ArticleMolecular biology and evolution2022
Controls for Phylogeny and Robust Analysis in Pareto Task Inference.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Functional trade-offs and innovation shape the adaptive landscape of aquatic mammal feeding.iScience · 2026Article
- The adaptive tasks and trade-offs that drive the human value system.Communications psychology · 2025Article
- AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral Heterogeneity.Cancer discovery · 2025Article
- Life history dynamics of evolving tumors: insights into task specialization, trade-offs, and tumor heterogeneity.Cancer cell international · 2024Review
- Tetrapod sperm length evolution in relation to body mass is shaped by multiple trade-offs.Nature communications · 2024Article
- Pareto task inference analysis reveals cellular trade-offs in diffuse large B-Cell lymphoma transcriptomic data.Frontiers in systems biology · 2024Article
- Sex-dependent control of pheromones on social organization within groups of wild house mice.Current biology : CB · 2023Article
- Pareto optimality, economy-effectiveness trade-offs and ion channel degeneracy: improving population modelling for single neurons.Open biology · 2022Review
- Signature of Pareto optimization in the Escherichia coli proteome.Scientific reports · 2018Article
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10 authors.
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Abstract
Understanding the tradeoffs faced by organisms is a major goal of evolutionary biology. One of the main approaches for identifying these tradeoffs is Pareto task inference (ParTI). Two recent papers claim that results obtained in ParTI studies are spurious due to phylogenetic dependence (Mikami T, Iwasaki W. 2021. The flipping t-ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution. Methods Ecol Evol. 12(4):696-706) or hypothetical p-hacking and population-structure concerns (Sun M, Zhang J. 2021. Rampant false detection of adaptive phenotypic optimization by ParTI-based Pareto front inference. Mol Biol Evol. 38(4):1653-1664). Here, we show that these claims are baseless. We present a new method to control for phylogenetic dependence, called SibSwap, and show that published ParTI inference is robust to phylogenetic dependence. We show how researchers avoided p-hacking by testing for the robustness of preprocessing choices. We also provide new methods to control for population structure and detail the experimental tests of ParTI in systems ranging from ammonites to cancer gene expression. The methods presented here may help to improve future ParTI studies.
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