Associate Professor Simon Ho

BSc (Hons) MSc (Sydney) DPhil (Oxford)

A08 - Heydon-Laurence Building
The University of Sydney

Telephone +61 2 9351 8681

Website Room 308, A11 - Edgeworth David Building
Molecular Ecology, Evolution, and Phylogenetics

Biographical details

I am an Australian Research Council QEII Fellow in the School of Biological Sciences, University of Sydney.

Until 2010, I was an Australian Postdoctoral Fellow and Lecturer at the Centre for Macroevolution and Macroecology (Research School of Biology, Australian National University). From mid-2006 to mid-2007, I was a Postdoctoral Researcher in the Department of Zoology, University of Oxford, working under the guidance of Beth Shapiro and Peter Holland. I was an Associate Researcher at Balliol College during this time.

I completed my D.Phil. degree in 2006 at the University of Oxford under the supervision of Andrew Rambaut, Alan Cooper, Alexei Drummond, and Richard Fortey. I was a Commonwealth Scholar and EPA Cephalosporin Scholar at Linacre College throughout my doctorate. My thesis dealt with various aspects of rate estimation, including the performance of different methods in estimating rates and divergence times among different species, as well as the roles of adaptive and stochastic processes in driving patterns of evolutionary rate variation.

Research interests

As a computational evolutionary biologist, my research interests include molecular clocks, evolutionary rates, phylogenetic methods, calibration techniques, and ancient DNA.

Scientific output

Teaching and supervision

  • Honours (committee member 2010-; acting chair 2014)
  • Scientific Research in Biology (BIOL4015)
  • Evolution & Biodiversity (BIOL3044)
  • Human Biology (Special Studies Program) (BIOL1993) - unit coordinator
  • Assembling the Tree of Life (BIOS3221; UNSW)
  • List of past Units of Study.

Awards and honours

  • NSW Young Tall Poppy of the Year, 2014
  • Eureka Prize for Outstanding Early Career Researcher, 2014
  • Early Career Award, Genetics Society of Australasia, 2011

University of Oxford

  • Edward Penley Abraham Cephalosporin Scholarship, Linacre College, 2004-2006
  • Domus Research Prize, Linacre College, 2004-2006
  • Commonwealth Scholarship Research Grant, British Council, 2003-2006
  • Commonwealth Scholarship, British Council, 2003-2006

University of Sydney

  • AE and FAQ Stephens Scholarship, Australian Postgraduate Awards, 2003
  • John H Elliot Memorial Prize for Best Thesis in Animal Biology, 2002
  • Professor Spencer Smith-White Prize in Biology Honours, 2002
  • GS Caird Scholarship in Zoology, 2001
  • Haswell Prize in Biology, 2001

Professional activities

Editorial Boards

  • Journal of Evolutionary Biology (2014-)
  • Biology Letters (2011-)
  • Human Origins Research (2010-)
  • PLOS ONE (2010-)
  • Mitochondrial DNA (2008-)

Professional Services

  • Reviewer, >200 papers for 46 journals, including Nature and Science
  • A “Top Referee” for Proceedings of the Royal Society B (2012, 2013) and Biology Letters (2009)
  • Reviewer for Australian Research Council and Natural Environment Research Council (UK)
  • Committee member, Genetics Society of Australasia (2014-)
  • Organising committee, Genetics Society of Australasia Conference (2014)

University Services

  • Research Committee, School of Biological Sciences, University of Sydney (2011-)
  • Honours Committee, School of Biological Sciences, University of Sydney (2010-)
  • Seminar organiser, School of Biological Sciences, University of Sydney (2010-2011)
  • Seminar organiser, School of Botany and Zoology, Australian National University (2009-2010)

University of Oxford

  • Edward Penley Abraham Cephalosporin Scholarship, Linacre College, 2004-2006
  • Domus Research Prize, Linacre College, 2004-2006
  • Commonwealth Scholarship Research Grant, British Council, 2003-2006
  • Commonwealth Scholarship, British Council, 2003-2006

University of Sydney

  • AE and FAQ Stephens Scholarship, Australian Postgraduate Awards, 2003
  • John H Elliot Memorial Prize for Best Thesis in Animal Biology, 2002
  • Professor Spencer Smith-White Prize in Biology Honours, 2002
  • GS Caird Scholarship in Zoology, 2001
  • Haswell Prize in Biology, 2001

University of Oxford

  • Edward Penley Abraham Cephalosporin Scholarship, Linacre College, 2004-2006
  • Domus Research Prize, Linacre College, 2004-2006
  • Commonwealth Scholarship Research Grant, British Council, 2003-2006
  • Commonwealth Scholarship, British Council, 2003-2006

University of Sydney

  • AE and FAQ Stephens Scholarship, Australian Postgraduate Awards, 2003
  • John H Elliot Memorial Prize for Best Thesis in Animal Biology, 2002
  • Professor Spencer Smith-White Prize in Biology Honours, 2002
  • GS Caird Scholarship in Zoology, 2001
  • Haswell Prize in Biology, 2001

PhD and master's project opportunities

Selected grants

2013

  • Refining the timescale of human evolution and dispersal using ancient DNA; Ho S; Australian Research Council (ARC)/Discovery Projects (DP).

2011

  • Estimating evolutionary time-scales using genomic data: Exploiting opportunities and meeting challenges; Ho S; Australian Research Council (ARC)/Discovery Projects (DP).

2010

  • Analysing and modelling molecular rate variation among nuclear and mitochondrial genomes; Ho S; Australian Research Council (ARC)/Discovery Projects (DP).

Selected publications

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Book Chapters

  • Ho, S. (2012). Phylogenetic Analysis of Ancient DNA using BEAST. In Beth Shapiro and Michael Hofreiter (Eds.), Methods in Molecular Biology, 840: Ancient DNA, (pp. 229-241). New York: Humana Press. [More Information]

Journals

  • Lee, T., Cameron, S., Evans, T., Ho, S., Lo, N. (2015). The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers. Molecular Phylogenetics and Evolution, 82, 234-244.
  • Hope, A., Ho, S., Malaney, J., Cook, J., Talbot, S. (2014). Accounting for rate variation among lineages in comparative demographic analyses. Evolution, 68-69, 2689-2700.
  • Duchene, S., Holmes, E., Ho, S. (2014). Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society B: Biological Sciences, 281(1786), 1-7. [More Information]
  • Shapiro, B., Ho, S. (2014). Ancient hyaenas highlight the old problem of estimating evolutionary rates. Molecular Ecology, 23, 499-501.
  • Duchene, S., Molak, M., Ho, S. (2014). ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics, 30(7), 1017-1019. [More Information]
  • Edwards, C., Ho, S., Barnett, R., Coxon, P., B̀radley, D., Lord, T., O'Connor, T. (2014). Continuity of brown bear maternal lineages in northern England through the Last-glacial period. Quaternary Science Reviews, 96(2014), 131-139. [More Information]
  • Zhang, F., Yu, D., Luo, Y., Ho, S., Wang, B., Zhu, C. (2014). Cryptic diversity, diversification and vicariance in two species complexes of Tomocerus (Collembola, Tomoceridae) from China. Zoologica Scripta, 43(2014), 393-404. [More Information]
  • Jaratlerdsiri, W., Isberg, S., Higgins, D., Ho, S., Salomonsen, J., Skjodt, K., Miles, L., Gongora, J. (2014). Evolution of MHC class i in the Order Crocodylia. Immunogenetics, 66(1), 53-65. [More Information]
  • Brito, R., Fransisco, F., Ho, S., Oldroyd, B. (2014). Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera: Apidae: Meliponini). Biological Journal of the Linnean Society, 113, 149-161.
  • Li, X., Zhang, Z., Yu, A., Ho, S., Carr, M., Zheng, W., Zhang, Y., Zhu, C., Lei, F., Shi, W. (2014). Global and local persistence of influenza A(H5N1) virus. Emerging Infectious Diseases, 20(8), 1287-1295. [More Information]
  • Stiller, M., Molak, M., Prost, S., Rabeder, G., Baryshnikov, G., Rosendahl, W., Münzel, S., Bocherens, H., Grandal d'Anglade, A., Hilpert, B., Ho, S., et al (2014). Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231. [More Information]
  • Foster, C., Conn, B., Henwood, M., Ho, S. (2014). Molecular data support Orianthera: a new genus of Australian Loganiaceae. Telopea, 16, 149-158.
  • Foster, C., Conn, B., Henwood, M., Ho, S. (2014). Molecular data support Orianthera: a new genus of Australian Loganiaceae. Telopea, 16, 149-158. [More Information]
  • Foster, C., Ho, S., Conn, B., Henwood, M. (2014). Molecular systematics and biogeography of Logania R.Br. (Loganiaceae). Molecular Phylogenetics and Evolution, 78(2014), 324-333. [More Information]
  • Martin, M., Ho, S., Wales, N., Ristaino, J., Gilbert, M. (2014). Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world Phytophthora infestans. Molecular Biology and Evolution, 31(6), 1414-1420. [More Information]
  • Lee, T., Ho, S., Wilson, G., Lo, N. (2014). Phylogeography and diversity of the terrestrial isopod Spherillo grossus (Oniscidea: Armadillidae) on the Australian East Coast. Zoological Journal of the Linnean Society, 170(2), 297-309. [More Information]
  • Barnett, R., Yamaguchi, N., Shapiro, B., Ho, S., Barnes, I., Sabin, R., Werdelin, L., Cuisin, J., Larson, G. (2014). Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evolutionary Biology, 14(1), 1-11. [More Information]
  • Ho, S. (2014). The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution, 29(9), 496-503. [More Information]
  • Duchene, S., Lanfear, R., Ho, S. (2014). The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phylogenetics and Evolution, 78(1), 277-289. [More Information]
  • Jia, F., Lo, N., Ho, S. (2014). The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales. PloS One, 9(5), 1-8. [More Information]
  • Yasaka, R., Nguyen, H., Ho, S., Duchene, S., Korkmaz, S., Katis, N., Takahashi, H., Gibbs, A., Ohshima, K. (2014). The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus. PloS One, 9(1), 1-12. [More Information]
  • Duchene, S., Ho, S. (2014). Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data. Molecular Phylogenetics and Evolution, 77(2014), 65-70. [More Information]
  • Lorion, J., Kiel, S., Faure, B., Kawato, M., Ho, S., Marshall, B., Tsuchida, S., Miyazaki, J., Fujiwara, Y. (2013). Adaptive radiation of chemosymbiotic deep-sea mussels. Proceedings of the Royal Society B: Biological Sciences, 280(1770), 1-10. [More Information]
  • Foote, A., Kaschner, K., Schultze, S., Garilao, C., Ho, S., Post, K., Higham, T., Stokowska, C., Van Der Es, H., Embling, C., et al (2013). Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications, 4, 1-7. [More Information]
  • Langford, S., Kraitsek, S., Baskerville, B., Ho, S., Gongora, J. (2013). Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens. BMC Genetics, 14(Article 91), 1-8. [More Information]
  • Miller, J., Murphy, D., Ho, S., Cantrill, D., Seigler, D. (2013). Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany, 61(6), 436-445. [More Information]
  • Keis, M., Remm, J., Ho, S., Davison, J., Tammeleht, E., Tumanov, I., Saveljev, A., Mannil, P., Kojola, I., Abramov, A., et al (2013). Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia. Journal of Biogeography, 40(5), 915-927. [More Information]
  • Paraskevis, D., Magiorkinis, G., Magiorkinis, E., Ho, S., Belshaw, R., Allain, J., Hatzakis, A. (2013). Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology, 57(3), 908-916. [More Information]
  • Martinkova, N., Barnett, R., Cucchi, T., Struchen, R., Pascal, M., Pascal, M., Fischer, M., Higham, T., Brace, S., Ho, S., et al (2013). Divergent evolutionary processes associated with colonization of offshore islands. Molecular Ecology, 22(20), 5205-5220. [More Information]
  • Huang, Y., Guo, X., Ho, S., Shi, H., Li, J., Li, J., Cai, B., Wang, Y. (2013). Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland. PloS One, 8(6), 1-13. [More Information]
  • Brotherton, P., Haak, W., Templeton, J., Brandt, G., Soubrier, J., Adler, C., Richards, S., Der Sarkissian, C., Ganslmeier, R., Friedrich, S., Ho, S., et al (2013). Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications, 4, 1-11. [More Information]
  • Avila-Arcos, M., Ho, S., Ishida, Y., Nikolaidis, N., Tsangaras, K., Honig, K., Medina, R., Rasmussen, M., Fordyce, S., Calvignac-Spencer, S., et al (2013). One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution, 30(2), 299-304. [More Information]
  • Molak, M., Lorenzen, E., Shapiro, B., Ho, S. (2013). Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages. Molecular Biology and Evolution, 30(2), 253-262. [More Information]
  • Jin, Q., Han, H., Hu, X., Li, X., Zhu, C., Ho, S., Ward, R., Zhang, A. (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One, 8(5), 1-13. [More Information]
  • Martin, M., Cappellini, E., Samaniego, J., Zepeda, M., Campos, P., Seguin-Orlando, A., Wales, N., Orlando, L., Ho, S., Dietrich, F., et al (2013). Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 4, 1-7. [More Information]
  • Yeoh, S., Ho, S., Thornhill, A., Foley, W. (2013). Regional population expansion in Eucalyptus globulus. Molecular Phylogenetics and Evolution, 68(3), 498-501. [More Information]
  • Lanfear, R., Ho, S., Jonathan, D., Moles, A., Aarssen, L., Swenson, N., Warman, L., Zanne, A., Allen, A. (2013). Taller plants have lower rates of molecular evolution. Nature Communications, 4, 1-7. [More Information]
  • Ho, S., Lo, N. (2013). The insect molecular clock. Australian Journal of Entomology, 52(2), 101-105. [More Information]
  • Basu Mallick, C., Mircea Iliescu, F., Mols, M., Hill, S., Tamang, R., Chaubey, G., Goto, R., Ho, S., Gallego Romero, I., Crivellaro, F., et al (2013). The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genetics, 9(11), 1-13. [More Information]
  • Zhao, Z., Su, T., Chesters, D., Wang, S., Ho, S., Zhu, C., Chen, X., Zhang, C. (2013). The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies. PloS One, 8(4), 1-15. [More Information]
  • Nguyen, H., Tomitaka, Y., Ho, S., Duchene, S., Vetten, H., Lesemann, D., Walsh, J., Gibbs, A., Ohshima, K. (2013). Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago. PloS One, 8(2), 1-13. [More Information]
  • Greenwood, A., Tsangaras, K., Ho, S., Szentkis, C., Nikolin, V., Ma, G., Damiani, A., East, M., Lawrenz, A., Hofer, H., et al (2012). A Potentially Fatal Mix of Herpes in Zoos. Current Biology, 22, 1727-1731. [More Information]
  • Thornhill, A., Popple, L., Carter, R., Ho, S., Crisp, M. (2012). Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Molecular Phylogenetics and Evolution, 63(1), 15-27. [More Information]
  • Dos Santos Ferreira Lins, L., Ho, S., Wilson, G., Lo, N. (2012). Evidence for Permo-Triassic colonization of the deep sea by isopods. Biology Letters, 8(6), 979-982. [More Information]
  • Gongora, J., Swan, A., Chong, A., Ho, S., Damayanti, C., Kolomyjec, S., Grant, T., Miller, E., Blair, D., Furlan, E., et al (2012). Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA. Journal of Zoology, 286, 110-119. [More Information]
  • Lanfear, R., Calcott, B., Ho, S., Guindon, S. (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701. [More Information]
  • Larson, G., Karlsson, E., Perri, A., Webster, M., Ho, S., Peters, J., Stahl, P., Piper, P., Lingaas, F., Fredholm, M., et al (2012). Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 109(23), 8878-8883. [More Information]
  • Mourier, T., Ho, S., Gilbert, M., Willerslev, E., Orlando, L. (2012). Statistical guidelines for detecting past population shifts using ancient DNA. Molecular Biology and Evolution, 29(9), 2241-2251. [More Information]
  • Edwards, C., Soulsbury, C., Statham, M., Ho, S., Wall, D., Dolf, G., Lossa, G., Baker, P., Harris, S., Sacks, B., et al (2012). Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles. Quaternary Science Reviews, 57, 95-104.
  • Sauquet, H., Ho, S., Gondolfo, M., Jordan, G., Wilf, P., Cantrill, D., Bayly, M., Bromham, L., Brown, G., Carpenter, R., et al (2012). Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of nothofagus (Fagales). Systematic Biology, 61(2), 289-313. [More Information]
  • Soubrier, J., Steel, M., Lee, M., Der Sarkissian, C., Guindon, S., Ho, S., Cooper, A. (2012). The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular Biology and Evolution, 29(11), 3345-3358. [More Information]
  • Shapiro, B., Ho, S., Drummond, A., Suchard, M., Pybus, O., Rambaut, A. (2011). A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. Molecular Biology and Evolution, 28(2), 879-887. [More Information]
  • Ho, S., Lanfear, R., Phillips, M., Barnes, I., Thomas, J., Kolokotronis, S., Shapiro, B. (2011). Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology, 60(3), 1-10. [More Information]
  • Wong, J., Ho, S., Hogg, P. (2011). Disulfide bond acquisition through eukaryotic protein evolution. Molecular Biology and Evolution, 28(1), 327-334. [More Information]
  • Molak, M., Ho, S. (2011). Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach. Journal of Molecular Evolution, 73(3-4), 244-255. [More Information]
  • Davison, J., Ho, S., Bray, S., Korsten, M., Tammeleht, E., Hindrikson, M., Ostbye, K., Ostbye, E., Lauritzen, S., Austin, J., et al (2011). Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews, 30(3-4), 418-430. [More Information]
  • Lanfear, R., Ho, S. (2011). Mito-communications. Mitochondrial DNA, 22(3), 39-40.
  • Vilstrup, J., Ho, S., Foote, A., Morin, P., Kreb, D., Krutzen, M., Parra, G., Robertson, K., de Stephanis, R., Verborgh, P., et al (2011). Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evolutionary Biology, 11(1, Article number 65), 65-1-65-10. [More Information]
  • Li, W., Shi, W., Qiao, H., Ho, S., Luo, A., Zhang, Y., Zhu, C. (2011). Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virology Journal, 8, 1-9. [More Information]
  • Luo, A., Zhang, A., Ho, S., Xu, W., Zhang, Y., Shi, W., Cameron, S., Zhu, C. (2011). Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals. BMC Genomics, 12, 1-13. [More Information]
  • Lanfear, R., Bromham, L., Ho, S. (2011). Reply to Englund: Molecular evolution and diversification - Counting species is better than counting nodes when the phylogeny is unknown. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 108(17), E85-E86. [More Information]
  • Gongora, J., Cuddahee, R., do Nascimento, F., Palgrave, C., Lowden, S., Ho, S., Simond, D., Damayanti, C., White, D., Tay, W., Rodrigues-Zarate, C., Moran, C., et al (2011). Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla). Zoologica Scripta, 40(4), 327-335. [More Information]
  • Ho, S., Shapiro, B. (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources, 11(3), 423-434. [More Information]
  • Lorenzen, E., Nogues-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K., Ugan, A., Borregaard, M., Gilbert, M., Nielsen, R., Ho, S., et al (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479(7373), 359-364. [More Information]
  • Pepper, M., Ho, S., Fujita, M., Keogh, S. (2011). The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate. Molecular Phylogenetics and Evolution, 61(3), 750-759. [More Information]
  • Ho, S., Lanfear, R., Bromham, L., Phillips, M., Soubrier, J., Rodrigo, A., Cooper, A. (2011). Time-dependent rates of molecular evolution. Molecular Ecology, 20(15), 3087-3101. [More Information]
  • Nguyen, J., Molak, M., Black, K., Fitzgerald, E., Travouillon, T., Ho, S. (2011). Vertebrate palaeontology of australasia into the twenty-first century. Biology Letters, 7(6), 804-806. [More Information]
  • Ho, S., Gilbert, M. (2010). Ancient mitogenomics. Mitochondrion, 10(1), 1-11. [More Information]
  • Ho, S., Lanfear, R. (2010). Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA, 21(3-4), 138-146. [More Information]
  • Ho, S., Lanfear, R. (2010). Mito-communications. Mitochondrial DNA, 21(5), 147-148. [More Information]
  • Lanfear, R., Ho, S., Love, D., Bromham, L. (2010). Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 107(47), 20423-20428. [More Information]
  • Luo, A., Qiao, H., Zhang, Y., Shi, W., Ho, S., Xu, W., Zhang, A., Zhu, C. (2010). Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evolutionary Biology, 10(242), 1-13. [More Information]
  • Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S., Vila, C., Hasegawa, M., et al (2010). Phylogeographic analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal of Biogeography, 37(12), 2332-2344. [More Information]
  • Salvo, G., Ho, S., Rosenbaum, G., Ree, R., Conti, E. (2010). Tracing the temporal and spatial origins of island endemics in the Mediterranean region: A case study from the citrus family (Ruta L., Rutaceae). Systematic Biology, 59(6), 705-722. [More Information]
  • Endicott, P., Ho, S., Stringer, C. (2010). Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and Modern Human origins. Journal of Human Evolution, 59(1), 87-95. [More Information]
  • Rambaut, A., Ho, S., Drummond, A., Shapiro, B. (2009). Accommodating the effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution, 26(2), 245-248. [More Information]
  • Ho, S., Phillips, M. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58(3), 367-380. [More Information]
  • Ho, S. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters, 5(3), 421-424. [More Information]
  • Willerslev, E., Gilbert, M., Binladen, J., Ho, S., Campos, P., Ratan, A., Tomsho, L., da Fonseca, R., Sher, A., Kuznetsova, T., et al (2009). Analysis of complete mitochondrial genome from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evolutionary Biology, 9, 1-11. [More Information]
  • Chatterjee, H., Ho, S., Barnes, I., Groves, C. (2009). Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evolutionary Biology, 9(1), 1-19. [More Information]
  • Endicott, P., Ho, S., Metspalu, M., Stringer, C. (2009). Evaluating the mitochondrial timescale of human evolution. Trends in Ecology and Evolution, 24(9), 515-521. [More Information]
  • Barnett, R., Shapiro, B., Barnes, I., Ho, S., Burger, J., Yamaguchi, N., Higham, T., Wheeler, H., Rosendahl, W., Sher, A., et al (2009). Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology, 18(8), 1668-1677. [More Information]
  • Steeman, M., Hebsgaard, M., Fordyce, R., Ho, S., Rabosky, D., Nielsen, R., Rahbek, C., Glenner, H., Sorensen, M., Willerslev, E. (2009). Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58(6), 573-585. [More Information]
  • Korsten, M., Ho, S., Davison, J., Pahn, B., Vulla, E., Roht, M., Tumanov, I., Kojola, I., Andersone-Lilley, Z., Ozolins, J., et al (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(9), 1963-1979. [More Information]
  • Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Ho, S., Shapiro, B., Pybus, O., Allain, J., Hatzakis, A. (2009). The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis. PLoS Medicine, 6(12), 1-12. [More Information]
  • Endicott, P., Ho, S. (2008). A Bayesian Evaluation of Human Mitochondrial Substitution Rates. American Journal of Human Genetics, 82(4), 895-902. [More Information]
  • Buckley, M., Walker, A., Ho, S., Yang, Y., Smith, C., Ashton, P., Oates, J., Cappellini, E., Koon, H., Penkman, K., et al (2008). Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry�? Science, 319(5859), 33-33. [More Information]
  • Ho, S., Larson, G., Edwards, C., Heupink, T., Lakin, K., Holland, P., Shapiro, B. (2008). Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biology Letters, 4(4), 370-374. [More Information]
  • Barik, S., Sahani, R., Prasad, B., Endicott, P., Metspalu, M., Sarkar, B., Bhattacharya, S., Annapoorna, P., Sreenath, J., Sun, D., et al (2008). Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. American Journal of Physical Anthropology, 136(1), 19-27. [More Information]
  • Ware, J., Ho, S., Kjer, K. (2008). Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models. Molecular Phylogenetics and Evolution, 47(1), 426-432. [More Information]
  • Gilbert, M., Drautz, D., Lesk, A., Ho, S., Qi, J., Ratan, A., Hsu, C., Sher, A., Dalen, L., Gotherstrom, A., et al (2008). Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 105(24), 8327-8332. [More Information]
  • Ho, S., Endicott, P. (2008). The crucial role of calibration in molecular date estimates for the peopling of the Americas. American Journal of Human Genetics, 83(1), 142-146. [More Information]
  • Ho, S., Saarma, U., Barnett, R., Haile, J., Shapiro, B. (2008). The effect of inappropriate calibration: Three case studies in molecular ecology. PloS One, 3(2), 1-8. [More Information]
  • Ho, S. (2008). The molecular clock and estimating species divergence. Nature Education Knowledge, 1(1), 168-168.
  • Haile, J., Holdaway, R., Oliver, K., Bunce, M., Gilbert, M., Nielsen, R., Munch, K., Ho, S., Shapiro, B., Willerslev, E. (2007). Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution, 24(4), 982-989. [More Information]
  • Ho, S., Heupink, T., Rambaut, A., Shapiro, B. (2007). Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution, 24(6), 1416-1422. [More Information]
  • Ho, S. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38(4), 409-414. [More Information]
  • Ho, S., Kolokotronis, S., Allaby, R. (2007). Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, 3(6), 702-705. [More Information]
  • Ho, S., Shapiro, B., Phillips, M., Cooper, A., Drummond, A. (2007). Evidence for time dependency of molecular rate estimates. Systematic Biology, 56(3), 515-522. [More Information]
  • Edwards, C., Bollongino, R., Scheu, A., Chamberlain, A., Tresset, A., Vigne, J., Baird, J., Larson, G., Ho, S., Heupink, T., et al (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 B: Biological Sciences, 274(1616), 1377-1385. [More Information]
  • Saarma, U., Ho, S., Pybus, O., Kaljuste, M., Tumanov, I., Kojola, I., Vorobiev, A., Markov, N., Saveljev, A., Valdmann, H., et al (2007). Mitogenetic structure of brown bears (Ursus arctos L.) in north-eastern Europe and a new time-frame for the formation of European brown bears. Molecular Ecology, 16(2), 401-413. [More Information]
  • Hyman, I., Ho, S., Jermiin, L. (2007). Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Molecular Phylogenetics and Evolution, 45(3), 792-812.
  • Binladen, J., Wiuf, C., Gilbert, M., Bunce, M., Barnett, R., Larson, G., Greenwood, A., Haile, J., Ho, S., Hansen, A., et al (2006). Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172(2), 733-741. [More Information]
  • Ho, S., Larson, G. (2006). Molecular clocks: when times are a-changin’. Trends in Genetics, 22(2), 79-83. [More Information]
  • Drummond, A., Ho, S., Phillips, M., Rambaut, A. (2006). Relaxed Phylogenetics and Dating with Confidence. PLoS Biology, 4(5), 0699-0710. [More Information]
  • Peng, Z., Ho, S., Zhang, Y., He, S. (2006). Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Molecular Phylogenetics and Evolution, 39(2), 568-572. [More Information]
  • Ho, S., Phillips, M., Drummond, A., 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(5), 1355-1363. [More Information]
  • Weinstock, J., Willerslev, E., Sher, A., Tong, W., Ho, S., Rubenstein, D., Storer, J., Burns, J., Martin, L., Bravi, C., et al (2005). Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective. PLoS Biology, 3(8), e241 - 1373-e241 - 1379. [More Information]
  • Murray, S., Flo Jorgensen, M., Ho, S., Patterson, D., Jermiin, L. (2005). Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist, 156(3), 269-286.
  • Ho, S., Phillips, M., Cooper, A., Drummond, A. (2005). Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22(7), 1561-1568. [More Information]
  • Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2004). The Biasing Effect Of Compositional Heterogeneity On Phylogenetic Estimates May Be Underestimated. Systematic Biology, 53(4), 638-643.
  • Ho, S., Jermiin, L. (2004). Tracing The Decay Of The Historical Signal In Biological Sequence Data. Systematic Biology, 53(4), 623-637.
  • Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2003). Hetero: a program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics, 2(3), 159-163.

2015

  • Lee, T., Cameron, S., Evans, T., Ho, S., Lo, N. (2015). The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers. Molecular Phylogenetics and Evolution, 82, 234-244.

2014

  • Hope, A., Ho, S., Malaney, J., Cook, J., Talbot, S. (2014). Accounting for rate variation among lineages in comparative demographic analyses. Evolution, 68-69, 2689-2700.
  • Duchene, S., Holmes, E., Ho, S. (2014). Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society B: Biological Sciences, 281(1786), 1-7. [More Information]
  • Shapiro, B., Ho, S. (2014). Ancient hyaenas highlight the old problem of estimating evolutionary rates. Molecular Ecology, 23, 499-501.
  • Duchene, S., Molak, M., Ho, S. (2014). ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics, 30(7), 1017-1019. [More Information]
  • Edwards, C., Ho, S., Barnett, R., Coxon, P., B̀radley, D., Lord, T., O'Connor, T. (2014). Continuity of brown bear maternal lineages in northern England through the Last-glacial period. Quaternary Science Reviews, 96(2014), 131-139. [More Information]
  • Zhang, F., Yu, D., Luo, Y., Ho, S., Wang, B., Zhu, C. (2014). Cryptic diversity, diversification and vicariance in two species complexes of Tomocerus (Collembola, Tomoceridae) from China. Zoologica Scripta, 43(2014), 393-404. [More Information]
  • Jaratlerdsiri, W., Isberg, S., Higgins, D., Ho, S., Salomonsen, J., Skjodt, K., Miles, L., Gongora, J. (2014). Evolution of MHC class i in the Order Crocodylia. Immunogenetics, 66(1), 53-65. [More Information]
  • Brito, R., Fransisco, F., Ho, S., Oldroyd, B. (2014). Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera: Apidae: Meliponini). Biological Journal of the Linnean Society, 113, 149-161.
  • Li, X., Zhang, Z., Yu, A., Ho, S., Carr, M., Zheng, W., Zhang, Y., Zhu, C., Lei, F., Shi, W. (2014). Global and local persistence of influenza A(H5N1) virus. Emerging Infectious Diseases, 20(8), 1287-1295. [More Information]
  • Stiller, M., Molak, M., Prost, S., Rabeder, G., Baryshnikov, G., Rosendahl, W., Münzel, S., Bocherens, H., Grandal d'Anglade, A., Hilpert, B., Ho, S., et al (2014). Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231. [More Information]
  • Foster, C., Conn, B., Henwood, M., Ho, S. (2014). Molecular data support Orianthera: a new genus of Australian Loganiaceae. Telopea, 16, 149-158.
  • Foster, C., Conn, B., Henwood, M., Ho, S. (2014). Molecular data support Orianthera: a new genus of Australian Loganiaceae. Telopea, 16, 149-158. [More Information]
  • Foster, C., Ho, S., Conn, B., Henwood, M. (2014). Molecular systematics and biogeography of Logania R.Br. (Loganiaceae). Molecular Phylogenetics and Evolution, 78(2014), 324-333. [More Information]
  • Martin, M., Ho, S., Wales, N., Ristaino, J., Gilbert, M. (2014). Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world Phytophthora infestans. Molecular Biology and Evolution, 31(6), 1414-1420. [More Information]
  • Lee, T., Ho, S., Wilson, G., Lo, N. (2014). Phylogeography and diversity of the terrestrial isopod Spherillo grossus (Oniscidea: Armadillidae) on the Australian East Coast. Zoological Journal of the Linnean Society, 170(2), 297-309. [More Information]
  • Barnett, R., Yamaguchi, N., Shapiro, B., Ho, S., Barnes, I., Sabin, R., Werdelin, L., Cuisin, J., Larson, G. (2014). Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evolutionary Biology, 14(1), 1-11. [More Information]
  • Ho, S. (2014). The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution, 29(9), 496-503. [More Information]
  • Duchene, S., Lanfear, R., Ho, S. (2014). The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phylogenetics and Evolution, 78(1), 277-289. [More Information]
  • Jia, F., Lo, N., Ho, S. (2014). The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales. PloS One, 9(5), 1-8. [More Information]
  • Yasaka, R., Nguyen, H., Ho, S., Duchene, S., Korkmaz, S., Katis, N., Takahashi, H., Gibbs, A., Ohshima, K. (2014). The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus. PloS One, 9(1), 1-12. [More Information]
  • Duchene, S., Ho, S. (2014). Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data. Molecular Phylogenetics and Evolution, 77(2014), 65-70. [More Information]

2013

  • Lorion, J., Kiel, S., Faure, B., Kawato, M., Ho, S., Marshall, B., Tsuchida, S., Miyazaki, J., Fujiwara, Y. (2013). Adaptive radiation of chemosymbiotic deep-sea mussels. Proceedings of the Royal Society B: Biological Sciences, 280(1770), 1-10. [More Information]
  • Foote, A., Kaschner, K., Schultze, S., Garilao, C., Ho, S., Post, K., Higham, T., Stokowska, C., Van Der Es, H., Embling, C., et al (2013). Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications, 4, 1-7. [More Information]
  • Langford, S., Kraitsek, S., Baskerville, B., Ho, S., Gongora, J. (2013). Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens. BMC Genetics, 14(Article 91), 1-8. [More Information]
  • Miller, J., Murphy, D., Ho, S., Cantrill, D., Seigler, D. (2013). Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany, 61(6), 436-445. [More Information]
  • Keis, M., Remm, J., Ho, S., Davison, J., Tammeleht, E., Tumanov, I., Saveljev, A., Mannil, P., Kojola, I., Abramov, A., et al (2013). Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia. Journal of Biogeography, 40(5), 915-927. [More Information]
  • Paraskevis, D., Magiorkinis, G., Magiorkinis, E., Ho, S., Belshaw, R., Allain, J., Hatzakis, A. (2013). Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology, 57(3), 908-916. [More Information]
  • Martinkova, N., Barnett, R., Cucchi, T., Struchen, R., Pascal, M., Pascal, M., Fischer, M., Higham, T., Brace, S., Ho, S., et al (2013). Divergent evolutionary processes associated with colonization of offshore islands. Molecular Ecology, 22(20), 5205-5220. [More Information]
  • Huang, Y., Guo, X., Ho, S., Shi, H., Li, J., Li, J., Cai, B., Wang, Y. (2013). Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland. PloS One, 8(6), 1-13. [More Information]
  • Brotherton, P., Haak, W., Templeton, J., Brandt, G., Soubrier, J., Adler, C., Richards, S., Der Sarkissian, C., Ganslmeier, R., Friedrich, S., Ho, S., et al (2013). Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications, 4, 1-11. [More Information]
  • Avila-Arcos, M., Ho, S., Ishida, Y., Nikolaidis, N., Tsangaras, K., Honig, K., Medina, R., Rasmussen, M., Fordyce, S., Calvignac-Spencer, S., et al (2013). One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution, 30(2), 299-304. [More Information]
  • Molak, M., Lorenzen, E., Shapiro, B., Ho, S. (2013). Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages. Molecular Biology and Evolution, 30(2), 253-262. [More Information]
  • Jin, Q., Han, H., Hu, X., Li, X., Zhu, C., Ho, S., Ward, R., Zhang, A. (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One, 8(5), 1-13. [More Information]
  • Martin, M., Cappellini, E., Samaniego, J., Zepeda, M., Campos, P., Seguin-Orlando, A., Wales, N., Orlando, L., Ho, S., Dietrich, F., et al (2013). Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 4, 1-7. [More Information]
  • Yeoh, S., Ho, S., Thornhill, A., Foley, W. (2013). Regional population expansion in Eucalyptus globulus. Molecular Phylogenetics and Evolution, 68(3), 498-501. [More Information]
  • Lanfear, R., Ho, S., Jonathan, D., Moles, A., Aarssen, L., Swenson, N., Warman, L., Zanne, A., Allen, A. (2013). Taller plants have lower rates of molecular evolution. Nature Communications, 4, 1-7. [More Information]
  • Ho, S., Lo, N. (2013). The insect molecular clock. Australian Journal of Entomology, 52(2), 101-105. [More Information]
  • Basu Mallick, C., Mircea Iliescu, F., Mols, M., Hill, S., Tamang, R., Chaubey, G., Goto, R., Ho, S., Gallego Romero, I., Crivellaro, F., et al (2013). The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genetics, 9(11), 1-13. [More Information]
  • Zhao, Z., Su, T., Chesters, D., Wang, S., Ho, S., Zhu, C., Chen, X., Zhang, C. (2013). The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies. PloS One, 8(4), 1-15. [More Information]
  • Nguyen, H., Tomitaka, Y., Ho, S., Duchene, S., Vetten, H., Lesemann, D., Walsh, J., Gibbs, A., Ohshima, K. (2013). Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago. PloS One, 8(2), 1-13. [More Information]

2012

  • Greenwood, A., Tsangaras, K., Ho, S., Szentkis, C., Nikolin, V., Ma, G., Damiani, A., East, M., Lawrenz, A., Hofer, H., et al (2012). A Potentially Fatal Mix of Herpes in Zoos. Current Biology, 22, 1727-1731. [More Information]
  • Thornhill, A., Popple, L., Carter, R., Ho, S., Crisp, M. (2012). Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Molecular Phylogenetics and Evolution, 63(1), 15-27. [More Information]
  • Dos Santos Ferreira Lins, L., Ho, S., Wilson, G., Lo, N. (2012). Evidence for Permo-Triassic colonization of the deep sea by isopods. Biology Letters, 8(6), 979-982. [More Information]
  • Gongora, J., Swan, A., Chong, A., Ho, S., Damayanti, C., Kolomyjec, S., Grant, T., Miller, E., Blair, D., Furlan, E., et al (2012). Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA. Journal of Zoology, 286, 110-119. [More Information]
  • Lanfear, R., Calcott, B., Ho, S., Guindon, S. (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701. [More Information]
  • Ho, S. (2012). Phylogenetic Analysis of Ancient DNA using BEAST. In Beth Shapiro and Michael Hofreiter (Eds.), Methods in Molecular Biology, 840: Ancient DNA, (pp. 229-241). New York: Humana Press. [More Information]
  • Larson, G., Karlsson, E., Perri, A., Webster, M., Ho, S., Peters, J., Stahl, P., Piper, P., Lingaas, F., Fredholm, M., et al (2012). Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 109(23), 8878-8883. [More Information]
  • Mourier, T., Ho, S., Gilbert, M., Willerslev, E., Orlando, L. (2012). Statistical guidelines for detecting past population shifts using ancient DNA. Molecular Biology and Evolution, 29(9), 2241-2251. [More Information]
  • Edwards, C., Soulsbury, C., Statham, M., Ho, S., Wall, D., Dolf, G., Lossa, G., Baker, P., Harris, S., Sacks, B., et al (2012). Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles. Quaternary Science Reviews, 57, 95-104.
  • Sauquet, H., Ho, S., Gondolfo, M., Jordan, G., Wilf, P., Cantrill, D., Bayly, M., Bromham, L., Brown, G., Carpenter, R., et al (2012). Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of nothofagus (Fagales). Systematic Biology, 61(2), 289-313. [More Information]
  • Soubrier, J., Steel, M., Lee, M., Der Sarkissian, C., Guindon, S., Ho, S., Cooper, A. (2012). The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular Biology and Evolution, 29(11), 3345-3358. [More Information]

2011

  • Shapiro, B., Ho, S., Drummond, A., Suchard, M., Pybus, O., Rambaut, A. (2011). A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. Molecular Biology and Evolution, 28(2), 879-887. [More Information]
  • Ho, S., Lanfear, R., Phillips, M., Barnes, I., Thomas, J., Kolokotronis, S., Shapiro, B. (2011). Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology, 60(3), 1-10. [More Information]
  • Wong, J., Ho, S., Hogg, P. (2011). Disulfide bond acquisition through eukaryotic protein evolution. Molecular Biology and Evolution, 28(1), 327-334. [More Information]
  • Molak, M., Ho, S. (2011). Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach. Journal of Molecular Evolution, 73(3-4), 244-255. [More Information]
  • Davison, J., Ho, S., Bray, S., Korsten, M., Tammeleht, E., Hindrikson, M., Ostbye, K., Ostbye, E., Lauritzen, S., Austin, J., et al (2011). Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews, 30(3-4), 418-430. [More Information]
  • Lanfear, R., Ho, S. (2011). Mito-communications. Mitochondrial DNA, 22(3), 39-40.
  • Vilstrup, J., Ho, S., Foote, A., Morin, P., Kreb, D., Krutzen, M., Parra, G., Robertson, K., de Stephanis, R., Verborgh, P., et al (2011). Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evolutionary Biology, 11(1, Article number 65), 65-1-65-10. [More Information]
  • Li, W., Shi, W., Qiao, H., Ho, S., Luo, A., Zhang, Y., Zhu, C. (2011). Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virology Journal, 8, 1-9. [More Information]
  • Luo, A., Zhang, A., Ho, S., Xu, W., Zhang, Y., Shi, W., Cameron, S., Zhu, C. (2011). Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals. BMC Genomics, 12, 1-13. [More Information]
  • Lanfear, R., Bromham, L., Ho, S. (2011). Reply to Englund: Molecular evolution and diversification - Counting species is better than counting nodes when the phylogeny is unknown. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 108(17), E85-E86. [More Information]
  • Gongora, J., Cuddahee, R., do Nascimento, F., Palgrave, C., Lowden, S., Ho, S., Simond, D., Damayanti, C., White, D., Tay, W., Rodrigues-Zarate, C., Moran, C., et al (2011). Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla). Zoologica Scripta, 40(4), 327-335. [More Information]
  • Ho, S., Shapiro, B. (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources, 11(3), 423-434. [More Information]
  • Lorenzen, E., Nogues-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K., Ugan, A., Borregaard, M., Gilbert, M., Nielsen, R., Ho, S., et al (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479(7373), 359-364. [More Information]
  • Pepper, M., Ho, S., Fujita, M., Keogh, S. (2011). The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate. Molecular Phylogenetics and Evolution, 61(3), 750-759. [More Information]
  • Ho, S., Lanfear, R., Bromham, L., Phillips, M., Soubrier, J., Rodrigo, A., Cooper, A. (2011). Time-dependent rates of molecular evolution. Molecular Ecology, 20(15), 3087-3101. [More Information]
  • Nguyen, J., Molak, M., Black, K., Fitzgerald, E., Travouillon, T., Ho, S. (2011). Vertebrate palaeontology of australasia into the twenty-first century. Biology Letters, 7(6), 804-806. [More Information]

2010

  • Ho, S., Gilbert, M. (2010). Ancient mitogenomics. Mitochondrion, 10(1), 1-11. [More Information]
  • Ho, S., Lanfear, R. (2010). Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA, 21(3-4), 138-146. [More Information]
  • Ho, S., Lanfear, R. (2010). Mito-communications. Mitochondrial DNA, 21(5), 147-148. [More Information]
  • Lanfear, R., Ho, S., Love, D., Bromham, L. (2010). Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 107(47), 20423-20428. [More Information]
  • Luo, A., Qiao, H., Zhang, Y., Shi, W., Ho, S., Xu, W., Zhang, A., Zhu, C. (2010). Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evolutionary Biology, 10(242), 1-13. [More Information]
  • Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S., Vila, C., Hasegawa, M., et al (2010). Phylogeographic analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal of Biogeography, 37(12), 2332-2344. [More Information]
  • Salvo, G., Ho, S., Rosenbaum, G., Ree, R., Conti, E. (2010). Tracing the temporal and spatial origins of island endemics in the Mediterranean region: A case study from the citrus family (Ruta L., Rutaceae). Systematic Biology, 59(6), 705-722. [More Information]
  • Endicott, P., Ho, S., Stringer, C. (2010). Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and Modern Human origins. Journal of Human Evolution, 59(1), 87-95. [More Information]

2009

  • Rambaut, A., Ho, S., Drummond, A., Shapiro, B. (2009). Accommodating the effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution, 26(2), 245-248. [More Information]
  • Ho, S., Phillips, M. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58(3), 367-380. [More Information]
  • Ho, S. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters, 5(3), 421-424. [More Information]
  • Willerslev, E., Gilbert, M., Binladen, J., Ho, S., Campos, P., Ratan, A., Tomsho, L., da Fonseca, R., Sher, A., Kuznetsova, T., et al (2009). Analysis of complete mitochondrial genome from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evolutionary Biology, 9, 1-11. [More Information]
  • Chatterjee, H., Ho, S., Barnes, I., Groves, C. (2009). Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evolutionary Biology, 9(1), 1-19. [More Information]
  • Endicott, P., Ho, S., Metspalu, M., Stringer, C. (2009). Evaluating the mitochondrial timescale of human evolution. Trends in Ecology and Evolution, 24(9), 515-521. [More Information]
  • Barnett, R., Shapiro, B., Barnes, I., Ho, S., Burger, J., Yamaguchi, N., Higham, T., Wheeler, H., Rosendahl, W., Sher, A., et al (2009). Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology, 18(8), 1668-1677. [More Information]
  • Steeman, M., Hebsgaard, M., Fordyce, R., Ho, S., Rabosky, D., Nielsen, R., Rahbek, C., Glenner, H., Sorensen, M., Willerslev, E. (2009). Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58(6), 573-585. [More Information]
  • Korsten, M., Ho, S., Davison, J., Pahn, B., Vulla, E., Roht, M., Tumanov, I., Kojola, I., Andersone-Lilley, Z., Ozolins, J., et al (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(9), 1963-1979. [More Information]
  • Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Ho, S., Shapiro, B., Pybus, O., Allain, J., Hatzakis, A. (2009). The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis. PLoS Medicine, 6(12), 1-12. [More Information]

2008

  • Endicott, P., Ho, S. (2008). A Bayesian Evaluation of Human Mitochondrial Substitution Rates. American Journal of Human Genetics, 82(4), 895-902. [More Information]
  • Buckley, M., Walker, A., Ho, S., Yang, Y., Smith, C., Ashton, P., Oates, J., Cappellini, E., Koon, H., Penkman, K., et al (2008). Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry�? Science, 319(5859), 33-33. [More Information]
  • Ho, S., Larson, G., Edwards, C., Heupink, T., Lakin, K., Holland, P., Shapiro, B. (2008). Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biology Letters, 4(4), 370-374. [More Information]
  • Barik, S., Sahani, R., Prasad, B., Endicott, P., Metspalu, M., Sarkar, B., Bhattacharya, S., Annapoorna, P., Sreenath, J., Sun, D., et al (2008). Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. American Journal of Physical Anthropology, 136(1), 19-27. [More Information]
  • Ware, J., Ho, S., Kjer, K. (2008). Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models. Molecular Phylogenetics and Evolution, 47(1), 426-432. [More Information]
  • Gilbert, M., Drautz, D., Lesk, A., Ho, S., Qi, J., Ratan, A., Hsu, C., Sher, A., Dalen, L., Gotherstrom, A., et al (2008). Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences (PNAS) of the United States of America, 105(24), 8327-8332. [More Information]
  • Ho, S., Endicott, P. (2008). The crucial role of calibration in molecular date estimates for the peopling of the Americas. American Journal of Human Genetics, 83(1), 142-146. [More Information]
  • Ho, S., Saarma, U., Barnett, R., Haile, J., Shapiro, B. (2008). The effect of inappropriate calibration: Three case studies in molecular ecology. PloS One, 3(2), 1-8. [More Information]
  • Ho, S. (2008). The molecular clock and estimating species divergence. Nature Education Knowledge, 1(1), 168-168.

2007

  • Haile, J., Holdaway, R., Oliver, K., Bunce, M., Gilbert, M., Nielsen, R., Munch, K., Ho, S., Shapiro, B., Willerslev, E. (2007). Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution, 24(4), 982-989. [More Information]
  • Ho, S., Heupink, T., Rambaut, A., Shapiro, B. (2007). Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution, 24(6), 1416-1422. [More Information]
  • Ho, S. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38(4), 409-414. [More Information]
  • Ho, S., Kolokotronis, S., Allaby, R. (2007). Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, 3(6), 702-705. [More Information]
  • Ho, S., Shapiro, B., Phillips, M., Cooper, A., Drummond, A. (2007). Evidence for time dependency of molecular rate estimates. Systematic Biology, 56(3), 515-522. [More Information]
  • Edwards, C., Bollongino, R., Scheu, A., Chamberlain, A., Tresset, A., Vigne, J., Baird, J., Larson, G., Ho, S., Heupink, T., et al (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 B: Biological Sciences, 274(1616), 1377-1385. [More Information]
  • Saarma, U., Ho, S., Pybus, O., Kaljuste, M., Tumanov, I., Kojola, I., Vorobiev, A., Markov, N., Saveljev, A., Valdmann, H., et al (2007). Mitogenetic structure of brown bears (Ursus arctos L.) in north-eastern Europe and a new time-frame for the formation of European brown bears. Molecular Ecology, 16(2), 401-413. [More Information]
  • Hyman, I., Ho, S., Jermiin, L. (2007). Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Molecular Phylogenetics and Evolution, 45(3), 792-812.

2006

  • Binladen, J., Wiuf, C., Gilbert, M., Bunce, M., Barnett, R., Larson, G., Greenwood, A., Haile, J., Ho, S., Hansen, A., et al (2006). Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172(2), 733-741. [More Information]
  • Ho, S., Larson, G. (2006). Molecular clocks: when times are a-changin’. Trends in Genetics, 22(2), 79-83. [More Information]
  • Drummond, A., Ho, S., Phillips, M., Rambaut, A. (2006). Relaxed Phylogenetics and Dating with Confidence. PLoS Biology, 4(5), 0699-0710. [More Information]
  • Peng, Z., Ho, S., Zhang, Y., He, S. (2006). Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Molecular Phylogenetics and Evolution, 39(2), 568-572. [More Information]

2005

  • Ho, S., Phillips, M., Drummond, A., 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(5), 1355-1363. [More Information]
  • Weinstock, J., Willerslev, E., Sher, A., Tong, W., Ho, S., Rubenstein, D., Storer, J., Burns, J., Martin, L., Bravi, C., et al (2005). Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective. PLoS Biology, 3(8), e241 - 1373-e241 - 1379. [More Information]
  • Murray, S., Flo Jorgensen, M., Ho, S., Patterson, D., Jermiin, L. (2005). Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist, 156(3), 269-286.
  • Ho, S., Phillips, M., Cooper, A., Drummond, A. (2005). Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22(7), 1561-1568. [More Information]

2004

  • Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2004). The Biasing Effect Of Compositional Heterogeneity On Phylogenetic Estimates May Be Underestimated. Systematic Biology, 53(4), 638-643.
  • Ho, S., Jermiin, L. (2004). Tracing The Decay Of The Historical Signal In Biological Sequence Data. Systematic Biology, 53(4), 623-637.

2003

  • Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2003). Hetero: a program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics, 2(3), 159-163.

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