A review of long-branch attraction

Bergsten, Johannes

doi:10.1111/j.1096-0031.2005.00059.x

Cited by 1,162Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesPlant Diversity and Evolution

The DOI matches its Crossref record; 208 of the 208 references it cites were found in a registry or an index.

A review of long-branch attraction

Bergsten, Johannes·2005·Cladistics

DOI 10.1111/j.1096-0031.2005.00059.x

Open this paper in CoChat — free account

Abstract

The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic "the guinea-pig is not a rodent" hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup.

Integrity signals

Registry

Crossref · 10.1111/j.1096-0031.2005.00059.x

Cites

208 of 208 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Inclusion of outgroups very distant from the ingroup can cause reconstruction artifacts by attracting fast-evolving (long-branched) ingroup species toward the root.
“the inclusion of outgroups very distant from the ingroup can cause reconstruction artifacts by attracting fast-evolving (long-branched) ingroup species toward the root (25, 27 -31)”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [25]

MrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 29,194
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,256
Inferring Phylogenies.
Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,093
Gene Trees in Species Trees
Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,039
A likelihood approach to estimating phylogeny from discrete morphological character data
Lewis, P. O. (2001) · Systematic Biology · doi:10.1080/106351501753462876 · Cited by 2,929
Glacial history and colonization of Europe by the blue tit Parus caeruleus
Kvist, L., Viiri, K. M., Dias, P. C., Rytkönen, S., & Orell, M. I. (2004) · Journal of Avian Biology · doi:10.1111/j.0908-8857.2004.03297.x · Cited by 2,798
Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe
Pinceel, J., Jordaens, K., Houtte, N. V., de Winter, A. J., & Backeljau, T. (2004) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2004.00368.x · Cited by 2,263
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230
Bayesian Phylogenetic Analysis of Combined Data
Nylander, J. A. A., Ronquist, F., Huelsenbeck, J. P., & Nieves‐Aldrey, J. L. (2004) · Systematic Biology · doi:10.1080/10635150490264699 · Cited by 1,845
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
Nixon, K. C. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00277.x · Cited by 1,748
Relationships between gene trees and species trees.
Pamilo, P., & Nei, M. (1988) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040517 · Cited by 1,615
Evidence for a clade of nematodes, arthropods and other moulting animals
Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512
A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)
Kluge, A. G. (1989) · Systematic Biology · doi:10.1093/sysbio/38.1.7 · Cited by 1,405
Molecular phylogenetics and the origins of placental mammals
Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y., Ryder, O. A., & O’Brien, S. J. (2001) · Nature · doi:10.1038/35054550 · Cited by 1,378
Estimating character weights during tree search
Goloboff, P. A. (1993) · Cladistics · doi:10.1111/j.1096-0031.1993.tb00209.x · Cited by 1,296
Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
Murphy, W. J., Eizirik, E., O’Brien, S. J., Madsen, O., Scally, M., Douady, C. J., Teeling, E. C., Ryder, O. A., Stanhope, M. J., JONG, W. W. D., et al. (2001) · Science · doi:10.1126/science.1067179 · Cited by 1,292
Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence
Alfaro, M. E. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg028 · Cited by 1,136
A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)
Kluge, A. G. (1989) · Systematic Zoology · doi:10.2307/2992432 · Cited by 1,011
Molecular Evolution: A Phylogenetic Approach
Page, R., & Holmes, E. C. (1998) · Medical Entomology and Zoology · Cited by 984
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
Zwickl, D. J., & Hillis, D. M. (2002) · Systematic Biology · doi:10.1080/10635150290102339 · Cited by 939
The Strepsiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology
Whiting, M. F., Carpenter, J. C., Wheeler, Q. D., & Wheeler, W. C. (1997) · Systematic Biology · doi:10.1093/sysbio/46.1.1 · Cited by 929
Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models
Huelsenbeck, J. P., & Rannala, B. H. (2004) · Systematic Biology · doi:10.1080/10635150490522629 · Cited by 902
The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes
Qiu, Y., Lee, J.-H., Bernasconi‐Quadroni, F., Soltis, P. S., Soltis, P. S., Zanis, M. J., Zimmer, E. A., Chen, Z., Savolainen, V., & Chase, M. W. (1999) · Nature · doi:10.1038/46536 · Cited by 842
Placental mammal diversification and the Cretaceous–Tertiary boundary
Springer, M. S., Murphy, W. J., Eduardo Eizirik, C., & O’Brien, S. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334222100 · Cited by 837
Potential Applications and Pitfalls of Bayesian Inference of Phylogeny
Huelsenbeck, J. P., Larget, B. R., Miller, R. E., & Ronquist, F. (2002) · Systematic Biology · doi:10.1080/10635150290102366 · Cited by 808
A Framework for the Quantitative Study of Evolutionary Trees
Hendy, M. D., & Penny, D. (1989) · Systematic Zoology · doi:10.2307/2992396 · Cited by 803
Success of Phylogenetic Methods in the Four-Taxon Case
Huelsenbeck, J. P., & Hillis, D. M. (1993) · Systematic Biology · doi:10.1093/sysbio/42.3.247 · Cited by 784
Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
Graybeal, A. (1998) · Systematic Biology · doi:10.1080/106351598260996 · Cited by 745
Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics
Erixon, P., Svennblad, B., Britton, T., & Oxelman, B. (2003) · Systematic Biology · doi:10.1080/10635150390235485 · Cited by 698
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
WILCOX, T. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00244-0 · Cited by 674
Gene trees and species trees are not the same
Nichols, R. A. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(01)02203-0 · Cited by 672
Performance of Phylogenetic Methods in Simulation
Huelsenbeck, J. P. (1995) · Systematic Biology · doi:10.1093/sysbio/44.1.17 · Cited by 659
Molecular Systematics of the Eastern Fence Lizard (Sceloporus undulatus): A Comparison of Parsimony, Likelihood, and Bayesian Approaches
Leaché, A. D., & Reeder, T. W. (2002) · Systematic Biology · doi:10.1080/106351502753475871 · Cited by 657
Parallel adaptive radiations in two major clades of placental mammals
Madsen, O., Scally, M., Douady, C. J., Kao, D. J., DeBry, R. W., Adkins, R., Amrine, H. M., Stanhope, M. J., de Jong, W. W., & Springer, M. S. (2001) · Nature · doi:10.1038/35054544 · Cited by 653
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
Suzuki, Y., Glazko, G. V., & Nei, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212646199 · Cited by 647
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
Kolaczkowski, B. D., & Thornton, J. W. (2004) · Nature · doi:10.1038/nature02917 · Cited by 617
ON OUTGROUPS
Nixon, K. C., & Carpenter, J. M. (1993) · Cladistics · doi:10.1111/j.1096-0031.1993.tb00234.x · Cited by 578
Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias
Hillis, D. M. (1998) · Systematic Biology · doi:10.1080/106351598260987 · Cited by 524
The Phylogeny of the Extant Hexapod Orders
Wheeler, W. C., Whiting, M., Wheeler, Q. D., & Carpenter, J. M. (2001) · Cladistics · doi:10.1111/j.1096-0031.2001.tb00115.x · Cited by 508
Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability
Douady, C. J. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg042 · Cited by 507
Split decomposition: A new and useful approach to phylogenetic analysis of distance data
Bandelt, H., & Dress, A. (1992) · Molecular Phylogenetics and Evolution · doi:10.1016/1055-7903(92)90021-8 · Cited by 504
Inferring complex phytogenies
Hillis, D. M. (1996) · Nature · doi:10.1038/383130a0 · Cited by 503
The Phylogeny of the Extant Hexapod Orders
Wheeler, W. C., Whiting, M. F., Wheeler, Q. D., & Carpenter, J. M. (2001) · Cladistics · doi:10.1006/clad.2000.0147 · Cited by 501
Phylogeny Reconstruction: The Role of Morphology
Scotland, R. W., Olmstead, R. G., & Bennett, J. R. (2003) · Systematic Biology · doi:10.1080/10635150390223613 · Cited by 497
Application and Accuracy of Molecular Phylogenies
Hillis, D. M., Huelsenbeck, J. P., & Cunningham, C. (1994) · Science · doi:10.1126/science.8171318 · Cited by 494
Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
Bowe, L. M., Coat, G., & dePamphilis, C. W. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4092 · Cited by 476
Increased Taxon Sampling Is Advantageous for Phylogenetic Inference
Pollock, D. D., Zwickl, D. J., McGuire, J. A., & Hillis, D. M. (2002) · Systematic Biology · doi:10.1080/10635150290102357 · Cited by 466
Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
Swofford, D. L., Waddell, P. J., Huelsenbeck, J. P., Foster, P. G., Lewis, P. O., & Rogers, J. S. (2001) · Systematic Biology · doi:10.1080/10635150117959 · Cited by 421
Molecules consolidate the placental mammal tree
Springer, M. S. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.05.006 · Cited by 408
Inferring phylogenies
Felsenstein, J. 1. (2004) · Cited by 405
The Role of Morphological Data in Phylogeny Reconstruction
Wiens, J. J. (2004) · Systematic Biology · doi:10.1080/10635150490472959 · Cited by 400
Sampling properties of DNA sequence data in phylogenetic analysis.
Cummings, M. P., Otto, S. P., & Wakeley, J. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040258 · Cited by 387
Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals
Stanhope, M. J., Waddell, V. G., Madsen, O., JONG, W. W. D., Hedges, S. B., Cleven, G. C., Kao, D. J., & Springer, M. S. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.17.9967 · Cited by 386
Mammalian mitogenomic relationships and the root of the eutherian tree
Árnason, Ú., Adegoke, J. A., Bodin, K., Born, E. W., Esa, Y. B., Gullberg, A., Nilsson, M. A., Short, R. V., Xu, X., & Janke, A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102164299 · Cited by 385
A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.
(1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040433 · Cited by 377
How Meaningful Are Bayesian Support Values?
Simmons, M. P., Pickett, K. M., & Miya, M. U. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh014 · Cited by 374
The guinea-pig is not a rodent
D’Erchia, A. M., Gissi, C., Pesole, G., Saccone, C., & Árnason, Ú. (1996) · Nature · doi:10.1038/381597a0 · Cited by 353
Endemic African mammals shake the phylogenetic tree
Springer, M. S., Cleven, G. C., Madsen, O., JONG, W. W. D., Waddell, V. G., Amrine‐Madsen, H., & Stanhope, M. J. (1997) · Nature · doi:10.1038/40386 · Cited by 329
How good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324
Ancient Phylogenetic Relationships
Gribaldo, S., & Philippe, H. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1593 · Cited by 314
Comparing Bootstrap and Posterior Probability Values in the Four-Taxon Case
Cummings, M. P., Handley, S. A., Myers, D. S., Reed, D. L., Rokas, A., & Winka, K. (2003) · Systematic Biology · doi:10.1080/10635150390218213 · Cited by 306
Molecular evidence regarding the origin of echolocation and flight in bats
Teeling, E. C., Scally, M., Kao, D. J., Romagnoli, M. L., Springer, M. S., & Stanhope, M. J. (2000) · Nature · doi:10.1038/35003188 · Cited by 304
Experimental Phylogenetics: Generation of a Known Phylogeny
Hillis, D. M., Bull, J. J., White, M. E., Badgett, M. R., & Molineux, I. J. (1992) · Science · doi:10.1126/science.1736360 · Cited by 300
Biological systematics: principles and applications
(2010) · Choice Reviews Online · doi:10.5860/choice.47-4406 · Cited by 299
Homoplasy Increases Phylogenetic Structure
Kälersjö, M., Albert, V. A., & Farris, J. S. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00400.x · Cited by 297
Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics
Sullivan, J. M., & Swofford, D. L. (1997) · Journal of Mammalian Evolution · doi:10.1023/a:1027314112438 · Cited by 283
Is the Felsenstein Zone a Fly Trap?
Huelsenbeck, J. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.1.69 · Cited by 278
The Rooting of the Universal Tree of Life Is Not Reliable
Philippe, H., & Forterre, P. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006573 · Cited by 267
Assessing the Relative Contribution of Molecular and Morphological Characters in Simultaneous Analysis Trees
Baker, R. H., Yu, X., & DeSalle, R. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0519 · Cited by 264
Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
Brinkmann, H., & Philippe, H. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026166 · Cited by 258
A phylogenetic foundation for comparative mammalian genomics.
Waddell, P. J., Kishino, H., & Ota, R. (2001) · PubMed · Cited by 255
Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting
Delsuc, F., Scally, M., Madsen, O., Stanhope, M. J., JONG, W. W. D., Catzeflis, F. M., Springer, M. S., & Douzery, E. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003989 · Cited by 254
Success of maximum likelihood phylogeny inference in the four-taxon case.
Gaut, B. S., & Lewis, P. O. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040183 · Cited by 245
NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS
Wheeler, W. C. (1990) · Cladistics · doi:10.1111/j.1096-0031.1990.tb00550.x · Cited by 245
The origin of red algae and the evolution of chloroplasts
Moreira, D., le Guyader, H., & Philippe, H. (2000) · Nature · doi:10.1038/35011054 · Cited by 245
Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm.
Goremykin, V., Hirsch-Ernst, K., Wölfl, S., & Hellwig, F. (2003) · Molecular biology and evolution · doi:10.1093/molbev/msg159 · Cited by 244
Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.
Lockhart, P. J., Larkum, A., Steel, M. A., Waddell, P., & Penny, D. (1996) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.93.5.1930 · Cited by 240
A Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character Optimization
Giribet, G., & Ribera, C. (2000) · Cladistics · doi:10.1111/j.1096-0031.2000.tb00353.x · Cited by 238
The Cytochrome b Gene as a Phylogenetic Marker: The Limits of Resolution for Analyzing Relationships Among Cichlid Fishes
Farias, I. P., Ortı́, G., Sampaio, I., Schneider, H., & Meyer, A. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010197 · Cited by 235
Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders
Cao, Y., Janke, A., Waddell, P. J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Pääbo, S., & Hasegawa, M. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006389 · Cited by 234
Success of Parsimony in the Four-Taxon Case: Long-Branch Repulsion by Likelihood in the Farris Zone
Siddall, M. E. (1998) · Cladistics · doi:10.1111/j.1096-0031.1998.tb00334.x · Cited by 233
Taxon Sampling and the Accuracy of Large Phylogenies
Rannala, B. H., Huelsenbeck, J. P., Yang, Z., & Nielsen, R. (1998) · Systematic Biology · doi:10.1080/106351598260680 · Cited by 233
General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa
Kim, J. (1996) · Systematic Biology · doi:10.1093/sysbio/45.3.363 · Cited by 232
The Early History of Modern Birds Inferred from DNA Sequences of Nuclear and Mitochondrial Ribosomal Genes
van Tuinen, M., Sibley, C. G., & Hedges, S. B. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026324 · Cited by 230
HomoplasyIncreasesPhylogenetic Structure*1
Kälersjö, M. (1999) · Cladistics · doi:10.1006/clad.1999.0085 · Cited by 230
Long-Branch Abstractions
Siddall, M. E., & Whiting, M. F. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00391.x · Cited by 229
Amphioxus Mitochondrial DNA, Chordate Phylogeny, and the Limits of Inference Based on Comparisons of Sequences
Naylor, G. J. P., & Brown, W. M. (1998) · Systematic Biology · doi:10.1080/106351598261030 · Cited by 224
Taxon sampling revisited
Poe, S., & Swofford, D. L. (1999) · Nature · doi:10.1038/18592 · Cited by 223
Inferring the root of a phylogenetic tree.
Huelsenbeck, J. P., Bollback, J. P., & Levine, A. M. (2002) · Systematic Biology · doi:10.1080/106351502753475862 · Cited by 221
Mitochondrial Versus Nuclear Gene Sequences in Deep-Level Mammalian Phylogeny Reconstruction
Springer, M. S., DeBry, R. W., Douady, C. J., Amrine‐Madsen, H., Madsen, O., JONG, W. W. D., & Stanhope, M. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003787 · Cited by 217
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
Barkman, T. J., Chenery, G., McNeal, J. R., Lyons‐Weiler, J., Elisens, W. J., Moore, G., Wolfe, A. D., & dePamphilis, C. W. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.220427497 · Cited by 216
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
Nixon, K. C. (1999) · Cladistics · doi:10.1006/clad.1999.0121 · Cited by 203
Combined Support for Wholesale Taxic Atavism in Gavialine Crocodylians
Gatesy, J., Amato, G., Norell, M. A., DeSalle, R., & Hayashi, C. Y. (2003) · Systematic Biology · doi:10.1080/10635150390197037 · Cited by 201
A Broad Survey of Recombination in Animal Mitochondria
Piganeau, G., Gardner, M., & Eyre‐Walker, A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh244 · Cited by 200
Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
Anderson, F. E., & Swofford, D. L. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.06.015 · Cited by 193
Data exploration in phylogenetic inference: scientific, heuristic, or neither
Grant, T., & Kluge, A. G. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00311.x · Cited by 186
PATTERNS IN TREE BALANCE AMONG CLADISTIC, PHENETIC, AND RANDOMLY GENERATED PHYLOGENETIC TREES
Heard, S. B. (1992) · Evolution · doi:10.1111/j.1558-5646.1992.tb01171.x · Cited by 184
EVOLUTION OF THE GALL WASP-HOST PLANT ASSOCIATION
Ronquist, F., & Liljeblad, J. (2001) · Evolution · doi:10.1111/j.0014-3820.2001.tb00765.x · Cited by 184
Spectral analysis of phylogenetic data
Hendy, M. D., & Penny, D. (1993) · Journal of Classification · doi:10.1007/bf02638451 · Cited by 182
Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium
Jenner, R. A. (2004) · Systematic Biology · doi:10.1080/10635150490423962 · Cited by 182
Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants
Sanderson, M. J., Wojciechowski, M. F., Hu, J., Khan, T. S., & Brady, S. G. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026357 · Cited by 180
A phylogenetic analysis of higher‐level gall wasp relationships (Hymenoptera: Cynipidae)
Liljeblad, J., & Ronquist, F. (1998) · Systematic Entomology · doi:10.1046/j.1365-3113.1998.00053.x · Cited by 176
Using Novel Phylogenetic Methods to Evaluate Mammalian mtDNA, Including Amino Acid-Invariant Sites-LogDet plus Site Stripping, to Detect Internal Conflicts in the Data, with Special Reference to the Positions of Hedgehog, Armadillo, and Elephant
Waddell, P. J., Cao, Y., Hauf, J., & Hasegawa, M. (1999) · Systematic Biology · doi:10.1080/106351599260427 · Cited by 171
Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
Maddison, D. R., And, M. D. B., & Ober, K. A. (1999) · Systematic Entomology · doi:10.1046/j.1365-3113.1999.00088.x · Cited by 168
Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification
Kluge, A. G. (1998) · Cladistics · doi:10.1111/j.1096-0031.1998.tb00328.x · Cited by 168
Trees within Trees: Genes and Species, Molecules and Morphology
Doyle, J. J. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.537 · Cited by 165
Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved?
Huelsenbeck, J. P. (1998) · PubMed · Cited by 163
Hobgoblin of phylogenetics?
Hillis, D. M., Huelsenbeck, J. P., & Swofford, D. L. (1994) · Nature · doi:10.1038/369363a0 · Cited by 162
Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)
Gontcharov, A. A. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msh052 · Cited by 162
Rooting Phylogenetic Trees with Distant Outgroups: A Case Study from the Commelinoid Monocots
Graham, S. W., Olmstead, R. G., & Barrett, S. C. H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003999 · Cited by 159
Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.
de Peer, Y. V., Rensing, S. A., Maier, U., & Wächter, R. D. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.15.7732 · Cited by 157
Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
Philippe* and, H., & Germot, A. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026362 · Cited by 154
Probabilism and Phylogenetic Inference
Siddall, M. E., & Kluge, A. G. (1997) · Cladistics · doi:10.1111/j.1096-0031.1997.tb00322.x · Cited by 148
Long-Branch Attraction and the rDNA Model of Early Eukaryotic Evolution
Stiller, J. W., & Hall, B. D. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026217 · Cited by 146
Four New Mitochondrial Genomes and the Increased Stability of Evolutionary Trees of Mammals from Improved Taxon Sampling
Lin, Y.-H., McLenachan, P. A., Gore, A. R., Phillips, M. J., Ota, R., Hendy, M. D., & Penny, D. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004031 · Cited by 146
Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
Chang, J. T. (1996) · Mathematical Biosciences · doi:10.1016/0025-5564(95)00172-7 · Cited by 145
Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal
Lyons‐Weiler, J., Hoelzer, G. A., & Tausch, R. J. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025635 · Cited by 143
Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock--A Simulation Study
Holland, B. R., Penny, D., & Hendy, M. D. (2003) · Systematic Biology · doi:10.1080/10635150390192771 · Cited by 143
A new perspective on lower metazoan relationships from 18S rDNA sequences
Kim, J., Kim, W., & Cunningham, C. W. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026124 · Cited by 143
ADAPTIVE RADIATION AND THE TOPOLOGY OF LARGE PHYLOGENIES
Guyer, C., & Slowinski, J. B. (1993) · Evolution · doi:10.1111/j.1558-5646.1993.tb01214.x · Cited by 142
Biological Systematics: Principles and Applications
Crowe, T. (2001) · Cladistics · doi:10.1006/clad.2001.0177 · Cited by 139
The Root of the Tree of Life in the Light of the Covarion Model
Lopez, P., Forterre, P., & Philippe, H. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006572 · Cited by 139
Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations
Luckett, W. P., & Hartenberger, J. (1993) · Journal of Mammalian Evolution · doi:10.1007/bf01041591 · Cited by 136
Maximum Likelihood Analysis of the Complete Mitochondrial Genomes of Eutherians and a Reevaluation of the Phylogeny of Bats and Insectivores
Nikaido, M., Kawai, K., Cao, Y., Harada, M., Tomita, S., Okada, N., & Hasegawa, M. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010241 · Cited by 134
How often do wrong models produce better phylogenies?
Yang, Z. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025695 · Cited by 133
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods
Reyes, A. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msh033 · Cited by 127
Where Do Rodents Fit? Evidence from the Complete Mitochondrial Genome of Sciurus vulgaris
Reyes, A., Gissi, C., Pesole, G., Catzeflis, F. M., & Saccone, C. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026379 · Cited by 125
The Phylogenetic Position of the Talpidae Within Eutheria Based on Analysis of Complete Mitochondrial Sequences
Mouchaty, S. K., Gullberg, A., Janke, A., & Árnason, Ú. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026238 · Cited by 119
Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case
Pol, D., & Siddall, M. E. (2001) · Cladistics · doi:10.1006/clad.2001.0172 · Cited by 118
War of the Iguanas: Conflicting Molecular and Morphological Phylogenies and Long-Branch Attraction in Iguanid Lizards
Wiens, J. J., & Hollingsworth, B. D. (2000) · Systematic Biology · doi:10.1080/10635150050207447 · Cited by 118
Complete Mitochondrial Genome of a Neotropical Fruit Bat, Artibeus jamaicensis, and a New Hypothesis of the Relationships of Bats to Other Eutherian Mammals
Pumo, D. E., Finamore, P. S., Franek, W. R., Phillips, C. J., Tarzami, S. T., & Balzarano, D. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006430 · Cited by 117
GROUNDPLANS AND EXEMPLARS: PATHS TO THE TREE OF LIFE
Yeates, D. K. (1995) · Cladistics · doi:10.1111/j.1096-0031.1995.tb00094.x · Cited by 117
Groundplans and exemplars: Paths to the tree of life
Yeates, D. K. (1995) · Cladistics · doi:10.1016/0748-3007(95)90020-9 · Cited by 116
The Accuracy of Methods for Coding and Sampling Higher-Level Taxa for Phylogenetic Analysis: A Simulation Study
Wiens, J. J. (1998) · Systematic Biology · doi:10.1080/106351598260789 · Cited by 116
Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data
Cao, Y., Fujiwara, M., Nikaido, M., Okada, N., & Hasegawa, M. (2000) · Gene · doi:10.1016/s0378-1119(00)00427-3 · Cited by 112
Additional Support for Afrotheria and Paenungulata, the Performance of Mitochondrial versus Nuclear Genes, and the Impact of Data Partitions with Heterogeneous Base Composition
Springer, M. S., Amrine‐Madsen, H., Burk, A., & Stanhope, M. J. (1999) · Systematic Biology · doi:10.1080/106351599260445 · Cited by 111
Highly Congruent Molecular Support for a Diverse Superordinal Clade of Endemic African Mammals
Stanhope, M. J., Madsen, O., Waddell, V. G., Cleven, G. C., JONG, W. W. D., & Springer, M. S. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0517 · Cited by 108
Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla
Krettek, A., Gullberg, A., & Árnason, Ú. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00173175 · Cited by 108
Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters
Bartosch-Härlid, A., & Árnason, Ú. (1999) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1999.0638 · Cited by 106
Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins
Culligan, K. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.2.463 · Cited by 104
Amborella not a “basal angiosperm”? Not so fast
Soltis, D. E., & Soltis, P. S. (2004) · American Journal of Botany · doi:10.3732/ajb.91.6.997 · Cited by 98
Cladistic analysis of languages: Indo‐European classification based on lexicostatistical data
Rexová, K., Frynta, D., & Zrzavý, J. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00299.x · Cited by 97
Relationships within Cornales and circumscription of Cornaceae—matK and rbcL sequence data and effects of outgroups and long branches
Xiang, Q., Moody, M. L., Soltis, P. S., Fan, C. Z., & Soltis, P. S. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00267-1 · Cited by 93
Covarion Shifts Cause a Long-Branch Attraction Artifact That Unites Microsporidia and Archaebacteria in EF-1α Phylogenies
Inagaki, Y., Susko, E., Fast, N. M., & Roger, A. J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh130 · Cited by 93
Estimating ancestral geographical distributions: a Gondwanan origin for aphid parasitoids?
Belshaw, R. D., Dowton, M. P., Quicke, D. L. J., & Austin, A. D. (2000) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2000.1027 · Cited by 92
Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data
Lyons‐Weiler, J., & Hoelzer, G. A. (1997) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1997.0450 · Cited by 91
Analyses of RNA Polymerase II Genes from Free-Living Protists: Phylogeny, Long Branch Attraction, and the Eukaryotic Big Bang
Dacks, J. B., Marinets, A., Doolittle, W. F., Cavalier‐Smith, T., & Logsdon, J. M., Jr. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004140 · Cited by 90
Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly
Reyes, A., Pesole, G., & Saccone, C. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025949 · Cited by 89
The phylogenetic position of Rhopalura ophiocomae (Orthonectida) based on 18S ribosomal DNA sequence analysis
Hanelt, B., Van Schyndel, D., Adema, C. M., Lewis, L. A., & Loker, E. S. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025683 · Cited by 88
Rodent monophyly: pitfalls of molecular phylogenies.
Philippe, H. (1997) · PubMed · Cited by 88
Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires
Lin, Y.-H., Waddell, P. J., & Penny, D. (2002) · Gene · doi:10.1016/s0378-1119(02)00695-9 · Cited by 87
Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches
Reed, D. L., Carpenter, K. E., & deGravelle, M. J. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00036-2 · Cited by 83
Phylogenetic Depth of the Bacterial Genera Aquifex and Thermotoga Inferred from Analysis of Ribosomal Protein, Elongation Factor, and RNA Polymerase Subunit Sequences
Bocchetta, M., Gribaldo, S., Sanangelantoni, A. M., & Cammarano, P. (2000) · Journal of Molecular Evolution · doi:10.1007/s002399910040 · Cited by 82
Invariable Sites Models and Their Use in Phylogeny Reconstruction
Steel, M., Huson, D. H., & Lockhart, P. J. (2000) · Systematic Biology · doi:10.1093/sysbio/49.2.225 · Cited by 82
Phylogeny of the Tree Swallow Genus, Tachycineta (Aves: Hirundinidae), by Bayesian Analysis of Mitochondrial DNA Sequences
Whittingham, L. A., Slikas, B., Winkler, D. W., & Sheldon, F. H. (2002) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2001.1073 · Cited by 82
On Outgroups
Nixon, K. C. (1993) · Cladistics · doi:10.1006/clad.1993.1028 · Cited by 82
Do long branches attract flies?
Carmean, D., & Crespi, B. J. (1995) · Nature · doi:10.1038/373666b0 · Cited by 80
Morphology versus molecules: resolution of the positions of Nymphalis, Polygonia, and related genera (Lepidoptera: Nymphalidae)
Wahlberg, N., & Nylin, S. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00364.x · Cited by 77
Rate Acceleration and Long-branch Attraction in a Conserved Gene of Cryptic Daphniid (Crustacea) Species
Omilian, A. R., & Taylor, D. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003767 · Cited by 75
Frequent Inconsistency of Parsimony Under a Simple Model of Cladogenesis
Huelsenbeck, J. P., & Lander, K. M. (2003) · Systematic Biology · doi:10.1080/10635150390235467 · Cited by 75
Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test
Wilcox, T. P., León, F. J. G.-D., Hendrickson, D. A., & Hillis, D. M. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.11.006 · Cited by 74
Molecules remodel the mammalian tree
JONG, W. W. D. (1998) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(98)01335-4 · Cited by 72
A Combined Analysis of the Cystic Fibrosis Transmembrane Conductance Regulator: Implications for Structure and Disease Models
Chen, J., Cutler, C., Jacques, C., Bœuf, G., Denamur, É., Lecointre, G., Mercier, B., Cramb, G., & Férec, C. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003965 · Cited by 71
Likelihood and Inconsistency, , , ,
Farris, J. S. (1999) · Cladistics · doi:10.1006/clad.1999.0104 · Cited by 70
Was the ANITA Rooting of the Angiosperm Phylogeny Affected by Long-Branch Attraction?
Qiu, Y., Lee, J., Whitlock, B. A., Bernasconi‐Quadroni, F., & Dombrovska, O. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003962 · Cited by 69
Accounting for Evolutionary Rate Variation among Sequence Sites Consistently Changes Universal Phylogenies Deduced from rRNA and Protein-Coding Genes
Tourasse, N. J., & Gouy, M. (1999) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1999.0675 · Cited by 68
EVOLUTION OF THE GALL WASP–HOST PLANT ASSOCIATION
Ronquist, F., & Liljeblad, J. (2001) · Evolution · doi:10.1554/0014-3820(2001)055[2503:eotgwh]2.0.co;2 · Cited by 68
Trees for bees
Lockhart, P. J., & Cameron, S. A. (2001) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)02054-1 · Cited by 67
Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla
Nikaido, M., Cao, Y., Harada, M., Okada, N., & Hasegawa, M. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00120-9 · Cited by 65
Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes
Moreira, D., Guyader, H. L., & Philippe, H. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026105 · Cited by 65
The Effectiveness of Mitochondrial rRNA Gene Sequences for the Reconstruction of the Phylogeny of an Insect Order (Orthoptera)
Flook, P. K., & Rowell, C. H. F. (1997) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1997.0425 · Cited by 65
Phylogenetic Inference
Leasure, B., Kuck, D. J., Gorlatch, S. P., Cole, M., Watson, G. R., Darte, A., Padua, D., Banerjee, U. K., Schenk, O., Gärtner, K., et al. (2011) · Springer eBooks · doi:10.1007/978-0-387-09766-4_2422 · Cited by 63
Are Red Algae Plants? A Critical Evaluation of Three Key Molecular Data Sets
Stiller, J. W., Riley, J., & Hall, B. D. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010183 · Cited by 62
EXPERIMENTAL MOLECULAR EVOLUTION OF BACTERIOPHAGE T7
Bull, J. J., Cunningham, C., Molineux, I. J., Badgett, M. R., & Hillis, D. M. (1993) · Evolution · doi:10.1111/j.1558-5646.1993.tb02130.x · Cited by 61
Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei)
Clements, K. D., Gray, R. D., & Choat, J. H. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00325-1 · Cited by 60
The Chaperonin Genes of Jakobid and Jakobid-Like Flagellates: Implications for Eukaryotic Evolution
Archibald, J. M., O’Kelly, C. J., & Doolittle, W. F. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004097 · Cited by 59
Identifying Conflicting Signal in a Multigene Analysis Reveals a Highly Resolved Tree: The Phylogeny of Rodentia (Mammalia)
DeBry, R. W. (2003) · Systematic Biology · doi:10.1080/10635150390235403 · Cited by 56
Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences
García‐Moreno, J., Sorenson, M. D., & Mindell, D. P. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-002-2443-9 · Cited by 55
Fourier transform Raman spectroscopic characterization of humic substances
Yang, Y., & Wang, T. (1997) · Vibrational Spectroscopy · doi:10.1016/s0924-2031(96)00044-6 · Cited by 54
Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10‐Taxon Case
Pol, D., & Siddall, M. E. (2001) · Cladistics · doi:10.1111/j.1096-0031.2001.tb00123.x · Cited by 53
Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree
Hampl, V., Čepička, I., Jaroslav Flegr, A., Tachezy, J., & Kulda, J. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.03.005 · Cited by 51
Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny
Reyes, A., Pesole, G., & Saccone, C. (2000) · Gene · doi:10.1016/s0378-1119(00)00438-8 · Cited by 50
The Phylogenetic Relationships of the Suborder Acanthuroidei (Teleostei: Perciformes) Based on Molecular and Morphological Evidence
Tang, K. L., Berendzen, P. B., WILEY, E. O., Morrissey, J. F., Winterbottom, R., & Johnson, G. D. (1999) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0596 · Cited by 48
Molecular phylogenetics of the allodapine bee genus Braunsapis: A–T bias and heterogeneous substitution parameters
Schwarz, M. P., Tierney, S. M., Cooper, S. J., & Bull, N. J. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.11.017 · Cited by 47
Relative Symmetry of Cladograms and Phenograms: An Experimental Study
Colless, D. H. (1995) · Systematic Biology · doi:10.1093/sysbio/44.1.102 · Cited by 46
The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina
Kennedy, M., Paterson, A. M., Morales, J. C., Parsons, S. E., Winnington, A. P., & Spencer, H. G. (1999) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1999.0660 · Cited by 44
Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi
Mouchaty, S. K., Gullberg, A., Janke, A., & Árnason, Ú. (2000) · Zoologica Scripta · doi:10.1046/j.1463-6409.2000.00045.x · Cited by 43
Lagomorphs Misplaced by More Characters and Fewer Taxa
Halanych, K. M. (1998) · Systematic Biology · doi:10.1080/106351598261085 · Cited by 42
The Effect of Taxonomic Sampling on Accuracy of Phylogeny Estimation: Test Case of a Known Phylogeny
Poe, S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026008 · Cited by 42
Phylogenetic Analysis of Evolutionary Relationships of the Planctomycete Division of the Domain Bacteria Based on Amino Acid Sequences of Elongation Factor Tu
Jenkins, C., & Fuerst, J. A. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010170 · Cited by 39
Implications for Bat Evolution from Two New Complete Mitochondrial Genomes
Lin, Y.-H., & Penny, D. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003850 · Cited by 37
Likelihood and Inconsistency
Farris, J. S. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00262.x · Cited by 33
Response of Colless's Tree Imbalance to Number of Terminal Taxa
Rogers, J. S. (1993) · Systematic Biology · doi:10.1093/sysbio/42.1.102 · Cited by 32
Inconsistency of Maximum Parsimony Revisited
Schulmeister, S. (2004) · Systematic Biology · doi:10.1080/10635150490445788 · Cited by 31
Long-Branch Distraction and the Strepsiptera
Whiting, M. F. (1998) · Systematic Biology · doi:10.1080/106351598261076 · Cited by 29
Evolution of Eukaryotic Translation Elongation and Termination Factors: Variations of Evolutionary Rate and Genetic Code Deviations
Moreira, D., Kervestin, S., Jean‐Jean, O., & Philippe, H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004071 · Cited by 28
Optimally recovering rate variation information from genomes and sequences: pattern filtering
Lake, J. A. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026030 · Cited by 20
Limitations of Relative Apparent Synapomorphy Analysis (RASA) for Measuring Phylogenetic Signal
Simmons, M. P., Randle, C. P., Freudenstein, J. V., & Wenzel, J. W. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003978 · Cited by 19

Flagged first, then by citations

Research works printed but not linked: 6

Bergsten J., 2004, Acilius phylogeny (Coleoptera: Dytiscidae), problems with long‐branch attraction and morphological intersexual coevlution, Cladistics, 20, 76
Goloboff P., 1999, NONA (NO NAME)
Goloboff P.A., 2004, Cases in which Bayesian phylogenetic analysis will be positively misleading, Cladistics, 20, 83
Huelsenbeck J.P., 1996, Parametric Bootstrapping in Molecular Phylogenetics: Application and Performance
Nixon K., 2002, WinClada
Pickett K.M., 2004, Do Bayesian support values reflect probability of the truth?, Cladistics, 20, 92

Sorted by citations

Insights into the phylogeny and coding potential of microbial dark matter
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature · doi:10.1038/nature12352 · Cited by 2,394
Reconstructing the early evolution of Fungi using a six-gene phylogeny
James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G. J., Gueidan, C., Fraker, E., Miądlikowska, J., et al. (2006) · Nature · doi:10.1038/nature05110 · Cited by 1,844
Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.
Adeolu, M., Alnajar, S., Naushad, S., & Gupta, R. S. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001485 · Cited by 1,049
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
Moore, M. J., Bell, C. D., Soltis, P. S., & Soltis, P. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708072104 · Cited by 702
Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion
LIVEZEY, B. C., & ZUSI, R. L. (2007) · Zoological Journal of the Linnean Society · doi:10.1111/j.1096-3642.2006.00293.x · Cited by 574
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553
Evaluating alternative hypotheses for the early evolution and diversification of ants
Brady, S. G., Schultz, T. R., Fisher, B. L., & Ward, P. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605858103 · Cited by 540
New approaches for unravelling reassortment pathways
Svinti, V., Cotton, J. A., & McInerney, J. O. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-1 · Cited by 498
Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology
Goloboff, P. A., Torres, A., & Arias, J. S. (2017) · Cladistics · doi:10.1111/cla.12205 · Cited by 478
Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times
Zeng, L., Zhang, Q., Sun, R., Kong, H., Zhang, N., & Mā, H. (2014) · Nature Communications · doi:10.1038/ncomms5956 · Cited by 430
Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
Soria‐Carrasco, V., Gompert, Z., Comeault, A. A., Farkas, T. E., Parchman, T. L., Johnston, J. S., Buerkle, C. A., Feder, J. L., Bast, J., Schwander, T., et al. (2014) · Science · doi:10.1126/science.1252136 · Cited by 420
An Extreme Case of Plant–Insect Codiversification: Figs and Fig-Pollinating Wasps
Cruaud, A., Rønsted, N., Chantarasuwan, B., Chou, L., Clement, W. L., Couloux, A., Cousins, B., Genson, G., Harrison, R. D., Hanson, P., et al. (2012) · Systematic Biology · doi:10.1093/sysbio/sys068 · Cited by 406
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
Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life
Wurdack, K. J., & Davis, C. “. (2009) · American Journal of Botany · doi:10.3732/ajb.0800207 · Cited by 368
Phylogeny in cryptic weevils: molecules, morphology and new genera of western Palaearctic Cryptorhynchinae (Coleoptera : Curculionidae)
Astrin, J. J., & Stüben, P. E. (2008) · Invertebrate Systematics · doi:10.1071/is07057 · Cited by 364
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
García-López, M., Meier‐Kolthoff, J. P., Tindall, B. J., Gronow, S., Woyke, T., Kyrpides, N. C., Hahnke, R. L., & Göker, M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02083 · Cited by 356
Molecular phylogeny of acariform mites (Acari, Arachnida): Strong conflict between phylogenetic signal and long-branch attraction artifacts
Dabert, M., Witaliński, W., Kaźmierski, A., Olszanowski, Z., & Dabert, J. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.12.020 · Cited by 339
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats
Simon, M., Scheuner, C., Meier‐Kolthoff, J. P., Brinkhoff, T., Wagner‐Döbler, I., Ulbrich, M., Klenk, H., Schomburg, D., Petersen, J., & Göker, M. (2017) · The ISME Journal · doi:10.1038/ismej.2016.198 · Cited by 348
Heterotachy and long-branch attraction in phylogenetics
Philippe, H., Zhou, Y., Brinkmann, H., Rodrigue, N., & Delsuc, F. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-50 · Cited by 336
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage
Marcet‐Houben, M., & Gabaldón, T. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002220 · Cited by 334
Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal
Sharma, P. P., Kaluziak, S. T., Pérez-Porro, A. R., González, V. L., Hormiga, G., Wheeler, W. C., & Giribet, G. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu235 · Cited by 328
Genomic data do not support comb jellies as the sister group to all other animals
Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N., & Wörheide, G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518127112 · Cited by 319
Inferring Phylogenies from RAD Sequence Data
Rubin, B. E., Ree, R. H., & Moreau, C. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033394 · Cited by 327
300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling
Song, H., Amédégnato, C., Cigliano, M. M., Desutter‐Grandcolas, L., Heads, S. W., Huang, Y., Otte, D., & Whiting, M. F. (2015) · Cladistics · doi:10.1111/cla.12116 · Cited by 319
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
Gatesy, J., & Springer, M. S. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.08.013 · Cited by 307
Arthropod fossil data increase congruence of morphological and molecular phylogenies
David, L., Sutton, M. D., & Edgecombe, G. D. (2013) · Nature Communications · doi:10.1038/ncomms3485 · Cited by 309
Colletotrichum gloeosporioidess.l. associated withTheobroma cacaoand other plants in Panamá: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes
Rojas, E. I., Rehner, S. A., Samuels, G. J., Bael, S. A. V., Herre, E. A., Cannon, P. F., Chen, R., Pang, J., Wang, R., Zhang, Y., et al. (2010) · Mycologia · doi:10.3852/09-244 · Cited by 304
Mapping the Tree of Life: Progress and Prospects
Pace, N. R. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00033-09 · Cited by 286
A rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285
A molecular phylogeny of annelids
Rousset, V., Pleijel, F., Rouse, G. W., Erséus, C., & Siddall, M. E. (2006) · Cladistics · doi:10.1111/j.1096-0031.2006.00128.x · Cited by 285
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Bolduc, B., Jang, H. B., Doulcier, G., You, Z.-Q., Roux, S., & Sullivan, M. B. (2017) · PeerJ · doi:10.7717/peerj.3243 · Cited by 285
Single-copy nuclear genes resolve the phylogeny of the holometabolous insects
Wiegmann, B. M., Trautwein, M., Kim, J., Cassel, B. K., Bertone, M. A., Winterton, S. L., & Yeates, D. K. (2009) · BMC Biology · doi:10.1186/1741-7007-7-34 · Cited by 283
The gene tree delusion
Springer, M. S., & Gatesy, J. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.07.018 · Cited by 281
Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies
Pelser, P. B., Kennedy, A. H., Tepe, E. J., Shidler, J. B., Nordenstam, B., Kadereit, J. W., & Watson, L. E. (2010) · American Journal of Botany · doi:10.3732/ajb.0900287 · Cited by 283
Genesis and Expansion of Metazoan Transcription Factor Gene Classes
Larroux, C., Luke, G. N., Koopman, P. A., Rokhsar, D. S., Shimeld, S. M., & Degnan, B. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn047 · Cited by 280
Phylogenomics provides robust support for a two-domains tree of life
Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., & Embley, T. M. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1040-x · Cited by 274
En route to a genome-based classification of Archaea and Bacteria?
Klenk, H., & Göker, M. (2010) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2010.03.003 · Cited by 276
Incongruence in the phylogenomics era
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 276
The Evolution of Organ Systems
Schmidt‐Rhaesa, A. (2007) · doi:10.1093/acprof:oso/9780198566687.001.0001 · Cited by 264
Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record
Park, E., Hwang, D., Lee, J., Song, J., Seo, T., & Won, Y. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.10.008 · Cited by 266
A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)
Weese, T. L., & Bohs, L. (2007) · Systematic Botany · doi:10.1600/036364407781179671 · Cited by 256
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
Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)
Ma, P.-F., Zhang, Y.-X., Zeng, C., Guo, Z., & Li, D.-Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu054 · Cited by 244
Multiple Sequence Alignment Accuracy and Phylogenetic Inference
Ogden, T. H., & Rosenberg, M. S. (2006) · Systematic Biology · doi:10.1080/10635150500541730 · Cited by 237
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
Nabhan, A. R., & Sarkar, I. N. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr014 · Cited by 243
Integrative modeling of gene and genome evolution roots the archaeal tree of life
Williams, T. A., Szöllősi, G. J., Spang, A., Foster, P. G., Heaps, S. E., Boussau, B., Ettema, T. J. G., & Embley, T. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618463114 · Cited by 233
Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
Dombrowski, N., Lee, J.-H., Williams, T. A., Offre, P., & Spang, A. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz008 · Cited by 230
Molecular phylogeny of the New World Dipsadidae (Serpentes: Colubroidea): a reappraisal
Grazziotin, F. G., Zaher, H., Murphy, R. W., Scrocchi, G., Altamirano-Benavides, M., Zhang, Y., & Bonatto, S. L. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00393.x · Cited by 222
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
Capella-Gutiérrez, S., Marcet‐Houben, M., & Gabaldón, T. (2012) · BMC Biology · doi:10.1186/1741-7007-10-47 · Cited by 216
Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence
Legendre, F., Nel, A., Svenson, G. J., Robillard, T., Pellens, R., & Grandcolas, P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130127 · Cited by 226
Taxonomy annotation and guide tree errors in 16S rRNA databases
Edgar, R. C. (2018) · PeerJ · doi:10.7717/peerj.5030 · Cited by 227
Added resolution among ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with complete small and large subunit nuclear ribosomal RNA genes
Waeschenbach, A., Webster, B. L., Bray, R. A., & Littlewood, D. T. J. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.019 · Cited by 214
The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids
Lyons, E. H., Pedersen, B. S., Kane, J., & Freeling, M. (2008) · Tropical Plant Biology · doi:10.1007/s12042-008-9017-y · Cited by 209
Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution
Nováková, E., Hypša, V., & Moran, N. A. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-143 · Cited by 206
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error
Kocot, K. M., Struck, T. H., Merkel, J., Waits, D. S., Todt, C., Brannock, P. M., Weese, D., Cannon, J. T., Moroz, L. L., Lieb, B., et al. (2016) · Systematic Biology · doi:10.1093/sysbio/syw079 · Cited by 211
Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia)
Huang, D., Benzoni, F., Fukami, H., Knowlton, N., Smith, N. D., & Budd, A. F. (2014) · Zoological Journal of the Linnean Society · doi:10.1111/zoj.12140 · Cited by 198
Plastid phylogenomic insights into the evolution of Caryophyllales
Yao, G., Jin, J., Li, H., Yang, J., Mandala, V. S., Croley, M., Mostow, R. S., Douglas, N. A., Chase, M. W., Christenhusz, M. J. M., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.12.023 · Cited by 189
Phylogeny of the Zygomycota based on nuclear ribosomal sequence data
White, M. M., James, T. Y., O'Donnell, K. L., Cafaro, M. J., Tanabe, Y., & Sugiyama, J. (2006) · Mycologia · doi:10.3852/mycologia.98.6.872 · Cited by 188
Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants
Harris, B. J., Clark, J. W., Schrempf, D., Szöllősi, G. J., Donoghue, P. C. J., Hetherington, A. M., & Williams, T. A. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01885-x · Cited by 187
Phylogeny, Evolution and Classification of Gall Wasps: The Plot Thickens
Ronquist, F., Nieves‐Aldrey, J. L., Buffington, M. L., Liu, Z., Liljeblad, J., & Nylander, J. A. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123301 · Cited by 187
Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models
Song, F., Li, H., Jiang, P., Zhou, X. J., Liu, J., Sun, C., Vogler, A. P., & Cai, W. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw086 · Cited by 191
Resolving an Ancient, Rapid Radiation in Saxifragales
Jian, S., Soltis, P. S., Gitzendanner, M. A., Moore, M. J., Li, R., Hendry, T. A., Qiu, Y., Dhingra, A., Bell, C. D., & Soltis, P. S. (2008) · Systematic Biology · doi:10.1080/10635150801888871 · Cited by 183
Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia
Struck, T. H., Wey-Fabrizius, A. R., Golombek, A., Hering, L., Weigert, A., Bleidorn, C., Klebow, S., Iakovenko, N., Hausdorf, B., Petersen, M., et al. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu143 · Cited by 178
Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
Foster, J. T., Beckstrom‐Sternberg, S. M., Pearson, T., Beckstrom‐Sternberg, J. S., Chain, P., Roberto, F. F., Hnath, J., Brettin, T., & Keim, P. (2009) · Journal of Bacteriology · doi:10.1128/jb.01581-08 · Cited by 177
Phylogeny, classification and evolutionary insights into pestiviruses
Liu, L., Xia, H., Wahlberg, N., Bélak, S., & Baule, C. (2009) · Virology · doi:10.1016/j.virol.2008.12.004 · Cited by 175
Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172
The Phylogeny and Evolution of Ants
Ward, P. S. (2014) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-120213-091824 · Cited by 180
'Candidatus Liberibacter solanacearum', associated with plants in the family Solanaceae
Liefting, L. W., Weir, B. S., Pennycook, S. R., & Clover, G. R. G. (2009) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.007377-0 · Cited by 170
Accurate Branch Length Estimation in Partitioned Bayesian Analyses Requires Accommodation of Among-Partition Rate Variation and Attention to Branch Length Priors
Marshall, D. C., Simon, C., & Buckley, T. R. (2006) · Systematic Biology · doi:10.1080/10635150601087641 · Cited by 170
Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics
Sheffield, N. C., Song, H., Cameron, S. L., & Whiting, M. F. (2009) · Systematic Biology · doi:10.1093/sysbio/syp037 · Cited by 170
A “Holistic” Kinesin Phylogeny Reveals New Kinesin Families and Predicts Protein Functions
Wickstead, B., & Gull, K. (2006) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-11-1090 · Cited by 175
Relict species: a relict concept?
Grandcolas, P., Nattier, R., & Trewick, S. A. (2014) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2014.10.002 · Cited by 165
Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha
Kapli, P., & Telford, M. J. (2020) · Science Advances · doi:10.1126/sciadv.abc5162 · Cited by 162
Relationships among major lineages of characid fishes (Teleostei: Ostariophysi: Characiformes), based on molecular sequence data
Javonillo, R., Malabarba, L. R., Weitzman, S. H., & Burns, J. R. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.026 · Cited by 161
A voltage-dependent chloride channel fine-tunes photosynthesis in plants
Herdean, A., Teardo, E., Nilsson, A., Pfeil, B. E., Johansson, O., Ünnep, R., Nagy, G., Zsíros, O., Dana, S., Solymosi, K., et al. (2016) · Nature Communications · doi:10.1038/ncomms11654 · Cited by 161
Newly discovered sister lineage sheds light on early ant evolution
Rabeling, C., Brown, J. M., & Verhaagh, M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806187105 · Cited by 164
A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error
Ballesteros, J. A., & Sharma, P. P. (2019) · Systematic Biology · doi:10.1093/sysbio/syz011 · Cited by 167
A genome Tree of Life for the Fungi kingdom
Choi, J., & Kim, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711939114 · Cited by 170
Phylogeny, classification, and species-level taxonomy of ants (Hymenoptera: Formicidae)*
Ward, P. S. (2007) · Zootaxa · doi:10.11646/zootaxa.1668.1.26 · Cited by 154
How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews
Göker, M., Voglmayr, H., Riethmüller, A., & Oberwinkler, F. (2006) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2006.07.005 · Cited by 154
Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny
Wu, C., Wang, Y., Hsu, C.-Y., Lin, C.-P., & Chaw, S. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr095 · Cited by 156
Re-assessing the diversity of negative strand RNA viruses in insects
Käfer, S., Paraskevopoulou, S., Zirkel, F., Wieseke, N., Donath, A., Petersen, M., Jones, T. C., Liu, S., Zhou, X. Y., Middendorf, M., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1008224 · Cited by 155
Vaccinia Virus Proteins A52 and B14 Share a Bcl-2–Like Fold but Have Evolved to Inhibit NF-κB rather than Apoptosis
Graham, S. C., Bahar, M. W., Cooray, S., Chen, R. A.-J., Whalen, D. M., Abrescia, N. G. A., Alderton, D., Owens, R. J., Stuart, D. I., Smith, G. L., et al. (2008) · PLoS Pathogens · doi:10.1371/journal.ppat.1000128 · Cited by 152
Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships
Shen, H., Braband, A., & Scholtz, G. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.11.002 · Cited by 149
Pushing short DNA fragments to the limit: Phylogenetic relationships of ‘hydrobioid’ gastropods (Caenogastropoda: Rissooidea)
Wilke, T., Haase, M., Hershler, R., Liu, H., Misof, B. Y., & Ponder, W. F. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.10.025 · Cited by 145
Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae
Barber, P. H., & Boyce, S. L. (2006) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2006.3540 · Cited by 145
When phylogenetic assumptions are violated: base compositional heterogeneity and among‐site rate variation in beetle mitochondrial phylogenomics
Song, H., Sheffield, N. C., Cameron, S. L., Miller, K. B., & Whiting, M. F. (2010) · Systematic Entomology · doi:10.1111/j.1365-3113.2009.00517.x · Cited by 144
An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life
Chang, J., Rabosky, D. L., Smith, S. A., & Alfaro, M. E. (2019) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13182 · Cited by 152
Measuring phylogenetic signal between categorical traits and phylogenies
Borges, R., Machado, J. P., Gomes, C., Rocha, A. P., & Antunes, A. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty800 · Cited by 144
Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 cp Protein-Coding Genes of Gnetum parvifolium: Insights into cpDNA Evolution and Phylogeny of Extant Seed Plants
Wu, C., Wang, Y., Liu, S., & Chaw, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm059 · Cited by 140
MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants
Gramzow, L., Weilandt, L., & Theißen, G. (2014) · Annals of Botany · doi:10.1093/aob/mcu066 · Cited by 139
Tree ferns: Monophyletic groups and their relationships as revealed by four protein-coding plastid loci
Korall, P., Pryer, K. M., Metzgar, J. S., Schneider, H., & Conant, D. S. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.01.001 · Cited by 139
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
Lang, J., Darling, A. E., & Eisen, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062510 · Cited by 144
Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
Rothfels, C. J., Larsson, A. O., Kuo, L., Korall, P., Chiou, W., & Pryer, K. M. (2012) · Systematic Biology · doi:10.1093/sysbio/sys001 · Cited by 138
Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes
Paps, J., Baguñà, J., & Riutort, M. (2009) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1574 · Cited by 138
Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data
Raupach, M. J., Mayer, C., Malyutina, M., & Wägele, J. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1063 · Cited by 138
Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera)
Heikkilä, M., Mutanen, M., Kekkonen, M., & Kaila, L. (2013) · Cladistics · doi:10.1111/cla.12064 · Cited by 136
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 138
Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus
Hubert, F. N., Grimm, G. W., Jousselin, E., Berry, V., Franc, A., & Kremer, A. (2014) · Systematics and Biodiversity · doi:10.1080/14772000.2014.941037 · Cited by 134
Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
Villaverde, T., Pokorny, L., Olsson, S., Barrado, M. R., Johnson, M. G., Gardner, E. M., Wickett, N. J., Molero, J., Riina, R., & Sanmartín, I. (2018) · New Phytologist · doi:10.1111/nph.15312 · Cited by 132

Authors: Bergsten, J.
Affiliations: Umeå University (SE)
Corresponding author: Bergsten, Johannes
ORCID: Bergsten, Johannes
Venue: Cladistics
Publisher: Wiley
Published: 2005-04
Volume: 21
Issue: 2
Pages: 163-193
ISSN: 0748-3007 (ISSN-L)
1096-0031
DOI: 10.1111/j.1096-0031.2005.00059.x
OpenAlex: W2101797035
Cited by: 1,162
References: 203
Citations by year: 2026: 32 · 2025: 50 · 2024: 64 · 2023: 54 · 2022: 57 · 2021: 50 · 2020: 71 · 2019: 62 · 2018: 59 · 2017: 72 · 2016: 50 · 2015: 57 · 2014: 69 · 2013: 49 · 2012: 59
FWCI: 17.82
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 60 d)
Locations: Cladistics (publishedVersion)
PubMed (publishedVersion)
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: long-branch attraction, outgroup rooting, rasa, split decomposition, spectral analysis, taxon sampling, placental mammals, Cynipidae, murid rodents, tenrecs, guinea pig, Glires, parsimony, Bayesian phylogenetics, codon position

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

A review of long-branch attraction

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks