Evidence map›Paper›PMID 40423579›Full record

ArticleMolecular biology and evolution2025

Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait.

Ammon Thompson, Michael R May, Ben R Hopkins, Nerisa Riedl, Olga Barmina, Benjamin J Liebeskind, Li Zhao, David Begun, Artyom Kopp

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PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular biology and evolution, 2025. 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. Review
  2. Review
  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

9 authors.

Ammon ThompsonDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0003-1825-4685
Michael R MayDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0002-5031-4820
Ben R HopkinsDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0002-9760-6185
Nerisa RiedlDepartment of Evolution and Ecology, University of California, Davis, CA, USA.
Olga BarminaDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0002-2297-4362
Benjamin J LiebeskindCenter for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.ORCID 0000-0002-8123-5260
Li ZhaoDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0001-6776-1996
David BegunDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0002-8809-1917
Artyom KoppDepartment of Evolution and Ecology, University of California, Davis, CA, USA.ORCID 0000-0001-5224-0741

Funding

Molecular Genetics of Evolutionary InnovationsR35GM122592 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI ARTYOM KOPP · 2017 to 2026
$4.5M
Human Frontier Science Program Organization LT000123/2020-LNIGMS NIH HHS R35 GM122592NIH HHS 5F32GM125107-02NIH HHS R35 GM122592
6 · The paper itself

Abstract

Changes in gene expression are a key driver of phenotypic evolution, leading to a persistent interest in the evolution of transcriptomes. Traditionally, gene expression is modeled as a continuous trait, leaving qualitative transitions largely unexplored. In this paper, we detail the development of new Bayesian inference techniques to study the evolutionary turnover of organ-specific transcriptomes, which we define as instances where orthologous genes gain or lose expression in a particular organ. To test these techniques, we analyze the transcriptomes of 2 male reproductive organs, testes and accessory glands, across 11 species of the Drosophila melanogaster species group. We first discretize gene expression states by estimating the probability that each gene is expressed in each organ and species. We then define a phylogenetic model of correlated transcriptome evolution in 2 or more organs and fit it to the expression state data. Inferences under this model imply that many genes have gained and lost expression in each organ, and that the 2 organs experienced accelerated transcriptome turnover on different branches of the Drosophila phylogeny.

Indexed as

Drosophila melanogasterModels, GeneticPhylogenyTranscriptomeAnimalsBayes TheoremDrosophilaEvolution, MolecularMaleTestisaccessory glandsDrosophilaevolutiongene expressionphylogeneticstestistranscriptome

Identifiers

PMID40423579
PMCPMC12108096

What Socratic holds

Textmetadata
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 Socratic graph.