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Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes

Yusuf, Leeban H, Saldívar Lemus, Yolitzi, Thorpe, Peter, Macías Garcia, Constantino, Ritchie, Michael G·2023·Molecular Biology and Evolution
DOI 10.1093/molbev/msad208PMC PMC10568250
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Abstract

The transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases of phenotypic convergence. However, whether the repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common signature in genomic divergence remains largely unknown. Although recent investigations into the evolution of viviparity have demonstrated striking similarity among the genes and molecular pathways involved across disparate vertebrate groups, quantitative tests for genome-wide convergent have provided ambivalent answers. Here, we investigate the potential role of molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes and utilized publicly available genomes of viviparous and oviparous species to test for molecular convergence across both coding and noncoding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and in rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, both statistical power and biological confounds could constrain our ability to detect significant correlated evolution. We therefore identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. Motif enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development, and immunity occurred alongside the evolution of viviparity. Overall, however, our findings indicate that independent transitions to viviparity in these fish are not strongly associated with an excess of molecular convergence, but a few genes show convincing evidence of convergent evolution.

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  • Together, findings of Yusuf et al. (2023) and Eastment et al. (2024) suggest that complex traits evolving over large timescales show limited genetic repeatability, likely reflecting redundancy in the genetic routes that can lead to viviparity.

    “Together, the findings of Yusuf et al. (2023) and Eastment et al. (2024) suggests that complex traits evolving over large timescales show limited genetic repeatability, likely reflecting redundancy in the genetic routes that can lead to viviparity.”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Yusuf et al. 2023

    The Discussion and Conclusions (pages unavailable) report no strong genome-wide signal of molecular convergence across the sampled transitions to viviparity, while also identifying a few repeatedly involved genes. That supports limited genetic repeatability in this system, but the paper does not establish the broader claim about complex traits over large timescales or show that redundant genetic routes explain the pattern. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Eastment et al. (2024) constructed a set of gene alignments from vertebrate genomes spanning over 400 million years of evolution that included 17 independent transitions to viviparity, a far larger number than earlier PhyloG2P studies.

    “Eastment et al. constructed a set of gene alignments from vertebrate genomes spanning over 400 million years of evolution that included 17 independent transitions to viviparity, a far larger number than earlier PhyloG2P studies (Yusuf et al. 2023).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Yusuf et al. 2023

  • In any group of lineages that have independently achieved similar phenotypic changes, some may have undergone similar or identical genetic changes, whereas others may have achieved the same phenotype through unique genetic changes.

    “In any group of lineages that have independently achieved similar phenotypic changes, some of them may have undergone similar or identical genetic changes, where as others may have achieved the same phenotype through unique genetic changes (Yusuf et al. 2023).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Yusuf et al. 2023

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Metadata

Authors
Yusuf, L. H., Saldívar Lemus, Y., Thorpe, P., Macías Garcia, C., & Ritchie, M. G.
Affiliations
  • Centre for Biological Diversity, School of Biology, University of St Andrews , St Andrews , UK
  • The Data Analysis Group, School of Life Sciences, University of Dundee , Dundee , UK
  • Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria , Mexico City CdMx , Mexico
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2023-10
Volume
40
Issue
10
ISSN
  • 0737-4038
  • 1537-1719
DOI
10.1093/molbev/msad208
PMC
PMC10568250
Cited by
22
References
4
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor, 3 d)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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