Experts and Doctors on molecular evolution in Brisbane, Queensland, Australia


Locale: Brisbane, Queensland, Australia
Topic: molecular evolution

Top Publications

  1. Smith A, Box N, Marks L, Chen W, Smit D, Wyeth J, et al. The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution. Gene. 2001;281:81-94 pubmed
  2. Tyagi R, Duquerroy S, Navaza J, Guddat L, Duggleby R. The crystal structure of a bacterial class II ketol-acid reductoisomerase: domain conservation and evolution. Protein Sci. 2005;14:3089-100 pubmed
    ..This contrasts with P. aeruginosa KARI, which forms a dodecamer, and spinach KARI, a dimer. In the E. coli KARI tetramer, a novel subunit-to-subunit interacting surface is formed by a symmetrical pair of bulbous protrusions. ..
  3. Degnan B, Vervoort M, Larroux C, Richards G. Early evolution of metazoan transcription factors. Curr Opin Genet Dev. 2009;19:591-9 pubmed publisher
  4. Richards G, Degnan B. The dawn of developmental signaling in the metazoa. Cold Spring Harb Symp Quant Biol. 2009;74:81-90 pubmed publisher
    ..Overall, this study highlights the stability and antiquity of the core cytosolic components of each pathway, juxtaposed with the more variable and recently evolved molecular interactions taking place at the cell surface. ..
  5. Collin S, Davies W, Hart N, Hunt D. The evolution of early vertebrate photoreceptors. Philos Trans R Soc Lond B Biol Sci. 2009;364:2925-40 pubmed publisher
  6. Woolfit M. Effective population size and the rate and pattern of nucleotide substitutions. Biol Lett. 2009;5:417-20 pubmed publisher
    ..Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N(e) is often substantial, however, and must be accounted for in analyses of molecular evolution. ..
  7. Jackson D, McDougall C, Woodcroft B, Moase P, Rose R, Kube M, et al. Parallel evolution of nacre building gene sets in molluscs. Mol Biol Evol. 2010;27:591-608 pubmed publisher
    ..The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa. ..
  8. Simonsen S, Sando L, Ireland D, Colgrave M, Bharathi R, Goransson U, et al. A continent of plant defense peptide diversity: cyclotides in Australian Hybanthus (Violaceae). Plant Cell. 2005;17:3176-89 pubmed
    ..The novel sequences provided substantial insight into the tolerance of the cystine knot framework in cyclotides to amino acid substitutions and will facilitate protein engineering applications of this framework...
  9. Morrow I, Parton R. Flotillins and the PHB domain protein family: rafts, worms and anaesthetics. Traffic. 2005;6:725-40 pubmed
    ..This review will discuss recent insights into the cell biology of flotillins and the large family of evolutionarily conserved PHB domain proteins. ..

More Information


  1. Takada S, Koopman P. Origin and possible roles of the Sox8 transcription factor gene during sexual development. Cytogenet Genome Res. 2003;101:212-8 pubmed
    ..Since a functional role(s) for Sox8 is implied by its conservation during evolution, the significance of Sox8 for sexual and other aspects of development will need to be uncovered through more directed lines of experimentation. ..
  2. Campbell N, Barker S. The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region. Mol Biol Evol. 1999;16:732-40 pubmed
    ..microplus. Instead, slipped-strand mispairing or recombination are the most plausible explanations for the evolution of these tandem repeats...
  3. Bateson M, Lines R, Revill P, Chaleeprom W, Ha C, Gibbs A, et al. On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus. J Gen Virol. 2002;83:2575-85 pubmed
  4. Ragan M. Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev. 2001;11:620-6 pubmed
    ..These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently. ..
  5. Cristino A, Nunes F, Barchuk A, Aguiar Coelho V, Simões Z, Bitondi M. Organization, evolution and transcriptional profile of hexamerin genes of the parasitic wasp Nasonia vitripennis (Hymenoptera: Pteromalidae). Insect Mol Biol. 2010;19 Suppl 1:137-46 pubmed publisher
    ..Temporal and spatial transcriptional profiles of N. vitripennis hexamerins suggest that they have physiological functions other than metamorphosis, which are arguably coupled with its lifestyle. ..
  6. Hill M, Bastiani M, Luetterforst R, Kirkham M, Kirkham A, Nixon S, et al. PTRF-Cavin, a conserved cytoplasmic protein required for caveola formation and function. Cell. 2008;132:113-24 pubmed publisher
    ..We conclude that PTRF-Cavin is required for caveola formation and sequestration of mobile caveolin into immobile caveolae. ..
  7. Etheridge N, Trusov Y, Verbelen J, Botella J. Characterization of ATDRG1, a member of a new class of GTP-binding proteins in plants. Plant Mol Biol. 1999;39:1113-26 pubmed
  8. Koopman P. Sry and Sox9: mammalian testis-determining genes. Cell Mol Life Sci. 1999;55:839-56 pubmed
  9. Ragan M, Beiko R. Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci. 2009;364:2241-51 pubmed publisher
    ..Here we identify and consider significant open questions concerning the role of LGT in genome evolution. ..
  10. Holmes R. Opossum aldehyde dehydrogenases: evidence for four ALDH1A1-like genes on chromosome 6 and ALDH1A2 and ALDH1A3 genes on chromosome 1. Biochem Genet. 2009;47:609-24 pubmed publisher
    ..It is proposed that the common ancestor for ALDH1A genes predates the appearance of birds during vertebrate evolution. ..
  11. Kolle G, Georgas K, Holmes G, Little M, Yamada T. CRIM1, a novel gene encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in vertebrate CNS development and organogenesis. Mech Dev. 2000;90:181-93 pubmed
    ..Our results suggest a role for CRIM1/Crim1 in CNS development possibly via growth factor binding. ..
  12. St Pierre L, Earl S, Filippovich I, Sorokina N, Masci P, de Jersey J, et al. Common evolution of waprin and kunitz-like toxin families in Australian venomous snakes. Cell Mol Life Sci. 2008;65:4039-54 pubmed publisher
  13. Blank L, Hugenholtz P, Nielsen L. Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci. J Mol Evol. 2008;67:13-22 pubmed publisher
    ..The intragene rearrangements appear to be ongoing events and the two has operons of the S. equi subspecies represent two alternatives of the same gene arrangement. A scenario for the evolution of streptococcal has operons is proposed...
  14. Glazov E, McWilliam S, Barris W, Dalrymple B. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol. 2008;25:939-48 pubmed publisher
    ..Overrepresentation of genes involved in regulation of neurogenesis among predicted miRNAs targets indicates an important role of the mir-379/mir-656 cluster in this biological process in the placental mammals. ..
  15. Gauthier M, Degnan B. The transcription factor NF-kappaB in the demosponge Amphimedon queenslandica: insights on the evolutionary origin of the Rel homology domain. Dev Genes Evol. 2008;218:23-32 pubmed publisher
    ..AmqNF-kappaB is expressed during A. queenslandica embryogenesis, suggesting a developmental role...
  16. Lawrence M, Lai J, Clements J. Kallikreins on steroids: structure, function, and hormonal regulation of prostate-specific antigen and the extended kallikrein locus. Endocr Rev. 2010;31:407-46 pubmed publisher
  17. Crowe M, Wang X, Rothnagel J. Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides. BMC Genomics. 2006;7:16 pubmed
  18. Rehli M, den Elzen N, Cassady A, Ostrowski M, Hume D. Cloning and characterization of the murine genes for bHLH-ZIP transcription factors TFEC and TFEB reveal a common gene organization for all MiT subfamily members. Genomics. 1999;56:111-20 pubmed
    ..Evolutionary aspects and implications for structure-function relationships are discussed. ..
  19. Beiko R, Harlow T, Ragan M. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A. 2005;102:14332-7 pubmed
    ..The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments. ..
  20. Mar J, Harlow T, Ragan M. Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. BMC Evol Biol. 2005;5:8 pubmed
  21. Koopman P, Schepers G, Brenner S, Venkatesh B. Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripes. Gene. 2004;328:177-86 pubmed publisher
  22. Oldmeadow C, Mengersen K, Mattick J, Keith J. Multiple evolutionary rate classes in animal genome evolution. Mol Biol Evol. 2010;27:942-53 pubmed publisher
  23. Bauer D, Buske F, Bailey T. Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. BMC Bioinformatics. 2010;11:366 pubmed publisher
  24. Jones A, Lowry K, Aaskov J, Holmes E, Kitchen A. Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy. J Gen Virol. 2010;91:182-8 pubmed publisher
    ..Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines...
  25. Gruber C, Elliott A, Ireland D, Delprete P, Dessein S, Goransson U, et al. Distribution and evolution of circular miniproteins in flowering plants. Plant Cell. 2008;20:2471-83 pubmed publisher
    ..We further predict that the number of cyclotides within the Rubiaceae may exceed tens of thousands, potentially making cyclotides one of the largest protein families in the plant kingdom. ..
  26. Chan C, Beiko R, Ragan M. Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics. 2006;7:412 pubmed
  27. Beiko R, Hamilton N. Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol. 2006;6:15 pubmed
    ..However, the edit paths inferred using EEEP suggest an important role for genetic transfer in the evolution of microbial genomes as well. ..
  28. Shao R, Dowton M, Murrell A, Barker S. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Mol Biol Evol. 2003;20:1612-9 pubmed publisher
    ..73, P = 0.01; Rs = 0.67, P < 0.05). We propose that increased rates of nucleotide substitution may lead to increased rates of gene rearrangement in the mt genomes of insects...
  29. Koopman P, Bullejos M, Loffler K, Bowles J. Expression-based strategies for discovery of genes involved in testis and ovary development. Novartis Found Symp. 2002;244:240-9; discussion 249-57 pubmed
    ..One of these, vanin 1, appears to play a role in mediating migration of mesonephric cells into the male genital ridge. Progress in characterizing other genes arising from the screen is discussed. ..