ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2008
Dealing with incongruence in phylogenomic analyses.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed.
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- AmpliPhy improves gene trees by adding homologous sequences without affecting alignments.Bioinformatics advances · 2026Article
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group.Molecular ecology · 2025Article
- Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus).Systematic biology · 2024Article
- A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes).GigaScience · 2024Article
- Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae).Plants (Basel, Switzerland) · 2023Article
- Evidence of horizontal gene transfer withinMicrobial genomics · 2023Article
- A plastid phylogenomic framework for the palm family (Arecaceae).BMC biology · 2023Article
- Evolution of a hybrid zone of two willow species (Ecology and evolution · 2023Article
- Phylogenomic analysis ofFrontiers in plant science · 2023Article
- Ghost Lineages Highly Influence the Interpretation of Introgression Tests.Systematic biology · 2022Article
- Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera.Innovation (Cambridge (Mass.)) · 2022Article
- Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.Genome biology and evolution · 2022Article
- Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations.Molecular ecology resources · 2022Article
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
32 more citing papers are in PubMed but not listed here.
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Abstract
Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
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