ArticleGenome biology and evolution2018
Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes.
Article in Genome biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 67 citations in OpenAlex.
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- Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis.Nature communications · 2025Article
- Cross-species single-cell transcriptomics reveals neuronal similarities and heterogeneity in amniote pallium.Zoological research · 2025Article
- Comparative transcriptomics in serial organs uncovers early and pan-organ developmental changes associated with organ-specific morphological adaptation.Nature communications · 2025Article
- Evolution and genetics of accessory gland transcriptome divergence between Drosophila melanogaster and D. simulans.Genetics · 2024Article
- Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data.Nature ecology & evolution · 2024Article
- Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts.iScience · 2024Article
- Benchmarking strategies for cross-species integration of single-cell RNA sequencing data.Nature communications · 2023Article
- The evolving definition of plant cell type.Frontiers in plant science · 2023Article
- Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.Developmental dynamics : an official publication of the American Association of Anatomists · 2022Article
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- Layered evolution of gene expression in "superfast" muscles for courtship.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Single-nucleus transcriptomes reveal evolutionary and functional properties of cell types in the Drosophila accessory gland.Genetics · 2022Article
- Cell types as species: Exploring a metaphor.Frontiers in plant science · 2022Review
- Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts.Nature ecology & evolution · 2022Article
- Evolution of higher mesenchymal CD44 expression in the human lineage: A gene linked to cancer malignancy.Evolution, medicine, and public health · 2022Article
- An ancient, conserved gene regulatory network led to the rise of oral venom systems.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology.iScience · 2021Article
- Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton.Frontiers in genetics · 2021Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolution and diversification of cell types is a key means by which animal complexity evolves. Recently, hierarchical clustering and phylogenetic methods have been applied to RNA-seq data to infer cell type evolutionary history and homology. A major challenge for interpreting this data is that cell type transcriptomes may not evolve independently due to correlated changes in gene expression. This nonindependence can arise for several reasons, such as common regulatory sequences for genes expressed in multiple tissues, that is, pleiotropic effects of mutations. We develop a model to estimate the level of correlated transcriptome evolution (LCE) and apply it to different data sets. The results reveal pervasive correlated transcriptome evolution among different cell and tissue types. In general, tissues related by morphology or developmental lineage exhibit higher LCE than more distantly related tissues. Analyzing new data collected from bird skin appendages suggests that LCE decreases with the phylogenetic age of tissues compared, with recently evolved tissues exhibiting the highest LCE. Furthermore, we show correlated evolution can alter patterns of hierarchical clustering, causing different tissue types from the same species to cluster together. To identify genes that most strongly contribute to the correlated evolution signal, we performed a gene-wise estimation of LCE on a data set with ten species. Removing genes with high LCE allows for accurate reconstruction of evolutionary relationships among tissue types. Our study provides a statistical method to measure and account for correlated gene expression evolution when interpreting comparative transcriptome data.
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