Bushes in the tree of life
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A discussion of how homoplasy (the frequency of independently evolved characters) and the spacing of cladogenetic events limit our ability to reconstruct the tree of life using existing phylogenetic methods.
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Cis-regulatory changes affecting yellow and ebony expression account for pigmentation pattern variation in Drosophila.
“Such processes account for variation in pigmentation patterns due to regulatory changes affecting expression of the yellow differentiation gene (Gompel et al., 2005; Rokas and Carroll, 2006); and the ebony differentiation gene (Rebeiz et al., 2009).”
From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Rokas and Carroll, 2006
Rokas and Carroll is cited alongside Gompel et al. for the yellow-gene portion of the sentence; the ebony portion has a separate citation. Our copy’s “Why Hundreds of Genes Might Not Suffice” section discusses phylogenetic characters and molecular evolution, not regulatory changes affecting yellow expression or Drosophila pigmentation. Searches for yellow, ebony, cis-regulatory changes, and pigmentation found no passage addressing the attributed point; the passages have no page numbers. (LLM, conf=0.78)
Experimental — accuracy not yet measuredRecent studies of Drosophila species have revealed cis-regulatory sequence microevolution underlying adaptive external trait variation.
“Recent studies that focused on the adaptive evolution of external traits in and among Drosophila species have revealed processes of cis-regulatory sequence microevolution.”
From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Rokas and Carroll, 2006
The section ‘Why Hundreds of Genes Might Not Suffice’ discusses positive selection and amino acid substitutions, while the Drosophila references concern protein evolution and genomic data. Searches for cis-regulatory microevolution and regulatory changes in external traits found no passage addressing the claimed finding; page numbers are unavailable in our copy. (LLM, conf=0.74)
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Cites
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
Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,093 · see citing works
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Huelsenbeck, J. P., Ronquist, F., Nielsen, R., & Bollback, J. P. (2001) · Science · doi:10.1126/science.1065889 · Cited by 2,737 · see citing works
THE MAJOR FEATURES OF EVOLUTION
Olson, E. C., & Simpson, G. G. (1954) · Evolution · doi:10.2307/2405671 · Cited by 2,029 · see citing works
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888 · see citing works
Natural Hybridization and Evolution
Arnold, M. L. (1997) · doi:10.1093/oso/9780195099744.001.0001 · Cited by 1,784 · see citing works
Natural hybridization and evolution
(1997) · Choice Reviews Online · doi:10.5860/choice.35-0883 · Cited by 1,742 · see citing works
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 · see citing works
Self-citationThe causes of molecular evolution
Gillespie, J. H. (1992) · Choice Reviews Online · doi:10.5860/choice.30-2064 · Cited by 1,244 · see citing works
Discordance of Species Trees with Their Most Likely Gene Trees
Degnan, J. H., & Rosenberg, N. A. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020068 · Cited by 977 · see citing works
Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals
Bazin, É., Glémin, S., & Galtier, N. (2006) · Science · doi:10.1126/science.1122033 · Cited by 923 · see citing works
Hearing silence: non-neutral evolution at synonymous sites in mammals
Chamary, J., Parmley, J. L., & Hurst, L. D. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1770 · Cited by 827 · see citing works
Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
Huelsenbeck, J. P., & Rannala, B. (1997) · Science · doi:10.1126/science.276.5310.227 · Cited by 781 · see citing works
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 · see citing works
Chen, F.-C., & Li, W. (2001) · The American Journal of Human Genetics · doi:10.1086/318206 · Cited by 720 · see citing works
Rare genomic changes as a tool for phylogenetics
Rokas, A., & Holland, P. W. H. (2000) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)01967-4 · Cited by 688 · see citing works
Self-citationAdaptive protein evolution in Drosophila
Smith, N. G. C., & Eyre‐Walker, A. (2002) · Nature · doi:10.1038/4151022a · Cited by 677 · see citing works
Performance of Phylogenetic Methods in Simulation
Huelsenbeck, J. P. (1995) · Systematic Biology · doi:10.1093/sysbio/44.1.17 · Cited by 659 · see citing works
The Causes of Molecular Evolution
Gillespie, J. H. (1992) · doi:10.1093/oso/9780195068832.001.0001 · Cited by 644 · see citing works
Unexpected complexity of the Wnt gene family in a sea anemone
Kusserow, A., Pang, K., Sturm, C., Hrouda, M., Lentfer, J., Schmidt, H. A., Technau, U., von Haeseler, A., Hobmayer, B., Martindale, M. Q., et al. (2005) · Nature · doi:10.1038/nature03158 · Cited by 599 · see citing works
Genetic evidence for complex speciation of humans and chimpanzees
Patterson, N. J., Richter, D. J., Gnerre, S., Lander, E. S., & Reich, D. (2006) · Nature · doi:10.1038/nature04789 · Cited by 582 · see citing works
Philippe, H., Lartillot, N., & Brinkmann, H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi111 · Cited by 551 · see citing works
Hillis, D. M. (1996) · Nature · doi:10.1038/383130a0 · Cited by 524 · see citing works
A Devonian tetrapod-like fish and the evolution of the tetrapod body plan
Daeschler, E. B., Shubin, N. H., & Jenkins, F. A. (2006) · Nature · doi:10.1038/nature04639 · Cited by 442 · see citing works
A critical reappraisal of the fossil record of the bilaterian phyla
BUDD, G. E., & JENSEN, S. (2000) · Biological Reviews of the Cambridge Philosophical Society · doi:10.1017/s000632310000548x · Cited by 428 · see citing works
Rokas, A., & Carroll, S. B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi121 · Cited by 424 · see citing works
Self-citation(2005) · Choice Reviews Online · doi:10.5860/choice.42-4627 · Cited by 421 · see citing works
Nikaido, M., Rooney, A. P., & Okada, N. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.10261 · Cited by 420 · see citing works
The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb
Shubin, N. H., Daeschler, E. B., & Jenkins, F. A. (2006) · Nature · doi:10.1038/nature04637 · Cited by 377 · see citing works
Exceptional Convergent Evolution in a Virus
Bull, J. J., Badgett, M. R., Wichman, H. A., Huelsenbeck, J. P., Hillis, D. M., Gulati, A., Ho, C., & Molineux, I. J. (1997) · Genetics · doi:10.1093/genetics/147.4.1497 · Cited by 375 · see citing works
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
Rokas, A., Krüger, D., & Carroll, S. B. (2005) · Science · doi:10.1126/science.1116759 · Cited by 371 · see citing works
Self-citationTesting the neutral theory of molecular evolution with genomic data from Drosophila
Fay, J. C., Wyckoff, G. J., & Wu, C. (2002) · Nature · doi:10.1038/4151024a · Cited by 357 · see citing works
Gaining ground: the origin and evolution of tetrapods
(2013) · Choice Reviews Online · doi:10.5860/choice.50-3274 · Cited by 340 · see citing works
Incomplete taxon sampling is not a problem for phylogenetic inference
Rosenberg, M. S., & Kumar, S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191248498 · Cited by 329 · see citing works
Early evolution of animal cell signaling and adhesion genes
Nichols, S., Dirks, W., Pearse, J. S., & King, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604065103 · Cited by 327 · see citing works
Troubleshooting Molecular Phylogenetic Analyses
Sanderson, M. J., & Shaffer, H. B. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150509 · Cited by 311 · see citing works
Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution
Penny, D., McComish, B. J., Charleston, M. A., & Hendy, M. D. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010258 · Cited by 287 · see citing works
SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES
Jennings, W. B., & Edwards, S. V. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb01072.x · Cited by 275 · see citing works
Detection of convergent and parallel evolution at the amino acid sequence level
Zhang, J., & Kumar, S. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025789 · Cited by 271 · see citing works
Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic AnalysisPreprint
Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2004) · Genome Research · doi:10.1101/gr.1347404 · Cited by 247 · see citing works
Amrine-Madsen, H., Koepfli, K., Wayne, R., & Springer, M. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00118-0 · Cited by 208 · see citing works
Alu elements and hominid phylogenetics
Salem, A., Ray, D. A., Xing, J.-C., Callinan, P. A., Myers, J. S., Hedges, D. J., Garber, R. K., Witherspoon, D., Jorde, L., & Batzer, M. (2003) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2133766100 · Cited by 193 · see citing works
Gaining ground: the origin and evolution of tetrapods
(2002) · Choice Reviews Online · doi:10.5860/choice.40-2180 · Cited by 192 · see citing works
Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates
Venkatesh, B., Erdmann, M. V., & Brenner, S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.201415598 · Cited by 175 · see citing works
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
Abouheif, E., Zardoya, R., & Meyer, A. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006397 · Cited by 167 · see citing works
Genomic and proteomic adaptations to growth at high temperature.
Hickey, D. A., & Singer, G. A. C. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-117 · Cited by 163 · see citing works
Patterns of speciation and limits to phylogenetic resolution
Hoelzer, G. A. (1994) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(94)90207-0 · Cited by 151 · see citing works
DNA Archives and Our Nearest Relative: The Trichotomy Problem Revisited
Satta, Y., Klein, J., & Takahata, N. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2000.0704 · Cited by 142 · see citing works
Takezaki, N., Figueroa, F., Zaleska-Rutczynska, Z., Takahata, N., & Klein, J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh150 · Cited by 141 · see citing works
Broad taxon and gene sampling indicate that chaetognaths are protostomes
Matus, D. Q., Copley, R. R., Dunn, C. W., Hejnol, A., Eccleston, H., Halanych, K. M., Martindale, M. Q., & Telford, M. J. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.017 · Cited by 138 · see citing works
Chaetognath phylogenomics: a protostome with deuterostome-like development
Marlétaz, F., Martin, E., Perez, Y., Papillon, D., Caubit, X., Lowe, C. J., Freeman, B., Fasano, L., Dossat, C., Wincker, P., et al. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.016 · Cited by 138 · see citing works
The Major Features of Evolution
Durrant, S. D., & Simpson, G. G. (1954) · Journal of Mammalogy · doi:10.2307/1375605 · Cited by 137 · see citing works
Structural biology and phylogenetic estimation
Naylor, G. J. P., & Brown, W. M. (1997) · Nature · doi:10.1038/41460 · Cited by 123 · see citing works
Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions
Averof, M., Rokas, A., Wolfe, K. H., & Sharp, P. M. (2000) · Science · doi:10.1126/science.287.5456.1283 · Cited by 119 · see citing works
Self-citationThe Stochastic Mode of Molecular Evolution: What Consequences for Systematic Investigations?
Lanyon, S. M. (1988) · The Auk · doi:10.1093/auk/105.3.565 · Cited by 116 · see citing works
A retroposon analysis of Afrotherian phylogeny.
Nishihara, H., Satta, Y., Nikaido, M., Thewissen, J., Stanhope, M. J., & Okada, N. (2005) · Molecular biology and evolution · doi:10.1093/molbev/msi179 · Cited by 100 · see citing works
Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators
Kim, J. (1998) · Systematic Biology · doi:10.1080/106351598261021 · Cited by 95 · see citing works
FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION
Fiala, K. L., & Sokal, R. R. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00398.x · Cited by 94 · see citing works
Genome-scale evidence of the nematode-arthropod clade
Dopazo, H., & Dopazo, J. (2005) · Genome biology · doi:10.1186/gb-2005-6-5-r41 · Cited by 93 · see citing works
Pupko, T., & Galtier, N. (2002) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2002.2025 · Cited by 74 · see citing works
Ó’hUigín, C., Satta, Y., Takahata, N., & Klein, J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004213 · Cited by 62 · see citing works
Gene Transfer: Gene Swapping Craze Reaches Eukaryotes
Gogarten, J. P. (2003) · Current Biology · doi:10.1016/s0960-9822(02)01426-4 · Cited by 61 · see citing works
How Much Can Evolved Characters Tell us about the Tree that Generated Them?
Mossel, E., & Steel, M. (2005) · doi:10.1093/oso/9780198566106.003.0014 · Cited by 58 · see citing works
Thermal Adaptation of the Small Subunit Ribosomal RNA Gene: A Comparative Study
Wang, H.-C., Xia, X., & Hickey, D. A. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-005-0255-4 · Cited by 58 · see citing works
Afrotherian phylogeny as inferred from complete mitochondrial genomes
Murata, Y., Nikaido, M., Sasaki, T., Cao, Y., Fukumoto, Y., Hasegawa, M., & Okada, N. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00035-6 · Cited by 56 · see citing works
Ancient origin for Hawaiian Drosophilinae inferred from protein comparisons.
Beverley, S. M., & Wilson, A. C. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.14.4753 · Cited by 52 · see citing works
Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results
Steel, M., Hendy, M. D., & Penny, D. (1998) · Discrete Applied Mathematics · doi:10.1016/s0166-218x(98)00080-8 · Cited by 43 · see citing works
The place of Amborella within the radiation of angiosperms
Lockhart, P. J., & Penny, D. (2005) · Trends in Plant Science · doi:10.1016/j.tplants.2005.03.006 · Cited by 42 · see citing works
The notion of the Cambrian pananimalia genome.
Ohno, S. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8475 · Cited by 33 · see citing works
Excessive homoplasy in an evolutionarily constrained protein
Wells, R. S. (1996) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1996.0060 · Cited by 13 · see citing works
WHERE HAVE ALL THE CLADES GONE? A SYSTEMATIST'S TAKE ON INFERRING PHYLOGENIES1
Sanderson, M. J. (2005) · Evolution · doi:10.1554/br05-7.1 · Cited by 5 · see citing works
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- Hillis DM 1996 Inferring complex phylogenies Nature 383 130 131 8774876
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Huerta‐Cepas, J., Szklarczyk, D., Forslund, S. K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1248 · Cited by 2,062 · see citing works
The Tree of Life and a New Classification of Bony Fishes
Betancur‐R, R., Broughton, R. E., WILEY, E. O., Carpenter, K. E., Lopez, J. A., Li, C., Holcroft, N. I., Arcila, D., Sanciangco, M. D. A., Cureton, J. C., et al. (2013) · PLoS Currents · doi:10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 · Cited by 841 · see citing works
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012) · Systematic Biology · doi:10.1093/sysbio/sys049 · Cited by 837 · see citing works
Inferring ancient divergences requires genes with strong phylogenetic signals
Salichos, L., & Rokas, A. (2013) · Nature · doi:10.1038/nature12130 · Cited by 616 · see citing works
Self-citationContentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520 · see citing works
Self-citationDeciphering ancient rapid radiations
Whitfield, J. B., & Lockhart, P. J. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.01.012 · Cited by 515 · see citing works
Evolution of Gene Regulatory Networks Controlling Body Plan Development
Peter, I. S., & Davidson, E. H. (2011) · Cell · doi:10.1016/j.cell.2011.02.017 · Cited by 417 · see citing works
Using genomic data to unravel the root of the placental mammal phylogenyPreprint
Murphy, W. J., Pringle, T. H., Crider, T. A., Springer, M. S., & Miller, W. (2007) · Genome Research · doi:10.1101/gr.5918807 · Cited by 436 · see citing works
Zeng, L., Zhang, Q., Sun, R., Kong, H., Zhang, N., & Mā, H. (2014) · Nature Communications · doi:10.1038/ncomms5956 · Cited by 423 · see citing works
Animal phylogeny and its evolutionary implications
Dunn, C. W., Giribet, G., Edgecombe, G. D., & Hejnol, A. (2014) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-120213-091627 · Cited by 401 · see citing works
Phylogenetic Insights on Adaptive Radiation
Glor, R. E. (2010) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.39.110707.173447 · Cited by 355 · see citing works
Multilocus phylogeography and phylogenetics using sequence-based markers
Brito, P. H., & Edwards, S. V. (2008) · Genetica · doi:10.1007/s10709-008-9293-3 · Cited by 347 · see citing works
The origin and early evolution of eukaryotes in the light of phylogenomics
Koonin, E. V. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-209 · Cited by 345 · see citing works
Leaché, A. D., Banbury, B. L., Felsenstein, J., de, A. N., & Stamatakis, A. (2015) · Systematic Biology · doi:10.1093/sysbio/syv053 · Cited by 340 · see citing works
Couvreur, T. L. P., Franzke, A., Al-Shehbaz, I. A., Bakker, F. T., Koch, М. A., & Mummenhoff, K. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp202 · Cited by 332 · see citing works
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 322 · see citing works
Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites, J. W., & Reeder, T. W. (2012) · Biology Letters · doi:10.1098/rsbl.2012.0703 · Cited by 324 · see citing works
Genome reduction as the dominant mode of evolution
Wolf, Y. I., & Koonin, E. V. (2013) · BioEssays · doi:10.1002/bies.201300037 · Cited by 312 · see citing works
The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development
Rokas, A. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091513 · Cited by 312 · see citing works
Self-citationNovel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
Salichos, L., Stamatakis, A., & Rokas, A. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu061 · Cited by 303 · see citing works
Self-citationReddy, S., Kimball, R. T., Pandey, A., Hosner, P. A., Braun, M. J., Hackett, S. J., Han, K.-L., Harshman, J. S., Huddleston, C. J., Kingston, S. E., et al. (2017) · Systematic Biology · doi:10.1093/sysbio/syx041 · Cited by 288 · see citing works
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
Puigbò, P., Wolf, Y. I., & Koonin, E. V. (2009) · Journal of Biology · doi:10.1186/jbiol159 · Cited by 276 · see citing works
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 267 · see citing works
Self-citationDeep 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 · see citing works
Understanding explosive diversification through cichlid fish genomics
Salzburger, W. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0043-9 · Cited by 266 · see citing works
Schierwater, B., Eitel, M., Jakob, W., Osigus, H.-J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S.-O., & DeSalle, R. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000020 · Cited by 260 · see citing works
Darwinian evolution in the light of genomics
Koonin, E. V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkp089 · Cited by 254 · see citing works
Wolf, Y. I., Novichkov, P. S., Karev, G. P., Koonin, E. V., & Lipman, D. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901808106 · Cited by 252 · see citing works
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements
Koonin, E. V., & Dolja, V. V. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00049-13 · Cited by 242 · see citing works
Ma, P.-F., Zhang, Y.-X., Zeng, C., Guo, Z., & Li, D.-Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu054 · Cited by 243 · see citing works
Advances in Insect Phylogeny at the Dawn of the Postgenomic Era
Trautwein, M., Wiegmann, B. M., BEUTEL, R. G., Kjer, K. M., & Yeates, D. K. (2011) · Annual Review of Entomology · doi:10.1146/annurev-ento-120710-100538 · Cited by 242 · see citing works
Ancient Rapid Radiations of Insects: Challenges for Phylogenetic Analysis
Whitfield, J. B., & Kjer, K. M. (2007) · Annual Review of Entomology · doi:10.1146/annurev.ento.53.103106.093304 · Cited by 221 · see citing works
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
Hime, P. M., Lemmon, A. R., Lemmon, E. C. M., Prendini, E., Brown, J. M., Thomson, R. C., Kratovil, J. D., Noonan, B. P., Pyron, R. A., Peloso, P. L. V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa034 · Cited by 213 · see citing works
Cretaceous origin and repeated tertiary diversification of the redefined butterflies
Heikkilä, M., Kaila, L., Mutanen, M., Peña, C., & Wahlberg, N. (2011) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2011.1430 · Cited by 219 · see citing works
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
Steenwyk, J. L., Buida, T. J., LaBella, A. L., Li, Y., Shen, X., & Rokas, A. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab096 · Cited by 205 · see citing works
Self-citationReconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
Shen, X., Zhou, X., Kominek, J., Kurtzman, C. P., Hittinger, C. T., & Rokas, A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.034744 · Cited by 211 · see citing works
Self-citationWhole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling
Srivastava, M., Mazza-Curll, K. L., van Wolfswinkel, J. C., & Reddien, P. W. (2014) · Current Biology · doi:10.1016/j.cub.2014.03.042 · Cited by 200 · see citing works
Wiens, J. J., Kuczynski, C. A., Smith, S. A., Mulcahy, D. G., Sites, J. W., Townsend, T. M., & Reeder, T. W. (2008) · Systematic Biology · doi:10.1080/10635150802166053 · Cited by 196 · see citing works
Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution
Broughton, R. E., Betancur‐R, R., Li, C., Gloria Arratia, F., & Ortı́, G. (2013) · PLoS Currents · doi:10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e · Cited by 191 · see citing works
The Deep Archaeal Roots of Eukaryotes
Yutin, N., Makarova, K. S., Mekhedov, S., Wolf, Y. I., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn108 · Cited by 181 · see citing works
The choice of model organisms in evo–devo
Jenner, R. A., & Wills, M. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2062 · Cited by 183 · see citing works
Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies
Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A., & Giraud, T. (2008) · Systematic Biology · doi:10.1080/10635150802306527 · Cited by 176 · see citing works
Huerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176 · see citing works
Zeng, L., Zhang, N., Zhang, Q., Endress, P. K., Huang, J., & Mā, H. (2017) · New Phytologist · doi:10.1111/nph.14503 · Cited by 171 · see citing works
Pervasive Cryptic Epistasis in Molecular Evolution
Lunzer, M., Golding, G. B., & Dean, A. M. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001162 · Cited by 168 · see citing works
Hamilton, C. A., Lemmon, A. R., Lemmon, E. M., & Bond, J. E. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0769-y · Cited by 167 · see citing works
Deep Phylogeny and Evolution of Sponges (Phylum Porifera)
Wörheide, G., Dohrmann, M., Erpenbeck, D., Larroux, C., Maldonado, M., Voigt, O., Borchiellini, C., & Lavrov, D. V. (2012) · Advances in Marine Biology · doi:10.1016/b978-0-12-387787-1.00007-6 · Cited by 166 · see citing works
Ballesteros, J. A., & Sharma, P. P. (2019) · Systematic Biology · doi:10.1093/sysbio/syz011 · Cited by 158 · see citing works
Koenen, E. J. M., Ojeda, D. I., Steeves, R., Migliore, J., Bakker, F. T., Wieringa, J. J., Kidner, C., Hardy, O. J., Pennington, R. T., Herendeen, P. S., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa041 · Cited by 159 · see citing works
Wan, Y., Schwaninger, H. R., Baldo, A. M., Labate, J. A., Zhong, G., & Simon, C. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-141 · Cited by 154 · see citing works
Meiklejohn, K. A., Faircloth, B. C., Glenn, T. C., Kimball, R. T., & Braun, E. L. (2016) · Systematic Biology · doi:10.1093/sysbio/syw014 · Cited by 153 · see citing works
Yu, L., Li, Y., Ryder, O. A., & Zhang, Y. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-198 · Cited by 151 · see citing works
Holzer, A. S., Bartošová‐Sojková, P., Born‐Torrijos, A., Lövy, A., Hartigan, A., & Fiala, I. (2018) · Molecular Ecology · doi:10.1111/mec.14558 · Cited by 150 · see citing works
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
Townsend, J. P., Su, Z., & Tekle, Y. I. (2012) · Systematic Biology · doi:10.1093/sysbio/sys036 · Cited by 146 · see citing works
Embracing Uncertainty in Reconstructing Early Animal Evolution
King, N., & Rokas, A. (2017) · Current Biology · doi:10.1016/j.cub.2017.08.054 · Cited by 144 · see citing works
Self-citationAnalysis of 142 genes resolves the rapid diversification of the rice genus
Zou, X.-H., Zhang, F., Zhang, J., Zang, L., Tang, L., Wang, J., Sang, T., & Ge, S. (2008) · Genome biology · doi:10.1186/gb-2008-9-3-r49 · Cited by 144 · see citing works
Pilgrim, E. M., von Dohlen, C. D., & Pitts, J. P. (2008) · Zoologica Scripta · doi:10.1111/j.1463-6409.2008.00340.x · Cited by 143 · see citing works
A Consistent Phylogenetic Backbone for the Fungi
Ebersberger, I., Simoes, R. D. M., Kupczok, A., Gube, M., Kothe, E., Voigt, K., & von Haeseler, A. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr285 · Cited by 141 · see citing works
Betancur‐R, R., Li, C., Munroe, T. A., Ballesteros, J. A., & Ortı́, G. (2013) · Systematic Biology · doi:10.1093/sysbio/syt039 · Cited by 140 · see citing works
Evolutionary developmental biology and genomics
Cañestro, C., Yokoi, H., & Postlethwait, J. H. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2226 · Cited by 134 · see citing works
The evolution of insect biodiversity
Tihelka, E., Cai, C., Giacomelli, M., Lozano-Fernández, J., Rota‐Stabelli, O., Huang, D., Engel, M. S., Donoghue, P. C. J., & Pisani, D. (2021) · Current Biology · doi:10.1016/j.cub.2021.08.057 · Cited by 138 · see citing works
Seiffert, E. R. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-224 · Cited by 133 · see citing works
Heinicke, M. P., Duellman, W. E., Trueb, L., Means, D. B., MacCulloch, R. D., & Hedges, S. B. (2009) · Zootaxa · doi:10.11646/zootaxa.2211.1.1 · Cited by 130 · see citing works
Meyer, B., Matschiner, M., & Salzburger, W. (2016) · Systematic Biology · doi:10.1093/sysbio/syw069 · Cited by 126 · see citing works
Molecular phylogeny and evolution of the Perissodactyla
Steiner, C., & Ryder, O. A. (2011) · Zoological Journal of the Linnean Society · doi:10.1111/j.1096-3642.2011.00752.x · Cited by 128 · see citing works
Heikkilä, M., Mutanen, M., Wahlberg, N., Sihvonen, P., & Kaila, L. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0520-0 · Cited by 126 · see citing works
Vrijenhoek, R. C. (2009) · Deep Sea Research Part II Topical Studies in Oceanography · doi:10.1016/j.dsr2.2009.05.016 · Cited by 123 · see citing works
Frequent and Widespread Parallel Evolution of Protein Sequences
Rokas, A., & Carroll, S. B. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn143 · Cited by 120 · see citing works
Self-citationError in Phylogenetic Estimation for Bushes in the Tree of Life
Patel, S. K. (2013) · Journal of Phylogenetics & Evolutionary Biology · doi:10.4172/2329-9002.1000110 · Cited by 118 · see citing works
The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of EukaryotesPreprint
Koonin, E. V., & Yutin, N. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016188 · Cited by 116 · see citing works
Post-molecular systematics and the future of phylogenetics
Pyron, R. A. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.04.016 · Cited by 112 · see citing works
The Biological Big Bang model for the major transitions in evolution
Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-21 · Cited by 115 · see citing works
Paleocene emergence of elephant relatives and the rapid radiation of African ungulates
Gheerbrant, E. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900251106 · Cited by 114 · see citing works
Sharma, P. P., & Giribet, G. (2011) · Invertebrate Systematics · doi:10.1071/is11002 · Cited by 112 · see citing works
Tang, L., Zou, X.-H., Achoundong, G., Potgieter, C. J., Second, G., Zhang, D., & Ge, S. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.007 · Cited by 109 · see citing works
Fournier, G. P., Huang, J., & Gogarten, J. P. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0033 · Cited by 108 · see citing works
Qin, L., Hu, Y., Wang, J., Wang, X., Zhao, R., Shan, H., Li, K., Xu, P., Wu, H., Yan, X., et al. (2021) · Nature Plants · doi:10.1038/s41477-021-00990-2 · Cited by 109 · see citing works
Back in time: a new systematic proposal for the Bilateria
Baguñà, J., Martinez, P., Paps, J., & Riutort, M. (2008) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2238 · Cited by 105 · see citing works
Nelson, D. R. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0430 · Cited by 104 · see citing works
Haddrath, O., & Baker, A. J. (2012) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.1630 · Cited by 99 · see citing works
Parks, M., Cronn, R., & Liston, A. (2012) · BMC Evolutionary Biology · doi:10.1186/1471-2148-12-100 · Cited by 98 · see citing works
Pyron, R. A., Hendry, C. R., Chou, V. M., Lemmon, E. M., Lemmon, A. R., & Burbrink, F. T. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.08.023 · Cited by 98 · see citing works
Whelan, N. V., & Halanych, K. M. (2016) · Systematic Biology · doi:10.1093/sysbio/syw084 · Cited by 96 · see citing works
Ontano, A. Z., Gainett, G., Aharon, S., Ballesteros, J. A., Benavides, L. R., Corbett, K. F., Gavish‐Regev, E., Harvey, M. S., Monsma, S. A., Santibáñez‐López, C. E., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab038 · Cited by 89 · see citing works
Lynch, V. J., & Wagner, G. P. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00790.x · Cited by 89 · see citing works
Rogozin, I. B., Basu, M. K., Csürös, M., & Koonin, E. V. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp011 · Cited by 88 · see citing works
Blanke, A., Wipfler, B., Letsch, H. O., Koch, M., Beckmann, F., BEUTEL, R. G., & Misof, B. Y. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00405.x · Cited by 88 · see citing works
Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers
Schenk, M., Thienpont, C., Koopman, W. J. M., Gilissen, L. J. W., & SMULDERS, M. J. M. (2008) · Tree Genetics & Genomes · doi:10.1007/s11295-008-0162-0 · Cited by 86 · see citing works
Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling
Bernot, J. P., Owen, C. L., Wolfe, J. M., Meland, K., Olesen, J., & Crandall, K. A. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad175 · Cited by 82 · see citing works
Taxogenomics of the order Chlamydiales
Pillonel, T., Bertelli, C., Salamin, N., & Greub, G. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.000090 · Cited by 82 · see citing works
Antoine Fouquet, A., Blotto, B. L., Maronna, M. M., Verdade, V. K., Juncá, F. A., de Sá, R., & Rodrigues, M. T. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.02.009 · Cited by 81 · see citing works
Winkler, I. S., Blaschke, J. D., Davis, D. J., Stireman, J. O., O’Hara, J. E., Cerretti, P., & Moulton, J. K. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.03.021 · Cited by 79 · see citing works
Diploid-dominant life cycles characterize the early evolution of Fungi
Amses, K. R., Simmons, D. R., Longcore, J. E., Mondo, S. J., Seto, K., Jerônimo, G. H., Bonds, A. E., Quandt, C. A., Davis, W. J., Chang, Y., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2116841119 · Cited by 78 · see citing works
Ocampo, G., & Columbus, J. T. (2010) · American Journal of Botany · doi:10.3732/ajb.1000227 · Cited by 78 · see citing works
Ringelberg, J. J., Koenen, E. J. M., Iganci, J. R. V., de Queiroz, L. P., Murphy, D. J., Gaudeul, M., Bruneau, A., Luckow, M., Lewis, G. P., & Hughes, C. E. (2022) · PhytoKeys · doi:10.3897/phytokeys.205.85866 · Cited by 78 · see citing works
Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions
Sims, G. E., Jun, S., Wu, G. A., & Kim, S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909377106 · Cited by 74 · see citing works
Heckman, K. L., Mariani, C., Rasoloarison, R. M., & Yoder, A. D. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.005 · Cited by 74 · see citing works
Chernikova, D., Motamedi, S., Csürös, M., Koonin, E. V., & Rogozin, I. B. (2011) · Biology Direct · doi:10.1186/1745-6150-6-26 · Cited by 72 · see citing works
Corolla Monosymmetry: Evolution of a Morphological Novelty in the Brassicaceae Family
Busch, A., Horn, S., Mühlhausen, A., Mummenhoff, K., & Zachgo, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr297 · Cited by 72 · see citing works
Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents
Roycroft, E., Moussalli, A., & Rowe, K. C. (2019) · Systematic Biology · doi:10.1093/sysbio/syz044 · Cited by 69 · see citing works
- Authors
- Rokas, A., & Carroll, S. B.
- Affiliations
- Broad Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Rokas, Antonis
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2006-11-14
- Volume
- 4
- Issue
- 11
- Pages
- e352
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC1637082
- OpenAlex
- W2090427748
- Cited by
- 315
- References
- 72
- Citations by year
- 2026: 11 · 2025: 2 · 2024: 13 · 2023: 8 · 2022: 10 · 2021: 13 · 2020: 15 · 2019: 7 · 2018: 9 · 2017: 16 · 2016: 11 · 2015: 17 · 2014: 22 · 2013: 19 · 2012: 16
- FWCI
- 12.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- 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
- homoplasy, phylogenetic inference, tree of life
- MeSH terms
- Animals, Classification, Humans, Phylogeny, Genetic Variation, Hominidae, Genome, Evolution, Molecular, Computational Biology
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