ArticlePLoS currents2015
Concatenation Analyses in the Presence of Incomplete Lineage Sorting.
Article in PLoS currents, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection.Journal of molecular evolution · 2026Article
- An updated phylogeny of Boraginales based on the Angiosperms353 probe set: a roadmap for understanding morphological evolution.Annals of botany · 2025Article
- Islands Promote Diversification of the Silvereye Species Complex: A Phylogenomic Analysis of a Great Speciator.Molecular ecology · 2025Article
- Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study inEcology and evolution · 2025Article
- MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing.Molecular biology and evolution · 2024Article
- Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.Molecular biology and evolution · 2024Article
- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
- Effect of Different Types of Sequence Data on Palaeognath Phylogeny.Genome biology and evolution · 2023Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq).Frontiers in plant science · 2022Article
- Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation.Algorithms for molecular biology : AMB · 2021Article
- Article
- Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae).Proceedings. Biological sciences · 2020Article
- Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.PLoS biology · 2020Article
- Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity.Proceedings. Biological sciences · 2020Article
- Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.Systematic biology · 2020Article
- An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.Applications in plant sciences · 2019Article
- Mammal madness: is the mammal tree of life not yet resolved?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.BMC genomics · 2015Article
- A comparative study of SVDquartets and other coalescent-based species tree estimation methods.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Incomplete lineage sorting (ILS), modelled by the multi-species coalescent, is a process that results in a gene tree being different from the species tree. Because ILS is expected to occur for at least some loci within genome-scale analyses, the evaluation of species tree estimation methods in the presence of ILS is of great interest. Performance on simulated and biological data have suggested that concatenation analyses can result in the wrong tree with high support under some conditions, and a recent theoretical result by Roch and Steel proved that concatenation using unpartitioned maximum likelihood analysis can be statistically inconsistent in the presence of ILS. In this study, we survey the major species tree estimation methods, including the newly proposed "statistical binning" methods, and discuss their theoretical properties. We also note that there are two interpretations of the term "statistical consistency", and discuss the theoretical results proven under both interpretations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.