Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

Goloboff, Pablo A.; Szumik, Claudia A.

doi:10.1016/j.ympev.2015.04.003

Cited by 73Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesPlant Diversity and Evolution

The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index.

Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

Open access

Goloboff, Pablo A., Szumik, Claudia A.·2015·Molecular Phylogenetics and Evolution

DOI 10.1016/j.ympev.2015.04.003

Open this paper in CoChat — free account Open PDF

Abstract

This paper describes an efficient implementation of triplet-based measures of stability, in the program TNT. The only available implementations of such measures are much slower than the present one, either because of an inefficient implementation (Phyutility, Thor) or because the stability is evaluated with quartets (RogueNaRok, requiring O(t(4)), instead of the O(t(3)) possible for triplets). The method to quickly calculate triplets is applied to solving IterPCR (Pol and Escapa, 2009). It is shown that, in some cases, IterPCR or other algorithms in the program TNT (e.g. commands prunnelsen, prunmajor, or chkmoves) produce more informative results than analysis with RogueNaRok.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1016/j.ympev.2015.04.003

Cites

33 of 33 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

The character information in the rogues can influence the relationships of the other taxa.
“The rogue taxa were excluded from the trees when calculating the consensus; they were never excluded from the matrix in any search for optimal trees (thus, the character information in the rogues can influence the relationships of the other taxa; see [105] for a recent discussion of this problem).”
From Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds (2020) · cites this paper as [105]
The rogue taxa were excluded from the trees when calculating the consensus; they were never excluded from the matrix in any search for optimal trees.
“The rogue taxa were excluded from the trees when calculating the consensus; they were never excluded from the matrix in any search for optimal trees (thus, the character information in the rogues can influence the relationships of the other taxa; see [105] for a recent discussion of this problem).”
From Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds (2020) · cites this paper as [105]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

TNT, a free program for phylogenetic analysis
Goloboff, P. A., Farris, J. S., & Nixon, K. C. (2008) · Cladistics · doi:10.1111/j.1096-0031.2008.00217.x · Cited by 5,352
Self-citation
Algorithms on strings, trees, and sequences computer science and computational biology
Gusfield, D. (1997) · Cited by 3,490
Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL
Chase, M. W., Soltis, P. S., Olmstead, R. G., Morgan, D., Les, D. H., Mishler, B. D., Duvall, M. R., Price, R. A., Hills, H. G., Qiu, Y., et al. (1993) · Annals of the Missouri Botanical Garden · doi:10.2307/2399846 · Cited by 2,033
Improvements to resampling measures of group support
Goloboff, P. A., Farris, J. S., Källersjö, M., Oxelman, B., Ramıacute;rez, M. J., & Szumik, C. A. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00376.x · Cited by 851
Self-citation
Phyutility: A phyloinformatics tool for trees, alignments and molecular data
Smith, S. A., & Dunn, C. W. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm619 · Cited by 629
On Finding Lowest Common Ancestors: Simplification and Parallelization
Schieber, B., & Vishkin, U. (1988) · SIAM Journal on Computing · doi:10.1137/0217079 · Cited by 535
Phylogenomic analyses unravel annelid evolution
Struck, T. H., Paul, C., Hill, N., Hartmann, S. A., Hösel, C., Kube, M., Lieb, B., Meyer, A., Tiedemann, R., Purschke, G., et al. (2011) · Nature · doi:10.1038/nature09864 · Cited by 416
Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
Aberer, A. J., Krompaß, D., & Stamatakis, A. (2012) · Systematic Biology · doi:10.1093/sysbio/sys078 · Cited by 398
Unstable taxa in cladistic analysis: identification and the assessment of relevant characters
Pol, D., & Escapa, I. H. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00258.x · Cited by 335
Methods for quick consensus estimation
Goloboff, P. (2001) · Cladistics · doi:10.1006/clad.2000.0156 · Cited by 274
Self-citation
Methods for Quick Consensus Estimation
Goloboff, P. A., & Farris, J. S. (2001) · Cladistics · doi:10.1111/j.1096-0031.2001.tb00102.x · Cited by 255
Self-citation
Deep metazoan phylogeny: When different genes tell different stories
Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254
Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony
Wilkinson, M. (1995) · Systematic Biology · doi:10.1093/sysbio/44.4.501 · Cited by 254
Common Cladistic Information and its Consensus Representation: Reduced Adams and Reduced Cladistic Consensus Trees and Profiles
Wilkinson, M. (1994) · Systematic Biology · doi:10.1093/sysbio/43.3.343 · Cited by 220
Problems due to missing data in phylogenetic analyses including fossils: a critical review
Kearney, M., & Clark, J. M. (2003) · Journal of Vertebrate Paleontology · doi:10.1671/0272-4634(2003)023[0263:pdtmdi]2.0.co;2 · Cited by 208
Majority-rule reduced consensus trees and their use in bootstrapping
Wilkinson, M. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025604 · Cited by 197
Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
Goloboff, P. A., Catalano, S. A., Mirande, J. M., Szumik, C., Arias, J. S., Källersjö, M., & Farris, J. S. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00255.x · Cited by 136
Self-citation
The Phylogenetic Trunk: Maximal Inclusion of Taxa with Missing Data in an Analysis of the Lepospondyli (Vertebrata, Tetrapoda)
Anderson, J. S. (2001) · Systematic Biology · doi:10.1080/10635150119889 · Cited by 136
RadCon: phylogenetic tree comparison and consensus
Thorley, J., & Page, R. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.5.486 · Cited by 129
Testing the phylogenetic stability of early tetrapods
THORLEY, J. L., & WILKINSON, M. (1999) · Journal of Theoretical Biology · doi:10.1006/jtbi.1999.0999 · Cited by 99
Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes
Lahr, D. J. G., Grant, J. R., Nguyen, T., Lin, J., & Katz, L. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022780 · Cited by 88
S uper T riplets : a triplet-based supertree approach to phylogenomics
Ranwez, V., Criscuolo, A., & Douzery, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq196 · Cited by 54
On the Three-Taxon Approach to Parsimony Analysis
Laet, J. E. D. (1998) · Cladistics · doi:10.1006/clad.1998.0075 · Cited by 53
Triplet supertree heuristics for the tree of life
Lin, H. T., Burleigh, J. G., & Eulenstein, O. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-s1-s8 · Cited by 52
A Simple and Accurate Method for Rogue Taxon Identification
Aberer, A. J., & Stamatakis, A. (2011) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2011.70 · Cited by 46
GB‐to‐TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT
Goloboff, P. A., & Catalano, S. A. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00400.x · Cited by 41
Self-citation
Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction
Siu-Ting, K., Pisani, D., Creevey, C. J., & Wilkinson, M. (2014) · Systematic Biology · doi:10.1093/sysbio/syu066 · Cited by 40
Uncovering Hidden Phylogenetic Consensus in Large Data Sets
Pattengale, N. D., Aberer, A. J., Swenson, K. M., Stamatakis, A., & Moret, B. M. E. (2011) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2011.28 · Cited by 40
Evaluating Undirected Positional Congruence of Individual Taxa Between Two Estimates of the Phylogenetic Tree for a Group of Taxa
Estabrook, G. F. (1992) · Systematic Biology · doi:10.1093/sysbio/41.2.172 · Cited by 28
Identifying stable reference taxa for phylogenetic nomenclature
Wilkinson, M. (2005) · Zoologica Scripta · doi:10.1111/j.1463-6409.2005.00213.x · Cited by 22
Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees
Sand, A., Holt, M. K., Johansen, J., Fagerberg, R., Brodal, G. S., Pedersen, C. R., & Mailund, T. (2013) · Biology · doi:10.3390/biology2041189 · Cited by 14
Abstracts of the 22nd Annual Meeting of the Willi Hennig Society
Stevenson, D. W. (2004) · Cladistics · doi:10.1111/j.1096-0031.2003.00006.x · Cited by 8
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms
Deepak, A., Dong, J., & Fernández‐Baca, D. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-30191-9_9 · Cited by 7

Flagged first, then by citations

Research works printed but not linked: 4

Aberer, A., 2011. Advanced Methods for Phylogenetic Post-Analysis. Master’s Thesis. Technische Universität München/Heidelberg Institute for Theoretical Studies, Germany, January 2011, 77 pp.
Dekker, M.C., 1986. Reconstruction Methods for Derivation Trees. Thesis submitted to the Department of Mathematics and Computer Science, Vrije Universiteit, Amsterdam.
Goloboff, 1995, A revision of the South American spiders of the family Nemesiidae (Araneae, Mygalomorphae). Part I: species from Peru, Chile, Argentina, and Uruguay, Bull. Am. Mus. Nat. Hist., 224, 1
Mosses, C., 2005. Triplet Supertrees. Thesis presented to the Department of Computer Science, University of Aarhus, Denmark, 6 June 2005, 94 pp.

Sorted by citations

TNT version 1.5, including a full implementation of phylogenetic morphometrics
Goloboff, P. A., & Catalano, S. A. (2016) · Cladistics · doi:10.1111/cla.12160 · Cited by 2,254
“…extension of implied weighting to take into account missing entries and average amounts of homoplasy in sets of characters (Goloboff, 2013), new search routines for difﬁcult data sets (Goloboff, 2014, 2015), or the implementation of algorithms to identify wildcard taxa (Goloboff and Szumik, 2015).”
BackgroundMethodSelf-citation
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
Mai, U., & Mirarab, S. (2018) · BMC Genomics · doi:10.1186/s12864-018-4620-2 · Cited by 387
Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)
Hosner, P. A., Faircloth, B. C., Glenn, T. C., Braun, E. L., & Kimball, R. T. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv347 · Cited by 241
Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds
Pei, R., Pittman, M., Goloboff, P. A., Dececchi, T. A., Habib, M. B., Kaye, T. G., Larsson, H. C. E., Norell, M. A., Brusatte, S. L., & Xu, X. (2020) · Current Biology · doi:10.1016/j.cub.2020.06.105 · Cited by 137
“The rogue taxa were excluded from the trees when calculating the consensus; they were never excluded from the matrix in any search for optimal trees (thus, the character information in the rogues can influence the relationships of the other taxa; see [105] for a recent discussion of this problem).”
Self-citation
Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
Smith, M. R. (2019) · Biology Letters · doi:10.1098/rsbl.2018.0632 · Cited by 131
Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction
(2016) · doi:10.1093/sysbio/syw041 · Cited by 120
“As rogue taxa can frequently have a negative impact on topology or in a bootstrap analysis (see a review in Goloboff and Szumik 2015), we also explored the presence of putative wild card taxa in our data set with RogueNaRok (Aberer et al. 2013), with the aim of identifying a set of taxa that, if…”
Method
Evolution in the Genus Rhinella: A Total Evidence Phylogenetic Analysis of Neotropical True Toads (Anura: Bufonidae)
Pereyra, M. O., Blotto, B. L., Baldo, D., Chaparro, J. C., Ron, S. R., Elias‐Costa, A. J., Iglesias, P. P., Venegas, P. J., Thomé, M. T. C., Ospina‐Sarria, J. J., et al. (2021) · Bulletin of the American Museum of Natural History · doi:10.1206/0003-0090.447.1.1 · Cited by 87
Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance
Godoy, P. L., Bronzati, M., Eltink, E., Marsola, J. C. A., Cidade, G. M., Langer, M. C., & Montefeltro, F. C. (2016) · PeerJ · doi:10.7717/peerj.2075 · Cited by 72
“This contribution used TNT v.1.1, a program made freely available thanks to a subsidy by the Willi Hennig Society.”
MethodInfluential
Africa’s oldest dinosaurs reveal early suppression of dinosaur distribution
Griffin, C. T., Wynd, B. M., Munyikwa, D., Broderick, T. J., Zondo, M., Tolan, S., Langer, M. C., Nesbitt, S. J., & Taruvinga, H. R. (2022) · Nature · doi:10.1038/s41586-022-05133-x · Cited by 73
New small-bodied ornithopods (Dinosauria, Neornithischia) from the Early Cretaceous Wonthaggi Formation (Strzelecki Group) of the Australian-Antarctic rift system, with revision of Qantassaurus intrepidus Rich and Vickers-Rich, 1999
Herne, M., Nair, J. P., Evans, A. R., & Tait, A. (2019) · Journal of Paleontology · doi:10.1017/jpa.2018.95 · Cited by 68
“Iterative PCR was assessed with the implementation of the original script (‘iterPCR.run’) available in TNT 1.5 (Goloboff and Szumik, 2015).”
MethodInfluential
Plasticity and Convergence in the Evolution of Short-Necked Plesiosaurs
Fischer, V., Benson, R., Zverkov, N. G., Soul, L. C., ARKHANGELSKY, M. S., Lambert, O., Stenshin, I. M., Uspensky, G. N., & Druckenmiller, P. S. (2017) · Current Biology · doi:10.1016/j.cub.2017.04.052 · Cited by 68
Phylogeny of the Caninae (Carnivora): Combining morphology, behaviour, genes and fossils
Zrzavý, J., Duda, P., Robovský, J., Okřinová, I., & Řičánková, V. P. (2018) · Zoologica Scripta · doi:10.1111/zsc.12293 · Cited by 59
Molecular phylogeny of the hyperdiverse genusSarcophaga(Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa
Buenaventura, E., Whitmore, D., & Pape, T. (2016) · Cladistics · doi:10.1111/cla.12161 · Cited by 55
“Goloboff and Szumik (2015) recommended against post-pruning analyses, as this will disregard the character information provided by the rogue taxa and may alter the retrieved relationships between the other taxa.”
BackgroundMethodResultInfluential
Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae)
Buenaventura, E., & Pape, T. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.12.028 · Cited by 51
New spinosaurids from the Wessex Formation (Early Cretaceous, UK) and the European origins of Spinosauridae
Barker, C. T., Hone, D. W. E., Naish, D., Cau, A., Lockwood, J. A. F., Foster, B., Clarkin, C., Schneider, P., & Gostling, N. J. (2021) · Scientific Reports · doi:10.1038/s41598-021-97870-8 · Cited by 49
Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology)
Torres, A., Goloboff, P. A., & Catalano, S. A. (2021) · Cladistics · doi:10.1111/cla.12477 · Cited by 45
Self-citation
The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition
Groh, S. S., Upchurch, P., Barrett, P. M., & Day, J. J. (2019) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlz117 · Cited by 46
Human population history revealed by a supertree approach
Duda, P., & Zrzavý, J. (2016) · Scientific Reports · doi:10.1038/srep29890 · Cited by 39
Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature
Madzia, D., & Cau, A. (2017) · PeerJ · doi:10.7717/peerj.3782 · Cited by 39
“Therefore, Pol & Escapa (2009) offered to use a TNT script, IterPCR, that provides a list of characters related to the instability of each unstable taxon.”
MethodInfluential
Identifying and addressing methodological incongruence in phylogenomics: A review
Fleming, J. F., Valero‐Gracia, A., & Struck, T. H. (2023) · Evolutionary Applications · doi:10.1111/eva.13565 · Cited by 41
“Roguenarok's focus on pruning based on tree support to improve a bootstrap score (Felsenstein, 1978; Goloboff & Szumik, 2015) can result in erroneous, but well- supported topologies being favoured by the algorithm, thus removing the uncertainty that would normally be expressed by a low bootstrap…”
Background
Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
Smith, M. R. (2021) · Systematic Biology · doi:10.1093/sysbio/syab099 · Cited by 31
“…Page: 1093 1088–1094 example by using other quantifications of leaf stability (e.g., Estabrook 1992; Thorley and Wilkinson 1999; Pol and Escapa 2009; Goloboff and Szumik 2015), or by integrating other heuristic methods, such as a “genetic” evolutionary approach (Srivastava et al. 2018).”
Method
The phylogenetic relationships and evolutionary history of the armoured dinosaurs (Ornithischia: Thyreophora)
Raven, T. J., Barrett, P. M., Joyce, C. B., & Maidment, S. C. R. (2023) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2023.2205433 · Cited by 29
Cricosaurus (Thalattosuchia, Metriorhynchidae) survival across the J/K boundary in the High Andes (Mendoza Province, Argentina)
Herrera, Y., Fernández, M., & Vennari, V. V. (2020) · Cretaceous Research · doi:10.1016/j.cretres.2020.104673 · Cited by 29
A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria
Pol, D., Baiano, M. A., Černý, D., Novas, F. E., Cerda, I. A., & Pittman, M. (2024) · Cladistics · doi:10.1111/cla.12583 · Cited by 28
“We carried out the IterPCR procedure (Pol and Escapa, 2009; see iterpcr.out in Supplementary Data) as implemented by Goloboff and Szumik (2015) in TNT in order to detect unstable taxa.”
Method
Braincase redescription of Efraasia minor Huene, 1908 (Dinosauria: Sauropodomorpha) from the Late Triassic of Germany, with comments on the evolution of the sauropodomorph braincase
Bronzati, M., & Rauhut, O. W. M. (2017) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlx029 · Cited by 28
Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages
Timilsena, P. R., Barrett, C. F., Piñeyro‐Nelson, A., Wafula, E. K., Ayyampalayam, S., McNeal, J. R., Yukawa, T., Givnish, T. J., Graham, S. W., Pires, J. C., et al. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac183 · Cited by 22
“Identifying unstable taxa: efficient implementation of triplet-based measures of stability, and comparison with phyutility and RogueNaRok.”
MethodInfluential
Phylogenetic relationships and time-calibration of the South American fossils and extant species of southern beeches (Nothofagus)
Vento, B., & Agraín, F. (2018) · Acta Palaeontologica Polonica · doi:10.4202/app.00493.2018 · Cited by 21
“This methodology was implemented in TNT under the “pcrprune” command (Goloboff and Szumik 2015).”
Method
Revision of Romanian sauropod dinosaurs reveals high titanosaur diversity and body-size disparity on the latest Cretaceous Haţeg Island, with implications for titanosaurian biogeography
Díaz, V. D., Mannion, P. D., Csiki‐Sava, Z., & Upchurch, P. (2025) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2024.2441516 · Cited by 21
Chatham Island Paleocene fossils provide insight into the palaeobiology, evolution, and diversity of early penguins (Aves, Sphenisciformes)
Blokland, J. C., Reid, C. M., Worthy, T. H., Tennyson, A. J. D., Clarke, J. A., & Scofield, R. P. (2019) · Palaeontologia Electronica · doi:10.26879/1009 · Cited by 20
Phylogenetic evaluation of Amynthas earthworms from South China reveals the initial ancestral state of spermathecae
Sun, J., James, S. W., Jiang, J., Yao, B., Zhang, L., Liu, M., Qiu, J., & Hu, F. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.07.026 · Cited by 19
Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina
Godoy, P. L., Cidade, G. M., Montefeltro, F. C., Langer, M. C., & Norell, M. A. (2020) · Papers in Palaeontology · doi:10.1002/spp2.1339 · Cited by 18
Rapid transformation in the braincase of sauropod dinosaurs: integrated evolution of the braincase and neck in early sauropods?
Bronzati, M., Benson, R., & Rauhut, O. W. M. (2017) · Palaeontology · doi:10.1111/pala.12344 · Cited by 18
“The PCRPrune command of TNT (Goloboff & Szumik 2015) was used to generate a reduced strict consensus tree depicting the alternative positions of the unstable OTUs (see Bronzati et al. 2017a).”
Method
Taxonomic and phylogenetic review of Necrosuchus ionensis (Alligatoroidea: Caimaninae) and the early evolution and radiation of caimanines
Cidade, G. M., Fortier, D., & Hsiou, A. S. (2019) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlz051 · Cited by 16
Catutosaurus gaspariniae , gen. et sp. nov. (Ichthyosauria, Thunnosauria) of the Upper Jurassic of Patagonia and the evolution of the ophthalmosaurids
Fernández, M., Campos, L., Maxwell, E. E., & Garrido, A. C. (2021) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.2021.1922427 · Cited by 13
“Most of the contributions dealing with missing data agree on the need to include all taxa (although incomplete) that may affect the topology (Wilkinson, 1995; Pol and Escapa, 2009; Goloboff and Szumik, 2015; Siu-Ting et al., 2015).”
Background
Phylogenetic analysis of Gondwanan basal eusauropods from the Early-Middle Jurassic of Patagonia, Argentina
Holwerda, F. M., & Pol, D. (2018) · Spanish Journal of Palaeontology · doi:10.7203/sjp.33.2.13604 · Cited by 13
Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total‐evidence dating analysis supports a Late Silurian‐Early Devonian origin and post‐Mesozoic morphological stasis
Flores, J. R., Bippus, A. C., de Ullivarri, C. F., Suárez, G. M., Hyvönen, J., & Tomescu, A. M. F. (2023) · New Phytologist · doi:10.1111/nph.19254 · Cited by 11
Theropod dinosaur diversity of the lower English Wealden: analysis of a tooth‐based fauna from the Wadhurst Clay Formation (Lower Cretaceous: Valanginian) via phylogenetic, discriminant and machine learning methods
Barker, C. T., Handford, L., Naish, D., Wills, S., Hendrickx, C., Hadland, P. T., Brockhurst, D., & Gostling, N. J. (2024) · Papers in Palaeontology · doi:10.1002/spp2.1604 · Cited by 11
“In the unconstrained analyses, wildcard taxa were identiﬁed using the iterPCR procedure (Pol & Escapa 2009; Goloboff & Szumik 2015), and Bremer supports were used to assess the nodal support of the resulting reduced consensus trees.”
The disadvantage of derivation: conserved systematic flaws in primary data have repeatedly biased the phylogenetic inference of Temnospondyli (Tetrapoda, Amphibia)Preprint
Gee, B. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.22.496729 · Cited by 11
“…by Schoch (2013) are clearly wildcards, either upon reanalysis of the original matrix or upon reanalysis of subsequent derivates, and it is not clear how “problematic” taxa were originally identified (e.g., with an Adams consensus or the IterPCR method of TNT; Goloboff and Szumik, 2015).”
Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)
Barker, C. T., Naish, D., & Gostling, N. J. (2023) · PeerJ · doi:10.7717/peerj.15453 · Cited by 10
“In the unconstrained analyses, wildcard OTUs were identified using the iterPCR function ( Goloboff & Szumik, 2015 ; Pol & Escapa, 2009 ), and Bremer support values were calculated as a measure of nodal support in the resulting reduced consensus.”
A new species ofCricosaurus(Thalattosuchia: Crocodylomorpha) from southern Germany: the first three-dimensionally preservedCricosaurusskull from the Solnhofen Archipelago
Herrera, Y., Aiglstorfer, M., & Bronzati, M. (2021) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2021.1883138 · Cited by 9
“The prunnelsen command (Goloboff & Szumik 2015) was used to identify the unstable OTUs, which consisted of Congosaurus bequaerti, Crocodylus acutus, Cr. intermedius, Cr. mindorensis, Cr. moreletti, Cr., rhombifer, Cr. suchus and the ‘Swiss rhacheosaurin’.”
Method
Measuring inferential importance of taxa using taxon influence indices
Denton, J. S. S., & Goolsby, E. W. (2018) · Ecology and Evolution · doi:10.1002/ece3.3941 · Cited by 9
“Systematic Biology, 62, 162–166. https://doi.org/10.1093/ sysbio/sys078 Aberer, A. J., Pattengale, N. D., & Stamatakis, A. (2010).”
BackgroundMethodInfluential
Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample
Song, N., Wei, S., & Wang, M. (2024) · Mitochondrial DNA Part A · doi:10.1080/24701394.2024.2345663 · Cited by 8
Scimitar-crested Spinosaurus species from the Sahara caps stepwise spinosaurid radiation
Sereno, P. C., Vidal, D., Myhrvold, N., Johnson‐Ransom, E., Real, M. C., Baumgart, S. L., Fontela, N. S., Green, T. L., Saitta, E. T., Adamou, B., et al. (2026) · Science · doi:10.1126/science.adx5486 · Cited by 8
TreeShrink: Efficient Detection of Outlier Tree Leaves
Mai, U., & Mirarab, S. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-67979-2_7 · Cited by 9
Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis
Kinateder, T., Drexler, L., Straub, K., Merkl, R., & Sterner, R. (2022) · Protein Science · doi:10.1002/pro.4536 · Cited by 8
“All possible combinations of the three filtering methods ( heatmap approach , rogue taxa and RogueNaRok ; Goloboff & Szumik, 2015) were applied to generate a data set with the best suitable selected sequences.”
Method
Phylogenetic relationships of Neogene hamsters (Mammalia, Rodentia, Cricetinae) revealed under Bayesian inference and maximum parsimony
Dirnberger, M., Peláez‐Campomanes, P., & López‐Antoñanzas, R. (2024) · PeerJ · doi:10.7717/peerj.18440 · Cited by 7
A new large hypercarnivorous crocodyliform from the Maastrichtian of Southern Patagonia, Argentina
Novas, F. E., Pol, D., Agnolín, F. L., Carvalho, I. D. S., Manabe, M., Tsuihiji, T., Rozadilla, S., Lio, G. L., & Isasi, M. P. (2025) · PLoS ONE · doi:10.1371/journal.pone.0328561 · Cited by 7
“Unstable taxa were detected using IterPCR [29,30] and nodal support was evaluated using parsimony jackknife [31] considering the impact of unstable taxa [32].”
A phylogenetic C interpreter for TNT
Goloboff, P. A., & Morales, M. E. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa214 · Cited by 7
Self-citation
Exploring the impact of unstable terminals on branch support values in paleontological data
Flores, J. R., Lehtonen, S., & Hyvönen, J. (2021) · Paleobiology · doi:10.1017/pab.2020.64 · Cited by 6
“Note that taxa that are unstable with minimum differences in fit are known to reduce branch support, and devising methods to efficiently deal with them has been challenging (Aberer and Stamatakis 2011; Aberer et al. 2013; Goloboff and Szumik 2015; Pei et al. 2020; Pol and Goloboff 2020).”
BackgroundMethod
Morphological phylogeny and review of the generic classification of Colletinae (Hymenoptera: Colletidae)
Ferrari, R. R., & Packer, L. (2020) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlaa128 · Cited by 5
A new pachyrukhine (Notoungulata: Typotheria) from the late Early Miocene of south-central Chile
Solórzano, A., Encinas, A., Kramarz, A., Carrasco, G., Núñez‐Flores, M., & Bobe, R. L. (2023) · Historical Biology · doi:10.1080/08912963.2023.2214568 · Cited by 5
“To improve the resolution of the phylogenetic tree, the method ‘Iterative Positional Congruence Reduced’ (IterPCR) of Pol and Escapa (2009), implemented in TNT 1.5 (Goloboff and Szumik 2015), was employed to detect possible unstable taxa.”
MethodInfluential
New insights into the phylogeny and skull evolution of stegosaurian dinosaurs: An extraordinary cranium from the European Late Jurassic (Dinosauria: Stegosauria)
Sánchez-Fenollosa, S., & Cobos, A. (2025) · Vertebrate Zoology · doi:10.3897/vz.75.e146618 · Cited by 4
“The Iter-PCR method (Pol and Escapa 2009) using the command ‘pcrprune’ (Goloboff and Szumik 2015) was employed to identify the rogue taxa.”
Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection
Wang, H.-C., Susko, E., & Roger, A. J. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.08.017 · Cited by 4
“In some cases the whole analysis will have to be re-conducted with the rogue taxa removed (Thomson and Shaffer, 2009; Aberer and Stamatakis, 2011; see also Goloboff and Szumik, 2015 for a discussion of pruning trees or matrices).”
Background
Two new compsognathid-like theropods show diversified predation strategies in theropod dinosaurs
Qiu, R., Wang, X., Jiang, S., Meng, J., & Zhou, Z. (2025) · National Science Review · doi:10.1093/nsr/nwaf068 · Cited by 4
Skeletons in the Forest: Using Entropy-Based Rogue Detection on Bayesian Phylogenetic Tree DistributionsPreprint
Klawitter, J., Bouckaert, R., & Drummond, A. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.25.615070 · Cited by 5
“The majority of rogue detection algorithms thus aim to improve both the resolution and the support of the clades (splits) in a consensus tree [1, 2, 13, 28, 31], which however is an NP-hard problem [9].”
Background
The oldest monofenestratan pterosaur from the Queso Rallado locality (Cañadón Asfalto Formation, Toarcian) of Chubut Province, Patagonia, Argentina
Fernandes, A. E., Pol, D., & Rauhut, O. W. M. (2024) · Royal Society Open Science · doi:10.1098/rsos.241238 · Cited by 2
PickMe : Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets
Rusinko, J., Cai, Y., Crysler, A., Thompson, K. L., Boutte, J., Fishbein, M., & Straub, S. C. K. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf017 · Cited by 1
“”Rogue” or ”wildcard” sam‑ ples whose inclusion reduces the resolution of and sup‑ port for splits in gene trees may be identified and re‑ moved (Aberer et al., 2012; Goloboff and Szumik, 2015, and e.g. Foley et al., 2019; Laumer et al., 2019; Li et al., 2021; Salichos and Rokas, 2013).”
Decoding the phylogeny of the genus Merodon Meigen (Diptera, Syrphidae): a synergistic approach with molecular and morphological data
Veselić, S., Vujić, A., Radenković, S., Zorić, L. Š., Djan, M., & Ståhls, G. (2025) · Cladistics · doi:10.1111/cla.70009 · Cited by 1
“These kinds of species could be considered as rogue taxa (Wilkinson, 1994; Goloboff and Szumik, 2015; Smith, 2022).”
A new fossil fish sheds light on the rapid evolution of early lungfishes
Qiao, T., Cui, X., Zhao, W., Liu, C., Li, M., Lü, J., Choo, B., & Zhu, M. (2025) · Current Biology · doi:10.1016/j.cub.2025.11.032 · Cited by 1
A comparison of two universal angiosperm bait sets and the phylogenomics of AlismatalesPreprint
Biffin, E., Waycott, M., Hammer, T., & van Dijk, K.-J. (2025) · bioRxiv · doi:10.1101/2025.09.15.676180 · Cited by 1
Revisão filogenética de Alligatoroidea (Crocodylia) e revisão taxonômica das espécies do clado Caimaninae
Cidade, G. M. (2020) · doi:10.11606/t.59.2020.tde-11122019-124833
Peer Review #3 of "Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance (v0.1)"
(2016) · PeerJ · doi:10.7287/peerj.2075v0.1/reviews/3
Peer Review #1 of "Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance (v0.2)"
(2016) · PeerJ · doi:10.7287/peerj.2075v0.2/reviews/1
Peer Review #1 of "Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance (v0.1)"
(2016) · PeerJ · doi:10.7287/peerj.2075v0.1/reviews/1
Peer Review #2 of "Postcranial anatomy of Pissarrachampsa sera (Crocodyliformes, Baurusuchidae) from the Late Cretaceous of Brazil: insights on lifestyle and phylogenetic significance (v0.2)"
(2016) · PeerJ · doi:10.7287/peerj.2075v0.2/reviews/2
On the effect of measures for comparing trees on the representation of treespace
Goloboff, P. A., & Morales, M. E. (2025) · Cladistics · doi:10.1111/cla.12614
“Triplets are fewer than quar-tets, and the existing code used by TNT for calculating IterPCR values (Goloboff and Szumik, 2015) can be adapted easily for checking triplets.”
Self-citation
Over‐reliance on Completeness exposes ultraconserved elements datasets to non‐randomly distributed missing data
Garzón‐Orduña, I. J., Brower, A. V. Z., Joele, F. R., & Torres, A. (2026) · Systematic Entomology · doi:10.1111/syen.70024
“%) and found in all nine datasets, are strong candidates to behave as wild cards or rogue taxa (Goloboff & Szumik, 2015; Sanderson et al., 2011; Wilkinson, 1995) during phylogenetic inference.”
Cladistic Analysis and a Revised Classification of the Family Anisembiidae (Embioptera) with a Catalog of the South American Species
Juárez, M. L., Goloboff, P. A., & Szumik, C. (2026) · American Museum Novitates · doi:10.1206/4048.1
Self-citation
Bicharracosaurus dionidei, gen. et sp. nov., a new macronarian (Dinosauria, Sauropoda) from the Late Jurassic Cañadón Calcáreo Formation of Argentina and the problematic early evolution of macronarians
reutter, A., Carballido, J. L., Windholz, G. J., Pol, D., & Rauhut, O. W. M. (2026) · PeerJ · doi:10.7717/peerj.20945
New unenlagiid from the Chorrillo Formation (Late Cretaceous, Maastrichtian), SW Patagonia, Argentina
Motta, M. J., Rolando, A. M. A., Rozadilla, S., Agnolín, F. L., Egli, F. B., Álvarez-Herrera, G. P., Chimento, N. R., Coco, G. L., Tsuihiji, T., Manabe, M., et al. (2026) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.2026.2656456 · Cited by 1
“Strict consensus and reduced strict consensus were produced, identifying unstable taxa using iterPCR (Pol & Escapa, 2009) as implemented in TNT (Goloboff & Szumik, 2015).”
Influential
A new nodosaurid ankylosaur (Dinosauria: Ornithischia) from the Upper Cretaceous Hikagenosawa Formation in Japan reveals dispersal pattern of Asian nodosaurid ankylosaurs
Oyabu, S., Kobayashi, Y., Zelenitsky, D. K., Fiorillo, A. R., & Kano, M. (2026) · Cretaceous Research · doi:10.1016/j.cretres.2026.106477
Phylogenetic relationships and Miocene diversification of the extinct rodent subfamily Democricetodontinae (Cricetidae)
Sualdea, L. R., López‐Antoñanzas, R., Sierra, M., & Peláez‐Campomanes, P. (2026) · Journal of Systematic Palaeontology · doi:10.1080/14772019.2026.2733171
Data from: Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction
Fernandez, R., Edgecombe, G. D., & Giribet, G. (2016) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.8mp17.1

Authors: Goloboff, P. A., & Szumik, C. A.
Affiliations: Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
Corresponding author: Goloboff, Pablo A.
ORCID: Goloboff, Pablo A.
Szumik, Claudia A.
Venue: Molecular Phylogenetics and Evolution
Publisher: Elsevier BV
Published: 2015-07
Volume: 88
Pages: 93-104
ISSN: 1055-7903 (ISSN-L)
DOI: 10.1016/j.ympev.2015.04.003
OpenAlex: W1975311257
Cited by: 73
References: 33
Citations by year: 2026: 7 · 2025: 9 · 2024: 6 · 2023: 5 · 2022: 4 · 2021: 7 · 2020: 6 · 2019: 5 · 2018: 5 · 2017: 6 · 2016: 12 · 2015: 1
FWCI: 3.47
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Molecular Phylogenetics and Evolution (publishedVersion)
PubMed (publishedVersion)
CONICET Digital (CONICET) (submittedVersion, cc-by-nc-nd)
Funders: CONICET (112 201101 00687)
NSF
NASA
Fundaçao de Amparo à Pesquisa do Estado de São Paulo
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords: phylogenetic stability, TNT, computational efficiency
MeSH terms: Algorithms, Phylogeny, Software

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks