ArticleProceedings of the National Academy of Sciences of the United States of America2015
Phylogenomics with paralogs.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories.PLoS computational biology · 2026Article
- Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ecology and evolution · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.Molecular biotechnology · 2026Article
- Genome-wide characterization and seasonal modulation of Hsp60 expression in juvenile Hilsa Shad across distinct upstream habitats.Journal, genetic engineering & biotechnology · 2025Article
- Orthology and near-cographs in the context of phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- Simplifying and Characterizing DAGs and Phylogenetic Networks via Least Common Ancestor Constraints.Bulletin of mathematical biology · 2025Article
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Clustering systems of phylogenetic networks.Theory in biosciences = Theorie in den Biowissenschaften · 2023Article
- Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling.Molecular biology and evolution · 2023Review
- Article
- Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat.International journal of molecular sciences · 2023Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies.Systematic biology · 2022Article
- Comprehensive identification of protein orthologs in the family Ascoviridae facilitates an understanding of phylogenomics, protein conservation, and phosphorylation.Archives of virology · 2022Article
- Distinguishing Evolutionary Conservation from Derivedness.Life (Basel, Switzerland) · 2022Review
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- Best match graphs and reconciliation of gene trees with species trees.Journal of mathematical biology · 2020Article
- Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.Systematic biology · 2020Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer.
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