ArticleBMC genomics2015
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ecology and evolution · 2026Article
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 2026Article
- Comparative population genomic analysis of Brevibacterium casei isolated from a tuberculosis patient.Folia microbiologica · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Comparative genomics and evolutionary analyses of Sphaeropleales.Frontiers in plant science · 2025Article
- Generation of accurate, expandable phylogenomic trees with uDance.Nature biotechnology · 2024Article
- Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.Systematic biology · 2023Article
- Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees.Molecular biology and evolution · 2022Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Article
- Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.Genome biology and evolution · 2022Article
- Comparative genomics of the Western Hemisphere soft tick-borne relapsing fever borreliae highlights extensive plasmid diversity.BMC genomics · 2022Article
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).Frontiers in plant science · 2022Article
- Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Temporal and palaeoclimatic context of the evolution of insular woodiness in the Canary Islands.Ecology and evolution · 2021Article
- Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set.American journal of botany · 2021Article
- Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae).Molecular biology and evolution · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundSpecies tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete lineage sorting (ILS), and horizontal gene transfer (HGT). Mathematical theory about reconstructing species trees in the presence of HGT alone or ILS alone suggests that quartet-based species tree methods (known to be statistically consistent under ILS, or under bounded amounts of HGT) might be effective techniques for estimating species trees when both HGT and ILS are present.
resultsWe evaluated several publicly available coalescent-based methods and concatenation under maximum likelihood on simulated datasets with moderate ILS and varying levels of HGT. Our study shows that two quartet-based species tree estimation methods (ASTRAL-2 and weighted Quartets MaxCut) are both highly accurate, even on datasets with high rates of HGT. In contrast, although NJst and concatenation using maximum likelihood are highly accurate under low HGT, they are less robust to high HGT rates.
conclusionOur study shows that quartet-based species-tree estimation methods can be highly accurate under the presence of both HGT and ILS. The study suggests the possibility that some quartet-based methods might be statistically consistent under phylogenomic models of gene tree heterogeneity with both HGT and ILS.
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