ArticleProceedings of the National Academy of Sciences of the United States of America2018
Pairwise comparisons across species are problematic when analyzing functional genomic data.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
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- The link between gene duplication and divergent patterns of gene expression across a complex life cycle.Evolution letters · 2024Article
- Gene Protein Sequence Evolution Can Predict the Rapid Divergence of Ovariole Numbers in the Drosophila melanogaster Subgroup.Genome biology and evolution · 2024Article
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- Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells.PLoS biology · 2024Article
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- Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data.Nature ecology & evolution · 2024Article
- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.Bioinformatics (Oxford, England) · 2023Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.Genome biology and evolution · 2023Article
- Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits.Genome research · 2023Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.bioRxiv : the preprint server for biology · 2023Article
- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis.bioRxiv : the preprint server for biology · 2023Article
- The GRN concept as a guide for evolutionary developmental biology.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2023Article
- A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data.Molecular biology and evolution · 2023Article
- The evolution of ovary-biased gene expression in Hawaiian Drosophila.PLoS genetics · 2023Article
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5 authors.
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Abstract
There is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here, we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to have more similar attributes (expression in this case) than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead, we find that they reflect species relationships. These reanalyses concretely show the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.
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