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Cited by 17Chromosomal and Genetic VariationsEvolution and Genetic DynamicsEvolution and Paleontology Studies

Effective population size does not explain long-term variation in genome size and transposable element content in animals

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Marino, Alba, Debaecker, Gautier, Fiston-Lavier, Anna-Sophie, Haudry, Annabelle, Nabholz, Benoit·2025·eLife
DOI 10.7554/elife.100574PMC PMC12274066

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Abstract

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such variation are still debated. As the effective population size (Ne e ) reflects the intensity of genetic drift, it is expected to be a key determinant of the fixation rate of nearly-neutral mutations. Accordingly, the Mutational Hazard Hypothesis postulates lineages with low Ne e to have bigger genome sizes due to the accumulation of slightly deleterious transposable elements (TEs), and those with high Ne e to maintain streamlined genomes as a consequence of a more effective selection against TEs. However, the existence of both empirical confirmation and refutation using different methods and different scales precludes its general validation. Using high-quality public data, we estimated genome size, TE content, and rate of non-synonymous to synonymous substitutions (dN/dS) as Ne e proxy for 807 species including vertebrates, molluscs, and insects. After collecting available life-history traits, we tested the associations among population size proxies, TE content, and genome size, while accounting for phylogenetic non-independence. Our results confirm TEs as major drivers of genome size variation, and endorse life-history traits and dN/dS as reliable proxies for Ne e . However, we do not find any evidence for increased drift to result in an accumulation of TEs across animals. Within more closely related clades, only a few isolated and weak associations emerge in fishes and birds. Our results outline a scenario where TE dynamics vary according to lineage-specific patterns, lending no support for genetic drift as the predominant force driving long-term genome size evolution in animals.

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  • Although efficient selection under large effective population sizes is predicted to purge TEs, recent animal-wide analyses find no association between effective population size and either genome size or TE content.

    “Although efficient selection under large effective population sizes is predicted to purge TEs (66), recent animal-wide analyses find no association between effective population size and either genome size or TE content (67).”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [67]

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Cited by

Sorted by citations

Authors
Marino, A., Debaecker, G., Fiston-Lavier, A.-S., Haudry, A., & Nabholz, B.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Lyon 1 Université (FR)
  • ISEM, Université de Montpellier, CNRS, IRD
Corresponding author
Marino, Alba
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2025-07-18
Volume
13
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.100574
PMC
PMC12274066
OpenAlex
W4402438594
Cited by
17
References
2
Citations by year
2026: 11 · 2025: 6
Type
posted content
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Agence Nationale de la Recherche (ANR-20-CE02-0008-01 "NeGA")
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
effective population size, genome size evolution, transposable elements, genetic drift, dN/dS, life-history traits, genome streamlining, vertebrates, Mollusca, insects, fish, birds
MeSH terms
Animals, DNA Transposable Elements, Phylogeny, Population Density, Genetic Variation, Evolution, Molecular, Genetic Drift, Genome Size

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