ArticleProceedings of the National Academy of Sciences of the United States of America2014
A critical appraisal of the use of microRNA data in phylogenetics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- At the Edge of Survival: Exploring the Frontiers of Tardigrade Extreme Stress Tolerance.Molecular ecology · 2026Review
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Genomics Sheds New Light on the Ancestral Bilaterian Opsin Repertoire and Suggests Rhabdomeric Phototransduction in Xenacoelomorpha.Genome biology and evolution · 2025Article
- A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data.Systematic biology · 2025Article
- Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.iScience · 2024Article
- Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine.Cell genomics · 2023Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- Small RNAs in Cnidaria: A review.Evolutionary applications · 2023Article
- MirGeneDB 2.1: toward a complete sampling of all major animal phyla.Nucleic acids research · 2022Article
- A new model of forelimb ecomorphology for predicting the ancient habitats of fossil turtles.Ecology and evolution · 2021Article
- Digging into bivalve miRNAomes: between conservation and innovation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions.Molecular biology and evolution · 2021Article
- Large-Scale Annotation and Evolution Analysis of MiRNA in Insects.Genome biology and evolution · 2021Article
- Programmed DNA Elimination in Vertebrates.Annual review of animal biosciences · 2021Review
- Article
- MirGeneDB 2.0: the metazoan microRNA complement.Nucleic acids research · 2020Article
- Evolutionary Implications of the microRNA- and piRNA Complement ofNon-coding RNA · 2019Article
- miRTrace reveals the organismal origins of microRNA sequencing data.Genome biology · 2018Article
- Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.Genome biology and evolution · 2018Article
- The evolutionary origin of plant and animal microRNAs.Nature ecology & evolution · 2017Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Recent progress in resolving the tree of life continues to expose relationships that resist resolution, which drives the search for novel sources of information to solve these difficult phylogenetic problems. A recent example, the presence and absence of microRNA families, has been vigorously promoted as an ideal source of phylogenetic data and has been applied to several perennial phylogenetic problems. The utility of such data for phylogenetic inference hinges critically both on developing stochastic models that provide a reasonable description of the process that give rise to these data, and also on the careful validation of those models in real inference scenarios. Remarkably, however, the statistical behavior and phylogenetic utility of microRNA data have not yet been rigorously characterized. Here we explore the behavior and performance of microRNA presence/absence data under a variety of evolutionary models and reexamine datasets from several previous studies. We find that highly heterogeneous rates of microRNA gain and loss, pervasive secondary loss, and sampling error collectively render microRNA-based inference of phylogeny difficult. Moreover, our reanalyses fundamentally alter the conclusions for four of the five studies that we reexamined. Our results indicate that the capacity of miRNA data to resolve the tree of life has been overstated, and we urge caution in their application and interpretation.
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