Potentially Interesting Websites and References
University of Maryland Libraries: http://www.lib.umd.edu/
Research Port
Databases
Find Database: Web of Science
Google Scholar: http://scholar.google.com
NCBI: National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/
follow taxonomy links
Integrated Taxonomic Information System
http://www.itis.gov/
more taxonomic information, not all species represented
Lab of Sudhir Kumar at ASU
http://kumarlab.net/index.html
Lab of James Elser at ASU
http://sols.asu.edu/faculty/jelser.php
http://lifesciences.asu.edu/irceb/stoichiometry/
Nature –omics resources
http://www.nature.com/omics/subjects/index.html
Genome Sizes, total of 10,000+ spp at these 3 sites:
University of Guelph
genomesize.com
Kew Gardens, plants and algae
www.kew.org/genomesize/homepage.html
Estonian University of Life Sciences, fungi
www.zbi.ee/fungal-genomesize
Tree of Life
http://www.tolweb.org/tree/
Eubacteria References, Tree of Life
Ahmad, S., A. Selvapandiyan, and R. K. Bhatnagar. 1999. A protein-based phylogenetic tree for Grampositive bacteria derived from hrcA, a unique heat-shock regulatory gene. International Journal of
Systematic Bacteriology 49:1387-1394.
Andersson, S. G. E., A. Zomorodipour, J. O. Andersson, T. Sicheritz-Ponten, U. C. M. Alsmark, R. M.
Podowski, A. K. Naslund, A. S. Eriksson, H. H. Winkler, and C. G. Kurland. 1998. The genome sequence
of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.
Balows, A., H.G. Träper, M. Dworkin, W. Harder, and K.-H. Schleifer (eds.). 1992. The Prokaryotes. A
Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. Second
edition, Volumes I-IV. Springer Verlag, New York.
Battistuzzi, F. U., A. Feijao, and A. B. Hedges. 2004. A genomic timescale of prokaryote evolution:
insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary
Biology 4:44-.
Bern, M. and D. Goldberg. 2005. Automatic selection of representative proteins for bacterial phylogeny.
BMC Evolutionary Biology 5:34-.
Boone, D. R., R.W. Castenholz, and G.M. Garrity. 2001. Bergey's Manual of Systematic Bacteriology.
Springer, New York.
Brochier, C., E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational
apparatus proteins.
Trends in Genetics 18:1-5.
Brown, J. R. , C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based
on large combined protein sequence data sets. Nature Genetics 28:281-285.
Bustard, K. and R. S. Gupta. 1997. The sequences of heat shock protein 40 (DnaJ) homologs provide
evidence for a close evolutionary relationship between the Deinococcus-Thermus group and cyanobacteria.
Journal of Molecular Evolution 45:193-205.
Castro, H. F., N. H. Williams, and A. Ogram. 2000. Phylogeny of sulfate-reducing bacteria. FEMS
Microbiology Ecology 31:1-9.
Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree
and bacterial megaclassification. International Journal of Systematic and Evolutionay Microbiology 52:776.
Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: Evidence
of a core of genes sharing a common history. Genome Research 2(7):1080-1090.
DeLong E. F. and N. R. Pace. 2001. Environmental diversity of Bacteria and Archaea. Systematic Biology
50:470-478.
Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria:
Comparison of trees of RecAs and 16S rRNAs from the same species. Journal of Molecular Evolution
41:1105-1123. Molecular Biology and Evolution 21(9):1643-1660.
Emelyanov, V. V. and B. V. Sinitsyn. 1999. A groE-based phylogenetic analysis shows very close
evolutionary relationship between mitochondria and Rickettsia. Russian Journal of Genetics 35:618-627.
Esser, C., N. Ahmadinejad, C. Wiegand, C. Rotte, F. Sebastiani, G. Gelius-Dietrich, K. Henze, E.
Kretschmann, E. Richly, D. Leister, D. Bryant, M. A. Steel, P. J. Lockhart, D. Penny and W. Martin. 2004.
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial
ancestry of yeast nuclear genes.
Fox, G. E., E. Stackebrandt, R. B. Hespell, J. Gibson, J. Maniloff, T. A. Dyer, R. S. Wolfe, W. E. Balch, R.
S. Tanner, L. J. Magrum, L. B. Zablen, R. Blakemore, R. Gupta, L. Bonen, B. J. Lewis, D. A. Stahl, K. R.
Luehrsen, K. N. Chen, and C. R. Woese. 1980. The phylogeny of prokaryotes. Science 209:457-463.
Garrity, G. M., J. A. Bell, and T. G. Lilburn. 2004. Taxonomic Outline of the Prokaryotes. Bergey's
Manual of Systematic Bacteriology, Second Edition. Release 5.0.
Gray, M. W., G. Burger, and B. F. Lang. 1999. Mitochondrial evolution. Science 283:1476-1481.
Gruber, T. M. and D. A. Bryant. 1997. Molecular systematic studies of eubacteria, using sigma(70)-type
sigma factors of group 1 and group 2. Journal of Bacteriology 179:1734-1747.
Gupta, R. S. 1997. Protein phylogenies and signature sequences: Evolutionary relationships within
prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek International Journal of
General and Molecular Microbiology 72:49-61.
Gupta, R. S. 1998. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships
among archaebacteria, eubacteria, and eukaryotes. Microbiology and Molecular Biology Reviews 62:14351491.
Gupta, R. S. 2000. The phylogeny of proteobacteria: relationships to other eubacterial phyla and
eukaryotes. FEMS Microbiology Reviews 24(4):367-402.
Gupta, R. S. 2004. The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and
Bacteroidetes. Critical Reviews in Microbiology 30(2):123-143.
Gupta, R.S., K. Bustard, M. Falah, D. Singh. 1997. Sequencing of heat shock protein 70 (DnaK) homologs
from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based
phylogeny of prokaryotes. Journal of Bacteriology 179:345-357.
Gupta, R.S. and E. Griffiths. 2002. Critical issues in bacterial phylogeny. Theoretical Population Biology
61(4):423-434.
Gupta, R. S., T. Mukhtar, and B. Singh. 1999. Evolutionary relationships among photosynthetic
prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and
proteobacteria): implications regarding the origin of photosynthesis. Molecular Microbiology 32:893-906.
Huang, W. M. 1996. Bacterial diversity based on type II DNA topoisomerase genes. Annual Review of
Genetics 30:79-107.
Huang, Y. P. and J. Ito. 1999. DNA polymerase C of the thermophilic bacterium Thermus aquaticus:
Classification and phylogenetic analysis of the family C DNA polymerases. Journal of Molecular Evolution
48:756-769.
Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of culture-independent studies on the
emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180:4765-4774.
Lawrence, J. G. and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proceedings
of the National Academy of Sciences of the United States of America 95:9413-9417.
Liu, R. and H. Ochman. 2007. Stepwise formation of the bacterial flagellar system. Proceedings of the
National Academy of Sciences of the United States of America 104(17):7116-7121.
Ludwig, W., J. Neumaier, N. Klugbauer, E. Brockmann, C. Roller, S. Jilg, K. Reetz, I. Schachtner, A.
Ludvigsen, M. Bachleitner, U. Fischer, and K. H. Schleifer. 1993. Phylogenetic relationships of Bacteria
based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes.
Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 64:285-305.
Ludwig, W., O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger , J. Neumaier, M. Bachleitner, and
K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis
19:554-568.
Moran, N. and P. Baumann. 1994. Phylogenetics of cytoplasmically inherited microorganisms of
arthropods. Trends in Ecology and Evolution 9:15-20.
Ochman, H., S. Elwyn, and N. A. Moran. 1999. Calibrating bacterial evolution. Proceedings of the National
Academy of Sciences of the United States of America 96:12638-12643.
Olsen, G. J. and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEB Journal 7:113-23.
Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life
into microbiology. Journal of Bacteriology 176:1-6.
Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
Pace, N. R. 1999. Microbial ecology and diversity. ASM News 65:328-333.
Pierson, B. K. 1994. The emergence, diversification, and role of photosynthetic bacteria. Pages 161-180 in
Early Life on Earth, Nobel Symposium No. 84 (Bengtson, S., ed.). Columbia University Press, New York.
Rappé, M. S. and S. J. Giovannoni. 2003. The uncultured microbial majority. Annual Review of
Microbiology 57:369-394.
Sapp, J. 2005) Microbial Phylogeny and Evolution: Concepts and Controversies. Oxford University Press,
New York.
Sicheritz-Ponten, T., C. G. Kurland, and S. G. E. Andersson. 1998. A phylogenetic analysis of the
cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the
Rickettsiaceae. Biochimica et Biophysica Acta Bioenergetics 1365:545-551.
Staley, J. T. and J. J. Gosink. 1999. Poles apart: Biodiversity and biogeography of sea ice bacteria. Annual
Review of Microbiology 53:189-215.
Stetter, K. O. 1996. Hypterthermophilic procaryotes. FEMS Microbiology Reviews 18:149-158.
Teichmann, S. A. and G. Mitchison. 1999. Is there phylogenetic signal in prokaryote proteins? Journal of
Molecular Evolution 49:98-107.
Viale, A. M. and A. K. Arakaki. 1994. The chaperone connection to the origins of the eukaryotic
organelles. FEBS Letters 341:146-151.
Viale, A. M., A. K. Arakaki, F. C. Soncini, and R. G. Ferreyra. 1994. Evolutionary relationships among
eubacterial groups as inferred from GroEL (chaperonin) sequence comparison. International Journal of
Systematic Bacteriology 44:527-533.
Woese, C. R. 1987. Bacterial evolution. Microbiological Reviews 51:221-271.
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed
using five different approaches suggest new major bacterial clades. BMC Evolutionary Biology 1:8-.
Yang, S., R. F. Doolittle, and P. E. Bourne. 2005. Phylogeny determined by protein domain content.
Proceedings of the National Academy of Science USA 102(2):373-378 .
Information on the Internet
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Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of
Life. The Institute for Genomic Research.
The Prokaryotes. An evolving electronic resource for the microbiological community.
Introduction to the Bacteria. UCMP Berkeley.
MicrobeWorld. American Society of Microbiology
Microbes.info. The Microbiology information portal.
Virtual Museum of Bacteria
Digital Learning Center for Microbial Ecology. A science education project at Michigan State
University.
Bacteriology 303. Study aids and background readings. University of Wisconsin - Madison.
The Microbial World: Profiles of Microorganism. An educational resource covering bacteria,
fungi, viruses, biological control, environmental microbiology, disease of plants, humans and
animals. Produced by Jim Deacon, Institute of Cell and Molecular Biology, and Biology Teaching
Organisation, University of Edinburgh.
Stalking the Mysterious Microbe. A kid-oriented site from the American Society for
Microbiology.
Bugs in the News!. Interesting facts about microbes compiled by John C. (Jack) Brown.
The Microbiology Network. A communication resource for the microbiologist.
List of Bacterial names with Standing in Nomenclature. J. P. Euzéby.
TIGR Microbial Database. A listing of microbial genomes and chromosomes completed and in
progress.
Bergey's Manual of Systematic Bacteriology, second edition. The taxonomic outline for the 5
volumes, including all species, type strains, and 16S rRNA sequence data can be downloaded from
this site.
Bacterial Nomenclature Up-To-Date. DSMZ-Deutsche Sammlung von Mikro-organismen und
Zellkulturen GmbH, Braunschweig, Germany.
The"Bad Bug Book". Foodborne Pathogenic Microorganisms and Natural Toxins Handbook. U.S.
Food & Drug Administration Center for Food Safety & Applied Nutrition.
Cells Alive!. Videos and images of bacteria and other organisms.
Public Health Image Library. Centers for Disease Control and Prevention (CDC).
Archaea References, Tree of Life
Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. 1998. Evidence for massive gene
exchange between archaeal and bacterial hyperthermophiles. Trends in Genetics 14:442-444.
Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity,
thermophily and monophyly from environmental rRNA sequences. Proceedings of The National Academy
of Sciences (U.S.A.) 93:9188-9193.
Barns, S. M., R. E. Fundyga, M. W. Jeffries and N. R. Pace. 1994. Remarkable archaeal diversity detected
in a Yellowstone National Park hot spring environment. Proceedings of the National Academy of Sciences
of the United States of America 91(5): 1609-1613.
Benachenhou, L. N., P. Forterre and B. Labedan. 1993. Evolution of glutamate dehydrogenase genes:
Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the
universal tree of life. Journal Of Molecular Evolution 36(4): 335-346.
Brown, J. R. and W. F. Doolittle. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiology
and Molecular Biology Reviews 61:456-502.
Cammarano, P., P. Palm, R. Creti, E. Ceccarelli, A. M. Sanangelantoni, and O. Tiboni. 1992. Early
evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences:
Phylogenetic coherence and structure of the Archaeal domain. Journal Of Molecular Evolution 34:396-405.
Delong, E. F. 1992. Archaea in coastal marine environments. Proceedings of The National Academy of
Sciences (U.S.A.) 89: 5685-5689.
DeLong E. F. and N. R. Pace. 2001. Environmental diversity of Bacteria and Archaea. Systematic Biology
50: 470-478.
Doolittle, W. F. and J. M. Logsdon. 1998. Archaeal genomics: Do archaea have a mixed heritage? Current
Biology 8: (6) R209-R211.
Graham, D. E., R. Overbeek, G. J. Olsen, and C. R. Woese. 2000. An archaeal genomic signature.
Proceedings of The National Academy of Sciences (U.S.A.) 97:3304-3308.
Huber, H., M. J. Hohn, R. Rachel, T. Fuchs, V. C. Wimmer, and K. O. Stetter. 2002. A new phylum of
Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67.
Kjems, J., N. Larsen, J. Z. Dalgaard, R. A. Garrett and K. O. Stetter. 1992. Phylogenetic relationships
amongst the hyperthermophilic Archaea determined from partial 23S rRNA gene sequences. Systematic
and Applied Microbiology 15(2): 203-208.
Klenk, H. P., C. Schleper, V. Schwass and R. Brudler. 1993. Nucleotide sequence, transcription and
phylogeny of the gene encoding the superoxide dismutase of Sulfolobus acidocaldarius. Biochimica Et
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Kyrpides, N. C. and G. J. Olsen. 1999. Archaeal and bacterial hyperthermophiles: horizontal gene exchange
or common ancestry? Trends in Genetics 15:298-299.
Kyrpides, N. C. and C. A. Ouzounis. 1999. Transcription in Archaea. Proceedings of The National
Academy of Sciences (U.S.A.) 96:8545-8550.
Macario, A. J. L. and E. C. de Macario. 1999. The archaeal molecular chaperone machine: Peculiarities and
paradoxes. Genetics 152:1277-1283.
Makarova, K. S., L. Aravind, M. Y. Galperin, N. V. Grishin, R. L. Tatusov, Y. I. Wolf, and E. V. Koonin.
1999. Comparative genomics of the archaea (Euryarchaeota): Evolution of conserved protein families, the
stable core, and the variable shell. Genome Research 9:608-628.
Matte-Tailliez, O., C. Brochier, P. Forterre, and H. Philippe. 2002. Archaeal phylogeny based on ribosomal
proteins. Molecular Biology and Evolution 19:631-639.
Stetter, K. O. 1996. Hypterthermophilic procaryotes. FEMS Microbiology Reviews 18:149-158.
Takai, K. and K. Horikoshi. 1999. Genetic diversity of archaea in deep-sea hydrothermal vent
environments. Genetics 152:1285-1297.
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ArchaeaWeb. Information resource for researchers working with Archaea and extremophiles.
Introduction to the Archaea: Life's extremists. . .. UCMP Berkeley.
ARCHAIC: ARCHAebacterial Information Collection. Database of archaebacterial genomic DNA
sequences. Structural Biology Centre, Tsukuba, Japan.
Jarrell Laboratory. Research on the ultrastructure and biochemistry of methanogenic archaea.
Department of Microbiology and Immunology at Queen's University in Kingston, Canada.
Molecular Biology of Extremophiles Laboratory. Institut de Génétique et Microbiologie,
Université Paris-Sud, Centre Universitaire d'Orsay, France.
Department of Microbiology and Archaeenzentrum. The Karl O. Stetter laboratory, Regensburg,
Germany.
Halophilic Microorganisms. Maintained by Robert Simon.
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Baldauf, S. L. 1999. A search for the origins of animals and fungi: Comparing and combining molecular
data. American Naturalist 154(suppl.):S178-S188.
Baldauf, S. L. and W. F. Doolittle. 1997. Origin and evolution of the slime molds (Mycetozoa).
Proceedings of the National Academy of Sciences (USA) 94:12007-12012.
Baldauf, S. L. and J. D. Palmer. 1993. Animals and fungi are each other's closest relatives: Congruent
evidence from multiple proteins. Proceedings of the National Academy of Sciences (USA) 90:1155811562.
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Borchiellini C., N. Boury-Esnault, J. Vacelet, and Y. Le Parco. 1998. Phylogenetic analysis of the Hsp70
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Budin, K. and H. Philippe. 1998. New insights into the phylogeny of eukaryotes based on Ciliate Hsp70
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Academy of Sciences (USA) 101(43):15386-15391.
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Embley T. M. and R. P. Hirt. 1998. Early branching eukaryotes? Curr. Opinion Gen. Dev. 8:624-629.
Fast, N. M., J. M. Logsdon, and W. F. Doolittle. 1999. Phylogenetic analysis of the TATA box binding
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Hampl, V., D. S. Horner, P. Dyal, J. Kulda, J. Flegr, P. G. Foster, and T. M. Embley. 2005. Inference of the
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Hirt, R. P., J. M. Logsdon, Jr., B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999.
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Huang, J., Y. Xu, and J. P. Gogarten. 2005. The presence of a haloarchaeal type tyrosyl-tRNA synthetase
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Kamaishi, T., T. Hashimoto, Y. Nakamura, F. Nakamura, S. Murata, N. Okada, K. Okamoto, and M.
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microsporidia evolved from within the fungi. Molecular Biology and Evolution 17:23-31.
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405:635-637.
Kim, J., W. Kim, and C. W. Cunningham. 1999. A new perspective on lower metazoan relationships from
18S rDNA sequences. Molecular Biology and Evolution 16:423-427.
Knoll, A. H. 1992. The early evolution of eukaryotes: a geological perspective. Science 256:622-627.
Kumar, S. and A. Rzhetsky. 1996. Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular
Evolution 42:183-193.
Lake, J. A. and M. C. Rivera. 1994. Was the nucleus the first endosymbiont? Proceedings of the National
Academy of Sciences (USA) 91:2880-2881.
Lang, B. F., G. Burger, C. J. O'Kelly, R. Cedergren, G. B. Golding, C. Lemieux, D. Sankoff, M. Turmel,
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Nature 387:493-497.
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Information on the Internet
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Eu-Tree. Assembling the Tree of Eukaryotic Diversity.
Protsville. Protist Research Laboratory, University of Sydney, Australia.
Protist Information Server. Japan Science and Technology Corporation.
o Protistologist's Home Pages.
o Digital Specimen Archives.
Eukaryota: Systematics. Museum of Paleontology, University of California, Berkeley, USA.
Malaria, Algae, Amoeba and You: Unravelling Eukaryotic Relationships. Joel B. Dacks.
ActionBioScience.org
Exploring Early Eukaryotic Evolution: Diversity and Relationships Among Novel DeepBranching Lineages . Virginia Edgcomb, Andrew Roger, Alastair G.B. Simpson, Jeffrey
Silberman and Mitchell Sogin, Marine Biological Laboratory, Woods Hole, USA.
Microbial Life - Educational Resources. Teaching and learning about the diversity, ecology and
evolution of the microbial world; discover the connections between microbial life, the history of
the earth and our dependence on micro-organisms.
Eukaryotes in extreme environments. Dave Roberts, the Natural History Museum, London, UK.
The Homeobox Page. Thomas R. Bürglin's page about the homeobox genes which play important
roles in the development of multicellular organisms.
Protist Image Data. Molecular Evolution and Organelle Genomics program at the University of
Montreal, Canada.