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The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA
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Statistical tests of models of DNA substitution
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Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests
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Comparison of phylogenetic trees
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A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals
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A Comprehensive and Dated Phylogenomic Analysis of Butterflies
inferredcites →https://doi.org/10.1016/j.dib.2018.04.094openalex-snapshot
Genome-scale DNA sequence data and the evolutionary history of placental mammals
inferredcites →https://doi.org/10.1016/j.ijpara.2018.07.001openalex-snapshot
Validity of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes) upheld in phylogenomic analysis
inferredcites →https://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2015.05.011openalex-snapshot
Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms
inferredcites →https://doi.org/10.1016/j.ympev.2015.10.027openalex-snapshot
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
inferredcites →https://doi.org/10.1016/j.ympev.2015.12.013openalex-snapshot
The effects of subsampling gene trees on coalescent methods applied to ancient divergences
inferredcites →https://doi.org/10.1016/j.ympev.2016.06.006openalex-snapshot
Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences
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Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
inferredcites →https://doi.org/10.1016/j.ympev.2018.10.003openalex-snapshot
Phylogenomics, life history and morphological evolution of ophiocomid brittlestars
inferredcites →https://doi.org/10.1016/j.ympev.2019.106539openalex-snapshot
Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/s41467-019-08822-wopenalex-snapshot
Model selection may not be a mandatory step for phylogeny reconstruction
inferredcites →https://doi.org/10.1038/s41559-016-0020openalex-snapshot
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1038/s41586-018-0708-8openalex-snapshot
Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes
inferredcites →https://doi.org/10.1073/pnas.0607004104openalex-snapshot
High-resolution species trees without concatenation
inferredcites →https://doi.org/10.1073/pnas.1211733109openalex-snapshot
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
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Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1073/pnas.1616744114openalex-snapshot
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
An Approximately Unbiased Test of Phylogenetic Tree Selection
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1080/10635150701429982openalex-snapshot
Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/14.9.819openalex-snapshot
GeneTree: comparing gene and species phylogenies using reconciled trees.
inferredcites →https://doi.org/10.1093/bioinformatics/btn484openalex-snapshot
BEST: Bayesian estimation of species trees under the coalescent model
inferredcites →https://doi.org/10.1093/bioinformatics/btq062openalex-snapshot
Phybase: an R package for species tree analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/bty633openalex-snapshot
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
inferredcites →https://doi.org/10.1093/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/isd/ixy013openalex-snapshot
Paleotropical Diversification Dominates the Evolution of the Hyperdiverse Ant Tribe Crematogastrini (Hymenoptera: Formicidae)
inferredcites →https://doi.org/10.1093/molbev/msi002openalex-snapshot
Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/msp296openalex-snapshot
Isolation with Migration Models for More Than Two Populations
inferredcites →https://doi.org/10.1093/molbev/mst116openalex-snapshot
Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals
inferredcites →https://doi.org/10.1093/molbev/msu331openalex-snapshot
Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1093/molbev/msv266openalex-snapshot
The Impact of Missing Data on Species Tree Estimation
inferredcites →https://doi.org/10.1093/molbev/msx324openalex-snapshot
Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syp055openalex-snapshot
Identifying Hybridization Events in the Presence of Coalescence via Model Selection
inferredcites →https://doi.org/10.1093/sysbio/syp057openalex-snapshot
Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)
inferredcites →https://doi.org/10.1093/sysbio/syr027openalex-snapshot
Estimating Species Trees from Unrooted Gene Trees
inferredcites →https://doi.org/10.1093/sysbio/syt057openalex-snapshot
Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syt068openalex-snapshot
Posterior Predictive Bayesian Phylogenetic Model Selection
inferredcites →https://doi.org/10.1093/sysbio/syv029openalex-snapshot
The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
inferredcites →https://doi.org/10.1093/sysbio/syw014openalex-snapshot
Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods
inferredcites →https://doi.org/10.1093/sysbio/syw082openalex-snapshot
Incomplete Lineage Sorting in Mammalian Phylogenomics
inferredcites →https://doi.org/10.1093/sysbio/syw089openalex-snapshot
Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards
inferredcites →https://doi.org/10.1093/sysbio/syw101openalex-snapshot
Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses
inferredcites →https://doi.org/10.1093/sysbio/syx001openalex-snapshot
PHRAPL: Phylogeographic Inference Using Approximate Likelihoods
inferredcites →https://doi.org/10.1093/sysbio/syy013openalex-snapshot
Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?
inferredcites →https://doi.org/10.1093/sysbio/syy019openalex-snapshot
The Biogeography of Deep Time Phylogenetic Reticulation
inferredcites →https://doi.org/10.1093/sysbio/syy033openalex-snapshot
Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations
inferredcites →https://doi.org/10.1093/sysbio/syy064openalex-snapshot
Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)
inferredcites →https://doi.org/10.1093/sysbio/syy074openalex-snapshot
Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)
inferredcites →https://doi.org/10.1093/sysbio/syz056openalex-snapshot
Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data
inferredcites →https://doi.org/10.1093/ve/vey016openalex-snapshot
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
inferredcites →https://doi.org/10.1098/rspb.2015.1413openalex-snapshot
Replicated divergence in cichlid radiations mirrors a major vertebrate innovation
inferredcites →https://doi.org/10.1109/tcbb.2004.10openalex-snapshot
Phylogenetic networks: modeling, reconstructibility, and accuracy
inferredcites →https://doi.org/10.1111/evo.12099openalex-snapshot
PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
inferredcites →https://doi.org/10.1111/evo.13558openalex-snapshot
Multiple origins of sexual dichromatism and aposematism within large carpenter bees
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05384.xopenalex-snapshot
Speciation in the White‐breasted Nuthatch (Sitta carolinensis): a multilocus perspective
inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00549.xopenalex-snapshot
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1111/jse.12160openalex-snapshot
Coalescent methods for estimating species trees from phylogenomic data
inferredcites →https://doi.org/10.1111/zsc.12210openalex-snapshot
Phylogenomic subsampling: a brief review
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110617-062249openalex-snapshot
Evaluating Model Performance in Evolutionary Biology
inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164407openalex-snapshot
Phylogenetic Inference Using Whole Genomes
inferredcites →https://doi.org/10.1186/1471-2105-15-273openalex-snapshot
A new method for modeling coalescent processes with recombination
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/s12859-019-2905-3openalex-snapshot
Testing adequacy for DNA substitution models
inferredcites →https://doi.org/10.1186/s12862-018-1155-8openalex-snapshot
Phylogenomic analysis of Apoidea sheds new light on the sister group of bees
inferredcites →https://doi.org/10.1186/s12862-018-1267-1openalex-snapshot
A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies
inferredcites →https://doi.org/10.1186/s12864-018-4619-8openalex-snapshot
The performance of coalescent-based species tree estimation methods under models of missing data
inferredcites →https://doi.org/10.1371/journal.pgen.1006006openalex-snapshot
Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent
inferredcites →https://doi.org/10.1371/journal.pone.0067001openalex-snapshot
Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
inferredcites →https://doi.org/10.1515/sagmb-2013-0048openalex-snapshot
Investigating the performance of AIC in selecting phylogenetic models
inferredcites →https://doi.org/10.3389/fgene.2017.00016openalex-snapshot
Analytical Biases Associated with GC-Content in Molecular Evolution
inferredcites →https://doi.org/10.4172/2329-9002.1000114openalex-snapshot
Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis
inferredcites →https://doi.org/10.7717/peerj.6399openalex-snapshot
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Coalescent-delimitation framework disentangles species boundaries within the Neotropical mouse-opossums subgenus Marmosops
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Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex
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The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species
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Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae
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Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss
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Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)
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Short branch attraction in phylogenomic inference under the multispecies coalescent
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Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea
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The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces
inferred← citeshttps://doi.org/10.3389/fpls.2021.765719openalex-snapshot
How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example
inferred← citeshttps://doi.org/10.3390/ani13030471openalex-snapshot
Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
inferred← citeshttps://doi.org/10.3390/bioengineering11050480openalex-snapshot
Common Methods for Phylogenetic Tree Construction and Their Implementation in R
inferred← citeshttps://doi.org/10.3767/persoonia.2023.51.07openalex-snapshot
Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution
inferred← citeshttps://doi.org/10.3897/phytokeys.205.85866openalex-snapshot
Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)
inferred← citeshttps://doi.org/10.4995/thesis/10251/176003openalex-snapshot
A genomic approach to the evolution, diversification and domestication of the genus Citrus
inferred← citeshttps://doi.org/10.6084/m9.figshare.24797896openalex-snapshot
Additional file 1 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.24798087openalex-snapshot
Additional file 2 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652528openalex-snapshot
Additional file 3 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652531openalex-snapshot
Additional file 4 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652534openalex-snapshot
Additional file 5 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652537openalex-snapshot
Additional file 6 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652540openalex-snapshot
Additional file 7 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652543openalex-snapshot
Additional file 8 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652546openalex-snapshot
Additional file 9 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652549openalex-snapshot
Additional file 10 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652552openalex-snapshot
Additional file 11 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652555openalex-snapshot
Additional file 12 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652558openalex-snapshot
Additional file 13 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652561openalex-snapshot
Additional file 14 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652564openalex-snapshot
Additional file 15 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652567openalex-snapshot
Additional file 16 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652570openalex-snapshot
Additional file 17 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652573openalex-snapshot
Additional file 18 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652576openalex-snapshot
Additional file 19 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652579openalex-snapshot
Additional file 20 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652582openalex-snapshot
Additional file 21 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652585openalex-snapshot
Additional file 22 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652588openalex-snapshot
Additional file 23 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.6084/m9.figshare.26652591openalex-snapshot
Additional file 24 of Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines
inferred← citeshttps://doi.org/10.64898/2026.04.29.721649openalex-snapshot
Phylogenomics reveals reticulate evolution in the Chenopodium album complex
inferred← citeshttps://doi.org/10.7554/elife.112129openalex-snapshot
Phylogenetic Mosaic of an Arms Race with Asymmetrical Sexual Conflict and Its Macroevolutionary Consequences in a Lineage of Small Water Striders
inferred← citeshttps://doi.org/10.7554/elife.72460openalex-snapshot
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
inferred← citeshttps://doi.org/10.7717/peerj.11502openalex-snapshot
Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation
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