ArticleIntegrative and comparative biology2013
Phylogenetic analysis of gene expression.
Article in Integrative and comparative biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Robust regression rescues poor phylogenetic decisions.BMC ecology and evolution · 2025Article
- Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes.Molecular biology and evolution · 2025Article
- MAFin: motif detection in multiple alignment files.Bioinformatics (Oxford, England) · 2025Article
- Leveraging graphical model techniques to study evolution on phylogenetic networks.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Transcriptomic Data Reveal Divergent Paths of Chitinase Evolution Underlying Dietary Convergence in Anteaters and Pangolins.Genome biology and evolution · 2025Article
- Article
- Comparative Analysis of Maternal Gene Expression Patterns Unravels Evolutionary Signatures Across Reproductive Modes.Molecular biology and evolution · 2024Article
- Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells.PLoS biology · 2024Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.Genome biology and evolution · 2023Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.bioRxiv : the preprint server for biology · 2023Article
- A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.Molecular biology and evolution · 2023Article
- An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation.Research (Washington, D.C.) · 2023Article
- The evolution of ovary-biased gene expression in Hawaiian Drosophila.PLoS genetics · 2023Article
- Family dinner: Transcriptional plasticity of five Noctuidae (Lepidoptera) feeding on three host plant species.Ecology and evolution · 2022Article
- Layered evolution of gene expression in "superfast" muscles for courtship.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora.Molecular biology and evolution · 2022Article
- The strength and form of natural selection on transcript abundance in the wild.Molecular ecology · 2021Article
- The Genomic Impact of Mycoheterotrophy in Orchids.Frontiers in plant science · 2021Article
- Adaptation of plasticity to projected maximum temperatures and across climatically defined bioregions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods.BMC genomics · 2020Article
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3 authors.
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Abstract
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. This will provide entirely new opportunities to identify genes related to particular phenotypes. There are, however, 3 key challenges that must be addressed for such studies to realize their potential. First, data on gene expression must be measured from multiple species, some of which may be field-collected, and parameterized in such a way that they can be compared across species. Second, it will be necessary to develop comparative phylogenetic methods suitable for large multidimensional datasets. In most phylogenetic comparative studies to date, the number n of independent observations (independent contrasts) has been greater than the number p of variables (characters). The behavior of comparative methods for these classic problems is now well understood under a wide variety of conditions. In studies of gene expression, and in studies based on other high-throughput tools, the number n of samples is dwarfed by the number p of variables. The estimated covariance matrices will be singular, complicating their analysis and interpretation, and prone to spurious results. Third, new approaches are needed to investigate the expression of the many genes whose phylogenies are not congruent with species phylogenies due to gene loss, gene duplication, and incomplete lineage sorting. Here we outline general considerations of project design for phylogenetic analyses of gene expression and suggest solutions to these three categories of challenges. These topics are relevant to high-throughput phenotypic data well beyond gene expression.
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