Research Publications

2004 Publication list




Asmussen, M.A., Cartwright, R.A. and Spencer, H.G. Frequency-dependent selection with dominance: A window onto the behavior of the mean fitness. Genetics 167: 499-512.
Bashford, J.D., Jarvis, P.D., Sumner, J. and Steel, M. U(1) x U(1) x U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes. J. Phys. A: Math. Gen. 37: L81–L89.
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. Developmental plasticity and human health. Nature 430: 419-421.
Collins, L.J. and Penny, D.  Lost in the RNA World – the genomics of ncRNA. New Zealand Bio Science 13, 38-40.
D. Penny and M. J. Phillips. The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?. Trends in Ecology and Evolution. 19(10):516-522.
Donald, K.M., Kennedy, M., Poulin, R. and Spencer, H.G. Host specificity and molecular phylogeny of larval Digenea isolated from New Zealand and Australian topshells (Gastropoda: Trochidae). Int J Parasitol. 34(5):557-68.
Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F., Gelius-Dietrich, G., Henze, K., Kretschmann, E., Richly, E., Leister, D., Bryant, D., Steel, M., Lockhart, P.J., Penny, D. and Martin, W. A genome phylogeny for mitochondria among a-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21(9): 1643--1660.
Guindon, S., Rodrigo, A.G., Dyer, K.A., and Huelsenbeck, J.P. Modeling the site-specific variation of selection patterns along lineages. PNAS 101: 12957-12962.
Hare, K.M., Miller, J.H. and Daugherty, C.H.   How do nocturnal lizards function at cool night temperatures? (abstract) New Zealand Journal of Zoology 31: 103-104.
Hare, K.M., Pledger, S., Thompson, M.B., Miller, J.H., and Daugherty, C.H.   Conditioning reduces metabolic rate and time to steady-state in the lizard Naultinus manukanus (Reptilia: Gekkonidae).   Comparative Biochemistry and Physiology, Part A 139: 245-250.
Harrison G.L., McLenachan P.A., Phillips M.J., Slack K.E., Cooper A., and Penny, D. Four new avian mitochondrial genomes help get to basic evolutionary questions in the Late Cretaceous. Mol. Biol. Evol. 21(6):974-983.
Hay, J.M., Sarre, S.D. and Daugherty, C.H.   Nuclear mitochondrial pseudogenes as molecular outgroups for phylogenetically isolated taxa: a case study in Sphenodon.   Heredity 93: 468-475.
Hoare, J.M., Pledger, S.A., Keall, S.N., Nelson, N.J., Mitchell, N.J., and Daugherty, C.H.  A long-term decline in body condition of the Brothers Island tuatara, Sphenodon guntheri. (abstract) New Zealand Journal of Zoology 31: 104.
Hordijk, W. and Steel, M. Detecting autocatalyctic, self-sustaining sets in chemical reaction systems. Journal of Theoretical Biology 227(4): 451-461.
Huson, D. H. Dezulian, T., Klöpper, T., Steel. M.A. Phylogenetic Super-Networks from Partial Trees IEEE/ACM Transactions on Computational Biology and Bioinformatics. Vol. 1(4): 151-158.
Huson, D.H. and Steel, M. Distances that perfectly mislead. Systematic Biology 53(2): 327-332.
Kennedy, M. and Spencer, H.G. 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
Longson, C., Hare, K.M., and Daugherty, C.H. Fluctuating assymetry is not a sensitive indicator of environmental stress in the egg-laying skink, Oligosoma suteri. (abstract) New Zealand Journal of Zoology 31: 105-106.
M. J. Phillips, F. Delsuc and D. Penny. Genome-Scale Phylogeny and the Detection of Systematic Biases. Mol. Biol. Evol. 21(7):1455–1458.
Matisoo-Smith, E. and Robins, J.H. Origins and Dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat. PNAS 101 (24): 9167-9172.
Miller, H.C and Lambert, D.M Gene duplication and gene conversion in class II MHC genes of New Zealand robins (Petroicidae). Immunogenetics. 56: 178-191.
Miller, H.C. and Lambert, D.M.   Genetic drift outweighs balancing selection in shaping post-bottleneck MHC variation in New Zealand robins (Petroicidae). Molecular Ecology 13: 3709-3721.
Morgan-Richards, M., Trewick, S. A., and Chapman, H. M. Evidence of hybridisation among Hieracium species in New Zealand from flow cytometry. Heredity 92: 1-9.
Mossel, E. and Steel, M. A phase transition for a random cluster model on phylogenetic trees. Mathematical Biosciences. 187: 189-203
Nelson, N.J. The “Tuatara Roadshow” and conservation in New Zealand.   2004 Annual report of the Center for Reproduction of Endangered Species, Zoological Society of San Diego.
Nelson, N.J. Tuatara conservation in New Zealand 2004 Annual report of the Center for Reproduction of Endangered Species, Zoological Society of San Diego.
Nelson, N.J., Cree, A., Thompson, M.B., Keall, S.N., and Daugherty, C.H. Temperature-dependent sex determination in tuatara.  In Temperature-Dependent Sex Determination, Valenzuela, N., and V. Lance (eds.). Smithsonian Institution Press.
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N. and Daugherty, C.H. Do TSD, sex ratios, and nest characteristics influence the vulnerability of tuatara to global warming? Pages 250-257 in S. Morris and A Vosloo, editors. Animals and Environments: Proceedings of the Third International Conference of Comparative Physiology and Biochemistry. Elsevier, KwaZulu-Natal, South Africa.
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N., and Daugherty, C.H. Do TSD, sex ratios, and nest characteristics influence the vulnerability of tuatara to global warming? International Congress Series 1275 (2004): 250-257.
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N., and Daugherty, C.H. Egg mass determines hatchling size, and incubation temperature influences post-hatching growth, of tuatara, Sphenodon punctatus.  Journal of Zoology, London 263: 77-87.
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N., and Daugherty, C.H.   Induction of oviposition produces smaller eggs in tuatara (Sphenodon punctatus). New Zealand Journal of Zoology 31: 283-289.
Norris, T.B., Rickards, G.K. and Daugherty C.H. Chromosomes of tuatara, Sphenodon, a chromosome heteromorphism and an archaic reptilian karyotype.   Cytogenetic and Genome Research 105: 93-99.
O’Shea, S., Bolstad, K. and Ritchie, P.A.   First records of egg masses of Nototodarus gouldi McCoy, 1888 (Mollusca: Cephalopoda: Ommastrephidae), with comments on egg-mass susceptibility to damage by fisheries trawl. New Zealand Journal of Zoology 31:161-166.
Penny, D. Our relative genetics. Nature 427, 208-209.
Prechtl, J., Kneip, C., Lockhart, P.J., Wenderoth, K. and Maier, U.-G. Intracellular sphaeroid bodies of Rhopalodia gibba have nitrogen fixing apparatus of cyanobacterial origin. Mol. Biol. Evol. 21(8): 1477-1481.
Ramstad, K.M., Nelson, N.J., Daugherty, C.H., and Allendorf, F.W.   Integrating traditional Māori and scientific ecological knowledge of the tuatara (Sphenodon). (abstract) New Zealand Journal of Zoology 31: 107.
Ritchie, P.A. and Lambert, D.M.   Late-Holocene penguin occupation and diet at King George Island, Antarctic Peninsula.   American Geophysical Union, Antarctic Research Series 79: 171-180.
Ritchie, P.A., Millar, C.D., Gibb, G., Baroni, C. and Lambert, D. M. Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adelie penguin lineages in Antarctica.  Molecular Biology and Evolution 21 (2): 240-248.
Semple, C. and Steel, M. Cyclic permutations and evolutionary trees. Advances in Applied Mathematics 32(4): 669-680.
Spencer, H.G., Feldman, M.W., Clark A.G. and Weisstein, A.E. The effect of genetic conflict on genomic imprinting and modification of expression at a sex-linked locus. Genetics166: 565-579.
Steel, M. and Penny. D. Two further links between MP and ML under the Poisson Model. Applied Mathematics Letters 17(7): 785-790.
Stevens, M.I., and Hogg, I.D. Population genetic structure of New Zealand’s endemic corophiid amphipods: evidence for allopatric speciation. Biological Journal of the Linnean Society 81: 119-133.
Trewick, S.A., Morgan-Richards, M. & Chapman, H.M.  DNA diversity of Hieracium pilosella (Asteraceae) introduced to New Zealand: reticulation, hybridization, and invasion. Chloroplast American Journal of Botany, 91: 73-85.
Woodhams, M.D. and Hendy, M.D. Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood. Bioinformatics 20(1): i348–i354.