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The supermatrix approach to systematics
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/ajpa.1330940111openalex-snapshot
Cladistic analysis of molecular and morphological data
inferredcites →https://doi.org/10.1002/cpe.954openalex-snapshot
RAxML‐II: a program for sequential, parallel and distributed inference of large phylogenetic trees
inferredcites →https://doi.org/10.1006/clad.1999.0111openalex-snapshot
Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa
inferredcites →https://doi.org/10.1006/clad.2000.0147openalex-snapshot
The Phylogeny of the Extant Hexapod Orders
inferredcites →https://doi.org/10.1007/978-1-4020-2330-9_18openalex-snapshot
A Critique of Matrix Representation with Parsimony Supertrees
inferredcites →https://doi.org/10.1007/bf00985205openalex-snapshot
Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants
inferredcites →https://doi.org/10.1007/bf02459467openalex-snapshot
Links between maximum likelihood and maximum parsimony under a simple model of site substitution
inferredcites →https://doi.org/10.1007/s10914-005-4963-8openalex-snapshot
Phylogenetic Relationships of Extinct Cetartiodactyls: Results of Simultaneous Analyses of Molecular, Morphological, and Stratigraphic Data
inferredcites →https://doi.org/10.1016/0025-5564(82)90125-0openalex-snapshot
Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time
inferredcites →https://doi.org/10.1016/j.cub.2004.09.027openalex-snapshot
Bayesian Inference of the Metazoan Phylogeny
inferredcites →https://doi.org/10.1016/j.jbi.2005.04.001openalex-snapshot
Missing data and the design of phylogenetic analyses
inferredcites →https://doi.org/10.1016/j.ode.2004.05.001openalex-snapshot
Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects
inferredcites →https://doi.org/10.1016/j.tig.2004.03.009openalex-snapshot
Genome mosaicism and organismal lineages
inferredcites →https://doi.org/10.1016/j.tree.2004.03.015openalex-snapshot
The evolution of supertrees
inferredcites →https://doi.org/10.1016/j.ympev.2003.10.008openalex-snapshot
Independence of alignment and tree search
inferredcites →https://doi.org/10.1016/s0169-5347(97)01242-1openalex-snapshot
Phylogenetic supertrees: Assembling the trees of life
inferredcites →https://doi.org/10.1016/s1055-7903(02)00033-7openalex-snapshot
Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes
inferredcites →https://doi.org/10.1016/s1055-7903(03)00109-xopenalex-snapshot
Gene tree parsimony vs. uninode coding for phylogenetic reconstruction
inferredcites →https://doi.org/10.1023/a:1025504124129openalex-snapshot
Relationships of Endemic African Mammals and Their Fossil Relatives Based on Morphological and Molecular Evidence
inferredcites →https://doi.org/10.1038/nature02053openalex-snapshot
Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1038/nature04134openalex-snapshot
The phylogenetic position of the ‘giant deer’ Megaloceros giganteus
inferredcites →https://doi.org/10.1038/nrg1603openalex-snapshot
Phylogenomics and the reconstruction of the tree of life
inferredcites →https://doi.org/10.1071/9780643090149openalex-snapshot
Monocots: Systematics and Evolution
inferredcites →https://doi.org/10.1071/is04004openalex-snapshot
Partitioned Bremer support localises significant conflict in bee flies (Diptera : Bombyliidae : Anthracinae)
inferredcites →https://doi.org/10.1073/pnas.162224399openalex-snapshot
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
inferredcites →https://doi.org/10.1080/10635150117959openalex-snapshot
Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
inferredcites →https://doi.org/10.1080/106351501753462876openalex-snapshot
A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
inferredcites →https://doi.org/10.1080/10635150252899824openalex-snapshot
Fragmentary Taxa, Missing Data, and Ambiguity: Mistaken Assumptions and Conclusions
inferredcites →https://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
inferredcites →https://doi.org/10.1080/10635150309349openalex-snapshot
Partitioned Likelihood Support and the Evaluation of Data Set Conflict
inferredcites →https://doi.org/10.1080/10635150490264699openalex-snapshot
Bayesian Phylogenetic Analysis of Combined Data
inferredcites →https://doi.org/10.1080/10635150490423971openalex-snapshot
Inconsistencies in Arguments for the Supertree Approach: Supermatrices versus Supertrees of Crocodylia
inferredcites →https://doi.org/10.1080/10635150500234534openalex-snapshot
Asynchronous Colonization of Madagascar by the Four Endemic Clades of Primates, Tenrecs, Carnivores, and Rodents as Inferred from Nuclear Genes
inferredcites →https://doi.org/10.1080/10635150500234625openalex-snapshot
Hylid Frog Phylogeny and Sampling Strategies for Speciose Clades
inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot
Inferring Phylogeny Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1080/10635150500433649openalex-snapshot
Tenrec Phylogeny and the Noninvasive Extraction of Nuclear DNA
inferredcites →https://doi.org/10.1080/10635150500541722openalex-snapshot
Supertree Bootstrapping Methods for Assessing Phylogenetic Variation among Genes in Genome-Scale Data Sets
inferredcites →https://doi.org/10.1080/10635150590905984openalex-snapshot
Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories
inferredcites →https://doi.org/10.1080/10635150590950362openalex-snapshot
Measuring Support and Finding Unsupported Relationships in Supertrees
inferredcites →https://doi.org/10.1080/10635150600697283openalex-snapshot
Differentiating between Hypotheses of Lineage Sorting and Introgression in New Zealand Alpine Cicadas (Maoricicada Dugdale)
inferredcites →https://doi.org/10.1080/106351598260798openalex-snapshot
Generalizing Phylogenetic Parsimony from the Tree to the Forest
inferredcites →https://doi.org/10.1080/106351598260987openalex-snapshot
Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.001.0001openalex-snapshot
Parsimony, Phylogeny, and Genomics
inferredcites →https://doi.org/10.1093/acprof:oso/9780199297306.003.0008openalex-snapshot
Parsimony and Bayesian phylogenetics
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/sysbio/38.1.7openalex-snapshot
A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)
inferredcites →https://doi.org/10.1093/sysbio/43.4.467openalex-snapshot
Combining Data in Phylogenetic Systematics: An Empirical Approach Using Three Molecular Data Sets in the Solanaceae
inferredcites →https://doi.org/10.1093/sysbio/46.4.654openalex-snapshot
Multiple Sources of Character Information and the Phylogeny of Hawaiian Drosophilids
inferredcites →https://doi.org/10.1098/rsbl.2004.0282openalex-snapshot
Molecular evidence and marine snake origins
inferredcites →https://doi.org/10.1098/rspb.2005.3124openalex-snapshot
Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers
inferredcites →https://doi.org/10.1109/csb.2004.1332422openalex-snapshot
Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees
inferredcites →https://doi.org/10.1109/tcbb.2004.44openalex-snapshot
Phylogenetic super-networks from partial trees
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb00453.xopenalex-snapshot
THE PHYLOGENY OF A SPECIES-LEVEL TENDENCY: SPECIES HERITABILITY AND POSSIBLE DEEP ORIGINS OF BERGMANN'S RULE IN TETRAPODS
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CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED
inferredcites →https://doi.org/10.1111/j.1096-0031.1994.tb00181.xopenalex-snapshot
TESTING SIGNIFICANCE OF INCONGRUENCE
inferredcites →https://doi.org/10.1111/j.1096-0031.1996.tb00196.xopenalex-snapshot
PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING
inferredcites →https://doi.org/10.1111/j.1096-0031.1999.tb00278.xopenalex-snapshot
Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
inferredcites →https://doi.org/10.1111/j.1096-0031.2003.tb00311.xopenalex-snapshot
Data exploration in phylogenetic inference: scientific, heuristic, or neither
inferredcites →https://doi.org/10.1111/j.1096-0031.2006.00096.xopenalex-snapshot
Dynamic homology and the likelihood criterion
inferredcites →https://doi.org/10.1111/j.1471-8286.2004.00829.xopenalex-snapshot
Phylomatic: tree assembly for applied phylogenetics
inferredcites →https://doi.org/10.1111/j.1472-4677.2004.00020.xopenalex-snapshot
Evolutionary timing of the origins of mesophilic sulphate reduction and oxygenic photosynthesis: a phylogenomic dating approach
inferredcites →https://doi.org/10.1126/science.1102036openalex-snapshot
Prospects for Building the Tree of Life from Large Sequence Databases
inferredcites →https://doi.org/10.1126/science.284.5423.2124openalex-snapshot
Phylogenetic Classification and the Universal Tree
inferredcites →https://doi.org/10.1142/9789814447362_0053openalex-snapshot
SCALING OF ACCURACY IN EXTREMELY LARGE PHYLOGENETIC TREES
inferredcites →https://doi.org/10.1146/annurev.ecolsys.27.1.423openalex-snapshot
GENE TREES, SPECIES TREES, AND SYSTEMATICS: A Cladistic Perspective
inferredcites →https://doi.org/10.1146/annurev.es.26.110195.003301openalex-snapshot
SEPARATE VERSUS COMBINED ANALYSIS OF PHYLOGENETIC EVIDENCE
inferredcites →https://doi.org/10.1186/1471-2148-5-58openalex-snapshot
The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support
inferredcites →https://doi.org/10.1371/journal.pbio.0000019openalex-snapshot
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
inferredcites →https://doi.org/10.1641/0006-3568(2003)053[0544:mtsott]2.0.co;2openalex-snapshot
Morphology: The Shape of Things to Come
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Chinchaysuyoa, a new genus of the fish family Ariidae (Siluriformes), with a redescription of Chinchaysuyoa labiata from Ecuador and a new species description from Peru
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Molecular Systematics of the Caniform Carnivora and its Implications for Conservation
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Phylogenetic Analyses: Comparing Species to Infer Adaptations and Physiological Mechanisms
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Disintegrating Portulacaceae: A new familial classification of the suborder Portulacineae (Caryophyllales) based on molecular and morphological data
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The application of cophylogenic tools to gene sets
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Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies
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Testing Phylogenetic Stability with Variable Taxon Sampling
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Phylogenomic Dating and the Relative Ancestry of Prokaryotic Metabolisms
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Species Tree Estimation from Genome-Wide Data with guenomu
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High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function
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Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model
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Genome Analysis of Plants
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Sources of Error and Incongruence in Phylogenomic Analyses
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Molecular Evidence of Primate Origins and Evolution
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Extracting Conflict-Free Information from Multi-labeled Trees
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Molecular Evidence on Primate Origins and Evolution
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Molecular Phylogenetic and Phylogenomic Approaches in Studies of Lichen Systematics and Evolution
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Phylogeny of Animals: Genomes Have a Lot to Say
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Molecular phylogeny of glass sponges (Porifera, Hexactinellida): increased taxon sampling and inclusion of the mitochondrial protein-coding gene, cytochrome oxidase subunit I
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Host range expansion is density dependent
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Deep divergences in the coffee family and the systematic position of Acranthera
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How to get off the mismatch at the generic rank in African Podostemaceae?
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Morphology and phylogenetics of two holoparasitic plants, Balanophora japonica and Balanophora yakushimensis (Balanophoraceae), and their hosts in Taiwan and Japan
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Ophiocordyceps pulvinata sp. nov., a pathogen with a reduced stroma
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Molecular phylogeny of glass sponges (Porifera, Hexactinellida): increased taxon sampling and inclusion of the mitochondrial protein-coding gene, cytochrome oxidase subunit I
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“Artiodactylans”: Phylogeny and the Fossil Record
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Anatomical, Ontogenetic, and Genomic Homologies Guide Reconstructions of the Teeth-to-Baleen Transition in Mysticete Whales
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Isoelectric point stabilization and protein mass compression are associated with antimicrobial resistance in the genus Acinetobacter
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Single-Gene Versus Double-Gene Tree Analyses in Molecular Classification of Saudi Venomous Snakes
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Consensus Methods, Phylogenetic
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Supertree Methods, Phylogenetic
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Building the Tree of Life
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Phylogenomic analysis and the origin and early evolution of viruses
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Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom
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An Introduction to Phylogenetics and the Tree of Life
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Re-evaluation of the systematic position of the Jurassic–Early Cretaceous fern genus Coniopteris
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SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences
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Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis
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Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field
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A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation
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A likelihood look at the supermatrix–supertree controversy
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Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae
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Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods
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Phylogenetic relationships of living and fossil African papionins: Combined evidence from morphology and molecules
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Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches
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Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: New insights on an old topic
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Dissecting the genome, secretome, and effectome repertoires of Monilinia spp.: The causal agent of brown rot disease: A comparative analysis
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A new Drynaria (Polypodiaceae) from the Upper Pliocene of Southwest China
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Diversity and distribution of rhizobia nodulated with Phaseolus vulgaris in two ecoregions of China
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Soil legacies of a primary invader strongly drive secondary invasions for species that are phylogenetically distant
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Genetic diversity and distribution of bradyrhizobia nodulating peanut in acid-neutral soils in Guangdong Province
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Clanistics: a multi-level perspective for harvesting unrooted gene trees
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Origin of land plants using the multispecies coalescent model
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Gene tree discordance, phylogenetic inference and the multispecies coalescent
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An Integrated Perspective on Phylogenetic Workflows
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Recombination-aware phylogenomics
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Organelle genomes as universal standard for phylogenetics: a sociotechnical perspective
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The effect of model choice on phylogenetic inference using mitochondrial sequence data: Lessons from the scorpions
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Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): Delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism
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Phylogenetic analysis of nuclear and mitochondrial genes reveals evolutionary relationships and mitochondrial introgression in the sertifer species group of the genus Neodiprion (Hymenoptera: Diprionidae)
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On the role of character loss in orbiniid phylogeny (Annelida): Molecules vs. morphology
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Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae)
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Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences
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Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography
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The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees
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A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes)
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Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data
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A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
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Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data
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Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)
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Species tree of a recent radiation: The subfamily Delphininae (Cetacea, Mammalia)
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Primate molecular phylogenetics in a genomic era
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A phylogenetic blueprint for a modern whale
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Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.02.009openalex-snapshot
Unexpected phylogenetic positions of the genera Rupirana and Crossodactylodes reveal insights into the biogeography and reproductive evolution of leptodactylid frogs
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.07.003openalex-snapshot
Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.11.011openalex-snapshot
Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.03.001openalex-snapshot
Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.05.018openalex-snapshot
Phylogenetics, ancestral state reconstruction, and a new infrafamilial classification of the pantropical Ochnaceae (Medusagynaceae, Ochnaceae s.str., Quiinaceae) based on five DNA regions
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.06.026openalex-snapshot
Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.12.005openalex-snapshot
Mitochondrial phylogeny shows multiple independent ecological transitions and northern dispersion despite of Pleistocene glaciations in meadow and steppe vipers (Vipera ursinii and Vipera renardi)
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.01.011openalex-snapshot
Multilocus species tree analyses resolve the ancient radiation of the subtribe Zizaniinae (Poaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.05.023openalex-snapshot
Re-evaluating the phylogeny of allopolyploid Gossypium L.
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.06.009openalex-snapshot
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.08.025openalex-snapshot
An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.09.028openalex-snapshot
Evolution of geographical place and niche space: Patterns of diversification in the North American sedge (Cyperaceae) flora
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.12.002openalex-snapshot
Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.12.003openalex-snapshot
Improved resolution and a novel phylogeny for the Neotropical triplefin blennies (Teleostei: Tripterygiidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.021openalex-snapshot
A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.06.007openalex-snapshot
Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.09.008openalex-snapshot
Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.12.021openalex-snapshot
Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.05.004openalex-snapshot
Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.06.002openalex-snapshot
Effects of tectonics and large scale climatic changes on the evolutionary history of Hyalomma ticks
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.10.004openalex-snapshot
Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.01.014openalex-snapshot
Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.06.008openalex-snapshot
Worldwide phylogeny of three-spined sticklebacks
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.06.035openalex-snapshot
Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.10.003openalex-snapshot
Phylogenomics, life history and morphological evolution of ophiocomid brittlestars
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.03.010openalex-snapshot
Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106529openalex-snapshot
Resolving the basal divisions in the stylommatophoran land snails and slugs with special emphasis on the position of the Scolodontidae
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106769openalex-snapshot
Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107091openalex-snapshot
A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107200openalex-snapshot
Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107342openalex-snapshot
How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107862openalex-snapshot
Phylogeny and Diversification of Planthoppers (Hemiptera Fulgoromorpha) Based on a Comprehensive Molecular Dataset and Large Taxon Sampling
inferred← citeshttps://doi.org/10.1017/9781139047678.002openalex-snapshot
Introduction: Carving Nature at Its Joints, or Why Birds Are Not Dinosaurs and Men Are Not Apes
inferred← citeshttps://doi.org/10.1017/9781139047678.003openalex-snapshot
The Interrelationships of Organisms
inferred← citeshttps://doi.org/10.1017/9781139047678.006openalex-snapshot
Systematics: Exposing Myths
inferred← citeshttps://doi.org/10.1017/9781139047678.009openalex-snapshot
Monothetic and Polythetic Taxa
inferred← citeshttps://doi.org/10.1017/9781139047678.010openalex-snapshot
Non-taxa or the Absence of –Phyly: Paraphyly and Aphyly
inferred← citeshttps://doi.org/10.1017/9781139047678.012openalex-snapshot
Parameters of Classification:Ordo Ab Chao
inferred← citeshttps://doi.org/10.1017/9781139047678.013openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.014openalex-snapshot
Modern Artificial Methods and Raw Data
inferred← citeshttps://doi.org/10.1017/9781139047678.015openalex-snapshot
How to Study Classification: Consensus Techniques and General Classifications
inferred← citeshttps://doi.org/10.1017/9781139047678.016openalex-snapshot
How to Study Classification: ‘Total Evidence’ vs. ‘Consensus’, Character Congruence vs. Taxonomic Congruence, Simultaneous Analysis vs. Partitioned Data
inferred← citeshttps://doi.org/10.1017/9781139047678.017openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.018openalex-snapshot
How to Study Classification
inferred← citeshttps://doi.org/10.1017/9781139047678.020openalex-snapshot
Beyond Classification: How to Study Phylogeny
inferred← citeshttps://doi.org/10.1017/9781139047678.021openalex-snapshot
The Separation of Classification and Phylogenetics
inferred← citeshttps://doi.org/10.1017/9781139047678.022openalex-snapshot
Further Myths and More Misunderstandings
inferred← citeshttps://doi.org/10.1017/9781139047678.025openalex-snapshot
Systematics Association Special Volumes
inferred← citeshttps://doi.org/10.1017/s001667231000008xopenalex-snapshot
A supermatrix-based molecular phylogeny of the family Drosophilidae
inferred← citeshttps://doi.org/10.1038/nature11050openalex-snapshot
Accelerated speciation in colour-polymorphic birds
inferred← citeshttps://doi.org/10.1038/npre.2008.2261.1openalex-snapshot
Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)
inferred← citeshttps://doi.org/10.1038/nprot.2014.063openalex-snapshot
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
inferred← citeshttps://doi.org/10.1038/nrg3186openalex-snapshot
Molecular phylogenetics: principles and practice
inferred← citeshttps://doi.org/10.1038/s41396-021-00941-xopenalex-snapshot
Prokaryotic taxonomy and nomenclature in the age of big sequence data
inferred← citeshttps://doi.org/10.1038/s41396-021-01007-8openalex-snapshot
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development
inferred← citeshttps://doi.org/10.1038/s41467-023-43964-yopenalex-snapshot
The formation of the Indo-Pacific montane avifauna
inferred← citeshttps://doi.org/10.1038/s41586-025-09740-2openalex-snapshot
An ancient recombination desert is a speciation supergene in placental mammals
inferred← citeshttps://doi.org/10.1038/s41597-026-06936-7openalex-snapshot
CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family
inferred← citeshttps://doi.org/10.1038/s41598-021-81926-wopenalex-snapshot
Total Ortholog Median Matrix as an alternative unsupervised approach for phylogenomics based on evolutionary distance between protein coding genes
inferred← citeshttps://doi.org/10.1038/s41598-022-11370-xopenalex-snapshot
Phylogenies from unaligned proteomes using sequence environments of amino acid residues
inferred← citeshttps://doi.org/10.1038/s42003-022-03482-xopenalex-snapshot
Molecular phylogenies map to biogeography better than morphological ones
inferred← citeshttps://doi.org/10.1038/srep18075openalex-snapshot
Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa)
inferred← citeshttps://doi.org/10.1071/is08035openalex-snapshot
Supertrees and the Tree of Life: generating a metaphylogeny for a diverse invertebrate family (Insecta : Diptera : Therevidae) using constraint trees and the parsimony ratchet to overcome low taxon overlap
inferred← citeshttps://doi.org/10.1071/is19002openalex-snapshot
The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores)
inferred← citeshttps://doi.org/10.1073/pnas.1211733109openalex-snapshot
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
inferred← citeshttps://doi.org/10.1073/pnas.1603941113openalex-snapshot
Comparative genomics of biotechnologically important yeasts
inferred← citeshttps://doi.org/10.1080/07352680802665297openalex-snapshot
Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress, Promise, and Future Prospects
inferred← citeshttps://doi.org/10.1080/10635150801910436openalex-snapshot
Testing Congruence in Phylogenomic Analysis
inferred← citeshttps://doi.org/10.1080/10635150802304787openalex-snapshot
The Vestigial Olfactory Receptor Subgenome of Odontocete Whales: Phylogenetic Congruence between Gene-Tree Reconciliation and Supermatrix Methods
inferred← citeshttps://doi.org/10.1080/10635150802580949openalex-snapshot
Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)
inferred← citeshttps://doi.org/10.1080/14772000.2020.1729894openalex-snapshot
Total-evidence phylogeny and divergence times of Vermilingua (Mammalia: Pilosa)
inferred← citeshttps://doi.org/10.1080/14772000.2023.2200306openalex-snapshot
Total evidence phylogenetic analysis of Leiosauridae (Squamata) with focus on the ‘para-anoles’ and description of a new Urostrophus species from the Bolivian Andes
inferred← citeshttps://doi.org/10.1080/14772019.2017.1394922openalex-snapshot
A new phylogeny of ichthyosaurs (Reptilia: Diapsida)
inferred← citeshttps://doi.org/10.1080/23802359.2016.1214553openalex-snapshot
Complete mitochondrial genome of the parrotfish Calotomus japonicus (Osteichthyes: Scaridae) with implications based on the phylogenetic position
inferred← citeshttps://doi.org/10.1080/23802359.2018.1424583openalex-snapshot
Complete mitochondrial genome sequence of Glaucosoma buergeri (Pempheriformes: Glaucosomatidae) with implications based on the phylogenetic position
inferred← citeshttps://doi.org/10.1080/23802359.2018.1534562openalex-snapshot
Complete F mitochondrial genomes of the Biwa pearl mussel, Hyriopsis schlegelii: the first report from the species’ native lake in Japan
inferred← citeshttps://doi.org/10.1080/23802359.2021.1914218openalex-snapshot
Complete female-transmitted mitochondrial genomes of two freshwater mussels from the Lake Biwa system in Japan: Nodularia douglasiae and N. nipponensis
inferred← citeshttps://doi.org/10.1080/23802359.2021.1955762openalex-snapshot
Complete F mitochondrial genomes of two freshwater mussels from the Lake Biwa system in Japan: Beringiana fukuharai and Sinanodonta tumens
inferred← citeshttps://doi.org/10.1089/cmb.2015.0146openalex-snapshot
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
inferred← citeshttps://doi.org/10.1093/aob/mcaa011openalex-snapshot
A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)
inferred← citeshttps://doi.org/10.1093/aob/mct109openalex-snapshot
The diversity, ecology and evolution of extrafloral nectaries: current perspectives and future challenges
inferred← citeshttps://doi.org/10.1093/aob/mcv135openalex-snapshot
Why should we investigate the morphological disparity of plant clades?
inferred← citeshttps://doi.org/10.1093/bib/bbs050openalex-snapshot
The impact of HGT on phylogenomic reconstruction methods
inferred← citeshttps://doi.org/10.1093/bib/bbu015openalex-snapshot
Causes, consequences and solutions of phylogenetic incongruence
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac326openalex-snapshot
Building alternative consensus trees and supertrees using k -means and Robinson and Foulds distance
inferred← citeshttps://doi.org/10.1093/botlinnean/boaa008openalex-snapshot
Phylogenetic position and evolution of glandular structures of the unusual and narrowly distributed genus Rhytidanthera (Ochnaceae)
inferred← citeshttps://doi.org/10.1093/gbe/evad213openalex-snapshot
Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees
inferred← citeshttps://doi.org/10.1093/gbe/evr050openalex-snapshot
Evaluating Phylogenetic Congruence in the Post-Genomic Era
inferred← citeshttps://doi.org/10.1093/gbe/evs104openalex-snapshot
Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data
inferred← citeshttps://doi.org/10.1093/gbe/evu031openalex-snapshot
Archaeal “Dark Matter” and the Origin of Eukaryotes
inferred← citeshttps://doi.org/10.1093/isd/ixaf020openalex-snapshot
Phylogeny, molecular species delimitation, and biogeography of the cryptic subgenus Ulopsina (Hemiptera: Cicadellidae: Ulopinae)
inferred← citeshttps://doi.org/10.1093/isd/ixx009openalex-snapshot
An Empirical Test of Reduced-Representation Genomics to Infer Species-Level Phylogenies for Two Ant Groups
inferred← citeshttps://doi.org/10.1093/jhered/esx089openalex-snapshot
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree
inferred← citeshttps://doi.org/10.1093/jpe/rtad007openalex-snapshot
Functional and phylogenetic similarities of co-occurring invaders affect the growth of an invasive forb
inferred← citeshttps://doi.org/10.1093/molbev/msaa159openalex-snapshot
Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment
inferred← citeshttps://doi.org/10.1093/molbev/msab254openalex-snapshot
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
inferred← citeshttps://doi.org/10.1093/molbev/msad109openalex-snapshot
Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs
inferred← citeshttps://doi.org/10.1093/molbev/msn043openalex-snapshot
Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
inferred← citeshttps://doi.org/10.1093/molbev/msp250openalex-snapshot
Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples
inferred← citeshttps://doi.org/10.1093/molbev/msr185openalex-snapshot
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
inferred← citeshttps://doi.org/10.1093/molbev/msr205openalex-snapshot
Phylogenetic Analysis Based on Spectral Methods
inferred← citeshttps://doi.org/10.1093/molbev/msu176openalex-snapshot
Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials
inferred← citeshttps://doi.org/10.1093/molbev/msu331openalex-snapshot
Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting
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