ArticleBMC genomics2018
The performance of coalescent-based species tree estimation methods under models of missing data.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 31 papers.
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31 citing papers in PubMed.
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- When the sand blossoms: Phylogeny, trait evolution, and geography of speciation in Linanthus.American journal of botany · 2025Article
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- Museum Genomics Reveals the Hybrid Origin of an Extinct Crater Lake Endemic.Systematic biology · 2024Article
- Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Evolutionary applications · 2024Article
- Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model.Algorithms for molecular biology : AMB · 2023Article
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- A Reinvestigation of Multiple Independent Evolution and Triassic-Jurassic Origins of Multicellular Volvocine Algae.Genome biology and evolution · 2023Article
- Weighted ASTRID: fast and accurate species trees from weighted internode distances.Algorithms for molecular biology : AMB · 2023Article
- Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads.Ecology and evolution · 2023Article
- Improving quartet graph construction for scalable and accurate species tree estimation from gene trees.Genome research · 2023Article
- Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.Systematic biology · 2023Article
- Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs.Molecular biology and evolution · 2023Article
- Taxonomic review ofPeerJ · 2023Article
- Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.Bioinformatics (Oxford, England) · 2023Article
- Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEstimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species phylogeny. Methods to estimate species trees in the presence of gene tree discord due to incomplete lineage sorting have been developed and proved to be statistically consistent when gene tree discord is due only to incomplete lineage sorting and every gene tree includes the full set of species.
resultsWe establish statistical consistency of certain coalescent-based species tree estimation methods under some models of taxon deletion from genes. We also evaluate the impact of missing data on four species tree estimation methods (ASTRAL-II, ASTRID, MP-EST, and SVDquartets) using simulated datasets with varying levels of incomplete lineage sorting, gene tree estimation error, and degrees/patterns of missing data.
conclusionsAll the species tree estimation methods improved in accuracy as the number of genes increased and often produced highly accurate species trees even when the amount of missing data was large. These results together indicate that accurate species tree estimation is possible under a variety of conditions, even when there are substantial amounts of missing data.
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