ArticleNature2010
A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns.
Article in Nature, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers.
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215 citing papers in PubMed.
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- Toward mechanisms underlying the developmental hourglass: evolvability and phylotypic conservation.EvoDevo · 2025Review
- The phylotranscriptomic profile of angiosperm seed development follows a reverse hourglass pattern.The Plant cell · 2025Article
- Polyploid giant cancer cells (PGCC): short-term return to multicellularity.Biological research · 2025Article
- A newly evolved small secretory peptide enhances mechanical properties of spider silk.Nature communications · 2025Article
- Recently Evolved, Stage-Specific Genes Are Enriched at Life-Stage Transitions in Flies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Developmental system drift and modular gene regulatory networks shape gastrulation inLife science alliance · 2025Article
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- Cell fate specification modes shape transcriptome evolution in the highly conserved spiral cleavage.EMBO reports · 2025Article
- Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis.Molecular biology and evolution · 2025Article
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
155 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Parallels between phylogeny and ontogeny have been discussed for almost two centuries, and a number of theories have been proposed to explain such patterns. Especially elusive is the phylotypic stage, a phase during development where species within a phylum are particularly similar to each other. Although this has formerly been interpreted as a recapitulation of phylogeny, it is now thought to reflect an ontogenetic progression phase, where strong constraints on developmental regulation and gene interactions exist. Several studies have shown that genes expressed during this stage evolve at a slower rate, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage. Here we use a combination of phylostratigraphy and stage-specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Notably, ageing animals express increasingly older genes. Comparisons with similar data sets from flies and nematodes show that this pattern occurs across phyla. Our results indicate that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.
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