The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

scientific article published on 23 March 2011

The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/bib/NabhanS12
P356DOI10.1093/BIB/BBR014
P932PMC publication ID3251835
P698PubMed publication ID21436145
P5875ResearchGate publication ID50850555

P2093author name stringIndra Neil Sarkar
Ahmed Ragab Nabhan
P2860cites workThe evolutionary position of nematodesQ21093615
Broad phylogenomic sampling improves resolution of the animal tree of lifeQ22337246
Incomplete taxon sampling is not a problem for phylogenetic inferenceQ24555203
The neighbor-joining method: a new method for reconstructing phylogenetic treesQ25939010
Confidence Limits on Phylogenies: an Approach using the BootstrapQ26778379
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesQ27860580
BEAST: Bayesian evolutionary analysis by sampling treesQ27860723
Evolutionary trees from DNA sequences: A maximum likelihood approachQ27860898
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum LikelihoodQ27861000
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzeesQ27861060
Increased taxon sampling greatly reduces phylogenetic errorQ28201637
Phylogenomics and the reconstruction of the tree of lifeQ28247594
Missing data and the design of phylogenetic analysesQ28253408
The logical basis of phylogenetic taxonomyQ28267959
Application of phylogenetic networks in evolutionary studiesQ28276801
The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogeniesQ28285586
Phylogenies from molecular sequences: inference and reliabilityQ28289703
Phylogenomics: the beginning of incongruence?Q28298382
The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST dataQ28754323
A review of long-branch attractionQ29397287
Conflicting phylogenetic signals at the base of the metazoan treeQ47388509
Large-scale sequencing and the new animal phylogenyQ47591330
The phylogenetic potential of entire 26S rDNA sequences in plantsQ48039586
Inferring complex phylogenies.Q52296474
Models of amino acid substitution and applications to mitochondrial protein evolution.Q52907382
Phylogenetic information and experimental design in molecular systematics.Q55435443
Branch Support and Tree StabilityQ55953534
Rapid Neighbour-JoiningQ56228814
Parsimony in Systematics: Philosophical IssuesQ56427363
More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic AccuracyQ57162900
When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomicsQ57531285
Rings of single-walled carbon nanotubesQ59060786
Computational complexity of inferring phylogenies from dissimilarity matricesQ69418195
Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methodsQ73454875
Taxonomic sampling, phylogenetic accuracy, and investigator biasQ74297965
Taxon sampling and the accuracy of large phylogeniesQ74304069
Genome-scale approaches to resolving incongruence in molecular phylogeniesQ29547249
Bayesian inference of phylogeny and its impact on evolutionary biologyQ29547502
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methodsQ29547744
Evidence for a clade of nematodes, arthropods and other moulting animalsQ29547800
Gene tree discordance, phylogenetic inference and the multispecies coalescentQ29614318
Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte CarloQ29614991
The tree of eukaryotesQ29616064
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and ProtostomiaQ29618582
A general comparison of relaxed molecular clock modelsQ29618908
Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiospermsQ30698104
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principleQ30875297
Resolution of phylogenetic conflict in large data sets by increased taxon samplingQ31049542
Sensitivity of phylogeny estimation to taxonomic samplingQ31077972
Genome trees and the tree of lifeQ31103613
Inconsistency of phylogenetic estimates from concatenated data under coalescenceQ31105795
Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?Q31108749
Missing data, incomplete taxa, and phylogenetic accuracyQ33187728
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysisQ33196499
Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC contentQ33279052
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomicsQ33320233
An even "newer" animal phylogenyQ33378161
The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inferenceQ33595529
The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data setsQ33615642
Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inferenceQ34019219
Increased taxon sampling is advantageous for phylogenetic inferenceQ34147941
A note on the neighbor-joining algorithm of Saitou and Nei.Q34170397
Phylogeny estimation: traditional and Bayesian approachesQ35097343
Taxon sampling, bioinformatics, and phylogenomicsQ37485746
Evolutionary relationships of eukaryotic kingdomsQ38560679
The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joiningQ38575927
Is sparse taxon sampling a problem for phylogenetic inference?Q42422738
Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inferenceQ42650662
The importance of taxon sampling in genomic studies: an example from the cyclooxygenases of teleost fishesQ43445994
Experimental design criteria in phylogenetics: where to add taxaQ43613051
Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationshipsQ44279794
Is it better to add taxa or characters to a difficult phylogenetic problem?Q44692911
Profiling phylogenetic informativenessQ45252022
Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?Q45421250
Large-scale phylogenies and measuring the performance of phylogenetic estimatorsQ45720973
Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin.Q46799456
How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruenceQ46894441
P433issue1
P921main subjectphylogeneticsQ171184
P304page(s)122-134
P577publication date2011-03-23
P1433published inBriefings in BioinformaticsQ4967031
P1476titleThe impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
P478volume13

Reverse relations

cites work (P2860)
Q91753464A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
Q28596153A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus
Q41671830A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation.
Q92399845A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers
Q93014326A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia
Q110696588A revised multilocus phylogeny of Old World sparrows (Aves: Passeridae)
Q35017606A test of Darwin's naturalization hypothesis in the thistle tribe shows that close relatives make bad neighbors
Q28652371A well-resolved phylogeny of the trees of Puerto Rico based on DNA barcode sequence data
Q35180768AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.
Q110697138An ocean yet to be discovered: increasing systematic knowledge of Indo-Pacific Okenia Menke, 1830 (Nudibranchia:Goniodorididae)
Q35066377Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses.
Q38709423Cross-platform compatibility of de novo-aligned SNPs in a nonmodel butterfly genus
Q54463074Ctenophore relationships and their placement as the sister group to all other animals.
Q42677698Delphinid systematics and biogeography with a focus on the current genus Lagenorhynchus: multiple pathways for antitropical and trans-oceanic radiation
Q104693653Diverse Phylogenomic Datasets Uncover a Concordant Scenario of Laurasiatherian Interordinal Relationships
Q35956691Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents
Q45749795Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers
Q21128724Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
Q61796024Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Q111629653Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)
Q46262735Expanded repertoire of kinetoplast associated proteins and unique mitochondrial DNA arrangement of symbiont-bearing trypanosomatids.
Q42670376Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses
Q110697307Global diversification and evolutionary history of onchidiid slugs (Gastropoda, Pulmonata)
Q64860724Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae)
Q28710489How to handle speciose clades? Mass taxon-sampling as a strategy towards illuminating the natural history of Campanula (Campanuloideae)
Q83515139ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies
Q41243559Identification of nuclear low-copy genes and their phylogenetic utility in rosids.
Q36222738Improved sampling at the subspecies level solves a taxonomic dilemma - A case study of two enigmatic Chinese tit species (Aves, Passeriformes, Paridae, Poecile).
Q110854585Insights into the Tricholomatineae (Agaricales, Agaricomycetes): a new arrangement of Biannulariaceae and Callistosporium, Callistosporiaceae fam. nov., Xerophorus stat. nov., and Pleurocollybia incorporated into Callistosporium
Q21132662Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.)
Q40172520Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.
Q122332133Kerkia Radoman, 1978 (Caenogastropoda: Hydrobiidae): endemism, apparently morphostatic evolution and cryptic speciation
Q31162062Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes
Q64065839Mitochondrial genome evolution in parasitic plants
Q28655630Mitogenomics of the Old World monkey tribe Papionini
Q104624996Molecular phylogenetic analysis of Punctoidea (Gastropoda, Stylommatophora)
Q59284530Molecular phylogeny of the hyperdiverse genusSarcophaga(Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa
Q64265523Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae
Q34649562Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes
Q91847510Out of Africa: The origins of the protozoan blood parasites of the Trypanosoma cruzi clade found in bats from Africa
Q110451122Phylogenetic analysis of the family Megalopodidae (Coleoptera: Chrysomeloidea): better taxon‐sampling facilitates detection of new relationships and new taxa
Q38907476Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes
Q49277100Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages
Q56865120Phylogenomic evidence overturns current conceptions of social evolution in wasps (Vespidae)
Q38751277Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella.
Q91178585Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling
Q91619552Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Q63507967Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error
Q57211864Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae)
Q89968579Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints
Q110697370Plastid phylogenomics of the Sansevieria Clade of Dracaena (Asparagaceae) resolves a recent radiation
Q28658139Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes
Q28603057Resolving the Phylogenetic Position of Coelacanth: The Closest Relative Is Not Always the Most Appropriate Outgroup
Q40924828Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae).
Q88741790Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution
Q57295484Sequencing HIV-neutralizing antibody exons and introns reveals detailed aspects of lineage maturation
Q110444858Single nucleotide polymorphism‐based species phylogeny of greater fritillary butterflies (Lepidoptera: Nymphalidae: Speyeria ) demonstrates widespread mitonuclear discordance
Q34549104Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray-Finned Fish as the Outgroup
Q110444822Systematics and origin of moths in the subfamily Arctiinae (Lepidoptera, Erebidae) in the Neotropical region
Q101439295Systematics of the Saharo‐Arabian clade of the Palearctic naked‐toed geckos with the description of a new species of Tropiocolotes endemic to Oman
Q93052372Tackling Rapid Radiations With Targeted Sequencing
Q95840948The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes
Q110451282The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus
Q38598738The components of biodiversity, with a particular focus on phylogenetic information.
Q38482267The impact of automated filtering of BLAST-determined homologs in the phylogenetic detection of horizontal gene transfer from a transcriptome assembly
Q41408546The lemur revolution starts now: the genomic coming of age for a non-model organism
Q111348147The phylogenetic history of the old world butterfly subtribe Mycalesina extended: the Mycalesis (Lepidoptera: Nymphalidae) of Sri Lanka
Q110445072The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes
Q38597500Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens
Q36206789dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees

Search more.