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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Phylogeny

  • Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss [1].
  • HFRS is primarily a Eurasian disease, whereas HPS appears to be confined to the Americas; these geographic distinctions correlate with the phylogenies of the rodent hosts and the viruses that coevolved with them [2].
  • In order to assess the validity of classifications of RNA viruses, published alignments and phylogenies of RNA-dependent RNA and DNA polymerase sequences were reevaluated by a Monte Carlo randomization procedure, bootstrap resampling, and phylogenetic signal analysis [3].
  • Several discrepancies between the probing data and the phylogeny suggest that E. coli tmRNA undergoes a conformational change [4].
  • Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus [5].

High impact information on Phylogeny

  • The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny [6].
  • Prion phylogeny revisited [7].
  • A phylogeny of these species based on the Adh sequence data is consistent with that based on polytene chromosome banding patterns [8].
  • Here a molecular phylogeny of the Scombroidei has been determined by direct sequencing of a portion of the mitochondrial cytochrome b gene [9].
  • Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny [10].

Chemical compound and disease context of Phylogeny


Biological context of Phylogeny

  • However, dimerization transforms an interdomain loop and beta-strand (monomeric RepE) into an alpha-helix (dimeric RepA). dRepA resemble the C terminus of eukaryotic and archaeal Cdc6, giving clues to the phylogeny of DNA replication initiators [16].
  • Despite the prevalence of store-operated Ca2+ entry, no vertebrate channel responsible for store-operated Ca2+ entry has been reported. trp (transient receptor potential), a Drosophila gene required in phototransduction, encodes the only known candidate for such a channel throughout phylogeny [17].
  • Amino acid sequence motifs exist within ST enzymes that are conserved throughout phylogeny [18].
  • Using nuclear (18S rDNA) and mitochondrial (16S and COI) DNA sequence data from 37 myzostomid species representing nine genera, we report here the first molecular phylogeny of the Myzostomida and investigate the evolution of their various symbiotic associations [19].
  • Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae) [20].

Anatomical context of Phylogeny


Associations of Phylogeny with chemical compounds


Gene context of Phylogeny

  • Transient receptor potential (TRP) homologs have been identified throughout animal phylogeny [31].
  • Diversity and phylogeny of gephyrin: tissue-specific splice variants, gene structure, and sequence similarities to molybdenum cofactor-synthesizing and cytoskeleton-associated proteins [32].
  • The phylogeny of pth2 homologs suggests that the gene has been vertically inherited throughout the archaeal and eukaryal domains [33].
  • Within the phylogeny of the RHD alleles, DAU formed an independent allele cluster, separate from the DIVa, weak D type 4, and Eurasian D clusters [34].
  • We report the cloning, genomic structure, phylogeny and embryonic expression of Dmbx genes from amphioxus and from Ciona, representing the two most closely related lineages to the vertebrates [35].

Analytical, diagnostic and therapeutic context of Phylogeny


  1. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Kiontke, K., Gavin, N.P., Raynes, Y., Roehrig, C., Piano, F., Fitch, D.H. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  2. Spectrum of hantavirus infection: hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. Peters, C.J., Simpson, G.L., Levy, H. Annu. Rev. Med. (1999) [Pubmed]
  3. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. Zanotto, P.M., Gibbs, M.J., Gould, E.A., Holmes, E.C. J. Virol. (1996) [Pubmed]
  4. Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). Felden, B., Himeno, H., Muto, A., McCutcheon, J.P., Atkins, J.F., Gesteland, R.F. RNA (1997) [Pubmed]
  5. Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus. Guymon, R., Pomerantz, S.C., Crain, P.F., McCloskey, J.A. Biochemistry (2006) [Pubmed]
  6. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Pasquinelli, A.E., Reinhart, B.J., Slack, F., Martindale, M.Q., Kuroda, M.I., Maller, B., Hayward, D.C., Ball, E.E., Degnan, B., Müller, P., Spring, J., Srinivasan, A., Fishman, M., Finnerty, J., Corbo, J., Levine, M., Leahy, P., Davidson, E., Ruvkun, G. Nature (2000) [Pubmed]
  7. Prion phylogeny revisited. Goldmann, W., Hunter, N., Somerville, R., Hope, J. Nature (1996) [Pubmed]
  8. Conservation and change in the DNA sequences coding for alcohol dehydrogenase in sibling species of Drosophila. Bodmer, M., Ashburner, M. Nature (1984) [Pubmed]
  9. Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny. Block, B.A., Finnerty, J.R., Stewart, A.F., Kidd, J. Science (1993) [Pubmed]
  10. Comparative genomic analyses of the bacterial phosphotransferase system. Barabote, R.D., Saier, M.H. Microbiol. Mol. Biol. Rev. (2005) [Pubmed]
  11. QuickTree: building huge Neighbour-Joining trees of protein sequences. Howe, K., Bateman, A., Durbin, R. Bioinformatics (2002) [Pubmed]
  12. Alternative schemes of butyrate production in Butyrivibrio fibrisolvens and their relationship to acetate utilization, lactate production, and phylogeny. Diez-Gonzalez, F., Bond, D.R., Jennings, E., Russell, J.B. Arch. Microbiol. (1999) [Pubmed]
  13. Sequencing, high-level expression and phylogeny of the pyrophosphate-dependent phosphofructokinase from the thermophilic spirochete Spirochaeta thermophila. Ronimus, R., de Heus, E., Rückert, A., Morgan, H. Arch. Microbiol. (2001) [Pubmed]
  14. Hepatitis B virus genotypes, phylogeny and occult infection in a region with a high incidence of hepatocellular carcinoma in China. Fang, Z.L., Zhuang, H., Wang, X.Y., Ge, X.M., Harrison, T.J. World J. Gastroenterol. (2004) [Pubmed]
  15. Characterisation of an Irish caprine lentivirus strain--SRLV phylogeny revisited. Rolland, M., Mooney, J., Valas, S., Perrin, G., Mamoun, R.Z. Virus Res. (2002) [Pubmed]
  16. A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Giraldo, R., Fernández-Tornero, C., Evans, P.R., Díaz-Orejas, R., Romero, A. Nat. Struct. Biol. (2003) [Pubmed]
  17. TRPC1, a human homolog of a Drosophila store-operated channel. Wes, P.D., Chevesich, J., Jeromin, A., Rosenberg, C., Stetten, G., Montell, C. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  18. Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes. Weinshilboum, R.M., Otterness, D.M., Aksoy, I.A., Wood, T.C., Her, C., Raftogianis, R.B. FASEB J. (1997) [Pubmed]
  19. Molecular phylogenetic analyses indicate multiple independent emergences of parasitism in myzostomida (protostomia). Lanterbecq, D., Rouse, G.W., Milinkovitch, M.C., Eeckhaut, I. Syst. Biol. (2006) [Pubmed]
  20. Phylogeny of frogs of the Physalaemus pustulosus species group, with an examination of data incongruence. Cannatella, D.C., Hillis, D.M., Chippindale, P.T., Weigt, L., Rand, A.S., Ryan, M.J. Syst. Biol. (1998) [Pubmed]
  21. Identification and localization of a novel, cytoskeletal, centrosome-associated protein in PtK2 cells. Baron, A.T., Salisbury, J.L. J. Cell Biol. (1988) [Pubmed]
  22. A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Freshwater, D.W., Fredericq, S., Butler, B.S., Hommersand, M.H., Chase, M.W. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  23. Nucleotide sequence diversity at the methionine synthase locus in endangered Dunnia sinensis (Rubiaceae): an evaluation of the positive selection hypothesis. Chiang, Y.C., Ge, X.J., Chou, C.H., Wu, W.L., Chiang, T.Y. Mol. Biol. Evol. (2002) [Pubmed]
  24. Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes. Gupta, R.S., Golding, G.B. J. Mol. Evol. (1993) [Pubmed]
  25. Adrenal and sex steroid receptor evolution: environmental implications. Baker, M.E. J. Mol. Endocrinol. (2001) [Pubmed]
  26. Gonadotropin-releasing hormone genes: phylogeny, structure, and functions. Fernald, R.D., White, R.B. Frontiers in neuroendocrinology. (1999) [Pubmed]
  27. Complex asparagine-linked oligosaccharides are required for morphogenic events during post-implantation development. Metzler, M., Gertz, A., Sarkar, M., Schachter, H., Schrader, J.W., Marth, J.D. EMBO J. (1994) [Pubmed]
  28. Intron phylogeny: a new hypothesis. Cavalier-Smith, T. Trends Genet. (1991) [Pubmed]
  29. Kainate-binding proteins: phylogeny, structures and possible functions. Henley, J.M. Trends Pharmacol. Sci. (1994) [Pubmed]
  30. Hormonal and immunological aspects of the phylogeny of sex steroid binding plasma protein. Renoir, J.M., Mercier-Bodard, C., Baulieu, E.E. Proc. Natl. Acad. Sci. U.S.A. (1980) [Pubmed]
  31. INAF, a protein required for transient receptor potential Ca(2+) channel function. Li, C., Geng, C., Leung, H.T., Hong, Y.S., Strong, L.L., Schneuwly, S., Pak, W.L. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  32. Diversity and phylogeny of gephyrin: tissue-specific splice variants, gene structure, and sequence similarities to molybdenum cofactor-synthesizing and cytoskeleton-associated proteins. Ramming, M., Kins, S., Werner, N., Hermann, A., Betz, H., Kirsch, J. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  33. Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Rosas-Sandoval, G., Ambrogelly, A., Rinehart, J., Wei, D., Cruz-Vera, L.R., Graham, D.E., Stetter, K.O., Guarneros, G., Söll, D. Proc. Natl. Acad. Sci. U.S.A. (2002) [Pubmed]
  34. The DAU allele cluster of the RHD gene. Wagner, F.F., Ladewig, B., Angert, K.S., Heymann, G.A., Eicher, N.I., Flegel, W.A. Blood (2002) [Pubmed]
  35. Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development. Takahashi, T., Holland, P.W. Development (2004) [Pubmed]
  36. Intraspecific phylogeny of the New Zealand short-tailed bat Mystacina tuberculata inferred from multiple mitochondrial gene sequences. Lloyd, B.D. Syst. Biol. (2003) [Pubmed]
  37. Diversity of beta-lactam resistance-conferring amino acid substitutions in penicillin-binding protein 3 of Haemophilus influenzae. Dabernat, H., Delmas, C., Seguy, M., Pelissier, R., Faucon, G., Bennamani, S., Pasquier, C. Antimicrob. Agents Chemother. (2002) [Pubmed]
  38. Localization of peroxidase mRNAs in soybean seeds by in situ hybridization. Gijzen, M., Miller, S.S., Bowman, L.A., Batchelor, A.K., Boutilier, K., Miki, B.L. Plant Mol. Biol. (1999) [Pubmed]
  39. The phylogeny of alpha-fetoprotein in vertebrates: survey of biochemical and physiological data. Mizejewski, G.J. Crit. Rev. Eukaryot. Gene Expr. (1995) [Pubmed]
  40. Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean. Matsumura, H., Watanabe, S., Harada, K., Senda, M., Akada, S., Kawasaki, S., Dubouzet, E.G., Minaka, N., Takahashi, R. Theor. Appl. Genet. (2005) [Pubmed]
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