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Institute of Molecular BioSciences, Massey University
   
 

Contact Details


Phone: +64 6 350 5033

Fax No. +64 6 350 5626

Email:d.penny@massey.ac.nz

Address:
Institute of Molecular
 BioSciences,
Massey University,
Private Bag 11222,
Palmerston North,
New Zealand

 
 
Links
 

Selected Publications

- Book chapters
- RNA publications
- Vertebrate publications
- Human Origins publications
- Theoretical publications
 

The Allan Wilson Centre
 

The Institute of Molecular Biosciences at
 
Massey University
 

 

D. Penny. (2007). Charles Darwin, evolution simple and testable. NZ Science Teacher (116): 23-27
Teacher Resource
 

Professor David Penny
Professor of Theoretical Biology

 

  
   

Background

BSc (Hons) 1961, PhD (Yale) 1965; FRSNZ 1990; Past-President New Zealand Association of Scientists; Past-President Society for Molecular Biology and Evolution.

    
         
   

Research Interests

"All organisms carry their history in their genes."

Our group is actively interested in a wide range of evolutionary questions where DNA sequences are critical. The two aspects of the research are devising better methods for extracting information from DNA sequences and asking important biological questions for testing.

The focus of our research is that DNA sequences carry a lot of information or 'signals'. The signals may result from common history (phylogeny), constraints from folding into 2 or 3D forms, constraints from structure of an active site, a systematic mutational bias (such as GC content), and so on. Our research group consists of biologists, molecular biologists and mathematicians. We interact in devising new mathematical methods, such as a discrete Fourier analysis, that helps detect signals that are biologically important.

The interests of our research students are very wide and include some with extensive field work (possibly overseas), some being mostly laboratory based, some mainly theoretical analysis, and others that are mainly involved in computer based. Current projects include: studying the origin and migration of early human populations; the origins of New Zealand biota; the origin of life and the RNA world; DNA evidence and the survival of land vertebrates across the Cretaceous/Tertiary boundary; an analytical study of complex algorithms for reconstructing evolutionary trees; computer simulations of the effectiveness of different methods.

What holds the interest of the group together is the love of science, and the excitement of aiming for quantitative answers to interesting biological questions.

   
         
 
 
         
   

Selected Publications

    
   


Please note that pdfs accessed via this site are for
personal use only and copyright rests with the publisher

- Book Chapters
- RNA publications
- Vertebrate publications
- Human Origins publications

- Theoretical publications
   
           
           
   

Book Chapters

     
             
    R. Egel and D. Penny (2007). On the Origin of Meiosis in Eukaryotic Evolution: Coevolution of Meiosis and Mitosis from Feeble Beginnings. In Recombination and Meiosis, R. Egel and D-H. Lankenau (eds), Springer. DOI 10.1007/7050_2007_036      
             
    Steel, M.A. and D. Penny. (2005) Maximum parsimony and the phylogenetic information in multistate characters. Pp 163-178, in Parsimony, Phylogeny and Genomics (V. Albert, ed), Oxford University Press.       (book purchase available online)
             
    D. Penny. (2002). Consequences of the continuity between the human and biological worlds. In “Learning, animals and the environment: changing the face of the future”. (M.Fisher, J. Marbrook and G. Sutherland eds) Pp 19-28 Royal Society of New Zealand, Wellington.        
             
    D. Penny and M.D.Hendy. (2001). Phylogenetics: parsimony and distance methods. Pp 445-483, In “Handbook of Statistical Genetics” (eds D J Balding, M Bishop and C. Cannings), Wiley.       (book purchase available online)
             
    E. E. Watson, S. Easteal and D. Penny. (2001). Homo genus: A review of the classification of humans and the great apes. Pp307-318, In Humanity from African Naissance to coming Millenia, (P.V. Tobias, M. A. Raath, J. Moggi-Cecchi and G. A. Doyle eds), Firenze University Press. Firenze.        
             
    Book Reviews        
    D. Penny. (2005). Biology and physics envy. EMBO reports. Vol 6, no 6:511       book review
             
    D. Penny. (2004) Life, the Universe, and Everything. Book review of “Life’s Solutions: Inevitable humans in a lonely world". Simon Conway Morris, Cambridge University Press. EMBO Reports 5, 134-135.       book review

(book purchase available online)
             
   

D. Penny. (2004) Darwin: I wish I were a Botanist. Book review of “The Correspondence of Charles Darwin, Volume 13 1865”, Cambridge University Press. Trends Ecol. Evol. 19, 67-68

      

read book review online

(book purchase available online)

             
             
             
   

From the RNA-world to the origin of eukaryotes

        
             
    Chen, X., Rozhdestvensky, T.S.,Collins, L.J., Schmitz, J., and D. Penny. (2007). Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research, Vol. 35, No. 14 4619–4628      
             
    Irimia, M., D. Penny, and Roy, S.W. (2007). Coevolution of genomic intron number and splice sites. TRENDS in Genetics Vol.23 No.7, 321-325
     
             
    Irimia, M., Rukov, J.L., D. Penny, and Roy, S.W. (2007). Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evolutionary Biology 2007, 7:188      
             
    Poole, A. and D. Penny.  2007.  Engulfed by speciation.  Nature 447:913.        
             
    Roy, S.W. and D. Penny. (2007). Intron length distributions and gene prediction. Nucleic Acids Research, Vol. 35, No. 14 4737–4742      
             
    Roy, S.W. and D. Penny. (2007). On the Incidence of Intron Loss and Gain in Paralogous Gene Families. Mol. Biol. Evol. 24(8):1579–1581.      
             
    Roy, S.W. and D. Penny. (2007). A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain. Mol. Biol. Evol. 24(7):1447–1457.      
             
    Roy, S.W. and D. Penny. (2007). Patterns of intron loss and gain in plants: intro loss-dominated evolution and a genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol 24(1), 171-81.      
             
    Woodhams, M.D., Stadler, P.F., D. Penny and Collins, L.J. (2007). RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evolutionary Biology, 7(Suppl 1):S13
doi:10.1186/1471-2148-7-S1-S13 (Abstract) 		     
             
    Matheson, J.W., Rich, F.J., Corbett, C., Greenwood, K., Huang, Q.S., D. Penny, and Hendy, M.D. (2006). Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years. J Medical Virology 78:1354-1364        
             
   

Roy S.W. and D. Penny. 2006. Smoke Without Fire: Most Reported Cases of Intron Gain in Nematodes Instead Reflect Intron Losses. Mol. Biol. Evol. 23(12):2259–2262.

      
             
    L. J. Collins and D. Penny. 2006. Investigating the Intron Recognition Mechanism in Eukaryotes. Mol. Biol. Evol. 23(5):901–910. (Abstract)      
             
    D.C. Jeffares, T. Mourier, and D. Penny. 2006. The biology of intron gain and loss. TRENDS in Genetics 22 (1): 16-22. (Abstract)      
             
    C.G. Kurland, L.J. Collins, and D. Penny. 2006. Genomics and the Irreducible Nature of Eukaryote Cells. Science 312: 1011-1014. (Abstract)      
             
    Penny, D. (2006). Why the resistance? EMBO report. Vol 7,no 10: 975.        
             
    L. J. Collins and D. Penny. 2005. Complex Spliceosomal Organization Ancestral to Extant Eukaryotes. Mol. Biol. Evol. 22(4):1053–1066. (Abstract)      
             
    D. Penny. 2005. An interpretive review of the origin of life research. Biology and Philosophy 20:633–671. (Abstract)      
             
    L. J. Collins, T. J. Macke, and D. Penny. 2004. Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif. Journal of Integrative Bioformatics http://journal.imbio.de/. (Abstract)      
             
    L. J. Collins. and D. Penny. 2004. Lost in the RNA World – the genomics of ncRNA. New Zealand Bio Science 13, 38-40        
             
    P. P. Gardner, B. R. Holland, V. Moulton, M. Hendy, and D. Penny. 2003. Optimal alphabets for an RNA world. Proc. R. Soc. Lond. B270, 1177–1182. (Abstract)      
             
    D. Penny and Poole, A.M. 2003. Lateral Gene Transfer: Some Theoretical Aspects. NZ Bioscience 32-35. (Abstract)      
             
    Poole, A.M., Phillips, M.J., and D. Penny. 2003. Prokarote and eukaryote evolvability. BioSystems 69: 163-185. (Abstract)      
             
    A. Poole, D. Penny and B.-M. Sjöberg. 2001 Confounded Cytosine! Tinkering and the evolution of DNA. Nature Reviews: Molecular Cellular Biology 2:147-151. (Abstract)      
             
    V. Moulton, Paul P. Gardner, R. F. Pointon, Lawrence K. Creamer, Geoffrey B. Jameson, and D. Penny. 2000. RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution 51:416-421. (Abstract)      
             
    A. Poole, D. Penny and B.-M. Sjöberg. 2000. Methyl-RNA: an evolutionary bridge between RNA and DNA? Chemistry and Biology 7: R207-R216. (Abstract)      
             
    D. Penny and A. Poole. 1999. The Nature of the Universal Ancestor. Curr Opin Genet Dev. Dec;9(6):672-7. (Abstract)      
             
    A. M. Poole, D.C. Jeffares and D. Penny. 1999. Early Evolution: Prokaryotes, the new kids on the block.BioEssays 21:880–889. (Abstract)      
             
   

A.M. Poole, D. C. Jeffares, and D. Penny. 1998. The path from the RNA world. Journal of Molecular Evolution 46: 1-17. (Abstract)

     
    (see Science,1 May 1998, Vol 280, pp 672-674 Genome Data Shake Tree of Life. also see New Scientist 16 Jan 1999, Making life simple. pp34-37)        
             
             
   

Vertebrate evolution/mass survival versus explosive radiations

        
             
    Gibb, G.C., Kardailsky, O., Kimball, R.T., Braun, E.L., and D. Penny. (2007). Mitochondrial Genomes and Avian Phylogeny: Complex Characters and Resolvability without Explosive Radiations. Mol. Biol. Evol. 24(1):269-280.
     
             
    Slack, K.E, Delsuc, F., Mclenachan, P.A., Arnason, U., and D. Penny. (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution 42:1-13.        
             
   

Phillips, M.J., McLenachan, P.A., Down, C., Gibb, G.C. and D. Penny. 2006. Combined Mitochondrial and Nuclear DNA Sequences Resolve the Interrelations of the Major Australasian Marsupial Radiations. Syst. Biol. 55(1):122–137. (Abstract)

     
             
   

G. L. (Abby) Harrison, P. A. McLenachan, M. J. Phillips, K. E. Slack, A. Cooper, and D. Penny. 2004. Four New Avian Mitochondrial Genomes Help Get to Basic Evolutionary Questions in the Late Cretaceous. Mol. Biol. Evol. 21(6):974–983. (Abstract)

     
             
    D. Penny and M. J. Phillips. 2004.The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?. Trends in Ecology and Evolution. 19(10):516-522. (Abstract)      
             
    Kerryn E. Slack, A. Janke, D. Penny and U. Arnason. 2003. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302: 43–52. (Abstract)
     
             
    Phillips, M.J. and D. Penny. 2003. The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution 28(2):171-85. (Abstract)      
             
    Y.-H. Lin, P.A McLenachan, M.J. Phillips, A.R. Gore, R. Ota, M.D. Hendy and D. Penny 2002. Four new mitochondrial genomes, and the stability of evolutionary trees of mammals. Molecular Biology and Evolution, 19: 2060-2070. (Abstract)      
             
    Y.-H. Lin, P.J. Waddell and D. Penny 2002. Pika and Vole mitochondrial genomes add support to both rodent monophyly and glires. Gene 294: 119-129. (Abstract)      
             
    Y.-H. Lin and D. Penny 2001. Implications for Bat Evolution from Two New Complete Mitochondrial Genomes. Molecular Biology and Evolution, 18: 684-688      
             
    L.D. Bromham, M.J. Phillips and D. Penny. 1999. Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology and Evolution 14: 113-118. (Abstract)      
             
    L. D. Bromham, A. Rambaut, R Fortey, A. Cooper and D. Penny. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proceedings National Academy of Sciences, USA. 95: 12386-12389. (Abstract)      
             
    A. Cooper and D. Penny. 1997. Mass survival of birds across the Cretaceous/Tertiary boundary. Science 275: 1109-1113. (Abstract)      
    (see also perspective by Ann Gibbons, Science 275: 1068 1997).        
             
             
   

Human origins and dispersal

        
             
    Clarke, A.C., Burtenshaw, M.K., McLenachan, P.A., Erickson, D.L., and D. Penny. 2006. Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria). Mol. Biol. Evol. 23(5):893–900. (Abstract)      
             
    D. Penny. 2004. Our relative genetics. Nature 427, 208-209.      
             
    Hurles, M.E., Matisso-Smith, E., Gray, R.D., and D. Penny. (2003). Untangling Oceanic settlement: the edge of the knowable. Trends in Ecology and Evolution 18(10): 531-540. (Abstract)      
             
    Watson, E. E. and D. Penny (2003). DNA and People: from East Africa to Aotearoa New Zealand. New Zealand Science Review 60(1): 29 - 35.      
             
    D. Penny, R. Murray-McIntosh and G. L. Harrison. 2002. Estimating the number of females the founding population of New Zealand: analysis of mtDNA variation. Journal of the Polynesian Society 111: 207-221        
             
    G.L. Harrison, R. Murray-McIntosh and D. Penny. 2001. Hepatitis B virus genotypes: A South Pacific perspective. Pacific Health Dialogue 8:188-192. (Abstract)        
             
    E. Matisoo-Smith, R. M. Roberts, G.J. Irwin, J.S. Allen, D. Penny. and D.M. Lambert. 1998. Patterns of prehistoric human mobility in Polynesia indicated by mtDNA from the Pacific rat. Proceedings of the National Academy of Sciences, USA. 95: 15145-15150. (Abstract)      
             
    R. P. Murray-McIntosh, B. J. Scrimshaw, P. J. Hatfield and D. Penny. 1998. Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences. Proceedings of the National Academy of Sciences USA. 95:9047-9052. (Abstract)      
             
    D. Penny, M. A. Steel, P. J. Waddell, and M. D. Hendy. 1995. Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. Molecular Biology Evolution 12:863-882. (Abstract)      
             
             
   

Theoretical Biology/phylogenetics

        
             
    Irimia, M., Maeso, I., D. Penny, Garcia-Ferna`ndez, J., and Roy, S.W. (2007). Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata. Mol. Biol. Evol. 24(8):1604–1607.
doi:10.1093/molbev/msm105
      
             
    K. E. Slack, C. M Jones, T. Ando, G. L. Harrison, E. Fordyce, U. Arnason and D. Penny. 2006. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Molecular Biology and Evolution 23: 1144-1155. (Abstract)      
             
    Holland, B.R., K.T. Huber, D. Penny, and V. Moulton. 2005. The MinMax Squeeze: Guaranteeing a minimal tree for population data. Mol. Biol. Evol. 22:235-242. (Abstract)      
             
    D. Penny. 2005. Relativity for Molecular Clocks. NATURE(436): 183-184      
             
    D. Penny. 2004. Evolutionary trees for all. Trends in Ecology and Evolution 19(6): 273      
             
    M. J. Phillips, F. Delsuc and D. Penny. 2004. Genome-Scale Phylogeny and the Detection of Systematic Biases. Mol. Biol. Evol. 21(7):1455–1458.      
             
    M. Steel and D. Penny. 2004. Two Further Links Between MP and ML Under the Poisson Model. Applied Mathematics Letters 17: 785-790. (Abstract)      
             
    Bromham, L. and D. Penny. 2003. The Modern Molecular Clock. Nature Reviews - Genetics 4:216-224.      
             
    Collins, L.J., Poole, A.M. and D. Penny . 2003. Using ancestral sequences to uncover potential gene homologs. Applied Bioinformatics 2, S85-S95.        
             
    Delsuc, F., Phillips, M.J. and D. Penny. 2003. Comment on "Hexapod Origins: Monophyletic or Paraphyletic?" Science 12 301: 1482-1483.      
             
    Edvardsson, S., Gardner, P. P., Poole, A. M., Hendy, M. D., D. Penny and Moulton, V.  2003.  A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19 (7): 865–873. (Abstract)      
             
    Ota, R. and D. Penny. (2003). Estimating changes in mutational mechanisms of evolution. Journal of Molecular Evolution 57:S233-S240. (Abstract)      
             
    D. Penny, Hendy, M. and Poole, A.  2003. Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 223(3): 377-385. (Abstract)      
             
    D. Penny  and Poole, A.M.  2003. Lateral gene transfer: some theoretical aspects. New Zealand Bio Science. 12: 32-35.        
             
    D. Penny, B J McComish, M A Charleston, M D Hendy. 2001. Mathematical elegance with biochemical realism: The covarion model of molecular evolution. Journal of Molecular Evolution. 53: 711-723. (Abstract)      
             
    B. Chor, B.R. Holland, D. Penny and M.D. Hendy. 2000. Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach. Molecular Biology and Evolution 17: 1529-1541. (Abstract)      
             
    L. J. Collins, V. Moulton and D. Penny. 2000. Use of RNA secondary structure for evolutionary relationships: the case of RNase P and RNase MRP. Journal of Molecular Evolution 51: 194-204. (Abstract)      
             
    V. Moulton, M. Zuker, M.A Steel, R. Pointon and D. Penny. 2000. Metrics on RNA secondary structures. Journal of Computational Biology. 7: 277-292. (Abstract)        
             
    M.A.Steel and D. Penny. 2000. Parsimony, likelihood and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17: 839-850. (Abstract)      
             
    M. A. Steel, M. D. Hendy, and D. Penny. 1999. Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results. Discrete Applied Mathematics. 88: 367-396.        
             
    P.J. Waddell, D. Penny, and T. Moore. 1997. Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Molecular Phylogenetics and Evolution 8: 33-50. (Abstract)      
             
    M. D. Hendy and D. Penny. 1996. Complete families of linear invariants for stochastic models of sequence evolution: with and without the molecular clock assumption. Journal of Computational Biology 3:19-31 (Abstract)        
             
    A. Bar-Hen and D. Penny. 1996. Estimating the bias on the Logdeterminant transformation for evolutionary trees. Applied Mathematics Letters 9: 1-5. (Abstract)      
             
    D. Penny, M. D. Hendy, P. J. Lockhart, and M. A. Steel. 1996. Corrected Parsimony, Minimum Evolution and Hadamard Conjugations. Systematic Biology 45: 593-603.        
             
             
             
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