · The paper itself

Abstract

Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.

Indexed as

Evolution, MolecularModels, GeneticBiological EvolutionGenomeGenomicsPhylogenyClockstaRevolutionary ratemolecular clockphylogenomicsrate heterogeneity

Identifiers

PMID38526019
PMCPMC10999959

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.