ArticleBMC bioinformatics2012
Gene trees and species trees: irreconcilable differences.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Adaptive evolution of stress response genes in parasites aligns with host niche diversity.BMC biology · 2025Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Phylogenomics and plastome evolution ofFrontiers in plant science · 2023Article
- Phylostat: a web-based tool to analyze paralogous clade divergence in phylogenetic trees.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- Primary orthologs from local sequence context.BMC bioinformatics · 2020Article
- Reconstructing the phylogeny of new world monkeys (Current zoology · 2019Article
- Advances and Applications in the Quest for Orthologs.Molecular biology and evolution · 2019Article
- Accurate prediction of orthologs in the presence of divergence after duplication.Bioinformatics (Oxford, England) · 2018Article
- Extracting functional trends from whole genome duplication events using comparative genomics.Biological procedures online · 2016Review
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Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReconciliation is the classical method for inferring a duplication and loss history from a set of extant genes. It is based upon the notion of embedding the gene tree into the species tree, the incongruence between the two indicating evidence for duplication and loss. However, results obtained by this method are highly dependent upon the considered species and gene trees. Thus, painstaking attention has been given to the development of methods for reconstructing accurate gene trees.
resultsThis paper highlights the fact that errors in gene trees are not the only reasons for the inference of an erroneous duplication-loss history. More precisely, we prove that, under certain reasonable hypotheses based on the widely accepted link between function and sequence constraints, even a well-supported gene tree yield a reconciliation that does not correspond to the true history. We then provide the theoretical underpinnings for a conservative approach to infer histories given such gene trees. We apply our method to the mammalian interleukin-1 (IL) gene tree, that has been used as a model example to illustrate the role of reconciliation.
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