Simon Y W Ho

Summary

Publications

  1. pmc The effect of inappropriate calibration: three case studies in molecular ecology
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS ONE 3:e1615. 2008
  2. doi request reprint Phylogenetic analysis of ancient DNA using BEAST
    Simon Y W Ho
    School of Biological Sciences, University of Sydney, Sydney, 2006, NSW, Australia
    Methods Mol Biol 840:229-41. 2012
  3. pmc Elevated substitution rates estimated from ancient DNA sequences
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Biol Lett 3:702-5. 2007
  4. doi request reprint Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity
    Ross Barnett
    Department of Zoology, University of Oxford, Oxford, UK
    Mol Ecol 18:1668-77. 2009
  5. ncbi request reprint Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
    James Haile
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
    Mol Biol Evol 24:982-9. 2007
  6. pmc Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, UK
    Biol Lett 4:370-4. 2008
  7. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
  8. ncbi request reprint Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
    Simon Y W Ho
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1561-8. 2005
  9. ncbi request reprint Bayesian estimation of sequence damage in ancient DNA
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:1416-22. 2007
  10. ncbi request reprint Hetero: a program to simulate the evolution of DNA on a four-taxon tree
    Lars S Jermiin
    School of Biological Sciences, University of Sydney, NSW, Australia
    Appl Bioinformatics 2:159-63. 2003

Collaborators

Detail Information

Publications37

  1. pmc The effect of inappropriate calibration: three case studies in molecular ecology
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS ONE 3:e1615. 2008
    ..Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events...
  2. doi request reprint Phylogenetic analysis of ancient DNA using BEAST
    Simon Y W Ho
    School of Biological Sciences, University of Sydney, Sydney, 2006, NSW, Australia
    Methods Mol Biol 840:229-41. 2012
    ..A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content...
  3. pmc Elevated substitution rates estimated from ancient DNA sequences
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Biol Lett 3:702-5. 2007
    ..Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels...
  4. doi request reprint Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity
    Ross Barnett
    Department of Zoology, University of Oxford, Oxford, UK
    Mol Ecol 18:1668-77. 2009
    ....
  5. ncbi request reprint Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
    James Haile
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
    Mol Biol Evol 24:982-9. 2007
    ..Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for...
  6. pmc Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, UK
    Biol Lett 4:370-4. 2008
    ..The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence...
  7. pmc Relaxed phylogenetics and dating with confidence
    Alexei J Drummond
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS Biol 4:e88. 2006
    ..From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution...
  8. ncbi request reprint Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
    Simon Y W Ho
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 22:1561-8. 2005
    ....
  9. ncbi request reprint Bayesian estimation of sequence damage in ancient DNA
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:1416-22. 2007
    ....
  10. ncbi request reprint Hetero: a program to simulate the evolution of DNA on a four-taxon tree
    Lars S Jermiin
    School of Biological Sciences, University of Sydney, NSW, Australia
    Appl Bioinformatics 2:159-63. 2003
    ..It has a simple user interface and output, making it equally useful in the teaching and research of phylogenetics...
  11. ncbi request reprint Evidence for time dependency of molecular rate estimates
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Syst Biol 56:515-22. 2007
  12. doi request reprint Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages
    Martyna Molak
    School of Biological Sciences, University of Sydney, Sydney, Australia
    Mol Biol Evol 30:253-62. 2013
    ..These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics...
  13. pmc Evidence for Permo-Triassic colonization of the deep sea by isopods
    Luana S F Lins
    School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
    Biol Lett 8:979-82. 2012
    ..The monophyly of the 'munnopsid radiation' within the isopods suggests that the ancestors of this group evolved in the deep sea and did not move to shallow-water refugia during anoxic events...
  14. doi request reprint Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach
    Martyna Molak
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
    J Mol Evol 73:244-55. 2011
    ..According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation...
  15. ncbi request reprint Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
    Simon Y W Ho
    Henry Wellcome Ancient Biomolecules Centre, Oxford, United Kingdom
    Mol Biol Evol 22:1355-63. 2005
    ..If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates...
  16. pmc Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective
    Jaco Weinstock
    Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
    PLoS Biol 3:e241. 2005
    ..Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species...
  17. ncbi request reprint Molecular clocks: when times are a-changin'
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Trends Genet 22:79-83. 2006
    ..We conclude that many studies involving recent divergence events will need to be reconsidered...
  18. pmc A Bayesian evaluation of human mitochondrial substitution rates
    Phillip Endicott
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Am J Hum Genet 82:895-902. 2008
    ..Our results also demonstrate that human mitochondrial genomes exhibit a number of molecular evolutionary complexities that necessitate the use of sophisticated analytical models for genetic analyses...
  19. ncbi request reprint Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
    Isabel T Hyman
    School of Biological Sciences, University of Sydney, NSW 2006, Australia
    Mol Phylogenet Evol 45:792-812. 2007
    ....
  20. doi request reprint Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins
    Phillip Endicott
    Départment Hommes, Natures, sociétés, Musée de l Homme, Paris, France
    J Hum Evol 59:87-95. 2010
    ..These results suggest that a reappraisal of key elements in the Pleistocene hominin fossil record may now be required...
  21. pmc Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
    M Thomas P Gilbert
    Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
    Proc Natl Acad Sci U S A 105:8327-32. 2008
    ..Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep...
  22. ncbi request reprint Evolution of MHC class I in the order Crocodylia
    Weerachai Jaratlerdsiri
    Faculty of Veterinary Science, University of Sydney, RMC Gunn Building B19, Sydney, NSW, 2006, Australia
    Immunogenetics 66:53-65. 2014
    ..These findings enhance our understanding of MHC class I evolution and provide a preliminary framework for comparative studies of other non-avian reptiles as well as diversity assessment within Crocodylia. ..
  23. pmc Adaptive radiation of chemosymbiotic deep-sea mussels
    Julien Lorion
    Marine Ecosystems Research Department, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka 237 0061, Japan, Geoscience Center, Geobiology Group, University of Gottingen, Goldschmidtstrasse 3, Göttingen 37077, Germany, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA, School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia, Museum of New Zealand Te Papa Tongarewa, PO Box 467, 169 Tory St, Te Aro, Wellington 6011, New Zealand, Faculty of Education and Human Sciences, University of Yamanashi, Kofu, Yamanashi 400 8510, Japan
    Proc Biol Sci 280:20131243. 2013
    ..Changes in habitat type resulted in adaptive trends in shell lengths (related to the availability of space and energy, and physiological trade-offs) and in the successive colonization of greater water depths. ..
  24. pmc Vertebrate palaeontology of Australasia into the twenty-first century
    Jacqueline M T Nguyen
    School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
    Biol Lett 7:804-6. 2011
    ..Nonetheless, further field exploration for new fossils and systematic descriptions will continue to shape our understanding of vertebrate evolution in this little-studied, but most unusual, part of the globe...
  25. doi request reprint Disulfide bond acquisition through eukaryotic protein evolution
    Jason W H Wong
    Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
    Mol Biol Evol 28:327-34. 2011
    ..Finally, we show that the acquisition of the functionally relevant disulfide bond in domain 2 of the CD4 protein occurred independently in primates and rodents...
  26. pmc Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
    Shannan M Langford S
    Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
    BMC Genet 14:91. 2013
    ..We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world...
  27. ncbi request reprint ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
    Sebastián Duchêne
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
    Bioinformatics 30:1017-9. 2014
    ..We present ClockstaR, a method for selecting the number of relaxed clocks for multigene datasets...
  28. ncbi request reprint Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
    Sebastián Duchêne
    School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia Electronic address
    Mol Phylogenet Evol 77:65-70. 2014
    ..Our analyses show strong statistical support for the clock-partitioning scheme chosen by ClockstaR. In addition, we find that the optimal clock-partitioning scheme produces more reliable estimates of node ages than other schemes. ..
  29. pmc The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales
    Fangzhi Jia
    School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
    PLoS ONE 9:e95722. 2014
    ....
  30. pmc The crucial role of calibration in molecular date estimates for the peopling of the Americas
    Simon Y W Ho
    Am J Hum Genet 83:142-6; author reply 146-7. 2008
  31. pmc Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
    Jonas Binladen
    Ancient DNA and Evolution Group, Centre for Ancient Genetics, Niels Bohr Institute, University of Copenhagen, Denmark
    Genetics 172:733-41. 2006
    ....
  32. pmc Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    Mike Buckley
    BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK
    Science 319:33; author reply 33. 2008
    ..rex does not...
  33. ncbi request reprint Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models
    Jessica L Ware
    Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, USA
    Mol Phylogenet Evol 47:426-32. 2008
  34. ncbi request reprint Uplift of the Tibetan plateau: evidence from divergence times of glyptosternoid catfishes
    Zuogang Peng
    Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Mol Phylogenet Evol 39:568-72. 2006
  35. ncbi request reprint Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages
    Urmas Saarma
    Department of Integrative Zoology, Institute of Zoology and Hydrobiology, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
    Mol Ecol 16:401-13. 2007
    ..Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations...
  36. ncbi request reprint Improving the analysis of dinoflagellate phylogeny based on rDNA
    Shauna Murray
    The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, 113 8657, Japan
    Protist 156:269-86. 2005
    ..The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments...
  37. pmc Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
    Ceiridwen J Edwards
    Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
    Proc Biol Sci 274:1377-85. 2007
    ..During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare...