Distinguished Professor David Penny

Distinguished Professor David Penny staff profile picture

Distinguished Professor

Institute of Fundamental Sciences

Telephone: +64 (06) 356 9099  ext. 84710
Email: 

Research Expertise

Research Interests

Biology

Thematics

Resource Development and Management

Area of Expertise

Field of Research Codes
Biological Sciences (060000)

Research Projects

Completed Projects

Project Title: Genome-scale plant phylogeny and the challenge of symmetric sequence

The research will gain a better understanding of plant phylogeny ¿ the development of a species over time as contrasted with the development of an individual. By measuring the impact of lineage-species molecular evolution for a range of time scales and gain a better understanding of deep plant phylogeny.
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Date Range: 2006 - 2009

Funding Body: Royal Society of New Zealand

Project Team:

Project Title: From Genomics to properties of the last Eukaryote common ancestor

Eukaryotes show a tremendous diversity of lifestyles, from plants and fungi that make all necessary chemical compounds from only very basic food sources, to animals that acquire many essential amino acids and enzyme cofactors (vitamins) by consuming other organisms. But which came first? The nature and origins of the earliest complex unicellular eukaryotes remains a mystery, and one with deep implications for the history of life on earth. We are using new genomic sequences from every group of eukaryotics to test information about the biosynthetic capabilities of two key early ancestors: (i) the last common ancestor of all modern eukaryotes; and (ii) the ancestral cell that engulfed the mitochondrion. These results will help resolve some of the most central questions of the origins of complex life. Our immediate goal is to reconstruct the biosynthetic enzymes present in early ancestors of all eukaryotes. The longer-term goal is to put real biology into genomics (or vice versa): to harness comparative genomics to yield useful information about the life history and cell biology of organisms.
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Date Range: 2011 - 2014

Funding Body: Marsden Fund - Full

Project Team:

Research Outputs

Creative Work

Penny, ED., Collins, L., & Shepherd, L.Ever wondered. [Video]. TV7
[Film or Video]Authored by: Penny, E.

Book

Daly, T., Penny, E., & Chen, X. (2011). How old are RNA networks?. In LJ. Collins (Ed.) RNA infrastructure and networks. (pp. 255 - 273). Texas, United States: Landes Bioscience and Springer
[Chapter]Authored by: Penny, E.
Read Abstract: abstract icon

Penny, E. (2010). Charles Darwin as a theoretical and mechanistic biologist. In D. Galloway, & J. Timmins (Eds.) Aspects of Darwin: A New Zealand celebration. (pp. 120 - 145). Dunedin: The friends of the Knox College Library
[Chapter]Authored by: Penny, E.

Penny, ED., & Collins, LJ. (2010). Evolutionary genomics leads the way. In . Gustavo Caetano Anolles (Ed.) Evolutionary Genomics and Systems Biology. (pp. 3 - 16). New Jersey: Wiley-VCH
[Chapter]Authored by: Penny, E.
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Penny, ED. (2008). Molecular evolution: Introduction. In DN. Cooper, & H. Kehrer-Sawatzki (Eds.) Handbook of Human Molecular Evolution. Chichester, UK: Wiley
[Chapter]Authored by: Penny, E.

Egel, R., & Penny, ED. (2008). On the origin of meiosis in eukaryotic evolution: Coevolution of meiosis and mitosis from feeble beginnings. In R. Egel, & DH. Lankenau (Eds.) Recombination and Meiosis: Models, Means, and Evolution. (pp. 249 - 288). Berlin, Germany: Springer
[Chapter]Authored by: Penny, E.

Penny, ED., Hendy, MD., & Holland, BR. (2007). Phylogenetics: Parsimony, networks, and distance methods. In DJ. Balding, M. Bishop, & C. Cannings (Eds.) Handbook of Statistical Genetics (3rd Ed.). (pp. 489 - 532). Chichester, UK: John Wiley and Sons
[Chapter]Authored by: Penny, E.

Penny, ED., & Meyer, A. (2006). DNA and the settlement of Polynesia. In KR. Howe (Ed.) Vaka Moana: Voyages of the ancestors - the discovery and settlement of the Pacific. (pp. 98 - 99). Auckland: David Bateman Ltd
[Chapter]Authored by: Penny, E.

Penny, DD., & Hendy, MD. (2001). Phylogenetics: Parsimony and distance methods. In DJ. Balding, M. Bishop, & C. Cannings (Eds.) Handbook of Statistical Genetics. (pp. 445 - 484). Chichester, UK: John Wiley & Sons
[Chapter]Authored by: Penny, E.

Penny, DD., & Hasegawa, M. (2001). Covarion model of molecular evolution. In S. Brenner, & JH. Miller (Eds.) Encyclopedia of Genetics. (pp. 473 - 477). San Diego, CA: Academic Press
[Chapter]Authored by: Penny, E.

Conference

Penny, ED. (2014, February). Loss of information at deeper divergences. Presented at 18th Annual New Zealand Phylogenetics Meeting. Waiheke Island.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED., & Harrison, A. (2013, November). Hepatitis B in the South Pacific. Presented at Communities of learning: riding with the changing tides. The centre, Manawatu Campus, Massey University.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2013, August). How many mutations between parents and offspring?. Presented at NZ Next Generation Sequencing Conference. Palmerston North.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2013, June). In silico resurrection of an ancestral protein in extant eukaryotes. Presented at Symposium - Molecules: Interaction & Evolution. University of Canterbury.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2013, November). Loss of information at deeper divergences. Presented at Phylomania 2013. University of Tasmania.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2013, February). Is it time to adopt an evolutionary species concept?. Presented at The interface of Mathematics and Biology - the 17th Annual New Zealand Phylogenomics Meeting. Mount Ruapehu, New Zealand.
[Conference Oral Presentation]Authored by: Penny, E.

Halliday, JS., Brown, A., Harrison, GL., Hunter, JG., Bendall, R., Penny, ED., . . . Dalton, HR. (2013). SEROPREVALENCE OF HEPATITIS E IN THE SOUTH PACIFIC ISLANDS. In Journal of Hepatology Vol. 58 (pp. S401 - S402). , The International Liver Congress™ 2013 – 48th Annual meeting of the European Association for the Study of the Liver: Elsevier
[Conference Abstract]Authored by: Penny, E.
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Penny, ED. (2011, November). What, if anything, is a fungus?. Presented at New Zealand Microbiological Society. Palmerston North.
[Conference Oral Presentation]Authored by: Penny, E.
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Penny, ED. (2010). The continuity of mind from great apes to humans. In International Conference on Mathematics Evolution and Development(pp. Unknown). : CAS-MPG Partner Institute for Computational Biology
[Conference Abstract]Authored by: Penny, E.
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Penny, ED. (2010, March). Integrating molecular evolution over different time scales. Presented at International Conference on Mathematics Evolution and Development. Shanghai, China.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2010, March). The continuity of mind, from great apes to humans. Presented at International Conference on Mathematics Evolution and Development. Shanghai, China.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2010). Integrating molecular evolution over different time scales. In International Conference on Mathematics Evolution and Development(pp. unknown). : CAS-MPG Partner Institute for Computational Biology
[Conference Abstract]Authored by: Penny, E.
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Gibb, GC., Penny, ED., & Trewick, SA. (2009). Niche stability in NZ birds: Integrating phylogeny, morphology, life history and paleontology. In GC. Gibb, D. Penny, & SA. Trewick (Eds.) Geogenes 4, Geological Society of New Zealand. (pp. 20 - 21).
[Conference Paper in Published Proceedings]Authored by: Penny, E., Trewick, S.

Gibb, GC., Goldberg, J., Trewick, SA., & Penny, D. (2008, February). The Multiscale Nature of Phylogeny: A case study using the New Zealand Pigeon (Kereru).. Presented at New Zealand Phylogenetics Conference. Whitianga, NZ.
[Conference Oral Presentation]Authored by: Penny, E., Trewick, S.

Penny, ED., Collins, LJ., & Chen, X. (2008). The ancestral eukaryote inferred from genomes. In Proceedings of the Genetics Society of AustralAsia 55th Annual Meeting(pp. 14 - 14). : GSA
[Conference Abstract]Authored by: Penny, E.

Penny, ED. (2008, June). Realism and Instrumentalism in theoretical models of molecular evolution. Presented at Mathmatics and Informatics in Evolution and Phylogeny. Hameau de I'Etoile.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED., Gibb, GC., Collins, LJ., & Biggs, PJ. (2008, June). Mass generation of new sequences and analysis. Presented at Evolution 2008. Minneapolis, Minnesota, United States of America.
[Conference Oral Presentation]Authored by: Biggs, P., Penny, E.

Penny, ED. (2008, May). Demonstrating the sufficiency of microevolutionary processes. Presented at From RNA to Humans: A Symposium on Evolution. Rockefeller University, New York, NY.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2008, March). Some applications of mathematics for phylogenetics. Presented at Adelaide Conference on Mathematical and Evolutionary Biology. Naracoorte Caves, South Australia.
[Conference Oral Presentation]Authored by: Penny, E.

Grievink, LS., Holland, BR., Hendy, MD., & Penny, ED. (2008). Lineage specific sequence evolution. In New Zealand Phylogenetics Conference 2008(pp. 17).
[Conference Abstract]Authored by: Penny, E.

Penny, ED. (2008). Questions. In New Zealand Phylogenetics Conference 2008(pp. 14).
[Conference Abstract]Authored by: Penny, E.

Penny, ED. (2008, February). Questions. Presented at New Zealand Phylogenetics Conference 2008. Whitianga, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Gibb, GC., Goldberg, J., Trewick, SA., & Penny, D. (2007, June). Pigeon evolution: integrating barcoding to the tree of life. Presented at Evolution 2007. Christchurch Convention Centre, Christchurch, NZ.
[Conference Oral Presentation]Authored by: Penny, E., Trewick, S.

Penny, ED.(2007). Deep mammal and bird divergences: Microevolution is sufficient for macroevolution. . Beijing, China
[Conference Paper]Authored by: Penny, E.

Penny, ED., & Collins, LJ. (2007). The RNA - infrastructure of the eukaryotic cell. In Proceedings of the 17th Queenstown Molecular Biology Meeting(pp. 41). : QMB
[Conference Abstract]Authored by: Penny, E.

Penny, ED. (2007, June). Using the tree, particularly of mammals and of birds, to study the question of the sufficiency of microevolutionary processes for explaining all of macroevolution. Presented at Satellite Workshop of the International Symposium for Evolutionary Biology in the 21st Century: Tracing Patterns of Evolution through the Tree of Life. Beijing, China.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2007, June). Multiscale processes in molecular evolution. Presented at Dumont D'Urville Workshop on Applied Evolutionary Bioinformatics. Kaikoura, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED. (2007, February). Evolution in four dimensions. Presented at Proteins: Structure, Function and Assembly in Health and Disease. Rotorua, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, ED., & Phillips, MJ.(2006). 'Nothing exists for one cause'; putting biology back into evolution. . Wellington, New Zealand
[Conference Other]Authored by: Penny, E.

Penny, ED. (2006, June). Why RNA? Why 4 nucleotides? Why proteins?. Presented at From Stars to Brains: Pathways to Consciousness in the Natural World. Canberra, ACT.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD., & Collins, LJ. (2004, September). RNA processing in the eukaryotic ancestor. Presented at International Conference on Bioinformatics 2004. The Aotea Centre, Auckland, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Gibb, GC., Kardailsky, O., Braun, E., & Penny, DD. (2004). Avian evolution using complete mitochondrial genome sequences. 7th New Zealand Molecular Ecology Conference. (pp. 6 - 6). Palmerston North, NZ
[Conference Paper in Published Proceedings]Authored by: Penny, E.

Penny, DD., Matheson, JW., & Collins, LJ. (2004, June). RNA processing in the eukaryotic ancestor. Presented at Society for Molecular Biology and Evolution Annual Meeting. Pennsylvania State University, University Park, PA.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2004, September). RNA processing in the eukaryotic ancestor. Presented at 3rd International Conference on Bioinformatics. Auckland, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2004, July). Where next in phylogeny?. Presented at Phylogenetic Combinatorics and Applications 2004. Uppsala University, Uppsala, Sweden.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2004, February). Where next in phylogeny?. Presented at 8th Annual New Zealand Phylogenetics Meeting. Whakapapa Village, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Collins, LJ., Shi, H., O'Toole, PW., Penny, DD., & Rakonjac, J. (2004). Secondary structure modelling of the replication initiator RNA pE1 of the prolate phages with the help of alignments of 95 pE1 sequences. Poster session presented at the meeting of New Zealand Society for Microbiology Annual Conference 2004. Palmerston North, NZ
[Conference Poster]Authored by: Penny, E., Rakonjac, J.

Collins, LJ., Poole, AM., Sogin, ML., & Penny, DD. (2003, February). Using ancestral sequences to uncover potential gene homologs. Presented at New Zealand Bioinformatics Conference 2003. Te Papa, Wellington, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Collins, LJ., Macke, TJ., & Penny, DD. (2003). Searching for ncRNAs in protist genomes. Poster session presented at the meeting of European Conference on Computational BIology in conjunction with the French National Conference on Bioinformatics 2003. Paris, France
[Conference Poster]Authored by: Penny, E.

Collins, LJ., Macke, TJ., & Penny, DD. (2003, September). Searching for ncRNAs in protist genomes. Presented at European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics 2003. Paris, France.
[Conference Oral Presentation]Authored by: Penny, E.

Collins, LJ., Poole, AM., Sogin, ML., & Penny, DD. (2003). Using ancestral sequences to uncover potential gene homologs. Poster session presented at the meeting of Pacific Symposium on Biocomputing 2003. Lihue, HI
[Conference Poster]Authored by: Penny, E.

Phillips, MJ., McClenachan, P., Ota, R., & Penny, DD. (2002, June). Integrating molecular, palaeontological and ecological data on mammalian interordinal diversification. Presented at Molecular Evolution: Evolution, Genomics, Bioinformatics. Sorrento (Naples), Italy.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2001, February). 10 years to sequence it - 100 years to understand it. Presented at Symposium for Bioinformatics and Computational Biology. City Campus, University of Auckland.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2001, February). Another major challenge to the classical multiregional model?. Presented at Doom01 - 5th annual New Zealand meeting on the interface of mathematics and biology in the study of phylogeny and molecular evolution. Whakapapa Village, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Penny, DD. (2001, June). Consequences of the continuity between the human and biological worlds. Presented at Joint ANZCCART/NAEAC Conference. Hamilton, NZ.
[Conference Oral Presentation]Authored by: Penny, E.

Watson, EE., Easteal, S., & Penny, DD. (2001). Homo genus: A review of the classification of humans and the great apes. 1998 Dual Congress of the International Association of Human Biologists and International Association for the Study of Human Palaeontology. (pp. 307 - 318). Firenze, Italy
[Conference Paper in Published Proceedings]Authored by: Penny, E.

Phillips, MJ., Lin, O., & Penny, DD. (2000). The complete mitochondrial genomes of two marsupials, a bandicoot and the brushtail possum. (pp. unpaged). , Society for Molecular Biology and Evolution and the American Genetic Association Joint Meeting: Society for Molecular Biology and Evolution
[Conference Abstract]Authored by: Penny, E.

Phillips, MJ., & Penny, DD. (2000). Mesozoic mammals: Phylogenetic instability of ecologically-divergent taxa. Poster session presented at the meeting of Evolution 2000. Indiana University, Bloomington, IN
[Conference Poster]Authored by: Penny, E.

Phillips, MJ., Lin, O., & Penny, DD. (2000, June). The complete mitochondrial genomes of two marsupials, a bandicoot and the brushtail possum. Presented at Society for Molecular Biology and Evolution (SMBE) and the American Genetic Association (AGA) Joint Meeting. Yale University, New Haven, CT.
[Conference Oral Presentation]Authored by: Penny, E.

Chor, B., Hendy, MD., Holland, BR., & Penny, DD. (2000). Multiple maxima of likelihood in phylogenetic trees: An analytic approach. In R. Shamir, S. Miyano, S. Istrail, P. Pevzner, & MW. Eds (Eds.) 4th International Conference on Computational Molecular Biology. (pp. 108 - 117). New York, NY
[Conference Paper in Published Proceedings]Authored by: Penny, E.

Journal

Robins, JH., Tintinger, V., Aplin, KP., Hingston, M., Matisoo-Smith, E., Penny, ED., . . . Lavery, SD. (2014). Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species. PLoS One. 9(5), 1-18
[Journal article]Authored by: Penny, E.
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Penny, ED. (2014). Rewriting Evolution—“Been There, Done That”. Genome Biology and Evolution. 5(5), 819-821 Retrieved from http://gbe.oxfordjournals.org/content/5/5.toc
[Journal article]Authored by: Penny, E.
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Daly, TK., Sutherland-Smith, AJ., & Penny, D. (2013). Beyond BLASTing: Tertiary and quaternary structure analysis helps identify major vault proteins. Genome Biology and Evolution. 5(1), 217-232
[Journal article]Authored by: Penny, E., Sutherland-Smith, A.

Shavit-Grievink, L., Penny, ED., & Holland, BR. (2013). Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice. Genome Biology and Evolution. 5, 681-687 Retrieved from http://gbe.oxfordjournals.org/content/5/4.toc
[Journal article]Authored by: Penny, E.
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Gibbs, G., Kennedy, M., & Penny, ED. (2013). Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability. Molecular Phylogenetics and Evolution. 68, 229-238 Retrieved from http://www.sciencedirect.com/science/article/pii/S1055790313001309
[Journal article]Authored by: Penny, E.
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Harrison, GL., Pryor, J., Malani, J., Supuri, M., Masta, A., Teriboriki, B., . . . Klenerman, P. (2013). Infection frequency of hepatitis C virus and IL28B haplotypes in Papua New Guinea, Fiji, and Kiribati. PLoS One. 8(8) Retrieved from http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066749
[Journal article]Authored by: Penny, E.
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Han, J., Collins, LJ., Biggs, PJ., White, WT., & Penny, ED. (2013). Are Signature Proteins the Key to Evaluating Eukaryotic Phylogeny?. Review of bioinformatics and biometrics. 2(2), 37-44 Retrieved from http://www.seipub.org/rbb/paperInfo.aspx?ID=6248
[Journal article]Authored by: Biggs, P., Penny, E.
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Zhong, B., Liu, L., Yan, Z., & Penny, ED. (2013). Origin of land plants using the multispecies coalescent model. Trends in Plant Science. 18(9), 492-495 Retrieved from http://www.cell.com/trends/plant-science/abstract/S1360-1385(13)00084-8
[Journal article]Authored by: Penny, E.
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White, WTJ., Zhong, B., & Penny, ED. (2013). Beyond Reasonable Doubt: Evolution from DNA Sequences. PLoS One. 8(8) Retrieved from http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069924
[Journal article]Authored by: Penny, E.
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Zhong, B., Xi, Z., Goremykin, VZ., Fong, R., McLenachan, PA., Novis, PM., . . . Penny, ED. (2013). Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. Molecular Biology and Evolution. 31(1), 177-183 Retrieved from http://mbe.oxfordjournals.org/content/31/1/177.abstract?sid=539ec6f1-9909-4b1a-826e-5ed23e02b4b0
[Journal article]Authored by: Penny, E.
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Daly, TK., Sutherland-Smith, AJ., & Penny, D. (2013). In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes. Genome Biology and Evolution. 5(8), 1567-1583
[Journal article]Authored by: Penny, E., Sutherland-Smith, A.

Tuffley, C., Timothy, W., White, J., Hendy, MD., & Penny, D. (2012). Correcting the apparent mutation rate acceleration at shorter time scales under a jukes-cantor model. Molecular Biology and Evolution. 29(12), 3703-3709
[Journal article]Authored by: Penny, E., Tuffley, C.

Kurland, CG., Collins, LJ., & Penny, D. (2007). Response [6]. Science. 316(5824), 543-543
[Journal article]Authored by: Penny, E.

Collins, L., & Penny, D. (2006). Investigating the intron recognition mechanism in eukaryotes. Molecular Biology and Evolution. 23(5), 901-910
[Journal article]Authored by: Penny, E.

Penny, ED. (2011). Darwin’s theory of descent with modification, versus the biblical tree of life. Plos Biology. 9(7), 1-4
[Journal article]Authored by: Penny, E.
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Penny, ED. (2010). Life as a natural property of matter. The Journal of Cosmology. 8, 24-26
[Journal article]Authored by: Penny, E.

Penny, E. (2010). 20 points on the structure and testability of Darwin's theory. Biology International. 47, 11-35
[Journal article]Authored by: Penny, E.
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Corser, CA., McLenachan, PA., Pierson, M., Harrison, GLA., & Penny, D. (2012). The Q2 Mitochondrial Haplogroup in Oceania. PLoS One. 7(12), 1-8 Retrieved from http://www.plosone.org/article/info%3Adoi/10.1371/journal.pone.0052022
[Journal article]Authored by: Penny, E.
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Saurabh, K., Holland, BR., Gibb, GC., & Penny, D. (2012). Gaps: An Elusive Source of Phylogenetic Information. Systematic Biology. 61(6), 1075-1082
[Journal article]Authored by: Penny, E.

Chen, XS., Penny, D., & Collins, LJ. (2011). Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. BMC Genomics. 12
[Journal article]Authored by: Penny, E.

Harrison, GL., Lemey, P., Hurles, M., Moyes, C., Horn, S., Pryor, J., . . . Shapiro, B. (2011). Genomic analysis of Hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses. 3(2), 83-101
[Journal article]Authored by: Penny, E.
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Penny, E. (2011). Taiwan and the origin of Polynesians. New Zealand Science Teacher. 126, 21-23
[Journal article]Authored by: Penny, E.

Penny, ED. (2010). Allan Wilson and testing the Out of Africa model for human origins. NZ Science Teacher. (125), 8-11
[Journal article]Authored by: Penny, E.

McComish, BJ., Hills, SFK., Biggs, PJ., & Penny, D. (2010). Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biology and Evolution. 2(1), 410-424
[Journal article]Authored by: Biggs, P., Hills, S., Penny, E.

Phillips, MJ., Gibb, GC., Crimp, EA., & Penny, D. (2010). Tinamous and moa flock together: Mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Systematic Biology. 59(1), 90-107
[Journal article]Authored by: Penny, E.

Grievink, LS., Penny, ED., Hendy, MD., & Holland, BR. (2010). Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree. Systematic Biology. 59, 288-297
[Journal article]Authored by: Penny, E.
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Steele, M., & Penny, ED. (2010). Origins of life: Common ancestry put to the test. Nature. 465, 168-169
[Journal article]Authored by: Penny, E.
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Gibb, GC., & Penny, D. (2010). Two aspects along the continuum of pigeon evolution: A South-Pacific radiation and the relationship of pigeons within Neoaves. Molecular Phylogenetics and Evolution. 56(2), 698-706
[Journal article]Authored by: Penny, E.

Penny, ED. (2010). The continuity of mind from great apes to humans. New Zealand Science Review. 67(2), 63-69
[Journal article]Authored by: Penny, E.
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Penny, ED. (2009). Charles Darwin as a theoretical biologist in the mechanistic tradition. Trends in Evolutionary Biology. 1(e1), 1-10
[Journal article]Authored by: Penny, E.
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Pratt, RC., Gibb, GC., Morgan-Richards, M., Phillips, MJ., Hendy, MD., & Penny, D. (2009). Toward resolving deep neoaves phylogeny: Data, signal enhancement, and priors. Molecular Biology and Evolution. 26(2), 313-326
[Journal article]Authored by: Morgan-Richards, M., Penny, E.

Collins, LJ., Kurland, CG., Biggs, P., & Penny, D. (2009). The modern RNP world of eukaryotes. Journal of Heredity. 100(5), 597-604
[Journal article]Authored by: Biggs, P., Penny, E.

Chen, XS., Collins, LJ., Biggs, PJ., & Penny, D. (2009). High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis. GENOME BIOLOGY AND EVOLUTION. 1, 165-175
[Journal article]Authored by: Biggs, P., Penny, E.
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Penny, ED., hoeppner, MP., Poole, AM., & Jeffares, DC. (2009). An overview of the introns-first theory. Journal of Molecular Evolution. 69(5), 527-540
[Journal article]Authored by: Penny, E.
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Waddell, PJ., Ota, R., & Penny, ED. (2009). Measuring fit of sequence data to phylogenetic model: Gain of power using marginal tests. Journal of Molecular Evolution. 69(4), 289-299
[Journal article]Authored by: Penny, E.
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Penny, ED. (2009). Charles Darwin as a scientist. New Zealand Science Review. 66(3), 87-92
[Journal article]Authored by: Penny, E.

De Nooijer, S., Holland, BR., & Penny, ED. (2009). The emergence of predators in early life: There was no Garden of Eden. PLoS One. 4(6), 1-10
[Journal article]Authored by: Penny, E.
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Collins, LJ., & Penny, D. (2009). The RNA infrastructure: dark matter of the eukaryotic cell?. Trends in Genetics.
[Journal article]Authored by: Penny, E.

Shavit Grievink, L., Penny, ED., Hendy, MD., & Holland, BR. (2008). LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evolutionary Biology. 8, 1-6
[Journal article]Authored by: Penny, E.

Chen, XS., White, WTJ., Collins, LJ., & Penny, D. (2008). Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS ONE. 3(8)
[Journal article]Authored by: Penny, E.

Irimia, M., Rukov, JL., Penny, ED., Vinther, J., Garcia Fernandez, J., & Roy, SW. (2008). Origin of introns by 'intronization' of exonic sequences. Trends in Genetics. 24(8), 378-381
[Journal article]Authored by: Penny, E.

Morgan-Richards, M., Trewick, SA., Bartosch-Harlid, A., Kardailsky, O., Phillips, MJ., McLenachan, P., . . . Penny, D. (2008). Bird evolution: Testing the Metaves clade with six new mitochondrial genomes. BMC Evolutionary Biology. 8(20) Retrieved from http://www.biomedcentral.com/1471-2148/8/20
[Journal article]Authored by: McLenachan, P., Morgan-Richards, M., Penny, E., Trewick, S.
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Irimia, M., Rukov, JL., Penny, ED., Garcia Fernandez, J., Vinther, J., & Roy, SW. (2008). Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Molecular Biology and Evolution. 25(2), 375-382
[Journal article]Authored by: Penny, E.

Penny, ED., White, W., Hendy, MD., & Phillips, MJ. (2008). A bias in ML estimates of branch lengths in the presence of multiple signals. Molecular Biology and Evolution. 25(2), 239-242
[Journal article]Authored by: Penny, E.

Penny, E., & Phillips, M. (2007). Evolutionary biology: Mass survivals. Nature. 446(7135), 501-502
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Kurland, CG., Collins, LJ., & Penny, ED. (2007). The evolution of Eukaryotes: Response. Science. 316(5824), 542-543
[Journal article]Authored by: Penny, E.

Gibb, GC., Kardailsky, O., Kimball, RT., Braun, EL., & Penny, D. (2007). Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Molecular Biology and Evolution. 24(1), 269-280
[Journal article]Authored by: Penny, E.

Roy, SW., & Penny, ED. (2007). Patterns of intron loss and gain in plants: Intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Molecular Biology and Evolution. 24(1), 171-181
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Slack, KE., Delsuc, F., Mclenachan, PA., Arnason, U., & Penny, D. (2007). Resolving the root of the avian mitogenomic tree by breaking up long branches. Molecular Phylogenetics and Evolution. 42(1), 1-13
[Journal article]Authored by: McLenachan, P., Penny, E.

Poole, A., & Penny, ED. (2007). Evaluating hypotheses for the origin of eukaryotes. BioEssays. 29(1), 74-84
[Journal article]Authored by: Penny, E.
Read Abstract: abstract icon

Woodhams, MD., Stadler, PF., Penny, D., & Collins, LJ. (2007). RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evolutionary Biology. 7(S13), 1-13 Retrieved from http://link.springer.com/article/10.1186/1471-2148-7-S1-S13#
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Chor, B., Hendy, MD., & Penny, ED. (2007). Analytic solutions for three taxon ML trees with variable rates across sites. Discrete Applied Mathematics. 155(4), 750-758
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Roy, SW., & Penny, ED. (2007). Evolutionary conservation of UTR intron boundaries in Cryptococcus. Molecular Biology and Evolution. 24(5), 1140-1148
[Journal article]Authored by: Penny, E.
Read Abstract: abstract icon

Poole, A., & Penny, ED. (2007). Testing hypotheses without considering predictions: Response to Dagan and Martin. BioEssays. 29, 611-614
[Journal article]Authored by: Penny, E.

Shavit, L., Penny, ED., Hendy, MD., & Holland, BR. (2007). The problem of rooting rapid radiations. Molecular Biology and Evolution. 24(11), 2400-2411
[Journal article]Authored by: Penny, E.

Irimia, M., Rukov, JL., Penny, ED., & Roy, SW. (2007). Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evolutionary Biology. 7(188)
[Journal article]Authored by: Penny, E.

Penny, ED. (2007). Charles Darwin, evolution simple and testable. NZ Science Teacher. 116, 23-27
[Journal article]Authored by: Penny, E.

Roy, SW., & Penny, ED. (2007). Intron length distributions and gene prediction. Nucleic Acids Research. 35(14), 4737-4742
[Journal article]Authored by: Penny, E.

White, WT., Hills, SF., Gaddam, R., Holland, BR., & Penny, D. (2007). Treeness triangles: Visualizing the loss of phylogenetic signal. Molecular Biology and Evolution. 24(9), 2029-2039
[Journal article]Authored by: Hills, S., Penny, E.

Roy, SW., & Penny, ED. (2007). Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Molecular Biology and Evolution. 24(9), 1926-1933
[Journal article]Authored by: Penny, E.

Roy, SW., & Penny, ED. (2007). On the incidence of intron loss and gain in paralogous gene families. Molecular Biology and Evolution. 24(8), 1579-1581
[Journal article]Authored by: Penny, E.

Irimia, M., Maeso, I., Penny, ED., Garcia Fernandez, J., & Roy, SW. (2007). Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Molecular Biology and Evolution. 24(8), 1604-1607
[Journal article]Authored by: Penny, E.

Chen, XS., Rozhdestvensky, TS., Collins, LJ., Schmitz, J., & Penny, D. (2007). Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research. 35(14), 4619-4628
[Journal article]Authored by: Penny, E.

Roy, SW., & Penny, ED. (2007). A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Molecular Biology and Evolution. 24(7), 1447-1457
[Journal article]Authored by: Penny, E.

Irimia, M., Penny, ED., & Roy, SW. (2007). Coevolution of genomic intron number and splice sites. Trends in Genetics. 23(7), 321-325
[Journal article]Authored by: Penny, E.

Poole, A., & Penny, ED. (2007). Engulfed by speculation. Nature. 447(7147), 913-913
[Journal article]Authored by: Penny, E.

Penny, ED., & Phillips, MJ. (2007). Mass survivals. Nature. 446(7135), 501-502
[Journal article]Authored by: Penny, E.

Penny, E. (2006). What are the major principles that controlled the origin of life?. Nature. 442(7104), 745-746
[Journal article]Authored by: Penny, E.
Read Online: DOI icon

Mourier, T., Penny, ED., & Jeffares, DC. (2006). The biology of intron gain and loss. Trends in Genetics. 22(1), 16-22
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Phillips, M., McLenachan, P., Down, C., Gibb, G., & Penny, D. (2006). Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Systematic Biology. 55(1), 122-137
[Journal article]Authored by: McLenachan, P., Penny, E.

Slack, KE., Jones, CM., Ando, T., Harrison, GL., Fordyce, RE., Arnason, U., . . . Penny, ED. (2006). Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Molecular Biology and Evolution. 23(6), 1144-1155
[Journal article]Authored by: Penny, E.
Read Online: DOI icon

Roy, SW., & Penny, ED. (2006). Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Research. 16, 1270-1275
[Journal article]Authored by: Penny, E.
Read Abstract: abstract icon

Pierson, MJ., Martinez-Arias, R., Holland, BR., Gemmell, NJ., Hurles, ME., & Penny, D. (2006). Deciphering past human population movements in Oceania: Provably optimal trees of 127 mtDNA genomes. Molecular Biology and Evolution. 23(10), 1966-1975
[Journal article]Authored by: Penny, E.

Matheson, JW., Rich, FJ., Cohet, C., Grimwood, K., Huang, QS., Penny, ED., . . . Kirman, JR. (2006). Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years. Journal of Medical Virology. 78(10), 1354-1364
[Journal article]Authored by: Penny, E.

Penny, ED. (2006). Darwin: The indelible stamp. New Zealand Science Review. 63(2), 48-50
[Journal article]Authored by: Penny, E.

Roy, SW., & Penny, ED. (2006). Smoke without fire: Most reported cases of intron gain in nematodes instead reflect intron losses. Molecular Biology and Evolution. 23(12), 2259-2262
[Journal article]Authored by: Penny, E.

Penny, ED. (2006). Why the resistance?. EMBO Reports. 7(10), 975-975
[Journal article]Authored by: Penny, E.

Kurland, CG., Collins, LJ., & Penny, D. (2006). Genomics and the irreducible nature of eukaryote cells. Science. 312(5776), 1011-1014
[Journal article]Authored by: Penny, E.

Roy, SW., Irimia, M., & Penny, ED. (2006). Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Molecular Biology and Evolution. 23(10), 1824-1827
[Journal article]Authored by: Penny, E.

Penny, ED. (2006). Defining moments: What are the major principles that controlled the origin of life?. Nature. 442(7104), 745-746
[Journal article]Authored by: Penny, E.

Clarke, AC., Burtenshaw, K., McLenachan, TA., Erickson, DL., & Penny, DD. (2005). Reconstructing the origins and dispersal of the polynesian bottle gourd (Lagenaria siceraria). Molecular Biology and Evolution. 23(1), 1-27
[Journal article]Authored by: Penny, E.

Collins, LJ., & Penny, DD. (2005). Investigating the intron recognition mechanism in eukaryotes. Molecular Biology and Evolution.
[Journal article]Authored by: Penny, E.

Penny, DD. (2005). An interpretative review of the origin of life research. Biology and Philosophy. 20, 633-671
[Journal article]Authored by: Penny, E.

Holland, BR., Huber, KT., Penny, DD., & Moulton, V. (2005). The MinMax Squeeze: Guaranteeing a minimal tree for population data. Molecular Biology and Evolution. 22(2), 235-242
[Journal article]Authored by: Penny, E.

Lockhart, PJ., & Penny, D. (2005). The place of Amborella within the radiation of angiosperms. Trends in Plant Science. 10(5), 201-202
[Journal article]Authored by: Lockhart, P., Penny, E.

Collins, L., & Penny, D. (2005). Complex spliceosomal organization ancestral to extant eukaryotes. Molecular Biology and Evolution. 22(4), 1053-1066
[Journal article]Authored by: Penny, E.

Phillips, MJ., Delsuc, F., & Penny, DD. (2004). Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution. 21(7), 1455-1458
[Journal article]Authored by: Penny, E.

Harrison, AL., McLenachan, TA., Phillips, MJ., Slack, KE., Cooper, A., & Penny, DD. (2004). Four new avian mitochondrial genomes help get to basic evolutionary questions in the late Cretacous. Molecular Biology and Evolution. 21(6), 974-983
[Journal article]Authored by: Penny, E.

Penny, DD., & Phillips, MJ. (2004). The rise of birds and mammals: Are microevolutionary processes sufficient for macroevolution?. Trends in Ecology and Evolution. 19(10), 516-522
[Journal article]Authored by: Penny, E.

Penny, DD. (2004). Darwin: I wish I were a botanist. TRENDS in Ecology and Evolution. 19(2), 67-68
[Journal article]Authored by: Penny, E.

Collins, LJ., & Penny, DD. (2004). Lost in the RNA world - The genomics of ncRNA. New Zealand Bioscience. 13(1), 38-40 Retrieved from http://www.nzms.org.nz/NZBiosciences/Backissues.html
[Journal article]Authored by: Penny, E.

Penny, DD. (2004). Life, the universe and everything. EMBO Reports. 5(2), 134-134
[Journal article]Authored by: Penny, E.

Penny, DD. (2004). Phylogeny in the comfort zone. Systematic Biology. 53(4), 669-670
[Journal article]Authored by: Penny, E.

Collins, LJ., Macke, TJ., & Penny, D. (2004). Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif. Journal of Intergative Bioinformatics. 1, 1-16 Retrieved from http://journal.imbio.de/article.php?aid=6
[Journal article]Authored by: Penny, E.
Read Online: DOI icon Read Abstract: abstract icon

Penny, DD. (2004). Our relative genetics. Nature. 427, 208-209
[Journal article]Authored by: Penny, E.

Steel, M., & Penny, DD. (2004). Two further links between MP and ML under the Poisson model. Applied Mathematics Letters. 17, 785-790
[Journal article]Authored by: Penny, E.

Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F., Gelius-Dietrich, G., . . . Martin, W. (2004). A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Molecular Biology and Evolution. 21(9), 1643-1660
[Journal article]Authored by: Lockhart, P., Penny, E.

Delsuc, F., Phillips, MJ., & Penny, DD. (2003). Comment on ''hexapod origins: Monophyletic or paraphyletic?''. Science. 301(5639)
[Journal article]Authored by: Penny, E.

Phillips, MJ., & Penny, DD. (2003). The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution. 28(2), 171-185
[Journal article]Authored by: Penny, E.

Poole, AM., Phillips, MJ., & Penny, DD. (2003). Prokaryote and eukaryote evolvability. BioSystems. 69(2-3), 163-185
[Journal article]Authored by: Penny, E.

Collins, L., Poole, AM., & Penny, D. (2003). Using ancestral sequences to uncover potential gene homologues. Applied Bioinformatics. 2(Supplement 3), S85-S95
[Journal article]Authored by: Penny, E.
Read Abstract: abstract icon

Ota, R., & Penny, DD. (2003). Estimating changes in mutational mechanisms of evolution. Journal of Molecular Evolution. 57(1), S233-S240
[Journal article]Authored by: Penny, E.

Lin, YH., McLenachan, PA., Gore, AR., Phillips, MJ., Ota, R., Hendy, MD., . . . Penny, DD. (2002). Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution. 19(12), 2060-2070
[Journal article]Authored by: Penny, E.

Penny, DD. (2002). A candle in the dark. EMBO Reports. 3(2), 1-1
[Journal article]Authored by: Penny, E.

Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., . . . Penny, DD. (2002). Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proceedings of the National Academy of Sciences. 99(19), 12246-12251
[Journal article]Authored by: Penny, E.

Lin, YH., Waddell, PJ., & Penny, DD. (2002). Pika and Vole mitochondrial genomes add support to both rodent monophyly and glires. Gene. 294, 119-129
[Journal article]Authored by: Penny, E.

Penny, DD., Murray McIntosh, RP., & Harrison, AL. (2002). Estimating the number of females in the founding population of New Zealand: Analysis of mtDNA variation. Journal of the Polynesian Society. 111(3), 207-221
[Journal article]Authored by: Penny, E.

Huber, KT., Langton, M., Penny, DD., Moulton, V., & Hendy, MD. (2002). Spectronet: A package for computing spectra and median networks. Applied BioInformatics. 1(3), 159-161
[Journal article]Authored by: Penny, E.

Phillips, MJ., Lin, YH., Harrison, GL., & Penny, DD. (2001). Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials. Proceedings of the Royal Society B: Biological Sciences. 268(1475), 1533-1538
[Journal article]Authored by: Penny, E.

Penny, DD. (2001). Genetic Engineering should be evaluated in same way as any other process - assessing benefits and risks. Laboratory News. 2, 19-19
[Journal article]Authored by: Penny, E.

Poole, AM., Penny, DD., & Sjoberg, BM. (2001). Confounded cytosine! Tinkering and the evolution of DNA. Nature Reviews: Molecular Cellular Biology. 2, 147-151
[Journal article]Authored by: Penny, E.

Lin, YH., & Penny, DD. (2001). Implications for bat evolution from two new complete mitochondrial genomes. Molecular Biology and Evolution. 18(4), 684-688
[Journal article]Authored by: Penny, E.

Penny, DD., & Holmes, SC. (2001). Doom01: Biological mathematics in evolutionary processes. Trends in Ecology and Evolution. 16(6), 275-276
[Journal article]Authored by: Penny, E.

Penny, DD. (2001). That was the name thereof. EMBO Reports. 2(4), 269-269
[Journal article]Authored by: Penny, E.

Poole, AM., & Penny, DD. (2001). Does endo-symbiosis explain the origin of the nucleus?. Nature Cell Biology. 3, 173-173
[Journal article]Authored by: Penny, E.

Penny, DD. (2001). The electrifying Australian: A review of Platypus - The extraordinary story of how a curious creature baffled the world. Nature. 412, 857-857
[Journal article]Authored by: Penny, E.

Penny, DD., McComish, BJ., Charleston, MA., & Hendy, MD. (2001). Mathematical elegance with biochemical realism: The covarion model of molecular evolution. Journal of Molecular Evolution. 53, 711-723
[Journal article]Authored by: Penny, E.

Bromham, LD., Penny, DD., Rambaut, A., & Hendy, MD. (2000). The power of relative rates tests depends on the data. Journal of Molecular Evolution. 50, 296-301
[Journal article]Authored by: Penny, E.

McConkey, EH., Fouts, R., Goodman, M., Nelson, D., Penny, DD., Ruvolo, M., . . . Wise, S. (2000). Proposal for a human genome evolution project. Molecular Phylogenetics and Evolution. 15(1), 1-4
[Journal article]Authored by: Penny, E.

Moulton, V., Zuker, M., Steel, MA., Pointon, RF., & Penny, DD. (2000). Metrics on RNA secondary structures. Journal of Computational Biology. 7(1/2), 277-292
[Journal article]Authored by: Penny, E.

Collins, LJ., Moulton, V., & Penny, D. (2000). Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. Journal of Molecular Evolution. 51(3), 194-204
[Journal article]Authored by: Penny, E.

Penny, DD. (2000). Throwim way leg. Embo Reports. 1(3), 215-216
[Journal article]Authored by: Penny, E.

Poole, AM., Penny, DD., & Sjoberg, BM. (2000). Methyl-RNA: An evolutionary bridge between RNA and DNA?. Chemistry and Biology. 7, 207-216
[Journal article]Authored by: Penny, E.

Moulton, V., Gardner, PP., Pointon, RF., Creamer, LK., Jameson, GB., & Penny, D. (2000). RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution. 51(4), 416-421
[Journal article]Authored by: Jameson, G., Penny, E.

Other

Penny, ED. (2013, May). Greek and Roman "science". In Classical world: A programme of seminars. Presented at Palmerston North, New Zealand.
[Oral Presentation]Authored by: Penny, E.
Read Abstract: abstract icon

Penny, D. (2013, May). Greek and Roman 'science'. In Classical World Programme of Seminars: University of the Third Age [U3A Manawatu], Palmerston North, New Zealand.
[Oral Presentation]Authored by: Penny, E.
Read Abstract: abstract icon

Penny, D. (2013, April). The pleasure and the frustration of DNA sequencing: The new revolution in biology. In Science for All, University of the Third Age [U3A], Palmerston North, New Zealand.
[Oral Presentation]Authored by: Penny, E.

Jameson, G., Edwards, P., & Penny, E. (2010, May). Origins of life. Presented at Radio New Zealand.
[Oral Presentation]Authored by: Edwards, P., Jameson, G., Penny, E.

Phillips, MJ., & Penny, ED. (2010). Mammalian phylogeny. (pp. 1 - 8). John Wiley & Sons Ltd
[Other]Authored by: Penny, E.

Penny, ED. (2010). DNA suggests Moa once flew. (pp. 1 - 1). Massey University
[Other]Authored by: Penny, E.

Penny, ED. (2006, April). From the RNA world to the origin of Eukaryotes. In The Kurland Symposium. Presented at Uppsala University, Sweden.
[Oral Presentation]Authored by: Penny, E.

Penny, ED. (2008). Molecular evolution: Introduction. John Wiley & Sons
[Other]Authored by: Penny, E.

Penny, ED. (2006, October). Estimating the size of the Maori founding population of New Zealand. In An Evening for Mathematics and Statistics Teachers and University Mathematics and Statistics Staff. Presented at Massey University, Palmerston North, NZ.
[Oral Presentation]Authored by: Penny, E.

Penny, ED. (2006). The next extinction?. Radio NZ
[Other]Authored by: Penny, E.

Collins, LJ., & Penny, DD. (2005, June). Aspects of genomic complexity in ancestral eukaryotes. : Society for Molecular Biology and Evolution.
[Oral Presentation]Authored by: Penny, E.

Penny, DD. (2002, July). The MinMax Squeeze: proving trees minimal for large numbers of closely related sequences. : Massey University.
[Oral Presentation]Authored by: Penny, E.

Supervision and Teaching

Papers Coordinated

Current Postgraduate Supervision

Supervisor of:

  • Simon Cox - PhD
    Plastid Genes Across the Great Divide
  • Toni Daly - PhD
    The Vault Ribonucleoprotein Particles

Completed Postgraduate Supervision

Supervisor of:

  • 2014 - Bojian Zhong- PhD
    Phylogenomics and Plant Evolution
  • 2013 - Bennet McComish- PhD
    Exploring biological sequence space: Selected problems in sequence analysis and phylogenetics
  • 2012 - Kerryn Slack- PhD
    Avian Phylogeny and & Divergence Times based on Mitogenomic Sequences
  • 2010 - Gillian Gibb- PhD
    Birds in a tree: A journey through avian phylogeny with particular emphasis on the birds of New Zealand
  • 2009 - Ang McGaughran- PhD
    Polar evolution: Molecular genetic and physiological parameters of Antartic arthropod populations
  • 2009 - Klaus Schliep- PhD
    Statistical phylogenetics
  • 2009 - Renae Pratt- PhD
    Patterns and processes in animal evoluation: Molecular phylogenetics of Southern Hemisphere fauna
  • 2009 - Andrew Clarke- PhD
    Origins and Dispersal of the Sweet Potato and Bottle Gourd in Oceania: Implications for Prehistoric Human Mobility
  • 2008 - Xiaowei Chen- PhD
    Non-protein-coding-RNA processing in the deep-branching protozoan parasite Giardia Intestinalis
  • 2004 - Mrs Lesley Joan Collins- PhD
    Lost in the RNA World: Non-coding RNA and the Spliceosome in the Eukaryotic Ancestor.
  • 2002 - Mr Matthew James Phillips- PhD
    Monotremata, Marsupialia and Placentalia: Inferring Phylogenetic Relationships From Molecular and Morphological Data.
  • 2001 - Mr Yu-Hsin Lin- PhD
    Mammalian Evolution and phylogeny from Complete Mitochondrial Genomes.
  • 2001 - Mr Anthony Masamu Poole- PhD
    The origin and evolution of prokaryotes and eukaryotes.
  • 1996 - Ms Elizabeth Evelyn Watson- PhD
    Threads From The Past: A Genetic Study of African Ethnic Groups and Human Origins.
  • 1996 - Mr Peter John Waddell- PhD
    Statistical Methods of Phylogenetic Analysis: Including Hadamard Conjugations, LogDet Transforms, and Maximum Likelihood.
  • 1993 - Mr Robert Eric Hickson- PhD
    Evolutionary Tails from the South Pacific

CoSupervisor of:

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