phylotree50

Publications (Supplementary Materials)

  • Wu, Chen, Ross N. Crowhurst, Alice B. Dennis, Victoria G. Twort, Shanlin Liu, Richard D. Newcomb, Howard A. Ross, and Thomas R. Buckley. 2016. De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus Hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction. PLOS ONE 11: e0157783.
  • Liu, Yang, Francesca Chiaromonte, Howard Ross, Raunaq Malhotra, Daniel Elleder, and Mary Poss. 2015. Error Correction and Statistical Analyses for Intra-Host Comparisons of Feline Immunodeficiency Virus Diversity from High-Throughput Sequencing Data. BMC Bioinformatics 16: 202.
  • Drummond, Alexei J., Richard D. Newcomb, Thomas R. Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, et al. 2015. Evaluating a Multigene Environmental DNA Approach for Biodiversity Assessment. GigaScience 4: 46.
  • Ranjard, Louis, Sarah J. Withers, Dianne H. Brunton, Howard A. Ross, and Stuart Parsons. 2015. Integration over Song Classification Replicates: Song Variant Analysis in the Hihi. The Journal of the Acoustical Society of America 137: 2542-2551.
  • Taylor, Michael W., Peter Tsai, Nicole Anfang, Howard A. Ross, and Matthew R. Goddard. 2014. Pyrosequencing Reveals Regional Differences in Fruit-Associated Fungal Communities: Vine Fungi Biogeography by Pyrosequencing. Environmental Microbiology 16: 2848-2858.
  • Ross, Howard A. 2014. The Incidence of Species-Level Paraphyly in Animals: A Re-Assessment. Molecular Phylogenetics and Evolution 76: 10-17.
  • Abbott, W. G., P. Tsai, H. A. Ross, M. 'Ofanoa, A. J. Trevarton, J. Hornell, S. R. Munn, and E. J. Gane. 2012. Selection pressure on the hepatitis B virus Pre-S/S and P open reading frames in Tongan subjects with a chronic hepatitis B virus infection. Antiviral Research 96:148-157.
  • Rose, C. J., J. Chapman, S. D. G. Marshall, S. F. Lee, P. Batterham, H. A. Ross, and R. D. Newcomb. 2011. Selective sweeps at the organophosphorus insecticide resistance locus, Rop-1, have affected variation across and beyond the alpha-esterase gene cluster in the Australian sheep blowfly, Lucilia cuprina. Molecular Biology and Evolution 28:1835-1846.
  • Gillman, L. N., P. McBride, D. J. Keeling, H. A. Ross, and S. D. Wright. 2011. Are rates of molecular evolution in mammals substantially accelerated in warmer environments? Reply. Proceedings of the Royal Society B 278:1294-1297.
  • Wright, S. D., H. A. Ross, D. J. Keeling, P. McBride, and L. N. Gillman. 2011. Thermal energy and the rate of genetic evolution in marine fishes. Evolutionary Ecology 25:525-530.
  • Masters, B. C., V. Fan, and H. A. Ross. 2011. Species Delimitation - a Geneious plugin for the exploration of species boundaries. Molecular Ecology Resources 11:154-157.
  • Robins, J. H., P. A. McLenachan, M. J. Phillips, B. J. McComish, E. Matisoo-Smith, and H. A. Ross. 2010. Evolutionary relationships and divergence times among the native rats of Australia. BMC Evolutionary Biology 10:375.
  • Ranjard, L., M. G. Anderson, M. J. Rayner, R. B. Payne, I. McLean, J. V. Briskie, H. A. Ross, D. H. Brunton, S. M. N. Wooley, and M. E. Hauber. 2010. Bioacoustic distances between the begging calls of brood parasites and their host species: a comparison of bioacoustic techniques. Behavioral Ecology and Sociobiology 64:1915-1926.
  • Padhi, A., H. A. Ross, J. A. Terwee, S. VandeWoude, and M. Poss. 2010. Profound differences in virus population genetics correspond to protection from CD4 decline resulting from Feline Lentivirus coinfection. Viruses 2:2663-2680.
  • Wright, S. D., L. N. Gillman, H. A. Ross, and D. J. Keeling. 2010. Energy and the tempo of evolution in amphibians. Global Ecology and Biogeography 19:733-740.
  • Gillman, L. N., D. J. Keeling, H. A. Ross, and S. D. Wright. 2009. Latitude, elevation and the tempo of molecular evolution in mammals. Proceedings of the Royal Society B-Biological Sciences 276: 3353-3359.
  • Wright, S. D., L. N. Gillman, H. A. Ross, and D. J. Keeling. 2009. Slower tempo of microevolution in island birds: implications for conservation biology. Evolution 63: 2275-2287.
  • Anderson, M. G., H. A. Ross, D. H. Brunton, and M. E. Hauber. 2009. Begging call matching between a specialist brood parasite and its host: A comparative approach to detect co-evolution. Biological Journal of the Linnean Society 98: 208-216.
  • Matisoo-Smith, E., M. Hingston, G. Summerhayes, J. H. Robins, H. A. Ross, M. D. Hendy. 2009 On the rat trail in Near Oceania: applying the commensal model to the question of Lapita colonization. Pacific Science 63: 465-475.
  • Robins, J. H., P. A. McLenachan, M. J. Phillips, L. Craig, H. A. Ross, and E. Matisoo-Smith. 2008. Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Molecular Phylogenetics and Evolution 49:460-466.
  • Ranjard, L., and H. A. Ross. 2008. Unsupervised bird song syllable classification using evolving neural networks. Journal of the Acoustical Society of America 123: 4358-4368.
  • Ross, H. A., S. Murugan and W. L. S. Li. 2008. Testing the reliability of genetic methods of species identification via simulation. Systematic Biology 57:216-230. (See also Supplementary Materials)
  • Poss, M., and H. A. Ross. 2008. Evolution of the long terminal repeat and regulatory genes of feline immunodeficiency virus genomes from naturally infected courgars. Virology 370:55-62
  • Poss, M., H. A. Ross, A. G. Rodrigo, J. A. Terwee and S. VandeWoude. 2008. The molecular biology and evolution of feline immunodeficiency viruses of cougars. Veterinary Immunology and Immunopathology 123:154-158 doi:10.1016/j.vetimm.2008.01.022
  • Robins, J. H., M. Hingston, E. Matisoo-Smith and H. A. Ross. 2007. Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes 7:717-729.
  • Poss, M., A. Idoine, H. A. Ross, J. A. Terwee, S. VandeWoude and A. G. Rodrigo. 2007. Recombination in feline lentiviral genomes during experimental cross-species infection. Virology 359:146-151.
  • Pyrc, K., R. Dijkman, L. Deng, M. F. Jebbink, H. A. Ross, B. Berkhout and L. Van Der Hoek. 2006. Mosaic structure of human coronavirus NL63, one thousand years of evolution. Journal of Molecular Biology 365: 964-973.
  • Ross, H. A., and S. Murugan. 2006. Using phylogenetic analyses and reference datasets to validate the species identities of cetacean sequences in GenBank. Molecular Phylogenetics and Evolution 40: 866-871.
  • Robins, J. H., H. A. Ross, M. S. Allen, and E. Matisoo-Smith. 2006. Sus bucculentus revisited. Nature 440: E7.
  • Poss, M., H. A. Ross, S. L. Painter, D. C. Holley, J. A. Terwee, S. VandeWoude, and A. G. Rodrigo. 2006. Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase. Journal of Virology 80: 2728-2737.
  • Ross, H. A., Nickle, D. C., Liu, Y., Heath, L., Jensen, M. A., Rodrigo, A. G., Mullins, J. I., 2006. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. Evolutionary Bioinformatics Online 2:18-41.
  • Ross, H. A., and A. G. Rodrigo. 2004. An assessment of matrix representation with compatibility in supertree construction. Pp. 35-63 in O. R. P. Bininda-Emonds, ed. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic Publishers, Boston.
  • Biek, R., A. G. Rodrigo, D. Holley, A. Drummond, C. R. Anderson Jr., H. A. Ross, and M. Poss. 2003. Epidemiology, genetic diversity, and evolution of endemic FIV in a wild population of cougars. Journal of Virology 77: 9578-9589.
  • Rodrigo, A. G., M. Goode, R. Forsberg, H. A. Ross, and A. Drummond. 2003. Inferring evolutionary rates using serially sampled sequences from several populations. Molecular Biology and Evolution 20:2010-2018.
  • Robins, J. H., E. Matisoo-Smith, and H. A. Ross. 2003. The origins of the feral pigs on the Auckland Islands. Proceedings of the Royal Society of New Zealand 33: 561-569.
  • 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. J. Heredity 94:111-114.
  • Baker, C. S., M. L. Dalebout, S. Lavery and H. A. Ross. 2003. www.DNA-surveillance: applied molecular taxonomy for species conservation and discovery. Trends in Ecology and Evolution 18: 271-272.
  • Baker, C. S., H. Ross and S. Lavery. 2002. Molecular taxonomy for conservation. Species 38: 12-13.
  • Ross, H. A., and A. G. Rodrigo. 2002. Immune-mediated positive selection drives Human Immunodeficiency Virus Type 1 molecular variation and predicts disease duration. Journal of Virology 76(22): 11715 - 11720.
  • Sheppard, S.C., H. A. Ross and J. L. Hawkins. 1992. Reciprocal transplant study of clones of strawberry proliferating in an irradiation field: morphometrics. Environmental and Experimental Botany 32:383-389.
  • Ross, H. A. 1986. Estimation of mating system parameters in plant populations using gene loci having null alleles. Theoretical and Applied Genetics 72: 322-327.
  • Ross, H. A. 1986. Genetic changes in an irradiated population of wild meadow voles (Microtus pennsylvanicus). Canadian Journal of Zoology 64: 698-703.
  • Ross, H. A., and J. L. Hawkins. 1986. Genetic variation among local populations of jack pine, Pinus banksiana. Canadian Journal of Genetics and Cytology 28: 453-458.
  • Ross, H. A. 1983. Genetic differentiation of starling (Sturnus vulgaris: Aves) populations in New Zealand and Great Britain. Journal of Zoology, London 201: 351-362.
  • Ross, H. A., and A. J. Baker. 1982. Variation in the size and shape of introduced starlings, Sturnus vulgaris (Aves: Sturninae), in New Zealand. Canadian Journal of Zoology 60: 3312-3325.
  • Ross, H. A., and I. A. McLaren. 1981. Lack of differential survival among young Ipswich Sparrows. Auk 98: 495-502.
  • Ross, H. A. 1980. Growth of nestling Ipswich Sparrows in relation to season, habitat, brood size, and parental age. Auk 97: 721-732.
  • Ross, H. A. 1980. The reproductive rates of yearling and older Ipswich Sparrows, Passerculus sandwichensis princeps. Canadian Journal of Zoology 58: 1557-1563.
  • Ross, H. A. 1979. Multiple clutches and shorebird egg and body weight. American Naturalist 113: 618-622.
  • Hunter, R. A., H. A. Ross, and A. J. S. Ball. 1975. A laboratory simulation of predator-induced incubation interruption using ring-billed gull eggs. Canadian Journal of Zoology 54: 628-633.

Technical Reports:

  • Ross, H. A., and H. Shearman. 2009. GenBank sequence assessment for species assignment - control region sequences published for baleen whales in 2007. Report SC/61/SD3 International Whaling Commission.
  • Ross, H. A., and H. Shearman. 2008. Validation of mtDNA control-region sequences in GenBank for large baleen whales. Report SC/60/SD6 Scientific Committee of the International Whaling Commission.
  • Ross, H. A., S. Murugan, and C. S. Baker. 2005. Are the species identities of cetacean sequences in GenBank correct? Report SC/57/SD4 Scientific Committee of the International Whaling Commission.
  • Dalebout, M. L., S. Lavery, C. S. Baker, S. Caballero, F. Cipriano, G. Ewing, M. Goode, R. G. LeDuc, G. M. Lento, F. B. Pichler, A. G. Rodrigo, P. E. Rosel, H. A. Ross, and D. Steel. 2003. www.DNA-surveillance Vs. 3.1: progress with a validated and comprehensive DNA database for species identification of whales, dolphins and porpoises. Report SC/55/SD8 Scientific Committee of the International Whaling Commission.
  • Lento, G. M., H. A. Ross, M. L. Dalebout, M. Goode, P. McLaren, A. G. Rodrigo, S. Lavery, and C. S. Baker. 2002. DNA Surveillance: A Web-based system for molecular identification of whales, dolphins and porpoises. Report SC/54/SD2 Scientific Committee of the International Whaling Commission.