How good are deep phylogenetic trees?

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128

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 3,261

Cases in which parsimony or compatibility methods will be positively misleading.

Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230

Molecular evidence for an ancient duplication of the entire yeast genome

Wolfe, K. H., & Shields, D. C. (1997) · Nature · doi:10.1038/42711 · Cited by 1,785

Evidence for a clade of nematodes, arthropods and other moulting animals

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Among-site rate variation and its impact on phylogenetic analyses

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Molecular archaeology of the Escherichia coli genome

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A Framework for the Quantitative Study of Evolutionary Trees

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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

Gene translocation links insects and crustaceans

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Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins.

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Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla

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Archaea and the prokaryote-to-eukaryote transition

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Molecular evidence from retroposons that whales form a clade within even-toed ungulates

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Evolutionary relationships among protozoa.

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Modeling the covarion hypothesis of nucleotide substitution

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The guinea-pig is not a rodent

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Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

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Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates

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The gain of three mitochondrial introns identifies liverworts as the earliest land plants

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Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies

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Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny

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Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics

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Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

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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

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General Time-Reversible Distances with Unequal Rates across Sites: Mixing Γ and Inverse Gaussian Distributions with Invariant Sites

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Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

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Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae1Note: Nucleotide sequence data reported in this paper has been submitted to the GenBank™ data base under the accession number U97520.1

Germot, A., Philippe, H., & Guyader, H. L. (1997) · Molecular and Biochemical Parasitology · doi:10.1016/s0166-6851(97)00064-9 · Cited by 238

Taxon Sampling and the Accuracy of Large Phylogenies

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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

A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans

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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

A mitochondrial Hsp70 orthologue in Vairimorpha necatrix : molecular evidence that microsporidia once contained mitochondria

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Aspects of the Genesis and Maintenance of Biological Diversity

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Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny

Hashimoto, T., Sánchez, L. B., Shirakura, T., Müller, M., & Hasegawa, M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6860 · Cited by 149

Vagaries of the molecular clock.

Ayala, F. J. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.15.7776 · Cited by 140

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

Lockhart, P. J., Steel, M., Barbrook, A. C., Huson, D. H., Charleston, M., & Howe, C. J. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026025 · Cited by 139

How often do wrong models produce better phylogenies?

Yang, Z. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025695 · Cited by 133

Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Pawlowski, J. W., Bolívar, I., Fahrni, J. F., de Vargas, C., Gouy, M., & Zaninetti, L. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025786 · Cited by 133

The molecular phylogeny of eukaryota: solid facts and uncertainties

Phillipe, H. (1998) · Parasitology International · doi:10.1016/s1383-5769(98)80093-7 · Cited by 126

Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.

Meyer, T. E., Cusanovich, M. A., & Kamen, M. D. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.2.217 · Cited by 125

Genome Data Shake Tree of Life

Pennisi, E. (1998) · Science · doi:10.1126/science.280.5364.672 · Cited by 124

Analyzing Large Data Sets: rbcL 500 Revisited

Rice, K. A., Donoghue, M. J., & Olmstead, R. G. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.554 · Cited by 118

The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships

Philippe, H., & Douzery, E. (1994) · Journal of Mammalian Evolution · doi:10.1007/bf01464365 · Cited by 112

Protein phylogeny of translation elongation factor EF-1α suggests microsporidians are extremely ancient eukaryotes

Kamaishi, T., Hashimoto, T., Nakamura, Y., Nakamura, F., Murata, S., Okada, N., Okamoto, K.-I., Shimizu, M., & Hasegawa, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02198852 · Cited by 106

Critical Analysis of Eukaryotic Phylogeny: A Case Study Based on the HSP70 Family

Germot, A., & Philippe, H. (1999) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.1999.tb04594.x · Cited by 102

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated.

Shoemaker, J. S., & Fitch, W. M. (1989) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040550 · Cited by 99

What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram‐positive bacteria? A new proposal for the classification of prokaryotic organisms

Gupta, R. S. (1998) · Molecular Microbiology · doi:10.1046/j.1365-2958.1998.00978.x · Cited by 97

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

Rodent monophyly: pitfalls of molecular phylogenies.

Philippe, H. (1997) · PubMed · Cited by 88

Hadamard Conjugations and Modeling Sequence Evolution with Unequal Rates across Sites

Waddell, P. J., Penny, D., & Moore, T. (1997) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1997.0405 · Cited by 78

Evolution of microbial life

Roberts, D., Sharp, P. J., Alderson, G., & Collins, M. (1997) · University of Groningen research database (University of Groningen / Centre for Information Technology) · Cited by 78

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution

Gu, X., & Li, W. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.11.5899 · Cited by 73

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

RNA Polymerase of Aquifex pyrophilus: Implications for the Evolution of the Bacterial rpoBC Operon and Extremely Thermophilic Bacteria

Klenk, H., Meier, T., Durovic, P., Schwass, V., Lottspeich, F., Dennis, P. P., & Zillig, W. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006496 · Cited by 64

New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences

Budin, K., & Philippe, H. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026010 · Cited by 61

A Critical Study of Homoplasy in Molecular Data with the Use of a Morpholoogically Based Cladogram, and Its Consequences for Character Weighting

Philippe, H., Lecointre, G., Lê, H. L. V., & Guyader, H. L. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025682 · Cited by 60

Molecular Phylogenetics at the Felsenstein Zone: Approaching the Strepsiptera Problem Using 5.8S and 28S rDNA Sequences

Hwang, U. W., Kim, W. D., Tautz, D., & Friedrich, M. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0518 · Cited by 59

The nonidentity of invariable positions in the cytochromes c of different species

Fitch, W. M. (1971) · Biochemical Genetics · doi:10.1007/bf00485794 · Cited by 50

Informational Suppression to Investigate Structural Functional and Evolutionary Aspects of the Cellulase EGZ

Bortoli‐German, I., Haiech, J., Chippaux, M., & Barras, F. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0068 · Cited by 47

Signature Sequences in Diverse Proteins Provide Evidence of a Close Evolutionary Relationship Between the Deinococcus-Thermus Group and Cyanobacteria

Gupta, R. S., & Johari, V. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006352 · Cited by 44

Lagomorphs Misplaced by More Characters and Fewer Taxa

Halanych, K. M. (1998) · Systematic Biology · doi:10.1080/106351598261085 · Cited by 42

Constraints on protein evolution and the age of the eubacteria/eukaryote split.

Miyamoto, M. M., & Fitch, W. M. (1996) · Systematic Biology · doi:10.1093/sysbio/45.4.568 · Cited by 35

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Donoghue, M. J., & Mathews, S. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0511 · Cited by 34

FIRST PRINCIPLES OF PHYLOGENETIC SYSTEMATICS, A BASIS FOR NUMERICAL METHODS USED FOR MORPHOLOGICAL AND MOLECULAR CHARACTERS

Wâgele, J.-W. (1996) · HAL (Le Centre pour la Communication Scientifique Directe) · Cited by 10

Higher ribosomal RNA substitution rates in Bacillariophyceae and Dasycladales than in Mollusca, Echinodermata, and Actinistia-Tetrapoda

Sörhannus, U. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025653 · Cited by 9

What can phylogenetic patterns tell us about the evolutionary processes generating biodiversity?

Philippe, H., & Adoutte, A. (1996) · doi:10.1093/oso/9780198548843.003.0004 · Cited by 5

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

Talavera, G., & Castresana, J. (2007) · Systematic Biology · doi:10.1080/10635150701472164 · Cited by 5,725

Phylogenetic Classification and the Universal Tree

Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888

Mitochondrial Evolution

Gray, M. W., Burger, G., & Lang, B. F. (1999) · Science · doi:10.1126/science.283.5407.1476 · Cited by 1,765

The Uncultured Microbial Majority

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Phylogenomics and the reconstruction of the tree of life

Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,264

DOI: 10.1080/10635150500234609 An Empirical Assessment of Long-Branch Attraction Artefacts in Deep

Phylogenomics, E., Brinkmann, H., Giezen, M. V. D., Zhou, Y., de Raucourt, G. P., & Philippe, H. (2013)

An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics

Brinkmann, H., van der Giezen, M., Zhou, Y., de Raucourt, G. P., & Philippe, H. (2005) · Systematic Biology · doi:10.1080/10635150500234609 · Cited by 286

Ancient Phylogenetic Relationships

Gribaldo, S., & Philippe, H. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1593 · Cited by 314

"Early-Diverging" Lineages Provide Little Information about Ancestors

Beaulieu, J. M., Alverson, A. J., & O’Meara, B. C. (2026) · Systematic Biology · doi:10.1093/sysbio/syag074

Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies

Rangel, L. T., & Fournier, G. P. (2023) · Microorganisms · doi:10.3390/microorganisms11102499 · Cited by 14