ArticleMolecular biology and evolution2021
Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed.
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- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.Molecular biology and evolution · 2026Article
- The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics.Systematic biology · 2026Article
- Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development.Molecular biology and evolution · 2026Article
- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive phylogenomic analyses of ciliated protists with a revised classification of the phylum Ciliophora (Eukaryota, Alveolata).Science China. Life sciences · 2026Article
- Integrative evidence reveals adaptive divergence and speciation in gentoo penguins.Communications biology · 2026Article
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating.Systematic biology · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).Molecular ecology resources · 2026Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- Article
- Identifying sets of phylogenetically informative markers for Anastrepha (Diptera: Tephritidae).Scientific reports · 2025Article
- Phylogenomics and macroevolution of a florally diverse Neotropical plant clade.Evolution; international journal of organic evolution · 2025Article
- Article
- Discordance Down Under: Combining Phylogenomics and Fungal Symbioses to Detangle Difficult Nodes in a Diverse Tribe of Australian Terrestrial Orchids.Systematic biology · 2025Article
- Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clamOpen biology · 2025Article
- Iguanas rafted more than 8,000 km from North America to Fiji.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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