The Closest Unicellular Relatives of Animals

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works

The rapid generation of mutation data matrices from protein sequences

Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,916 · see citing works

PAML: a program package for phylogenetic analysis by maximum likelihood

Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,344 · see citing works

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 3,221 · see citing works

An approximately unbiased test of phylogenetic tree selection

Shimodaira, H. (2002) · Systematic Biology · doi:10.1080/10635150290069913 · Cited by 2,791 · see citing works

Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies

Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531 · see citing works

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

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

CONSEL: for assessing the confidence of phylogenetic tree selection

Shimodaira, H., & Hasegawa, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1246 · Cited by 2,051 · see citing works

[5] Rapid and sensitive sequence comparison with FASTP and FASTA

Pearson, W. R. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83007-v · Cited by 1,934 · see citing works

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Gascuel, O. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025808 · Cited by 1,850 · see citing works

The staden sequence analysis package

Staden, R. (1996) · Molecular Biotechnology · doi:10.1007/bf02900361 · Cited by 1,264 · see citing works

A kingdom-level phylogeny of eukaryotes based on combined protein data.

Baldauf, S., Roger, A., Wenk-Siefert, I., & Doolittle, W. (2000) · Science · doi:10.1126/science.290.5493.972 · Cited by 1,243 · see citing works

Mitochondrial Genome Evolution and the Origin of Eukaryotes

Lang, B. F., Gray, M. W., & Burger, G. (1999) · Annual Review of Genetics · doi:10.1146/annurev.genet.33.1.351 · Cited by 724 · see citing works

Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi

Wainright, P. O., Hinkle, G., Sogin, M. L., & Stickel, S. K. (1993) · Science · doi:10.1126/science.8469985 · Cited by 653 · see citing works

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

Baldauf, S. L., & Palmer, J. D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.24.11558 · Cited by 543 · see citing works

Molecular phylogenetics: state-of-the-art methods for looking into the past

Whelan, S., Lió, P., & Goldman, N. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02272-7 · Cited by 413 · see citing works

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171316998 · Cited by 395 · see citing works

Evolutionary relationships among protozoa.

Coombs, G. H., Vickerman, K., Sleigh, M. A., & Warren, A. (1998) · Kluwer Academic Publishers eBooks · Cited by 383 · see citing works

Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA

de Peer, Y. V., & Wächter, R. D. (1997) · Journal of Molecular Evolution · doi:10.1007/pl00006266 · Cited by 254 · see citing works

Phylogenetic Analysis of Rhinosporidium seeberi ’s 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade

Herr, R. A., Ajello, L., Taylor, J. W., Arseculeratne, S. N., & Mendoza, L. (1999) · Journal of Clinical Microbiology · doi:10.1128/jcm.37.9.2750-2754.1999 · Cited by 247 · see citing works

Molecular Evidence That the Myxozoan Protists Are Metazoans

Smothers, J. F., von Dohlen, C. D., Smith, L. H., & Spall, R. D. (1994) · Science · doi:10.1126/science.8085160 · Cited by 239 · see citing works

A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution

King, N., & Carroll, S. B. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.261477698 · Cited by 234 · see citing works

Evolutionary Biology of the Fungi

Motta, J. J., RAYNER, A. D. M., Brasier, C. M., & Moore, D. (1989) · Mycologia · doi:10.2307/3760095 · Cited by 227 · see citing works

A novel clade of protistan parasites near the animal-fungal divergence.

Ragan, M. A., Goggin, C. L., Cawthorn, R. J., Cerenius, L., Jamieson, A., Plourde, S. M., Rand, T. G., Söderhäll, K., & Gutell, R. R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11907 · Cited by 170 · see citing works

The Mitochondrial Genome of the Sea Anemone Metridium senile (Cnidaria): Introns, a Paucity of tRNA Genes, and a Near-Standard Genetic Code

Beagley, C. T., Okimoto, R., & Wolstenholme, D. R. (1998) · Genetics · doi:10.1093/genetics/148.3.1091 · Cited by 150 · see citing works

Evolutionary relationships of eukaryotic kingdoms

Kumar, S., & Rzhetsky, A. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02198844 · Cited by 142 · see citing works

Amoebidium parasiticum Is a Protozoan, Not a Trichomycete

Benny, G. L., & O'Donnell, K. L. (2000) · Mycologia · doi:10.2307/3761480 · Cited by 91 · see citing works

Hyaloraphidium curvatum is not a Green Alga, but a Lower Fungus; Amoebidium parasiticum is not a Fungus, but a Member of the DRIPs

Ustinova, I., Krienitz, L., & Huss, V. A. R. (2000) · Protist · doi:10.1078/1434-4610-00023 · Cited by 90 · see citing works

Neomonada and the origin of animals and fungi.

Cavalier‐Smith, T., Coombs, G. H., Vickerman, K., Sleigh, M. A., & Warren, A. (1998) · Cited by 82 · see citing works

Hsp70 sequences indicate that choanoflagellates are closely related to animals

Snell, E. A., Furlong, R. F., & Holland, P. W. H. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00275-5 · Cited by 73 · see citing works

Sequence Analysis of the Mitochondrial Genome of Sarcophyton glaucum: Conserved Gene Order Among Octocorals

Beaton, M. J., Roger, A. J., & Cavalier‐Smith, T. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006429 · Cited by 68 · see citing works

Note on the Infusoria flagellata and the Spongiae ciliatae

James‐Clark, H. (1871) · American Journal of Science · doi:10.2475/ajs.s3-1.2.113 · Cited by 52 · see citing works

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 1,807 · see citing works

The Revised Classification of Eukaryotes

Adl, S. M., Simpson, A. G. B., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., et al. (2012) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2012.00644.x · Cited by 1,680 · see citing works

A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

Lartillot, N., & Philippe, H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh112 · Cited by 1,516 · see citing works

Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis

Gregoretti, I., Lee, Y.-M., & Goodson, H. V. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.006 · Cited by 1,456 · see citing works

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 1,228 · see citing works

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139 · see citing works

The new tree of eukaryotes

Burki, F., Roger, A. J., Brown, M. W., & Simpson, A. G. B. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2019.08.008 · Cited by 913 · see citing works

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

Lutzoni, F. M., Kauff, F., Cox, C. J., McLaughlin, D. J., Celio, G. J., Dentinger, B. T. M., Padamsee, M., Hibbett, D. S., James, T. Y., Baloch, E., et al. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1446 · Cited by 816 · see citing works

Structure, regulation and evolution of Nox‐family NADPH oxidases that produce reactive oxygen species

Sumimoto, H. (2008) · FEBS Journal · doi:10.1111/j.1742-4658.2008.06488.x · Cited by 718 · see citing works

Mitochondrial genomes: anything goes

Burger, G., Gray, M. W., & Lang, B. F. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.10.012 · Cited by 631 · see citing works

The tree of eukaryotes

Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579 · see citing works

The evolution of cell types in animals: emerging principles from molecular studies

Arendt, D. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2416 · Cited by 525 · see citing works

The Unicellular Ancestry of Animal Development

King, N. (2004) · Developmental Cell · doi:10.1016/j.devcel.2004.08.010 · Cited by 482 · see citing works

The evolution of signalling pathways in animal development

Pires-daSilva, A., & Sommer, R. J. (2003) · Nature Reviews Genetics · doi:10.1038/nrg977 · Cited by 466 · see citing works

Myosin domain evolution and the primary divergence of eukaryotes

Richards, T. A., & Cavalier‐Smith, T. (2005) · Nature · doi:10.1038/nature03949 · Cited by 432 · see citing works

Evolution of Key Cell Signaling and Adhesion Protein Families Predates Animal Origins

King, N., Hittinger, C. T., & Carroll, S. B. (2003) · Science · doi:10.1126/science.1083853 · Cited by 424 · see citing works

Ancient gene linkages support ctenophores as sister to other animals

Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362 · see citing works

Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments

Philippe, H., Snell, E. A., Bapteste, E. P., Lopez, P., Holland, P. W. H., & Casañe, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh182 · Cited by 398 · see citing works

Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion

Cavalier‐Smith, T. (2004) · Annals of Botany · doi:10.1093/aob/mci010 · Cited by 397 · see citing works

The Evolution of Sex: a Perspective from the Fungal Kingdom

Lee, S. C., Ni, M., Li, W., Shertz, C. A., & Heitman, J. (2010) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00005-10 · Cited by 369 · see citing works

Only six kingdoms of life

Cavalier‐Smith, T. (2004) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2004.2705 · Cited by 333 · see citing works

The origin of Metazoa: a unicellular perspective

Sebé-Pedrós, A., Degnan, B. M., & Ruiz-Trillo, I. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.21 · Cited by 332 · see citing works

Mitochondria of Protists

Gray, M. W., Lang, B. F., & Burger, G. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.142526 · Cited by 321 · see citing works

The Capsaspora genome reveals a complex unicellular prehistory of animals

Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M. W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., et al. (2013) · Nature Communications · doi:10.1038/ncomms3325 · Cited by 317 · see citing works

The Protistan Origins of Animals and Fungi

Steenkamp, E. T., Wright, J., & Baldauf, S. L. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj011 · Cited by 307 · see citing works

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 · see citing works

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 281 · see citing works

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 275 · see citing works

Multigene Phylogeny of Choanozoa and the Origin of Animals

Shalchian‐Tabrizi, K., Minge, M. A., Espelund, M., Orr, R. J. S., Ruden, T. A., Jakobsen, K. S., & Cavalier‐Smith, T. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002098 · Cited by 263 · see citing works

THE SYMBIOTIC BIRTH AND SPREAD OF PLASTIDS: HOW MANY TIMES AND WHODUNIT?

Palmer, J. D. (2003) · Journal of Phycology · doi:10.1046/j.1529-8817.2003.02185.x · Cited by 271 · see citing works

A Phylogenomic Investigation into the Origin of Metazoa

Ruiz‐Trillo, I., Roger, A. J., Burger, G., Gray, M. W., & Lang, B. F. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn006 · Cited by 269 · see citing works

The Evolution of Organ Systems

Schmidt‐Rhaesa, A. (2007) · doi:10.1093/acprof:oso/9780198566687.001.0001 · Cited by 262 · see citing works

Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses

Pritham, E. J., Sharma, T. P., & Feschotte, C. (2006) · Gene · doi:10.1016/j.gene.2006.08.008 · Cited by 258 · see citing works

Early central nervous system evolution: an era of skin brains?

Holland, N. D. (2003) · Nature reviews. Neuroscience · doi:10.1038/nrn1175 · Cited by 250 · see citing works

Ancient origin of the integrin-mediated adhesion and signaling machinery

Sebé-Pedrós, A., Roger, A. J., Lang, B. F., King, N., & Ruiz‐Trillo, I. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002257107 · Cited by 250 · see citing works

Mitochondrial genome of <i>Trichoplax adhaerens</i> supports Placozoa as the basal lower metazoan phylum

Dellaporta, S. L., Xu, A., Sagasser, S., Jakob, W., Moreno, M. A., Buss, L. W., & Schierwater, B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602076103 · Cited by 252 · see citing works

Protist phylogeny and the high-level classification of Protozoa

Cavalier‐Smith, T. (2003) · European Journal of Protistology · doi:10.1078/0932-4739-00002 · Cited by 251 · see citing works

The Evolution of Eukaryotic Cilia and Flagella as Motile and Sensory Organelles

Mitchell, D. R. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_11 · Cited by 246 · see citing works

Evolution of Filamentous Plant Pathogens: Gene Exchange across Eukaryotic Kingdoms

Richards, T. A., Dacks, J. B., Jenkinson, J. M., Thornton, C. R., & Talbot, N. J. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.052 · Cited by 226 · see citing works

Unique mitochondrial genome architecture in unicellular relatives of animals

Burger, G., Forget, L., Zhu, Y. J., Gray, M. W., & Lang, B. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0336115100 · Cited by 221 · see citing works

Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life

Berbee, M. L., James, T. Y., & Strullu‐Derrien, C. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-030117-020324 · Cited by 218 · see citing works

Molecular phylogeny of choanoflagellates, the sister group to Metazoa

Carr, M., Leadbeater, B. S. C., Hassan, R., Nelson, M., & Baldauf, S. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801667105 · Cited by 205 · see citing works

Choanoflagellates, choanocytes, and animal multicellularity

Maldonado, M. (2004) · Invertebrate Biology · doi:10.1111/j.1744-7410.2004.tb00138.x · Cited by 207 · see citing works

Dynamical patterning modules: a "pattern language" for development and evolution of multicellular form

Newman, S. A., & Bhat, R. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.072481sn · Cited by 208 · see citing works

The origins of multicellularity: a multi-taxon genome initiative

Ruiz‐Trillo, I., Burger, G., Holland, P. W. H., King, N., Lang, B. F., Roger, A. J., & Gray, M. W. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.01.005 · Cited by 206 · see citing works

Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements

Richards, T. A., Dacks, J. B., Campbell, S. A., Blanchard, J. L., Foster, P. G., McLeod, R. L., & Roberts, C. W. (2006) · Eukaryotic Cell · doi:10.1128/ec.00106-06 · Cited by 205 · see citing works

Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata

Moreira, D., von der Heyden, S., Bass, D., López‐García, P., Chao, E. E. Y., & Cavalier‐Smith, T. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.11.001 · Cited by 201 · see citing works

The Genomic and Cellular Foundations of Animal Origins

Richter, D. J., & King, N. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133456 · Cited by 196 · see citing works

Emergence, development and diversification of the TGF-β signalling pathway within the animal kingdom

Huminiecki, Ł., Goldovsky, L., Freilich, S., Moustakas, A., Ouzounis, C. A., & Heldin, C. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-28 · Cited by 183 · see citing works

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169 · see citing works

Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of “Primitive” Eukaryotes

Simpson, A. G. B., Inagaki, Y., & Roger, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj068 · Cited by 178 · see citing works

Histone modifications and chromatin dynamics: a focus on filamentous fungi

Brosch, G., Loidl, P., & Graessle, S. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2007.00100.x · Cited by 174 · see citing works

Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium

Cavalier‐Smith, T., Chao, E. E. Y., & Oates, B. R. (2004) · European Journal of Protistology · doi:10.1016/j.ejop.2003.10.001 · Cited by 171 · see citing works

The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa

Philip, G. K., Creevey, C. J., & McInerney, J. O. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi102 · Cited by 170 · see citing works

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

Pincus, D., Letunić, I., Peer Bork, B., & Lim, W. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803161105 · Cited by 165 · see citing works

The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition

Ros-Rocher, N., Pérez-Posada, A., Leger, M. M., & Ruiz‐Trillo, I. (2021) · Open Biology · doi:10.1098/rsob.200359 · Cited by 160 · see citing works

The origin of Metazoa: a transition from temporal to spatial cell differentiation

Mikhailov, K. V., Константинова, А. В., Nikitin, M. A., Troshin, P. V., Rusin, L. Y., Lyubetsky, V., Panchin, Y. V., Mylnikov, A. P., Moroz, L. L., Kumar, S., et al. (2009) · BioEssays · doi:10.1002/bies.200800214 · Cited by 151 · see citing works

The Evolution of SMC Proteins: Phylogenetic Analysis and Structural Implications

Cobbe, N., & Heck, M. M. S. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh023 · Cited by 146 · see citing works

Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

Brown, M. W., Spiegel, F. W., & Silberman, J. D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp185 · Cited by 149 · see citing works

Evolution of networks and sequences in eukaryotic cell cycle control

Cross, F. R., Buchler, N. E. G., & Skotheim, J. M. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0078 · Cited by 144 · see citing works

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

Liu, Y., Steenkamp, E. T., Brinkmann, H., Forget, L., Philippe, H., & Lang, B. F. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-272 · Cited by 140 · see citing works

Impact of DNA sequence-data on the taxonomy of anamorphic fungi

Shenoy, B. M., Jeewon, R., & Hyde, K. (2007) · Cited by 142 · see citing works

The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling

Wållberg, A., Thollesson, M., Farris, J. S., & Jondelius, U. (2004) · Cladistics · doi:10.1111/j.1096-0031.2004.00041.x · Cited by 141 · see citing works

Bacterial lipids activate, synergize, and inhibit a developmental switch in choanoflagellates

Woznica, A., Cantley, A. M., Beemelmanns, C., Freinkman, E., Clardy, J., & King, N. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1605015113 · Cited by 136 · see citing works

Alternative oxidase: an inter-kingdom perspective on the function and regulation of this broadly distributed ‘cyanide-resistant’ terminal oxidase

McDonald, A. E. (2008) · Functional Plant Biology · doi:10.1071/fp08025 · Cited by 130 · see citing works

Origins, evolutionary history, and taxonomic distribution of alternative oxidase and plastoquinol terminal oxidase

McDonald, A. E., & Vanlerberghe, G. C. (2006) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2006.08.001 · Cited by 128 · see citing works

The mechanisms of codon reassignments in mitochondrial genetic codes

Sengupta, S., Yang, X., & Higgs, P. G. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0284-7 · Cited by 121 · see citing works

Conflicting phylogenetic signals at the base of the metazoan tree

Rokas, A., King, N., Finnerty, J. R., & Carroll, S. B. (2003) · Evolution & Development · doi:10.1046/j.1525-142x.2003.03042.x · Cited by 125 · see citing works

Evolution of microtubule organizing centers across the tree of eukaryotes

Naoji Yubuki, A., & Leander, B. S. (2013) · The Plant Journal · doi:10.1111/tpj.12145 · Cited by 123 · see citing works

Evolution of the mitochondrial genome: protist connections to animals, fungi and plants

Bullerwell, C. E., & Gray, M. W. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.08.008 · Cited by 120 · see citing works

Branched Mitochondrial Electron Transport in the Animalia: Presence of Alternative Oxidase in Several Animal Phyla

McDonald, A. E., & Vanlerberghe, G. C. (2004) · IUBMB Life · doi:10.1080/1521-6540400000876 · Cited by 118 · see citing works

Crystal Structure of Human Spermine Synthase

Wu, H., Min, J., Zeng, H., McCloskey, D. E., Ikeguchi, Y., Loppnau, P., Michael, A. J., Pegg, A. E., & Plotnikov, A. N. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m710323200 · Cited by 118 · see citing works

Fungal evolution: the case of the vanishing mitochondrion

Bullerwell, C. E., & Lang, B. F. (2005) · Current Opinion in Microbiology · doi:10.1016/j.mib.2005.06.009 · Cited by 115 · see citing works

Comparative Genomics of Large Mitochondria in Placozoans

Signorovitch, A. Y., Buss, L. W., & Dellaporta, S. L. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030013 · Cited by 115 · see citing works

Dynamical patterning modules: physico-genetic determinants of morphological development and evolution

Newman, S. A., & Bhat, R. (2008) · Physical Biology · doi:10.1088/1478-3975/5/1/015008 · Cited by 111 · see citing works

The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

Férandon, C., Moukha, S., Callac, P., Benedetto, J.-P., Castroviejo, M., & Barroso, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014048 · Cited by 112 · see citing works

Twinkle, the Mitochondrial Replicative DNA Helicase, Is Widespread in the Eukaryotic Radiation and May Also Be the Mitochondrial DNA Primase in Most Eukaryotes

Shutt, T. E., & Gray, M. W. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0162-8 · Cited by 111 · see citing works

The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa

Cavalier‐Smith, T. (2003) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.02548-0 · Cited by 111 · see citing works

Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals.

Hehenberger, E., Tikhonenkov, D., Kolísko, M., del Campo, J., Esaulov, A., Mylnikov, A. P., & Keeling, P. (2017) · Current Biology · doi:10.1016/j.cub.2017.06.006 · Cited by 99 · see citing works

Functional development of Src tyrosine kinases during evolution from a unicellular ancestor to multicellular animals

Segawa, Y., Suga, H., Iwabe, N., Oneyama, C., Akagi, T., Miyata, T., & Okada, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600021103 · Cited by 108 · see citing works

Speculations on the evolution of 9+2 organelles and the role of central pair microtubules

Mitchell, D. R. (2004) · Biology of the Cell · doi:10.1016/j.biolcel.2004.07.004 · Cited by 107 · see citing works

Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa

Medina, M., Collins, A. G., Taylor, J. W., Valentine, J. W., Lipps, J. H., Amaral‐Zettler, L., & Sogin, M. L. (2003) · International Journal of Astrobiology · doi:10.1017/s1473550403001551 · Cited by 107 · see citing works

Reconstructing the Evolution of the Endocytic System: Insights from Genomics and Molecular Cell Biology

Field, M. C., Gabernet‐Castello, C., & Dacks, J. B. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_7 · Cited by 105 · see citing works

Molecular Phylogeny of Unikonts: New Insights into the Position of Apusomonads and Ancyromonads and the Internal Relationships of Opisthokonts

Paps, J., Medina-Chacón, L. A., Marshall, W. L., Suga, H., & Ruiz‐Trillo, I. (2012) · Protist · doi:10.1016/j.protis.2012.09.002 · Cited by 104 · see citing works

The telomere repeat motif of basal Metazoa

Traut, W., Szczepanowski, M., Zrzavá, M., Opitz, C., Marec, F., & Zrzavý, J. (2007) · Chromosome Research · doi:10.1007/s10577-007-1132-3 · Cited by 104 · see citing works

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

Liu, Y., Leigh, J., Brinkmann, H., Cushion, M. T., Rodríguez‐Ezpeleta, N., Philippe, H., & Lang, B. F. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn221 · Cited by 104 · see citing works

Development of ichthyosporeans sheds light on the origin of metazoan multicellularity

Suga, H., & Ruiz‐Trillo, I. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.01.009 · Cited by 102 · see citing works

Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem‐cell differentiation

Hemmrich, G., & Bosch, T. C. G. (2008) · BioEssays · doi:10.1002/bies.20813 · Cited by 100 · see citing works

Molecular phylogeny of Zygomycota based on EF-1α and RPB1 sequences: limitations and utility of alternative markers to rDNA

Tanabe, Y., Saikawa, M., Watanabe, M. M., & Sugiyama, J. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00185-4 · Cited by 97 · see citing works

Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms

Seif, E. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki199 · Cited by 100 · see citing works

Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi

Cafaro, M. J. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.12.019 · Cited by 95 · see citing works

Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea)

Glockling, S. L., Marshall, W. L., & Gleason, F. H. (2013) · Fungal ecology · doi:10.1016/j.funeco.2013.03.005 · Cited by 94 · see citing works

Phylogenetic Analysis of Eukaryotes Using Heat-Shock Protein Hsp90

Stechmann, A., & Cavalier‐Smith, T. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2490-x · Cited by 93 · see citing works

The rosetteless gene controls development in the choanoflagellate S. rosetta

Levin, T. C., Greaney, A. J., Wetzel, L. A., & King, N. (2014) · eLife · doi:10.7554/elife.04070 · Cited by 93 · see citing works

Biocommunication of Fungi

Palková, Z., & Váchová, L. (. (2012) · Springer eBooks · doi:10.1007/978-94-007-4264-2 · Cited by 92 · see citing works

On the origin and evolution of RNA editing in metazoans

Zhang, P., Zhu, Y., Guo, Q., Li, J., Zhan, X., Yu, H., Xie, N., Tan, H., Lundholm, N., Garcia‐Cuetos, L., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112112 · Cited by 87 · see citing works

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

O'Brien, E. A., Koski, L. B., Zhang, Y., Yang, L., Wang, E. H.-H., Gray, M. W., Burger, G., & Lang, B. F. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl770 · Cited by 87 · see citing works

The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG)

Megarioti, A. H., & Kouvelis, V. N. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa126 · Cited by 86 · see citing works

Capsaspora owczarzaki is an independent opisthokont lineage

Ruiz‐Trillo, I., Inagaki, Y., Davis, L. A., Sperstad, S. V., Landfald, B., & Roger, A. J. (2004) · Current Biology · doi:10.1016/j.cub.2004.10.037 · Cited by 86 · see citing works

How was the notochord born?

Satoh, N., Tagawa, K., & Takahashi, H. (2012) · Evolution & Development · doi:10.1111/j.1525-142x.2011.00522.x · Cited by 82 · see citing works

Mitochondrial Genomes in Unicellular Relatives of Animals

Lavrov, D. V., & Lang, B. F. (2018) · Springer eBooks · doi:10.1007/978-1-4614-1531-2_178 · Cited by 5 · see citing works

Animals and Their Unicellular Ancestors

Paps, J., & Ruiz‐Trillo, I. (2010) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0022853 · Cited by 13 · see citing works

Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi

Wainright, P. O., Hinkle, G., Sogin, M. L., & Stickel, S. K. (1993) · Science · doi:10.1126/science.8469985 · Cited by 653 · see citing works

Multigene Phylogeny of Choanozoa and the Origin of Animals

Shalchian‐Tabrizi, K., Minge, M. A., Espelund, M., Orr, R. J. S., Ruden, T. A., Jakobsen, K. S., & Cavalier‐Smith, T. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002098 · Cited by 263 · see citing works

Multigene phylogeny of choanozoa and the origin of animals. PLoS

Shalchian‐Tabrizi, K., Minge, M. A., Espelund, M., Orr, R., Ruden, T. A., Kjetill, S., & Cavalier-smith, J. T. (2008)