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Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability

https://doi.org/10.1093/molbev/msg042
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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PHYLIP (Phylogeny Inference Package)
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Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
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Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis
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Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks
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Major fungal lineages are derived from lichen symbiotic ancestors
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Three retrotransposon families in the genome of Giardia lamblia : Two telomeric, one dead
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Bootstrap confidence levels for phylogenetic trees.
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Bootstrap confidence levels for phylogenetic trees
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Molecular Systematics of the Eastern Fence Lizard (Sceloporus undulatus): A Comparison of Parsimony, Likelihood, and Bayesian Approaches
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Model Misspecification and Probabilistic Tests of Topology: Evidence from Empirical Data Sets
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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
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MODELTEST: testing the model of DNA substitution.
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MRBAYES: Bayesian inference of phylogenetic trees
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Bacterial Origin for the Isoprenoid Biosynthesis Enzyme HMG-CoA Reductase of the Archaeal Orders Thermoplasmatales and Archaeoglobales
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Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting
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The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
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Testing a Covariotide Model of DNA Substitution
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Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
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Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
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Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees
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Is There Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull
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Gene Trees in Species Trees
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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The Closest Living Relatives of Land Plants
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Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
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Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
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Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences
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An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta)
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.11.015openalex-snapshot
Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.12.005openalex-snapshot
Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT–trnF sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.01.013openalex-snapshot
Molecular and morphological evolution of the amphipod radiation of Lake Baikal
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.05.009openalex-snapshot
Molecular phylogeny of the benthic shallow-water octopuses (Cephalopoda: Octopodinae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.05.012openalex-snapshot
A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.07.019openalex-snapshot
A molecular phylogeny of the Canidae based on six nuclear loci
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.08.019openalex-snapshot
Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.09.012openalex-snapshot
Phylogeny of Arthropoda inferred from mitochondrial sequences: Strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.11.008openalex-snapshot
New insights into the phylogeny of fig pollinators using Bayesian analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.12.014openalex-snapshot
Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes)
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.12.015openalex-snapshot
Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.01.001openalex-snapshot
Tree ferns: Monophyletic groups and their relationships as revealed by four protein-coding plastid loci
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.01.029openalex-snapshot
Basal relationships in the Drosophila melanogaster species group
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.04.006openalex-snapshot
Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.08.020openalex-snapshot
Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis)
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.10.012openalex-snapshot
Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.10.019openalex-snapshot
Novel phylogeny of the raccoon family (Procyonidae: Carnivora) based on nuclear and mitochondrial DNA evidence
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.11.001openalex-snapshot
Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata
inferred← citeshttps://doi.org/10.1016/j.ympev.2006.12.009openalex-snapshot
Molecular phylogenetic dating supports an ancient endemic speciation model in Australia’s biodiversity hotspot
inferred← citeshttps://doi.org/10.1016/j.ympev.2007.02.015openalex-snapshot
Phylogeny of “core Gruiformes” (Aves: Grues) and resolution of the Limpkin–Sungrebe problem
inferred← citeshttps://doi.org/10.1016/j.ympev.2007.03.011openalex-snapshot
A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach
inferred← citeshttps://doi.org/10.1016/j.ympev.2007.07.015openalex-snapshot
Filling the European gap: Biosystematics of the eusocial system Reticulitermes (Isoptera, Rhinotermitidae) in the Balkanic Peninsula and Aegean area
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.01.010openalex-snapshot
Phylogenetic relationships and heterogeneous evolutionary processes among phrynosomatine sand lizards (Squamata, Iguanidae) revisited
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.01.019openalex-snapshot
Random local neighbor joining: A new method for reconstructing phylogenetic trees
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.03.036openalex-snapshot
Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.05.013openalex-snapshot
A molecular phylogeny of the Sylvia cantillans complex: Cryptic species within the Mediterranean basin
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.10.018openalex-snapshot
Phylogenetic relationships among iguanian lizards using alternative partitioning methods and TSHZ1: A new phylogenetic marker for reptiles
inferred← citeshttps://doi.org/10.1016/j.ympev.2008.12.015openalex-snapshot
Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.01.006openalex-snapshot
Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.06.003openalex-snapshot
Accounting for molecular stochasticity in systematic revisions: Species limits and phylogeny of Paroaria
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.07.008openalex-snapshot
Phylogenetic relationships of Ceratitis fruit flies inferred from nuclear CAD and tango/ARNT gene fragments: Testing monophyly of the subgenera Ceratitis (Ceratitis) and C. (Pterandrus)
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.08.019openalex-snapshot
Deciphering and dating the red panda’s ancestry and early adaptive radiation of Musteloidea
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.10.022openalex-snapshot
Phylogeny of ladybirds (Coleoptera: Coccinellidae): Are the subfamilies monophyletic?
inferred← citeshttps://doi.org/10.1016/j.ympev.2009.12.020openalex-snapshot
Molecular phylogeny of acariform mites (Acari, Arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.01.015openalex-snapshot
Placing the mountain goat: A total evidence approach to testing alternative hypotheses
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.02.029openalex-snapshot
Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.04.015openalex-snapshot
Arthropod colonization of land – Linking molecules and fossils in oribatid mites (Acari, Oribatida)
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.07.003openalex-snapshot
Evolutionary history and taxonomy of a short-horned grasshopper subfamily: The Melanoplinae (Orthoptera: Acrididae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.08.018openalex-snapshot
Genetic variation and phylogeny of the cosmopolitan marine genus Tubificoides (Annelida: Clitellata: Naididae: Tubificinae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.08.032openalex-snapshot
Towards a molecular phylogeny of Mollusks: Bivalves’ early evolution as revealed by mitochondrial genes
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.02.014openalex-snapshot
Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.08.028openalex-snapshot
Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.09.011openalex-snapshot
Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.01.020openalex-snapshot
Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.08.019openalex-snapshot
Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.07.001openalex-snapshot
Phylogenomics supports Panpulmonata: Opisthobranch paraphyly and key evolutionary steps in a major radiation of gastropod molluscs
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.08.011openalex-snapshot
Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera)
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.09.009openalex-snapshot
Inside the Melanoplinae: New molecular evidence for the evolutionary history of the Eurasian Podismini (Orthoptera: Acrididae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.11.010openalex-snapshot
Phylogeny of the family Aglajidae (Pilsbry, 1895) (Heterobranchia: Cephalaspidea) inferred from mtDNA and nDNA
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.09.018openalex-snapshot
Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.10.004openalex-snapshot
When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.08.023openalex-snapshot
Effects of missing data on topological inference using a Total Evidence approach
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.11.021openalex-snapshot
Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.12.014openalex-snapshot
Molecular phylogeny of the Ellobiidae (Gastropoda: Panpulmonata) supports independent terrestrial invasions
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.04.001openalex-snapshot
Back to solitude: Solving the phylogenetic position of the Diazonidae using molecular and developmental characters
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.04.020openalex-snapshot
Resolution of inter and intra-species relationships of the West Indian fruit fly Anastrepha obliqua
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.004openalex-snapshot
Higher-level molecular phylogeny of the water mites (Acariformes: Prostigmata: Parasitengonina: Hydrachnidiae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.02.027openalex-snapshot
A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume “killer algae”
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.05.018openalex-snapshot
Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.05.025openalex-snapshot
Using a multi-gene approach to infer the complicated phylogeny and evolutionary history of lorises (Order Primates: Family Lorisidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.12.020openalex-snapshot
Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106699openalex-snapshot
Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107061openalex-snapshot
A phylogeny for the Drosophila montium species group: A model clade for comparative analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107115openalex-snapshot
Phylogeny and classification of Odonata using targeted genomics
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107523openalex-snapshot
Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107758openalex-snapshot
A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107913openalex-snapshot
Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data
inferred← citeshttps://doi.org/10.1016/s0065-308x(06)63001-7openalex-snapshot
Phylogenetic Analyses of Parasites in the New Millennium
inferred← citeshttps://doi.org/10.1016/s0743-7315(03)00079-0openalex-snapshot
Parallel algorithms for Bayesian phylogenetic inference
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00108-8openalex-snapshot
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00111-8openalex-snapshot
Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00115-5openalex-snapshot
Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00259-8openalex-snapshot
Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae)
inferred← citeshttps://doi.org/10.1017/cbo9780511614927.002openalex-snapshot
Molecular phylogenetics for conservation biology
inferred← citeshttps://doi.org/10.1017/s0024282911000375openalex-snapshot
Phylogenetic relations of European shrubby taxa of the genusUsnea
inferred← citeshttps://doi.org/10.1017/s0024282912000448openalex-snapshot
Testing morphology-based delimitation of Vulpicida juniperinus and V. tubulosus (Parmeliaceae) using three molecular markers
inferred← citeshttps://doi.org/10.1017/s0031182011000485openalex-snapshot
Trypanosomatids are common and diverse parasites ofDrosophila
inferred← citeshttps://doi.org/10.1017/s0952836904005278openalex-snapshot
A molecular approach to discerning the phylogenetic placement of the enigmatic snake Xenophidion schaeferi among the Alethinophidia
inferred← citeshttps://doi.org/10.1017/s0953756204001625openalex-snapshot
Disintegration of the Micareaceae (lichenized Ascomycota): a molecular phylogeny based on mitochondrial rDNA sequences
inferred← citeshttps://doi.org/10.1023/b:jomm.0000015105.96065.f0openalex-snapshot
Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)
inferred← citeshttps://doi.org/10.1038/nrg1603openalex-snapshot
Phylogenomics and the reconstruction of the tree of life
inferred← citeshttps://doi.org/10.1038/s41467-019-08822-wopenalex-snapshot
Model selection may not be a mandatory step for phylogeny reconstruction
inferred← citeshttps://doi.org/10.1038/s41467-020-20507-3openalex-snapshot
Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants
inferred← citeshttps://doi.org/10.1038/s41598-017-12300-yopenalex-snapshot
Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwin’s Favourite Orchids
inferred← citeshttps://doi.org/10.1038/s41598-022-08983-7openalex-snapshot
Systematic identification and expression profiles of the BAHD superfamily acyltransferases in barley (Hordeum vulgare)
inferred← citeshttps://doi.org/10.1038/s41598-022-13856-0openalex-snapshot
African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing
inferred← citeshttps://doi.org/10.1038/s41598-024-73703-2openalex-snapshot
The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species
inferred← citeshttps://doi.org/10.1046/j.1365-294x.2003.02085.xopenalex-snapshot
Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae)
inferred← citeshttps://doi.org/10.1051/ps/2017014openalex-snapshot
Qualitative Robustness in Bayesian Inference
inferred← citeshttps://doi.org/10.1071/9781486314935.bk08025_part1openalex-snapshot
Biodiversity
inferred← citeshttps://doi.org/10.1071/is11026openalex-snapshot
Genes, morphology, development and photosynthetic ability support the resurrection of Elysia cornigera (Heterobranchia : Plakobranchoidea) as distinct from the ‘solar-powered’ sea slug, E. timida
inferred← citeshttps://doi.org/10.1071/is17080openalex-snapshot
Phylogenetic systematics of the shelled sea slug genus Oxynoe Rafinesque, 1814 (Heterobranchia : Sacoglossa), with integrative descriptions of seven new species
inferred← citeshttps://doi.org/10.1071/mu03047openalex-snapshot
When DNA throws a spanner in the taxonomic works: testing for monophyly in the Dusky-capped Flycatcher, Myiarchus tuberculifer, and its South American subspecies, M. t. atriceps
inferred← citeshttps://doi.org/10.1071/mu05035openalex-snapshot
Molecular resolution of population history, systematics and historical biogeography of the Australian ringneck parrotsBarnardius: are we there yet?
inferred← citeshttps://doi.org/10.1071/sb05019openalex-snapshot
Phylogenetic relationships of Rhododendron section Vireya (Ericaceae) inferred from the ITS nrDNA region
inferred← citeshttps://doi.org/10.1073/pnas.0305562101openalex-snapshot
Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia , the world's largest flower
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