ArticleProceedings of the National Academy of Sciences of the United States of America2007
High-resolution species trees without concatenation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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147 citing papers in PubMed.
- Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).PLoS computational biology · 2026Article
- RIFinder reveals widespread adaptive remote introgression in grass genomes.Plant communications · 2026Article
- Impact of incomplete lineage sorting and natural selection on the phylogenetic and taxonomic uncertainties of Aspidistra in Taiwan.Botanical studies · 2025Article
- Investigations into the Diversity and Distribution of tRNA and Phylogenetics of Translation Factors in Amoebozoa-InfectingViruses · 2025Article
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- Terraces in species tree inference from gene trees.BMC ecology and evolution · 2024Article
- Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.Systematic biology · 2023Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Performance of intron 7 of theZooKeys · 2023Article
- Continent-wide patterns of song variation predicted by classical rules of biogeography.Ecology letters · 2022Article
- Phylogenomic analysis does not support a classic but controversial hypothesis of progenitor-derivative origins for the serpentine endemic Clarkia franciscana.Evolution; international journal of organic evolution · 2022Article
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- The evolution of social parasitism inProceedings of the National Academy of Sciences of the United States of America · 2021Article
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- A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae.Applications in plant sciences · 2020Article
- Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin.Developmental biology · 2020Article
- The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets.Systematic biology · 2020Article
- A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae).Annals of botany · 2020Article
- STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency.BMC genomics · 2020Article
- Fungal species boundaries in the genomics era.Fungal genetics and biology : FG & B · 2019Review
87 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.
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