The origin and evolution of model organisms

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,735

Molecular Evolution and Phylogenetics

Nei, M., & Kumar, S. (2000) · doi:10.1093/oso/9780195135848.001.0001 · Cited by 8,012

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

Inferring the historical patterns of biological evolution

Pagel, M. (1999) · Nature · doi:10.1038/44766 · Cited by 5,200

Life with 6000 Genes

Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., et al. (1996) · Science · doi:10.1126/science.274.5287.546 · Cited by 4,423

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

Woese, C. R., & Fox, G. E. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.11.5088 · Cited by 4,131

A Molecular View of Microbial Diversity and the Biosphere

Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797

A Neoproterozoic Snowball Earth

Hoffman, P. F., Kaufman, A. J., Halverson, G. P., & Schrag, D. P. (1998) · Science · doi:10.1126/science.281.5381.1342 · Cited by 2,693

Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach.

Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977

A molecular timescale for vertebrate evolution

Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936

Phylogenetic Classification and the Universal Tree

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

Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference

Rannala, B. H., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,751

The genome sequence of Schizosaccharomyces pombe

Wood, V., Gwilliam, R., Rajandream, M.-A., Lyne, M. H., Lyne, R., Stewart, A., SGOUROS, J. G., Peat, N., Hayles, J., Baker, S. G., et al. (2002) · Nature · doi:10.1038/nature724 · Cited by 1,671

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

Mitochondrial genome variation and the origin of modern humans

Ingman, M., Kaessmann, H., Pääbo, S., & Gyllensten, U. B. (2000) · Nature · doi:10.1038/35047064 · Cited by 1,546

Evolution of the angiosperms: calibrating the family tree

Wikström, N., Savolainen, V., & Chase, M. W. (2001) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2001.1782 · Cited by 1,508

ORIGIN OF EUKARYOTIC CELLS

Raven, P. H., & Margulis, L. (1971) · Evolution · doi:10.1111/j.1558-5646.1971.tb01930.x · Cited by 1,483

The origin and early evolution of plants on land

Kenrick, P., & Crane, P. R. (1997) · Nature · doi:10.1038/37918 · Cited by 1,466

Evidence for life on Earth before 3,800 million years ago

Mojzsis, S. J., Arrhenius, G., McKeegan, K. D., Harrison, T. M., Nutman, A. P., & Friend, C. R. L. (1996) · Nature · doi:10.1038/384055a0 · Cited by 1,370

Microfossils of the early Archean apex chert: New evidence of the antiquity of life

Schopf, J. W. (1993) · Science · doi:10.1126/science.260.5108.640 · Cited by 1,363

Estimating the rate of evolution of the rate of molecular evolution

Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317

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 1,306

Archean Molecular Fossils and the Early Rise of Eukaryotes

Brocks, J. J., Logan, G. A., Buick, R., & Summons, R. E. (1999) · Science · doi:10.1126/science.285.5430.1033 · Cited by 1,275

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

Glomalean Fungi from the Ordovician

Redecker, D., Kodner, R. B., & Graham, L. E. (2000) · Science · doi:10.1126/science.289.5486.1920 · Cited by 1,176

A nonparametric approach to estimating divergence times in the absence of rate constancy.

Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156

A new hominid from the Upper Miocene of Chad, Central Africa

Brunet, M., Guy, F., Pilbeam, D. R., Mackaye, H. T., Likius, A., Djimdoumalbaye, A., Beauvilain, A., Blondel, C., Bocherens, H., Boisserie, J., et al. (2002) · Nature · doi:10.1038/nature00879 · Cited by 1,095

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

Katinka, M., Duprat, S., Cornillot, E., Méténier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E., Brottier, P., Wincker, P., et al. (2001) · Nature · doi:10.1038/35106579 · Cited by 1,051

Molecular Evidence for the Early Colonization of Land by Fungi and Plants

Heckman, D. S., Geiser, D. M., Eidell, B. R., Stauffer, R. L., Kardos, N. L., & Hedges, S. B. (2001) · Science · doi:10.1126/science.1061457 · Cited by 1,020

Questioning the evidence for Earth's oldest fossils

Brasier, M. D., Green, O. R., Jephcoat, A. P., Kleppe, A., Kranendonk, M. J. V., Lindsay, J. F., Steele, A., & Grassineau, N. V. (2002) · Nature · doi:10.1038/416076a · Cited by 979

2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis

Summons, R. E., Jahnke, L. L., Hope, J. M., & Logan, G. A. (1999) · Nature · doi:10.1038/23005 · Cited by 975

ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES

Magallón, S., & Sanderson, M. J. (2001) · Evolution · doi:10.1111/j.0014-3820.2001.tb00826.x · Cited by 942

The habitat and nature of early life

Nisbet, E. G., & Sleep, N. H. (2001) · Nature · doi:10.1038/35059210 · Cited by 930

Intra- and Interspecific Variation in Primate Gene Expression Patterns

Enard, W., Khaitovich, P., Klose, J., Zöllner, S. K., Heißig, F., Giavalisco, P., Nieselt, K., Muchmore, E. A., Varki, A. P., Ravid, R., et al. (2002) · Science · doi:10.1126/science.1068996 · Cited by 845

Phylogenetic test of the molecular clock and linearized trees.

Takezaki, N., Rzhetsky, A., & Nei, M. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040259 · Cited by 826

Early animal evolution: emerging views from comparative biology and geology

Knoll, A. H., & Carroll, S. B. (1999) · Science · doi:10.1126/science.284.5423.2129 · Cited by 821

The origin and early diversification of angiosperms

Crane, P. R., Friis, E. M., & Pedersen, K. R. (1995) · Nature · doi:10.1038/374027a0 · Cited by 796

Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees

Chen, F.-C., & Li, W. (2001) · The American Journal of Human Genetics · doi:10.1086/318206 · Cited by 720

Genome phylogeny based on gene content

Snel, ‎., Peer Bork, B., & Huynen, M. A. (1999) · Nature Genetics · doi:10.1038/5052 · Cited by 708

Phylogenetic Meaning of the Kingdom Concept: an Unusual Ribosomal RNA from Giardia lamblia

Sogin, M. L., Gunderson, J. H., Elwood, H. J., Alonso, R. A., & Peattie, D. A. (1989) · Science · doi:10.1126/science.2911720 · Cited by 707

The Early Evolution of Eukaryotes: A Geological Perspective

Knoll, A. H. (1992) · Science · doi:10.1126/science.1585174 · Cited by 684

Performance of a divergence time estimation method under a probabilistic model of rate evolution.

Kishino, H., Thorne, J. L., & Bruno, W. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003811 · Cited by 633

Laser–Raman imagery of Earth's earliest fossils

Schopf, J. W., Kudryavtsev, A. B., Agresti, D. G., Wdowiak, T. J., & Czaja, A. D. (2002) · Nature · doi:10.1038/416073a · Cited by 603

Mutation rates in mammalian genomes

Kumar, S., & Subramanian, S. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.022629899 · Cited by 601

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

Gupta, R. S. (1998) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.62.4.1435-1491.1998 · Cited by 598

Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome

Brenner, S., Elgar, G. S., Sanford, R. A., Macrae, A. D., Venkatesh, B., & Aparicio, S. A. J. R. (1993) · Nature · doi:10.1038/366265a0 · Cited by 572

New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya

Leakey, M. G., Feibel, C. S., McDougall, I., & Walker, A. (1995) · Nature · doi:10.1038/376565a0 · Cited by 556

Hox genes in brachiopods and priapulids and protostome evolution

de Rosa, R., Grenier, J. K., Andreeva, T., Cook, C. E., Adoutte, A., Akam, M., Carroll, S. B., & Balavoine, G. (1999) · Nature · doi:10.1038/21631 · Cited by 541

Continental breakup and the ordinal diversification of birds and mammals

Hedges, S. B., Parker, P. H., Sibley, C. G., & Kumar, S. (1996) · Nature · doi:10.1038/381226a0 · Cited by 529

The new animal phylogeny: Reliability and implications

Adoutte, A., Balavoine, G., Lartillot, N., Lespinet, O., Prud'homme, B., & de Rosa, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.9.4453 · Cited by 512

Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla

Wray, G. A., Levinton, J. S., & Shapiro, L. H. (1996) · Science · doi:10.1126/science.274.5287.568 · Cited by 511

Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi

Wang, D. Y.-C., Kumar, S., & Hedges, S. B. (1999) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.1999.0617 · Cited by 493

Megascopic Eukaryotic Algae from the 2.1-Billion-Year-Old Negaunee Iron-Formation, Michigan

Han, T.-M., & Runnegar, B. N. (1992) · Science · doi:10.1126/science.1631544 · Cited by 463

Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers

Chaw, S., Parkinson, C. L., Cheng, Y., Vincent, T. M., & Palmer, J. D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4086 · Cited by 462

Systematics and the Fossil Record

Smith, A. B. (1994) · Wiley eBooks · doi:10.1002/9781444313918 · Cited by 457

A Nonhyperthermophilic Common Ancestor to Extant Life Forms

Galtier, N., Tourasse, N., & Gouy, M. (1999) · Science · doi:10.1126/science.283.5399.220 · Cited by 442

A mitochondrial remnant in the microsporidian Trachipleistophora hominis

Williams, B., Hirt, R. P., Lucocq, J. M., & Embley, T. M. (2002) · Nature · doi:10.1038/nature00949 · Cited by 421

Morphological and ecological complexity in early eukaryotic ecosystems

Javaux, E. J., Knoll, A. H., & Walter, M. R. (2001) · Nature · doi:10.1038/35083562 · Cited by 418

Determining divergence times with a protein clock: Update and reevaluation

Feng, D.-F., Cho, G. S., & Doolittle, R. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.24.13028 · Cited by 416

Early life on earth

Bengtson, S. (1994) · Columbia University Press eBooks · Cited by 400

From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (review)

Laubichler, M. D. (2003) · Perspectives in biology and medicine · doi:10.1353/pbm.2003.0012 · Cited by 387

Universal trees based on large combined protein sequence data sets

Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E., & Stanhope, M. J. (2001) · Nature Genetics · doi:10.1038/90129 · Cited by 381

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba

Bapteste, E. P., Brinkmann, H., Lee, J. A., Moore, D. V., Sensen, C. W., Gordon, P. M. K., Duruflé, L., Gaasterland, T., Lopez, P., Müller, M., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032662799 · Cited by 380

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life.

Margulis, L. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.3.1071 · Cited by 358

Evidence that eukaryotes and eocyte prokaryotes are immediate relatives

Rivera, M. C., & Lake, J. A. (1992) · Science · doi:10.1126/science.1621096 · Cited by 342

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

Qiu, Y., Cho, Y., Cox, J. C., & Palmer, J. D. (1998) · Nature · doi:10.1038/29286 · Cited by 336

Rooting the Eukaryote Tree by Using a Derived Gene Fusion

Stechmann, A., & Cavalier‐Smith, T. (2002) · Science · doi:10.1126/science.1071196 · Cited by 332

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

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 328

A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common HistoryPreprint

Daubin, V., Gouy, M., & Perrière, G. (2002) · Genome Research · doi:10.1101/gr.187002 · Cited by 318

Genomic Regulatory Systems

(2001) · Elsevier eBooks · doi:10.1016/b978-0-12-205351-1.x5000-9 · Cited by 315

Genome trees constructed using five different approaches suggest new major bacterial clades

Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L., & Koonin, E. V. (2001) · BMC Evolutionary Biology · doi:10.1186/1471-2148-1-8 · Cited by 304

Fossils, molecules and embryos: new perspectives on the Cambrian explosion

Valentine, J. W., Jablonski, D., & Erwin, D. H. (1999) · Development · doi:10.1242/dev.126.5.851 · Cited by 300

Evidence from Beta-Tubulin Phylogeny that Microsporidia Evolved from Within the Fungi

Keeling, P. J., Luker, M. A., & Palmer, J. D. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026235 · Cited by 299

Nature And Human Society: The Quest For A Sustainable World

Raven, P. H., & Williams, T. (1997) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.293001 · Cited by 289

Molecular Phylogeny and Divergence Time Estimates for Major Rodent Groups: Evidence from Multiple Genes

Adkins, R. M., Gelke, E. L., Rowe, D. L., & Honeycutt, R. L. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003860 · Cited by 284

Reconstructing Early Events in Eukaryotic Evolution

Roger, A. J. (1999) · The American Naturalist · doi:10.1086/303290 · Cited by 283

Fungal Molecular Evolution: Gene Trees and Geologic Time

Berbee, M. L., & Taylor, J. W. (2001) · Springer eBooks · doi:10.1007/978-3-662-10189-6_10 · Cited by 280

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

The art and design of genetic screens: yeast

Forsburg, S. L. (2001) · Nature Reviews Genetics · doi:10.1038/35088500 · Cited by 265

A non-hyperthermophilic ancestor for Bacteria

Brochier‐Armanet, C., & Philippe, H. (2002) · Nature · doi:10.1038/417244a · Cited by 254

Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora and molecular clocks.

Li, W., Gouy, M., Sharp, P. M., Ó’hUigín, C., & Yang, Y. W. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.17.6703 · Cited by 247

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

Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants

Nickrent, D. L., Parkinson, C. L., Palmer, J. D., & Duff, R. J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026290 · Cited by 244

The Genomic Tree as Revealed from Whole Proteome ComparisonsPreprint

Tekaia, F., Lazcano, A., & Dujon, B. (1999) · Genome Research · doi:10.1101/gr.9.6.550 · Cited by 242

Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data

Sanderson, M. J., & Doyle, J. A. (2001) · American Journal of Botany · doi:10.2307/3558458 · Cited by 240

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

A genomic timescale for the origin of eukaryotes

Hedges, S. B., Chen, H., Kumar, S., Wang, D. Y.-C., Thompson, A. S., & Watanabe, H. (2001) · BMC Evolutionary Biology · doi:10.1186/1471-2148-1-4 · Cited by 230

Vertebrate Palaeontology

Benton, M. J. (1997) · Springer eBooks · doi:10.1007/978-1-4899-2865-8 · Cited by 221

The evolutionary position of nematodes

Blair, J. E., Ikeo, K., Gojobori, T., & Hedges, S. B. (2002) · BMC Evolutionary Biology · doi:10.1186/1471-2148-2-7 · Cited by 218

Molecular evidence for pre-Cretaceous angiosperm origins

Martin, W. F., Gierl, A., & Saedler, H. (1989) · Nature · doi:10.1038/339046a0 · Cited by 204

Metasomatic Origin of Quartz-Pyroxene Rock, Akilia, Greenland, and Implications for Earth's Earliest Life

Fedo, C. M., & Whitehouse, M. J. (2002) · Science · doi:10.1126/science.1070336 · Cited by 204

The Cambrian evolutionary ‘explosion’: decoupling cladogenesis from morphological disparity

Fortey, R. A., Briggs, D. E. G., & WILLS, M. A. (1996) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.1996.tb01693.x · Cited by 200

The phylogeny of plant and animal pathogens in the Ascomycota

Berbee, M. L. (2001) · Physiological and Molecular Plant Pathology · doi:10.1006/pmpp.2001.0355 · Cited by 199

Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record

Smith, A. B., & Peterson, K. J. (2002) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.30.091201.140057 · Cited by 193 · cited 1×

Systematics and the Fossil Record

Wagner, P. J., & Smith, A. B. (1995) · Palaios · doi:10.2307/3515163 · Cited by 189

Archaeal Phylogeny Based on Ribosomal Proteins

Matte-Tailliez, O., Brochier‐Armanet, C., Forterre, P., & Philippe, H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004122 · Cited by 180

Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics

James, T. Y., Porter, D. D., Leander, C. A., Vilgalys, R. J., & Longcore, J. E. (2000) · Canadian Journal of Botany · doi:10.1139/b00-009 · Cited by 180

Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes

Mushegian, A. R., Garey, J. R., Martin, J., & Liu, L. X. (1998) · Genome Research · doi:10.1101/gr.8.6.590 · Cited by 164

Eubacterial phylogeny based on translational apparatus proteins

Brochier‐Armanet, C., Bapteste, E. P., Moreira, D., & Philippe, H. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(01)02522-7 · Cited by 157

Detection of lateral gene transfer among microbial genomes

Ragan, M. A. (2001) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00244-6 · Cited by 151

A critical reappraisal of the fossil record of the bilaterian phyla

BUDD, G. E., & JENSEN, S. (2000) · Biological Reviews · doi:10.1111/j.1469-185x.1999.tb00046.x · Cited by 145

Discoidal Impressions and Trace-Like Fossils More Than 1200 Million Years Old

Rasmussen, B., Bengtson, S., Fletcher, I. R., & McNaughton, N. J. (2002) · Science · doi:10.1126/science.1070166 · Cited by 145

Using Homolog Groups to Create a Whole-Genomic Tree of Free-Living Organisms: An Update

House, C. H., & Fitz‐Gibbon, S. T. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0054-5 · Cited by 128

Fossil Evidence for a Late Cretaceous Origin of “Hoofed” Mammals

Archibald, J. D. (1996) · Science · doi:10.1126/science.272.5265.1150 · Cited by 122

Human and Ape Molecular Clocks and Constraints on Paleontological Hypotheses

Stauffer, R. L., Walker, A., Ryder, O. A., Lyons‐Weiler, M. A., & Hedges, S. B. (2001) · Journal of Heredity · doi:10.1093/jhered/92.6.469 · Cited by 122

Vertebrate Genomes Compared

Hedges, S. B., & Kumar, S. (2002) · Science · doi:10.1126/science.1076231 · Cited by 111

The Comparison of β-Thymosin Homologues Among Metazoa Supports an Arthropod-Nematode Clade

Manuel, M., Kruse, M., Müller, W. E. G., & Parco, Y. L. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010100 · Cited by 110

Molecular Estimates of Primate Divergences and new Hypotheses for Primate Dispersal and the Origin of Modern Humans*

Árnason, Ú., Gullberg, A., Burguete, A. S., & Janice, A. (2004) · Hereditas · doi:10.1111/j.1601-5223.2000.00217.x · Cited by 109

Genetic Algorithm-Based Maximum-Likelihood Analysis for Molecular Phylogeny

Katoh, K., Kuma, K., & Miyata, T. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010238 · Cited by 103

Bacterial molecular phylogeny using supertree approach.

Daubin, V., Gouy, M., & Perrière, G. (2001) · PubMed · Cited by 100

Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.

Hansmann, S., & Martin, W. (2000) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/00207713-50-4-1655 · Cited by 99

Hominid revelations from Chad

Wood, B. A. (2002) · Nature · doi:10.1038/418133a · Cited by 92

Early Evolution of the Bilateria

Hausdorf, B. (2000) · Systematic Biology · doi:10.1080/10635150050207438 · Cited by 83

Retortamonad Flagellates are Closely Related to Diplomonads—Implications for the History of Mitochondrial Function in Eukaryote Evolution

Silberman, J. D., Simpson, A. G. B., Kulda, J., Čepička, I., Hampl, V., Johnson, P. J., & Roger, A. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004135 · Cited by 73

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

Chaperonin 60 Phylogeny Provides Further Evidence for Secondary Loss of Mitochondria Among Putative Early-Branching Eukaryotes

Horner, D. S., & Embley, T. M. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003737 · Cited by 66

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

Determining the Relative Rates of Change for Prokaryotic and Eukaryotic Proteins with Anciently Duplicated Paralogs

Kollman, J. M., & Doolittle, R. F. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010078 · Cited by 36

Large scale analysis of sequences from Neurospora crassa

Schulte, U., Becker, I., Mewes, H., & Mannhaupt, G. (2002) · Journal of Biotechnology · doi:10.1016/s0168-1656(01)00415-1 · Cited by 29

Genomics: Lessons from the Aeropyrum pernix genome

Faguy David, M., & Doolittle, W. F. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80074-3 · Cited by 27

The Archaea Monophyly Issue: A Phylogeny of Translational Elongation Factor G(2) Sequences Inferred from an Optimized Selection of Alignment Positions

Cammarano, P., Creti, R., Sanangelantoni, A. M., & Palm, P. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006574 · Cited by 22

Molecular evidence from the nuclear genome for the time frame of human evolution

Easteal, S., & Herbert, G. (2009) · Journal of Molecular Evolution · doi:10.1007/pl00000066 · Cited by 12

Untitled work

Collins, A. G. (2000) · doi:10.1666/0094-8373(2000)026

Application of Phylogenetic Networks in Evolutionary Studies

Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,895

The COG database: an updated version includes eukaryotes

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. (2004) · Nature · doi:10.1038/nature03025 · Cited by 1,966

Living in a fungal world: impact of fungi on soil bacterial niche development

de Boer, W., Folman, L. B., Summerbell, R. C., & Boddy, L. (2004) · FEMS Microbiology Reviews · doi:10.1016/j.femsre.2004.11.005 · Cited by 1,862

A new timeline of life’s early evolution

York, A. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0080-6 · Cited by 1

Exploiting genomics in evolutionary developmental biology

Holland, P. W. H., Copley, R. R., Snell, E. A., Furlong, R. F., & Agapow, P. (2002) · International Congress Series · doi:10.1016/s0531-5131(02)01134-2

BMC Evolutionary Biology BioMed Central

Hedges, S. B., Blair, J. E., Venturi, M. L., Access, J. L. S. O., & Shoe Jason, L. (2003)

Developing Evolutionary Cell Biology

Titus, M. A., & Goodson, H. V. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.11.006 · Cited by 5

Genomics

Davis, R. H. (2003) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780195154368.003.0018