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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
Multiple resampled genomic matrices provide mixed support for arachnid monophyly
Marc Domènech1,2,3, Mattia Giacomelli1,2, Inés Galán-Luque1,2
1Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.
Biology Letters
|May 26, 2026
Summary
Developing a resolved tree of life is computationally challenging. Our new method for analyzing phylogenies reveals that chelicerate evolutionary history remains unresolved despite genomic data.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Constructing a comprehensive tree of life is hindered by computational demands and inadequate modeling of large genomic datasets.
- Phylogenetic analysis aims to resolve evolutionary relationships between species, but ancient clades often present challenges due to data complexity and computational intensity.
Purpose of the Study:
- To develop and apply a systematic approach for identifying robust and challenging nodes in ancient phylogenies.
- To investigate the unresolved phylogeny of chelicerates, specifically the contentious sister-group relationship between marine horseshoe crabs and arachnids.
- To assess the impact of different analytical strategies and data types on phylogenetic resolution.
Main Methods:
- Inferred single-copy orthologues from multi-protein, clade-specific matrices containing diverse taxa and genes.
- Analyzed concatenated supermatrices using mixture models, incorporating one randomly selected species per major clade.
- Assessed node support for competing topologies using amino acid and nucleotide data, employing strategies like removing distant relatives and recoding.
Main Results:
- Applied the novel approach to chelicerates, molluscs, and vertebrates.
- Chelicerate phylogenies demonstrated method and dataset dependency, indicating unresolved evolutionary history.
- Phylogenies for molluscs and vertebrates showed stable support, serving as benchmarks for well-resolved groups.
Conclusions:
- The developed approach systematically identifies challenging nodes in phylogenies, aiding in the resolution of the tree of life.
- Despite extensive genomic data and advanced analytical methods, the evolutionary history of chelicerates remains unresolved.
- Phylogenetic resolution is highly dependent on the chosen methods and datasets, particularly for ancient and complex clades.
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