ArticleGenome research2012
Unified modeling of gene duplication, loss, and coalescence using a locus tree.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Analysis of phylogenetic signal in protein language model embeddings.Scientific reports · 2026Article
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Phylogenetic Insights from a NovelPlants (Basel, Switzerland) · 2025Article
- Revealing Reassortment in Influenza A Viruses with TreeSort.Molecular biology and evolution · 2025Article
- Ages, sizes and (trees within) trees of taxa and of urns, from Yule to today.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- Unifying duplication episode clustering and gene-species mapping inference.Algorithms for molecular biology : AMB · 2024Article
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference.Molecular biology and evolution · 2022Article
- Embedding gene trees into phylogenetic networks by conflict resolution algorithms.Algorithms for molecular biology : AMB · 2022Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes.Systematic biology · 2022Article
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.Molecular biology and evolution · 2022Article
- Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.Molecular biology and evolution · 2021Article
4 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic model, DLCoal, that defines gene duplication and loss in a population setting, such that coalescence and ILS can be directly addressed. Interestingly, this model implies that in addition to the usual gene tree and species tree, there exists a third tree, the locus tree, which will likely have many applications. Using this model, we develop the first general reconciliation method that accurately infers gene duplications and losses in the presence of ILS, and we show its improved inference of orthologs, paralogs, duplications, and losses for a variety of clades, including flies, fungi, and primates. Also, our simulations show that gene duplications increase the frequency of ILS, further illustrating the importance of a joint model. Going forward, we believe that this unified model can offer insights to questions in both phylogenetics and population genetics.
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