Current Publications at AWCMEE

 

Books and Book Chapters
 
  

Allen, R., Cree, A., Darby, J., Davis, L., Patrick, B. and Spencer, H. (2003). Chapter 8: Forests and Shrublands. Pages 153-190 In: The Natural History of Southern New Zealand, J. Darby, R.E. Fordyce, A. Mark, K. Probert and C. Townsend (eds). Otago University Press, Dunedin.
(book purchase available online)

Barker, M., Brett, T., Darby, J., Dugan J., Hubbard, D., Johnson, P., Mladenov, P., Patrick, B., Peake, B., Probert, K., Smith, A., Spencer, H. and Walker, S. (2003). Chapter 11: The coast. Pages 267-311 in The Natural History of Southern New Zealand, J. Darby, R.E. Fordyce, A. Mark, K. Probert and C. Townsend (eds). Otago University Press, Dunedin.
(book purchase available online)

Brett, T., Carter, L., Carter, R.M., Darby, J., Davis, L., Dawson, S., Jillett, J., Probert, K. and Spencer, H. (2003). Chapter 12: The open sea. Pages 313-338 in The Natural History of Southern New Zealand, J. Darby, R.E. Fordyce, A. Mark, K. Probert and C. Townsend (eds). Otago University Press, Dunedin
(book purchase available online)

Bryant, D., Semple, C. and Steel, M. (2003). Combining trees with divergence times. Chapter for book in Kluwer computational biology series (ed. O Bininda-Edmonds).
(Visit M. Steel website to view pdf) also (book purchase available online)

Goode, M., and Rodrigo, A. G. (2004) Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences. In Current Protocols in Bioinformatics (ed. A. Baxevanis). J. Wiley.
(book purchase available online)

Mark, A., Lee, W., Patrick, B., Cree, A., Darby, J. and Spencer, H. (2003). Chapter 9: Tussock grasslands and associated mountain lands. Pages 191-235 in The Natural History of Southern New Zealand, J. Darby, R.E. Fordyce, A. Mark, K. Probert and C. Townsend (eds). Otago University Press, Dunedin.
(book purchase available online)

Penny, D. (2003). Molecular Biology: introduction. In: Encyclopaedia of Life Sciences. Macmillan Reference, London.Penny, D. and Hendy, M.D. (2003) Phylogenetics: parsimony and distance methods. Pp 348-388, in “Handbook of Statistical Genetics, 2nd Ed” (eds D J Balding, M Bishop and C. Cannings), Wiley.
(book purchase available online)

Penny, D. (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.

Phillips, M.J. and Penny, D. (2003). Mammal Phylogeny. In: Encyclopedia of the Human Genome, Macmillan, London.

Ross, H.A., and Rodrigo, A.G (2003). An assessment of matrix representation with compatibility in supertree construction. In O. R. P. Bininda-Emonds (ed.), Phylogenetic Supertrees, Kluwer Academic Publishers, Boston. (in press).

Semple, C. and Steel. M. (2003). Phylogenetics. Oxford University Press.
(book purchase available online)

Spencer, H. and Darby, J. (2003). Birds of Freshwater Habitats in Southern New Zealand. Pages 264-265 in Chapter 10: Inland Water and Wetlands, The Natural History of Southern New Zealand, J. Darby, R.E. Fordyce, A. Mark, K. Probert and C. Townsend (eds). Otago University Press, Dunedin
(book purchase available online)

Spencer, H.G. (2004). Population genetics. In Biometrics, S.R. Wilson and C. Burden (eds), in Encyclopedia of Life Support Systems, Developed under the Auspices of UNESCO, EOLSS Publishers, Oxford. http://www.eolss.net

Spencer, H.G. (2003). Imprinting: Evolution. Volume 3, pages 430-433 in Nature Encyclopedia of the Human Genome, D.N. Cooper (ed.). Nature Publishing Group, London.

Spencer, H.G. (2002). Intragenomic conflict. In Encyclopedia of Life Sciences, G. Fullerlove (ed.). http://www.els.net Nature Publishing Group, London
(Visit H. Spencer website to view pdf)

Spencer, H.G. (2002). Mutation-selection balance. Volume 12, pages 529-533 in Encyclopedia of Life Sciences, G. Fullerlove (ed.). http://www.els.net Nature Publishing Group, London.
(Visit H. Spencer website to view pdf)

Spencer, H.G., and Paul, D.B. (2002). Eugenics. Pages 317-322 in Encyclopedia of Evolution, M. Pagel (ed.). Oxford University Press, New York.
 
 
 
 
 
 
 
 
 
   

Journal Publications

All available publications online are for viewing purposes only

 

Anderson, J.P., Learn, G.H., Rodrigo, A.G., He, X., Wang, Y., Weinstock, H., Kalish, M.L., Robbins, K.E., Hood, L. and Mullins, J.I. (2003). Predicting Demographic Group Structures Based on DNA Sequence Data. Molecular Biology and Evolution 20: 1168-1180
(abstract) (view pdf)

Asmussen, M.A., Cartwright, R.A. and Spencer, H.G. (2004). Frequency-dependent selection with dominance: A window onto the behavior of the mean fitness. Genetics 167: 499-512.
(abstract) (Visit H. Spencer website to view pdf)

Bateson, P., Barker, D., Clutton-Brock, T., Deb, D., Foley, R.A., Gluckman, P., Godfrey, K., Kirkwood, T., Mirazón Lahr, M., Macnamara, J., Metcalfe, N.B., Monaghan, P., Spencer, H.G. and Sultan, S.E. (2004). Developmental plasticity and human health. Nature 430: 419-421.
(abstract) (Visit H. Spencer website to view pdf)

Bininda-Emonds, O.R.P., Gittleman, J.L. and Steel, M. (2003). The (super) tree of life: procedures, probems and prospects. Annual Review of Ecology and Systematics 33: 265-289.
(abstract) (Visit M. Steel website to view pdf)

Bromham, L. and Penny. D.(2003). The Modern Molecular Clock. Nature Reviews - Genetics 4:216-224.
(abstract) (Visit L. Bromham website to view pdf)

Charteris, S.C. and Ritchie, P.A. (2002). Identification of galaxiid nests, emigrating larvae and whitebait, using mitochondrial DNA control region sequences. New Zealand Journal of Marine and Freshwater Research 36: 789-795.
(available online)

Collins, L.J. and Penny, D. (2004) Lost in the RNA World – the genomics of ncRNA. New Zealand Bio Science 13, 38-40

Collins, L.J., Poole, A.M. and Penny, D.P. (2003). Using ancestral sequences to uncover potential gene homologs. Applied Bioinformatics 2, S85-S95.

Delsuc, F., Phillips, M.J.,. Penny, D. (2003) Comment on "Hexapod Origins: Monophyletic or Paraphyletic?" Science 12 301: 1482-1483.
(available online)

Donald, K.M., Kennedy, M., Poulin, R. and Spencer, H.G. (2004). Host specificity and molecular phylogeny of larval Digenea isolated from New Zealand and Australian topshells (Gastropoda: Trochidae). Int J Parasitol. 34(5):557-68
(abstract) (Visit H. Spencer website to view pdf)

Drummond, A.J., Nicholls, G.K., Rodrigo, A.G. and Solomon. Genealogies from time-stamped sequence data. In Tools for Constructing Chronologies (Eds. C. Buck and A. Millard) Springer Lecture Notes in Statistics, vol 171:pp. 151-174
(available online)

Edvardsson, S, Gardner, P.P., Poole, A.M., Hendy, M.D., Penny, D, and Moulton, V. (2003). A Search for H/ACA SnoRNAs in Yeast Using Predicted MFE Secondary Structures. BioInformatics 19: 865-873.
(available online)

Gardner, P.P., Holland, B.R., Moulton, V., Hendy, M.D. and Penny, D. (2003). On the optimal number of nucleotides in an RNA-world. Proceedings of the Royal Society, London, Series B 270:1177-1182.
(available online)

Gascuel, O., Hendy, M.D., Jean-Marie, A. and McLachlan, R. (2003). The combinatorics of tandem duplication trees. Systematic Biology 52:110-118.
(available online)

Hare, K. and Daugherty. C. (2002). Incubation regime affects juvenile morphology and hatching success, but not sex, of the oviparous lizard Oligosoma suteri (Lacertilia: scincidae). Conservation Biology 16 (4): 887-894.
(available online)

Harrison G.L., McLenachan P.A., Phillips M.J., Slack K.E., Cooper A., Penny D. (2004) Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous. Mol. Biol. Evol. 21(6):974-983.
(available online)

Holland, B.R., Penny, D. and Hendy, M.D. (2003). Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock - A Simulation Study. Systematic Biology. 52(2): 229-238.
(available online)

Holland, B.R., Huber, K.T., Dress, A. and Moulton, V. (2002). Delta Plots: A Tool for Analyzing Phylogenetic Distance Data. Molecular Biology and Evolution 19:2051-2059.
(available online)

Huber, K.T., Langton, M., Penny, D. Moulton, V and Hendy, M. (2002). SpectroNet: a package for computing spectra and median networks. Applied BioInformatics 1: 159-161.
(available online)

Hurles, M.E., Matisso-Smith, E., Gray, R.D., and Penny, D. (2003). Untangling Oceanic settlement: the edge of the knowable. Trends in Ecology and Evolution 18(10): 531-540.
(abstract) (download pdf - 512KB)

Huynen, L.; Lambert, D.M.; McLennan, J.A.; Rickard, C.; Robertson, H.A. (2003). A DNA test for sex assignment in kiwi (Apteryx spp.). Notornis 50(4): 231-233.

Huynen, L., Millar, C.D., Scofield, R.P. and Lambert, D.M. (2003). Nuclear DNA sequences detect species limits in ancient moa. Nature 425: 175 -178.
(available online)

Kennedy, M. and Spencer, H.G. (2004). Phylogeny of the Frigatebirds (Fregatidae) and Tropicbirds (Phaethonidae), two divergent groups of the traditional order Pelecaniformes, inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 31(1):31-8
(abstract) (Visit H. Spencer website to view pdf)

Kleine, T., Lockhart, P. and Batschauer, A. (2003). An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. The Plant Journal. 35 (1): 93-103.
(available online)

Lambert, D.M., Ritchie, P.A., Millar, C.D., Holland, B., Drummond, A.J. and Baroni, C. (2002). Rates of Evolution in Ancient DNA from Adelie penguins. Science 295: 2270-2773.
(available online)

Lettink M, Jamieson IG, Millar CD, Lambert DM. (2002). Mating system and genetic variation in endangered New Zealand takahe. Conservation Genetics 3(4): 427-434.
(available online)

Lin, Y.H., McLenachan, P.A., Gore, A.R., Phillips, M.J., Ota, R., Hendy, M.D. and David Penny (2002). Four New Mitochondrial Genomes and the Increased Stability of Evolutionary Trees of Mammals from Improved Taxon Sampling. Molecular Biology and Evolution 19: 2060-2070.
(available online)

Lin, Y-H., Waddell, P.J., and Penny, D. (2002). Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene 294: 119-129.
(available online)

McBreen, K., Lockhart, P.J., McLenachan, P., Scheele, S., Robertson, A.W. (2003) The use of molecular techniques to resolve relationships among traditional weaving cultivars of Phormium. NZ J Bot. 41:301-310
(available online)

Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., Leister, D., Stoebe, B., Hasegewa, M., and Penny, D. (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 99:12246-122451.
(available online)

Matisoo-Smith, E. and Robins, J.H. (2004). Origins and Dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat. PNAS 101 (24): 9167-9172.
(abstract) (download pdf - 371KB)

Matisoo-Smith, E. (2002). Something Old, Something New: Do Genetic Studies of Contemporary Populations Reliably Represent Prehistoric Populations of Pacific Rattus exulans. Human Biology 74 (3): 489-496.
(abstract) (download pdf - 272KB)

Miller, H.C., Lambert, D.M., Millar, C.D., Robertson, B.C., and Minot. E.O. (2002). Minisatellite DNA profiling detects lineages and parentage in the endangered kakapo (Strigops habroptilus) despite low microsatellite DNA variation. Conservation Genetics 3: 427-434.
(available online)

Morgan-Richards, M. and Wallis, G.P. (2003). Degree of cytogenetic differentiation fails to predict hybrid zone width in the weta Hemideina thoracica (Orthoptera: Anostostomatidae) Evolution 57: 849-861
(available online)

Nelson, N.J., Keall, S. N., Brown, B., and Daugherty, C. H. (2002). Establishing a new wild population of tuatara (Sphenodon guntheri). Conservation Biology Vol. 16, No. 4: 887-894.
(abstract) (view pdf)

Nelson, N.J., Keall, S. N., Pledger, S., and Daugherty, C. H. (2002). Male-biased sex ratio in a small tuatara population. Journal of Biogeography 29: 633-640.
(available online)

Nickle, D.C., Jensen, M.A., Gottlieb, G.S., Shriner, D., Learn, G.H., Rodrigo, A.G., and Mullins.J.I. (2003). Consensus and ancestral state HIV vaccines. Science 299: 1515-1518.
(available online)

Ota, R. and Penny, D. (2003). Estimating changes in mutational mechanisms of evolution. Journal of Molecular Evolution 57:1-8.
(available online)

Penny, D. (2004) Evolutionary trees for all. Trends in Ecology and Evolution 19(6): 273

Penny, D. (2004) Our relative genetics. Nature 427, 208-209.

Penny, D. (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.

Penny, D. (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.

Penny, D., Hendy, M. and Poole, A. (2003). Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 223(3): 377-385.
(available online)

Penny, D. and Poole, A.M. (2003) Lateral gene transfer: some theoretical aspects. New Zealand Bio Science. 12: 32-35.

Penny, D., Murray-McIntosh, R. and Harrison, G.L. (2002). Estimating the number of females in the founding population of New Zealand:Analysis of mtDNA variation. Journal of the Polynesian Society 111:207-221.

Perrie, L.R., Brownsey, P.J., Lockhart, P.J., Brown, E.A. and Large, M.F. (2003). Biogeography of temperate Australasian Polystichum ferns as inferred from chloroplast sequence and AFLP. Journal of Biogeography 30: 1729-1736 .
(available online)

Perrie, L.R., Brownsey, P.J., Lockhart, P.J. and Large, M.F. (2003). Evidence for an allopolyploid complex in New Zealand Polystichum (Dryopteridaceae). New Zealand Journal of Botany 41: 189-215.
(available online)

Perrie, L.R., Brownsey, P.J., Lockhart, P.J. and Large, M.F. (2003). Morphological and genetic diversity in the New Zealand fern Polystichum vestitum (Dryopteridaceae), with special reference to the Chatham Islands. New Zealand Journal of Botany 41: 581-602.
(available online)

Phillips, M.J. and Penny D. (2003). The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution 28(2):171-85
(available online)

Poole, A.M., Phillips, M.J., and Penny, D. (2003). Prokarote and eukaryote evolvability. BioSystems 69: 163-185.

Poole, A.M., Derek T. Logan, D.T., Britt-Marie Sjoberg, B. (2002). The Evolution of the Ribonucleotide Reductases: Much Ado About Oxygen. Journal of Molecular Evolution 55:180-196
(available online)

Poole, A.M. (2000). What is the Last Universal Common Ancestor (LUCA)? ActionBioScience.org Productions
http://www.actionbioscience.org/newfrontiers/poolearticle.html

Prechtl, J., Kneip, C., Lockhart, P.J., Wenderoth, K. and Maier, U.-G. (2004) Intracellular sphaeroid bodies of Rhopalodia gibba have nitrogen fixing apparatus of cyanobacterial origin. Mol. Biol. Evol. (in press)
(available online- abstract ahead of print)

Ritchie, P.A., Anderson, I.A. and Lambert, D.M. (2003). Evidence for specificity of psittacine beak and feather disease viruses among avian hosts. Virology 306: 109-115.

Robins, J.H., Matisoo-Smith, E., Ross, H. (2003) The origins of the feral pigs on the Auckland Islands. Journal of the Royal Society of New Zealand 33(2): 561-569.
(abstract) (download pdf - 238KB)

Rodrigo, A.G., Goode, M., Forsberg, R., Ross, H.A. & Drummond, A. (2003) Inferring evolutionary rates using serially sampled sequences from several populations. Mol. Biol. Evol., 20:2010–2018
(available online)

Roeder, A., Ritchie, P.A. and Lambert, D.M. (2002) New DNA markers for penguins. Conservation Genetics (3): 341-344.

Ross, H. A., G. M. Lento, M. L. Dalebout, M. Goode, G. Ewing, P. McLaren, A. G. Rodrigo, S. Lavery, and C. S. Baker. (2003) DNA Surveillance: Web-based molecular identification of whales, dolphins and porpoises. Journal of Heredity 94(2): 111-114.
(available online)

Slack, K.E., Janke, A., Penny, D. and Arnason. U. (2003). Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene 302:43-52.

Smissen, R., Breitwieser, I., Ward, J., McLenachan, P. and Lockhart, P.J. (2003). Use of ISSR profiles and ITS sequences to study the biogeography alpine cushion in the genus Raoulia. Plant Systematics and Evolution 239: 79-94.

Sober, E. and Steel, M. (2002) Testing the hypothesis of common ancestry. J. Theor. Biol. 218: 395-408
(available online)

Spencer, H.G., Feldman, M.W., Clark A.G. and Weisstein, A.E. (2004). The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus. Genetics 166: 565-579.
(abstract) (Visit H. Spencer website to view pdf)

Spencer, H.G. (2003). Further properties of Gavrilets’s one-locus two-allele model of maternal selection. Genetics 164: 1689-1692.
(abstract) (Visit H. Spencer website to view pdf)

Spencer, H.G. (2002). The correlation between relatives on the supposition of genomic imprinting. Genetics 161: 411-417.
(abstract) (Visit H. Spencer website to view pdf)

Stevens, M.I., and Hogg, I.D. (2004) Population genetic structure of New Zealand’s endemic corophiid amphipods: evidence for allopatric speciation. Biological Journal of the Linnean Society 81: 119-133.
(available online)

Stevens, M.I., and Hogg, I.D. (2003) Long-term isolation and recent range expansion revealed for the endemic springtail Gomphiocephalus hodgsoni from southern Victoria Land, Antarctica. Molecular Ecology 12: 2357-2369.
(available online)

Stockler, K., Daniel, I.L. and Lockhart, P.J. (2002). New Zealand Kauri (Agathis australis (D.Ddon) Lindl., Araucariaceae) Survives Oligocene Drowning. Academic Press: Molecular Phylogenetics and Evolution 24: 180-193.

Sultan, S.E. and Spencer, H.G. (2002). Metapopulation structure favors plasticity over local adaptation. American Naturalist 160: 271-283.
(abstract) (Visit H. Spencer website to view pdf)

Trewick, S.A., Morgan-Richards, M. & Chapman, H.M. (2004) Chloroplast DNA diversity of Hieracium pilosella (Asteraceae) introduced to New Zealand: reticulation, hybridization, and invasion. American Journal of Botany, 91: 73-85
(available online)

Watson, E.E. and Penny, D. (2003). DNA and people: From East Africa to Aotearoa New Zealand. New Zealand Science Review 60: 29-35.

Weisstein, A.E., and Spencer, H.G. (2003). The evolution of genomic imprinting via variance minimization: An evolutionary genetic model. Genetics 165: 205-222.
(abstract) (Visit H. Spencer website to view pdf)

Weisstein, A.E., Feldman, M.W. and Spencer, H.G. (2002). Evolutionary genetic models of the ovarian time bomb hypothesis for the evolution of genomic imprinting. Genetics 162: 425-439.
(abstract) (Visit H. Spencer website to view pdf)

Winkworth, R.C., Grau, J., Robertson, A.W. and Lockhart, P.J. (2002). The origins and evolution of the genus Myosotis L. (Boraginaceae). Academic Press: Molecular Phylogenetics and Evolution 24: 180-193.

Winkworth, R.C., Wagstaff, S.J., Glenny, D., and Lockart, P.J. (2002). Plant dispersal N.E.W.S from New Zealand. Trends in Ecology and Evolution.

Woodhams, M.D. and Hendy, M.D. (2004). Reconstructing phylogeny by Quadratically
Approximated Maximum Likelihood. Bioinformatics 20(1): i348–i354
(abstract) (view pdf)
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