PUBLICATIONS FROM THE EVOLUTIONARY PHYLOINFORMATICS GROUP

For links to PDFs of these publications, please click here

 

  • Ho SYW, and Gilbert MTP (2010) Ancient mitogenomics. Mitochondrion 10: 1-11.
  • Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SYW, Shapiro B, Pybus O, Allain JP, and Hatzakis A (2009) The global dynamics and phylogeography of Hepatitis C Virus 1a and 1b. PLoS Medicine 6: e1000198.
  • Steeman ME, Hebsgaard MB, Fordyce RE, Ho SYW, Rabosky DL, Nielsen R, Rahbek C, Glenner H, Sorensen MV, and Willerslev E (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology 58: 573-585.
  • Chatterjee HJ, Ho SYW, Barnes I, and Groves C (2009) Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evolutionary Biology 9: 259.
  • Ho SYW, and Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58: 367-380.
  • Endicott P, Ho SYW, Metspalu M, and Stringer C (2009) Evaluating the mitochondrial timescale of human evolution. Trends in Ecology and Evolution 24: 515-521.
  • Phillips MJ (2009) Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 441: 132-140.
  • Phillips MJ (2009) Mammalian and avian survival across the Cretaceous-Tertiary boundary. New Zealand Science Review 66: 34-38.
  • Willerslev E, Gilbert MTP, Binladen J, Ho SYW, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, and Schuster SC (2009) Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evolutionary Biology 9: 95.
  • Ho SYW (2009) An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters 5: 421-424.
  • Bromham L (2009) Why do species vary in their rate of molecular evolution? Biology Letters 5: 401-404.
  • Bromham L (2009) Putting the 'bio' into bioinformatics. Biology Letters 5: 391-393.
  • Korsten M, Ho SYW, Burger J, Yamaguchi N, Higham TFG, Wheeler HT, Rosendahl W, Sher AV, Sotnikova M, Kuznetsova T, Baryshnikov GF, Martin LD, Harington CR, Burns JA, and Cooper A (2009) Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Molecular Ecology 18: 1963-1979.
  • Barnett R, Shapiro B, Barnes I, Ho SYW, Davison J, Pahn B, Vulla E, Roht M, Tumanov IL, Kojola I, Andersone-Lilley Z, Ozolins J, Pilot M, Mertzanis Y, Giannakopoulos A, Vorobiev AA, Markov NI, Saveljev AP, Lyapunova EA, Abramov AV, Mannil P, Valdmann H, Pazetnov SV, Pazetnov VS, Rokov AM, and Saarma U (2009) Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology 18: 1668-1677.
  • Rambaut A, Ho SYW, Drummond AJ, and Shapiro B (2009) Accommodating the effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution 26: 245-248.
  • Pueyo JI*, Lanfear R*, and Couso JP (2008) Ancestral notch-mediated segmentation revealed in the cockroach P. americana. Proceedings of the National Academy of Sciences of the USA 105: 16614-16619. (* equal first authors)
  • Lanfear R, and Bromham L (2008) Statistical tests between competing hypotheses of Hox cluster evolution. Systematic Biology, 57(5):708-718.
  • Davies TJ, Fritz SA, Grenyer R, Orme CDL, Bielby J, Bininda-Emonds ORP, Cardillo M, Jones KE, Gittleman JL, Mace GM, and Purvis A. (2008) Phylogenetic trees and the future of mammalian biodiversity. Proceedings of the National Academy of Sciences of the USA, 105: 11564-11570.
  • Cardillo M, Gittleman JL, and Purvis A (2008) Global patterns in the phylogenetic structure of island mammal assemblages. Proceedings of the Royal Society B, 275: 1549-1556.
  • Cardillo M, Mace GM, Gittleman JL, Jones KE, Bielby J, and Purvis A (2008) The predictability of extinction: biological and external correlates of decline in mammals. Proceedings of the Royal Society B, 275: 1441-1448.
  • Bromham L (2008) Reading the story in DNA: a beginner’s guide to molecular evolution. Oxford University Press.
  • Ho SYW and Endicott P (2008) The crucial role of calibration in molecular date estimates for the peopling of the Americas. American Journal of Human Genetics, 83: 142-146.
  • Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PWH, and Shapiro B (2008) Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biology Letters, 4: 370-374.
  • Bromham L (2008) Molecular Evolution: Rates. In: Encylopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0001802.pub2].
  • Bromham L (2008) Molecular Evolution: Patterns and Rates. In: Encylopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0001799.pub3]
  • Gilbert MTP, Drautz DI, Lesk AM, Ho SYW, Qi J, Ratan A, Hsu C-H, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova T, Shidlovskiy F, Tikhonov A, Willerslev E, Iacumin P, Buigues B, Ericson PGP, Germonpré M, Kosintsev P, Nikolaev V, Nowak-Kemp M, Knight JR, Irzyk GP, Perbost CS, Fredrikson KM, Harkins TT, Sheridan S, Miller W, and Schuster SC (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the USA, 105: 8327-8332.
  • Welch JJ, Bininda-Emonds ORP, Bromham L (2008) Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evolutionary Biology 8:53.