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SCIENTIFIC PUBLICATIONS

In press

39     Mito-communications: (i) Mitochondrial phylogeography of house mice, (ii) Two migration routes for the first Americans, (iii) The influence of altitude on mitochondrial evolution in mammals, (iv) Extreme organisation, (v) The effective population size of mitochondrial DNA
Ho SYW, and Lanfear R. Mitochondrial DNA, in press.

38     Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
Ho SYW, and Phillips MJ. Systematic Biology, in press.

37     Evaluating the mitochondrial timescale of human evolution
Endicott P, Ho SYW, Metspalu M, and Stringer C. Trends in Ecology and Evolution, in press.

2009

36     Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
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. BMC Evolutionary Biology, 9: 95.

35     Mito-communications: (i) Age-related selection in mitochondrial genomes, (ii) Mitochondrial evolution in tuatara, (iii) Mitochondrial genome of the thylacine
Lanfear R and Ho SYW. Mitochondrial DNA, 20: 27-28.

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

33     Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?
Korsten M, Ho SYW, Davison J, Pähn 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, Männil P, Valdmann H, Pazetnov SV, Pazetnov VS, Rõkov AM, and Saarma U. Molecular Ecology, 18: 1963-1979.

32     Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity
Barnett R, Shapiro B, Barnes I, 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. Molecular Ecology, 18: 1668-1677.

31     Mito-communications: (i) Report on the 3rd International Symposium on Biomolecular Archaeology, (ii) Ursid mitogenomics, (iii) Ancient human mitogenomics, (iv) Goat domestication, (v) Partial deletion of the mitochondrial control region
Ho SYW. Mitochondrial DNA, 20: 2-6.

30     Accommodating the effect of ancient DNA damage on inferences of demographic histories
Rambaut A, Ho SYW, Drummond AJ, and Shapiro B. Molecular Biology and Evolution, 26: 245-248.

2008

29     The crucial role of calibration in molecular date estimates for the peopling of the Americas
Ho SYW and Endicott P. American Journal of Human Genetics, 83: 142-146.

28     Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PWH, and Shapiro B. Biology Letters, 4: 370-374.

27     Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
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. Proceedings of the National Academy of Sciences of the USA, 105: 8327-8332.

26     A Bayesian evaluation of human mitochondrial substitution rates
Endicott P and Ho SYW. American Journal of Human Genetics, 82: 895-902.

25     The molecular clock and estimating species divergence
Ho SYW. Nature Education, 1.

24     Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands
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. American Journal of Physical Anthropology, 136: 19-27.

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

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

21     Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
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 B, Zylber MI, Gilbert MTP, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, and Collins MJ. Science, 319: 33c.

 20    Confounding factors in phylogenetic analysis
Ho SYW. VDM Verlag, Saarbrücken, Germany. 87 pages. ISBN 978-3-639-04610-6.

2007

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

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

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

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

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

14     Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
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, Döle H-J, Göldner H, Hartz S, Helmer D, Herzig B, Hongo H, Mashkour M, Özdogan M, Pucher E, Roth G, Schade-Lindig S, Schmölcke U, Schulting RJ, Stephan E, Uerpmann H-P, Vörös I, Voytek B, Bradley DG, and Burger J. Proceedings of the Royal Society of London B, 274: 1377-1385.

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

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

2006

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

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

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

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

2005

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

06     Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective
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. PLoS Biology, 3: e241.

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

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

2004

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

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

2003

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

 


PRESENTATIONS

Invited Talks and Workshops

08     Title pending
Keynote speaker, Australasian Evolution Society Conference, Canberra, Australia. Sep 2009.

07     Vegetation Function Working Group 60: Rates of Molecular Evolution in Plants, Sydney, Australia. May 2009.

06     Recalibrating the time-scale of human evolution using mitochondrial DNA
 Genetics Society of Australasia Conference, Adelaide, Australia. Jul 2008.

05     Vegetation Function Working Group 32: Calibrating the Evolutionary History of Southern Hemisphere Plant Clades, Melbourne, Australia. May 2008.

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

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

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

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

 

Other Talks

11     Evaluating the mitochondrial timescale of human evolution
Conference on Australasian Vertebrate Evolution Palaeontology and Systematics, Sydney, Australia. Jun 2009.

10     Evaluating the mitochondrial timescale of human evolution
Quaternary Forum, Canberra, Australia. Jun 2009.

09     Recalibrating the time-scale of human evolution using mitochondrial DNA
Session chair, International Symposium on Biomolecular Archaeology, York, UK. Sep 2008.

08     Ancient DNA: 'Molecular fossils' provide a window on the past
Tempo and Mode, Canberra, Australia. Sep 2008.

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

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

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

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

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

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

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

 

COMPUTER PROGRAMS AND MANUALS

 

03     A Rough Guide to BEAST 1.4
Drummond AJ, Ho SYW, Rawlence N, and Rambaut A. 2007. University of Auckland, New Zealand.

02     Sequescence
Ho SYW. 2007. University of Oxford, UK.

01     RateEvolver
Ho SYW. 2005. University of Oxford, UK.