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Convergent genomic signatures associated with vertebrate viviparity

Eastment, Rhiannon V., Wong, Bob B. M., McGee, Matthew D.·2024·BMC Biology
DOI 10.1186/s12915-024-01837-wPMC PMC10854053
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Abstract

Background: Viviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? Results: We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes—be it at the nucleotide or protein level—common to all viviparous lineages. Conclusions: Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.

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  • 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 Eastment et al. 2024

    The Background states that the study used vertebrate whole-genome data spanning more than 400 million years and accounting for 17 independent transitions to viviparity. But the Methods (Whole genome alignments) say the default alignment used for substitution-rate analysis accounted for 14 transitions; the 17-transition figure describes the broader dataset, not specifically its coding-gene alignments. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • 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 Eastment et al. 2024

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  • Eastment et al. identified diverse molecular changes associated with viviparity, but only some were replicated, and even then only across a subset of lineages.

    “In addition, they identified diverse molecular changes associated with viviparity, but only some of these genetic changes were replicated, and even then only across a subset of lineages.”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Eastment et al. 2024

  • Several recent studies have applied multiple complementary PhyloG2P methods.

    “This diversity has been actively embraced with several recent studies applying multiple complementary PhyloG2P methods (Eliason et al. 2023; Zhang et al. 2023; Eastment et al. 2024; Matsuda and Makino 2024)”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Eastment et al. 2024

  • If a replicated change in phenotype has been achieved through changes in different genetic elements, PhyloG2P methods will fail to identify them unless considerable prior knowledge of the genetic elements involved can be leveraged to identify genetic replication at the network or pathway level.

    “If a replicated change in phenotype has been achieved through changes in different genetic elements, then PhyloG2P methods will fail to identify them unless considerable prior knowledge of the genetic elements involved can be leveraged to identify genetic replication at the network or pathway level (Lamichhaney et al. 2019; Wheeler et al. 2022; Eastment et al. 2024; Shakya et al. 2025).”

    From From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions (2025) · cites this paper as Eastment et al. 2024

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Metadata

Authors
Eastment, R. V., Wong, B. B. M., & McGee, M. D.
ORCID
Eastment, Rhiannon V.
Venue
BMC Biology
Publisher
Springer Science and Business Media LLC
Published
2024-02-08
Volume
22
Issue
1
ISSN
1741-7007
DOI
10.1186/s12915-024-01837-w
PMC
PMC10854053
Cited by
9
References
7
Language
en
Licence
Funders
  • Australian Government (Research Training Program Scholarship)
  • Australian Research Council (DP220100245, FT190100014, DP180104195, DE180101558)

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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.

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