Genome-scale coestimation of species and gene trees
Open accessAbstract
Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current methods to reconstruct phylogenies fail to model the two-way dependency between gene trees and the species tree, they often misrepresent gene and species histories. We present a new probabilistic model to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families. We use simulations to show that this method accurately infers the species tree and gene trees, is robust to misspecification of the models of sequence and gene family evolution, and provides a precise historic record of gene duplications and losses throughout genome evolution. We simultaneously reconstruct the history of mammalian species and their genes based on 36 completely sequenced genomes, and use the reconstructed gene trees to infer the gene content and organization of ancestral mammalian genomes. We show that our method yields a more accurate picture of ancestral genomes than the trees available in the authoritative database Ensembl.
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The novel OrthoFinder method outperformed all methods other than DLCpar (full) in terms of accuracy on two independent simulated datasets.
“In terms of accuracy, the novel OrthoFinder method outperformed all methods other than DLCpar (full) (Fig. 5a, Additional file 1: Table S2).”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [34]
The Results > Simulations passage reports that PHYLDOG produced more accurate gene trees than PhyML, not an accuracy ranking for OrthoFinder. Searches for OrthoFinder, DLCpar, and the claimed comparison across two independent simulated datasets found no passage addressing it in our copy. (LLM, conf=0.76)
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“Potential alternatives include the use of molecular clocks [16], gene tree parsimony [17] and, most recently, probabilistic gene tree/species tree reconciliation [18].”
- Authors
- Boussau, B., Szöllősi, G. J., Duret, L., Gouy, M., Tannier, E., & Daubin, V.
- Affiliations
- Lyon 1 Université (FR)
- Corresponding author
- Boussau, Bastien
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2012-11-06
- Volume
- 23
- Issue
- 2
- Pages
- 323-330
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3561873
- OpenAlex
- W1972157500
- Cited by
- 258
- References
- 2
- Citations by year
- 2026: 7 · 2025: 15 · 2024: 12 · 2023: 5 · 2022: 14 · 2021: 17 · 2020: 21 · 2019: 21 · 2018: 22 · 2017: 26 · 2016: 21 · 2015: 29 · 2014: 25 · 2013: 22 · 2012: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- HighWire Press Open Archive (submittedVersion)
- Funders
- European Commission (253642)
- Agence Nationale de la Recherche (011-03, ANR- 10-BINF-01-01, ANR-08-EMER-0011, ANR-10-BINF-0001, ANR-10)
- Centre National de la Recherche Scientifique
- Institut National de Physique Nucléaire et de Physique des Particules
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- species tree estimation, gene tree estimation, gene duplication, gene loss, coalescent models, ancestral genome reconstruction, mammalian phylogeny, gene family evolution, genome evolution
- MeSH terms
- Algorithms, Animals, Computer Simulation, Genes, Humans, Models, Genetic, Phylogeny, Models, Statistical, Genome, Gene Deletion, Evolution, Molecular, Computational Biology, Gene Duplication
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