Dr Simon Ho ARC Postdoctoral Fellow Current web site: http://www.simonho.org

Background
I completed a B.Sc. at the University of Sydney, with my Honours project focusing on phylogenetics and the Cambrian Explosion. After staying to complete an M.Sc. thesis on phylogenetic methods, I moved to the U.K. to read for a D.Phil. at the University of Oxford. My doctoral thesis, which was based on research conducted in the Ancient Biomolecules Centre, was entitled 'Estimating rates of molecular evolution'. I was a member of Linacre College during my doctorate, but was employed by several other colleges as a tutor in Evolution. I also demonstrated in Statistics for the Department of Zoology. I remained in the same research group as a postdoctoral researcher for 12 months, also becoming an Associate Researcher at Balliol College, before returning to Australia in August 2007. I spent the remaining months of 2007 as an Honorary Researcher at the University of Sydney before taking up an ARC-funded Australian Postdoctoral Fellowship at the Australian National University at the beginning of 2008.

Research Interests
My research primarily concerns phylogenetic methods and their application. Much of my work has been on methods for estimating rates of molecular evolution, as well as divergence dating techniques. Due to the theoretical nature of my research, I have not focused on a specific group of organisms, but have a broad interest in evolution at the molecular level.

Journal Articles
Barnett, R., Shapiro, B., Barnes, I., Ho, S.Y.W., Burger, J., Yamaguchi, N., Higham, T.F.G., Wheeler, H.T., Rosendahl, W., Sher, A.V., Sotnikova, M., Kuznetsova, T., Baryshnikov, G.F., Martin, L.D., Harington, C.R., Burns, J.A., Cooper, A. 2009. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology 18: 1668-1677.

Endicott, P., Ho, S.Y.W., Metspalu, M., Stringer, C. 2009. Evaluating the mitochondrial timescale of human evolution. Trends in Ecology and Evolution 24(9): 515-521.

Ho, S. 2009. An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters 5: 421-424.

Ho, S.Y.W., Phillips, M.J. 2009. Accountiing for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times. Systematic Biology 58(3): 367-380.

Korsten, M., Ho, S.Y.W., Davison, J., Pahn, B., Vulla, E., Roht, M., Tumanov, I.L., Kojola, I., Andersone-Lilley, Z., Ozolins, J., Pilot, M., Mertzanis, Y., Giannakopoulos, A., Vorobiev, A.A., Markov, N.I., Saveljev, A.P., Lyapunova, E.A., Abramov, A.V., Mannil, P., Valdmann, H., Pazetnov, S.V., Pazetnov, V.S., Rokov, A.M., Saarma, U. 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.

Rambaut, A., Ho, S.Y.W., Drummond, A.J., Shapiro, B. 2009. Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories. Molecular Biology and Evolution 26(2): 245-248.

Willerslev, E., Gilbert, M.T.P., Binladen, J., Ho, S.Y.W., Campos, P.F., Ratan, A., Tomsho, L.P., da Fonseca R.R., Sher, A., Kuznetsova, T.V., Nowak-Kemp, M., Roth, T.L., Miller, W., Schuster, S.C. 2009. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evolutionary Biology 9: 95.

Gilbert, M.T.P., Drautz, D.I., Lesk, A.M., Ho, S.Y.W., Qi, J., Ratan, A., Hsu, C-H., Sher, A., Dalén, L., Götherström, A., Tomsho, L.P., Rendulic, S., Packard, M., Campos, P.F., Kuznetsova, T.V., Shidlovskiy, F., Tikhonov, A., Willerslev, E., Iacumin, P., Buigues, B., Ericson, P.G.P., Germonpré, M., Kosintsev, P., Nikolaev, V., Nowak-Kemp, M., Knight, J.R., Irzyk, G.P., Perbost, C.S., Fredrikson, K.M., Harkins, T.T., Sheridan, S., Miller, W., Schuster, S.C. 2008. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. PNAS 105(24): 8327-8332.

Ho, S.Y.W., Endicott, P. 2008. The Crucial Role of Calibration in Molecular Date Estimates for the Peopling of the Americas. The American Journal of Human Genetics 83: 142-146.

Ho, S.Y.W., Larson, G., Edwards, C.J., Heupink, T.H., Lakin, K.E., Holland, P.W.H., Shapiro, B. 2008. Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biology Letters 4: 370-374.

Endicott P and Ho SYW. 2008. A Bayesian evaluation of human mitochondrial substitution rates. American Journal of Human Genetics, in press.

Barik SS, Sahani R, Prasad BVR, Endicott P, Metspalu M, Bhattacharya S, Sarkar BN, Annapoorna PCH, Sreenath J, Sun D, Sanchez JJ, Ho SYW, Chandrasekar A, and Rao VR. 2008. Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. American Journal of Physical Anthropology, 136: 19-27.

Ware JL, Ho SYW, and Kjer K. 2008. Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models. Molecular Phylogenetics and Evolution, 47: 426-432.

Ho SYW, Saarma U, Barnett R, Haile J, and Shapiro B. 2008. The effect of inappropriate calibration: Three case studies in molecular ecology. PLoS ONE, 3: e1615.

Buckley M, Walker A, Ho SYW, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney Bm Zylber MI, Gilbert MTP, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, and Collins MJ. 2008. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science, 319: 33c.

Hyman IT, Ho SYW, and Jermiin LS. 2007. Molecular phylogeny of Australian Helicarionidae, Euconulidae, and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Molecular Phylogenetics and Evolution, 45: 792-812.

Ho SYW, Kolokotronis S-O, and Allaby RG. 2007. Elevated substitution rates estimated from ancient DNA. Biology Letters, 3: 702-705.

Ho SYW. 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38: 409-414.

Ho SYW, Shapiro B, Phillips MJ, Cooper A, and Drummond AJ. 2007. Evidence for time dependency of molecular rate estimates. Systematic Biology, 56: 515-522.

Ho SYW, Heupink TH, Rambaut A, and Shapiro B. 2007. Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution, 24: 1416-1422.

Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne J-D, Baird JF, Larson G, Ho SYW, Heupink TH, Shapiro B, Freeman AR, Thomas MG, Arbogast R-M, Arndt B, Bartosiewicz L, Benecke N, Budja M, Chaix L, Choyke AM, Coqueugniot R, Dohle H-J, G??ldner H, Hartz S, Helmer D, Herzig B, Hongo H, Mashkour M, Ozdogan, Pucher E, Roth G, Schade-Lindig S, Schmolcke U, Schulting RJ, Stephan E, Uerpmann H-P, Voros I, Voytek B, Bradley DG, and Burger J. 2007. Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proceedings of the Royal Society of London B, 274: 1377-1385.

Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, Nielsen R, Munch K, Ho SYW, Shapiro B, and Willerslev E.. 2007. Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a problem? Molecular Biology and Evolution, 24: 982-989.

Saarma U, Ho SYW, Pybus OG, Kaljust M, Tumanov IM, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann A, Lyapunova EA, Abramov AV, M?§nnil P, Korsten M, Vulla E, Pazetnov SV, Pazetnov VS, Putchkovskiy SV, and Rokov AM. 2007. Mitogenetic structure of brown bears (Ursus arctos L.) in north-eastern Europe and a new time-frame for the formation of brown bear lineages. Molecular Ecology , 16: 401-413.

Peng Z*, Ho SYW*(equal first authors), Zhang Y, and He S. 2006. Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Molecular Phylogenetics and Evolution, 39: 568-572.

Drummond AJ, Ho SYW, Phillips MJ, and Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology, 4: e88.

Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SYW, Hansen AJ, Willerslev E. 2006. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172: 733-741.

Ho SYW and Larson G. 2006. Molecular clocks: When times are a-changin'. Trends in Genetics, 22: 79-83.

Murray S, Jorgensen MF, Ho SYW, Patterson DJ, and Jermiin LS. 2005. Improving the analysis of dinoflagellate phylogeny based on rRNA. Protist, 156: 269-286.

Weinstock J, Willerslev E, Sher A, Tong W, Ho SYW, Rubinstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, and Cooper A. 2005. Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective. PLoS Biology, 3: e241.

Ho SYW, Phillips MJ, Cooper A, and Drummond AJ.. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22: 1561-1568.

Ho SYW, Phillips MJ, Drummond AJ, and Cooper A. 2005. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution, 22: 1355-1363.

Jermiin LS, Ho SYW, Ababneh F, Robinson J, and Larkum AWD. 2004. The biasing effect of composition heterogeneity on phylogenetic estimates may be underestimated. Systematic Biology, 53: 638-643.

Ho SYW and Jermiin LS. 2004. Tracing the decay of the historical signal in biological sequence data. Systematic Biology, 53: 623-637.

Jermiin LS, Ho SYW, Ababneh F, Robinson J, and Larkum AWD. 2003. Hetero: A program to simulate the evolution of DNA on four-taxon trees. Applied Bioinformatics, 2: 159-163

Invited Talks

Relaxed molecular clocks and probabilistic calibrations
Session chair, Structural, Functional, and Evolutionary Genomics Conference , Cambridge, UK. Jul 2007.

Bayesian phylogenetic analysis using BEAST
Natural History Museum , London, UK. Jul 2007.

The molecular clock: Theory and application
Session Biostatistics M.Sc. Course , University of Athens, Greece. Jun 2007.

A biologist's guide to dating, with a discussion of uncorrelated relaxed-clock models
Dating the Tree of Life Symposium, Geneva, Switzerland. Sep 2006.

Conference Talks

Applications of phylogenetics in ancient DNA analysis
Evolution 2007 , Christchurch, New Zealand. Jun 2007.

Measuring rates of molecular evolution from ancient DNA
Australasian Evolution Society Conference, Sydney, Australia. Jun 2007.

Testing a Bayesian model of sequence damage using ancient DNA data sets
International Symposium on Biomolecular Archaeology, Stockholm, Sweden. Sep 2006.

A biologist's guide to dating
Evolution 2006, New York, USA. Jun 2006.

Relaxed-clock phylogenetics
PhyloGroup V, London, UK. Apr 2006.

Phylogenetic inference in a relaxed clock framework
Molecular Biology and Evolution 2005, Auckland, New Zealand. Jun 2005.

Re-evaluating the Cambrian explosion hypothesis
Annual New Zealand Phylogenetics Meeting, Kaikoura, New Zealand. Feb 2003.

Computer Programmes and Manuals

A Rough Guide to BEAST 1.4
Drummond AJ, Ho SYW, Rawlence N, and Rambaut A. University of Auckland, Auckland, New Zealand.

Sequescence
Ho SYW. University of Oxford, Oxford, United Kingdom.

RateEvolver
Ho SYW. University of Oxford, Oxford, United Kingdom.