Simon Ho

Publications

Further information about these publications, including citation details, can be found on Google Scholar.

In press

109  Global and local persistence featuring the migration dynamics of highly pathogenic avian influenza A H5N1 viruses
        Li X, Zhang Z, Yu A, Ho SYW, Carr MJ, Zheng W, Zhang Y, Zhu C, Lei F, Shi W (in press) Emerging Infectious Diseases.

108  Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
        Duchene S & Ho SYW (in press) Molecular Phylogenetics and Evolution.

107  The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and         timescales
        Jia F, Lo N, & Ho SYW (in press) PLOS ONE.

106  Cryptic diversity, diversification, and vicariance in the two species complexes of Tomocerus (Collembola, Tomoceridae)         from China)
        Zhang F, Yu D, Luo Y, Ho SYW, Wang B, & Zhu C (in press) Zoologica Scripta.

105  Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera, Apidae,         Meliponini)
        Brito RM, de Oliveira Francisco F, Ho SYW, & Oldroyd BP (in press) Biological Journal of the Linnean Society.

104  Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora         infestans
        Martin MD, Ho SYW, Wales N, Ristaino JB, Gilbert MTP (in press) Molecular Biology and Evolution.

103  Molecular clocks
        Ho SYW (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag, Berlin-Heidelberg.

102  Molecular clocks, human evolution
        Ho SYW, & Endicott P (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag,         Berlin-Heidelberg.

101  Molecular clocks, relaxed variant
        Ho SYW (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag, Berlin-Heidelberg.

100  Continuity of brown bear maternal lineages in northern England through the Last-glacial period
        Edwards CJ, Ho SYW, Barnett R, Coxon P, Bradley DG, Lord TC, & O'Connor T (in press) Quaternary Science Reviews.

99    Mitochondrial DNA diversity and the evolution of the Pleistocene cave bear complex
        Stiller M, Molak M, Prost S, Rabeder G, Baryshnikov G, Rosendahl W, Munzel S, Bocherens H, Grandal-d'Anglade A, Hilpert B,         Germonpré M, Stasyk O, Pinhasi R, Tintori A, Rohland N, Mohandesan E, Ho SYW, Hofreiter M, & Knapp M (in press)         Quaternary International.
 


2014

98    Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical         analysis
        Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Burger J, Sabin R, Werdelin L, Cuisin J, & Larson G (2014) BMC         Evolutionary Biology, 14: 70.

97    ClockstaR: Choosing the number of relaxed-clock models in molecular phylogenetic analysis
        Duchene S*, Molak M, & Ho SYW* (*equal first authors) (2014) Bioinformatics, 30: 1017-1019.

96    Phylogeography and diversity of the terrestrial isopod Spherillo grossus (Oniscidea: Armadillidae) on the Australian East         Coast
        Lee TRC, Ho SYW, Wilson GDF, & Lo N (2014) Zoological Journal of the Linnean Society, 170: 297-309.

95    Ancient hyaenas highlight the old problem of estimating evolutionary rates
        Shapiro B*, & Ho SYW* (*equal first authors) (2014) Molecular Ecology, 23: 499-501.

94    The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus
        Yasaka R, Nguyen HD, Ho SYW, Duchene S, Korkmaz S, Katis N, Takahashi H, Gibbs AJ, & Ohshima K (2014) PLOS ONE, 9:         e85641.

93    Human evolution: Molecular timescale
        Ho SYW, Endicott P, & Molak M (2014) Encyclopedia of Global Archaeology, ed. Smith C. Springer, New York. Pp 3511-3514.

92    DNA interpretation constraints in archaeology
        Ho SYW, Endicott P, & Molak M (2014) Encyclopedia of Global Archaeology, ed. Smith C. Springer, New York. Pp 2155-2159.

91    Evolution of MHC class I in the Order Crocodylia
        Jaratlerdsiri W, Isberg SR, Higgins DP, Ho SYW, Salomonsen J, Skjodt K, Miles LG, & Gongora J (2014) Immunogenetics, 66:         53-65.


2013

90    The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent
        Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, Chaubey G, Goto R, Ho SYW, Gallego Romero I, Crivellaro F, Hudjashov G,         Rai N, Metspalu M, Mascie-Taylor CGN, Pitchappan R, Singh L, Mirazon-Lahr M, Kumarasamy T, Villems R, & Kivisild T (2013)         PLOS Genetics, 9: e1003912.

89    Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil         records
        Miller JT, Murphy DJ, Ho SYW, Cantrill DJ, & Seigler D (2013) Australian Journal of Botany, 61: 436-445.

88    Divergent evolutionary processes associated with colonization of offshore islands
        Martínkova N, Barnett R, Cucchi T, Struchen R, Pascal M, Pascal M, Fischer MC, Higham T, Brace S, Ho SYW, Quéré JP,         O'Higgins P, Excoffier L, Heckel G, Hoelzel AR, Dobney KM, & Searle JB (2013) Molecular Ecology, 22: 5205-5220.

87    Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
        Langford SM, Kraitsek S, Baskerville B, Ho SYW, & Gongora J (2013) BMC Genetics, 14: 91.

86    Adaptive radiation of chemosymbiotic deep-sea mussels
        Lorion J, Kiel S, Faure B, Masaru K, Ho SYW, Marshall B, Rsuchida S, Miyazaki JI, & Fujiwara Y (2013) Proceedings of the         Royal Society of London B, 280: 20131243.

85    Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
        Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF, Seguin-Orlando A, Wales N, Orlando L, Ho SYW, Dietrich FS,         Mieczkowski PA, Heitman J, Willerslev E, Krogh A, Ristaino JB, & Gilbert MTP (2013) Nature Communications, 4: 2172.

84    Diversification and demography of the Oriental garden lizard (Calotes versicolor) on Hainan Island and the adjacent         mainland
        Huang Y, Guo X, Ho SYW, Shi H, Li J, Li J, Cai B, & Wang Y (2013) PLOS ONE, 8: e64754.

83    Regional population expansion in Eucalyptus globulus
        Yeoh SH, Ho SYW, Thornhill AH, & Foley WJ (2013) Molecular Phylogenetics and Evolution, 68: 498-501.

82    Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the
        Qinghai-Tibetan Plateau
        Jin Q, Han H, Hu X, Li X, Zhu C, Ho SYW, Ward RD, & Zhang A-B (2013) PLOS ONE, 8: e64428.

81    Taller plants have lower rates of molecular evolution
        Lanfear R, Ho SYW, Davies TJ, Moles AT, Aarsen L, Swenson NG, Warman L, Zanne AE, & Allen AP (2013) Nature         Communications, 4: 1879.

80    The insect molecular clock
        Ho SYW, & Lo N (2013) Australian Journal of Entomology, 52: 101-105.

79    Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
        Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Adler CJ, Richards SM, Der Sarkissian CSI, Ganslmeier R, Friederich S,         Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt         KW, Cooper A, & The Genographic Consortium (2013) Nature Communications, 4: 1764.

78    The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of tachinid         flies
        Zhao Z, Su TJ, Chesters D, Wang SD, Ho SYW, Zhu CD, Chen XL, & Zhang CT (2013) PLOS ONE, 8: e61814.

77    Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographic structure and         migration patterns among brown bears in north-western Eurasia
        Keis M, Remm J, Ho SYW, Davison J, Tammeleht E, Tumanov IL, Saveljev AP, Männil P, Kojola I, Abramov AV, Margus T, &         Saarma U (2013) Journal of Biogeography, 40: 915-927.

76    Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts
        Foote AD, Kaschner K, Schultze SE, Garilao C, Ho SYW, Post K, Higham TFG, Stokowska C, van der Es H, Embling CB,         Gregersen K, Johansson F, Willerslev E, & Gilbert MTP (2013) Nature Communications, 4: 1677.

75    Dating the origin and dispersal of hepatitis B virus infection in humans and primates
        Paraskevis D, Magiorkinis G, Magiorkinis E, Ho SYW, Belshaw R, Allain J-P, & Hatzakis A (2013) Hepatology, 57: 908-916.

74    Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago
        Nguyen HD, Tomitaka Y, Ho SYW, Duchêne S, Vetten H-J, Lesemann D, Walsh JA, Gibbs AJ, & Ohshima K (2013) PLOS ONE, 8:         e55336.

73    One hundred twenty years of koala retrovirus evolution determined from museum skins
        Ávila-Arcos MC*, Ho SYW*, Ishida Y*, Nikolaidis N*, Tsangaras K* (equal first authors), Hönig K, Medina R, Rasmussen M,         Fordyce SL, Calvignac-Spencer S, Willerslev E, Gilbert MTP, Helgen KM, Roca AL, & Greenwood AD (2013) Molecular Biology         and Evolution, 30: 299-304.

72    Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in         sample ages
        Molak M, Lorenzen ED, Shapiro B, & Ho SYW (2013) Molecular Biology and Evolution, 30: 253-262.


2012

Cover of "Systematic Biology", March 2012

71    Evidence for Permo-Triassic colonization of the deep sea by isopods
        Lins LSF, Ho SYW, Wilson GDF, & Lo N (2012) Biology Letters, 8: 979-982.

70    Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the         British Isles
        Edwards CJ, Soulsbury CD, Statham MJ, Ho SYW, Wall D, Dolf G, Iossa G, Baker PJ, Harris S,         Sacks BN, & Bradley DG (2012) Quaternary Science Reviews, 57: 95-104.

69    The influence of rate heterogeneity among sites on the time dependence of molecular rates
        Soubrier J, Steel M, Lee MSY, Der Sarkissian C, Guindon S, Ho SYW, & Cooper A (2012) Molecular         Biology and Evolution, 29: 3345-3358.

68    A potentially fatal mix of herpes in zoos
        Greenwood AD, Tsangaras K, Ho SYW, Szentiks CA, Nikolin VM, Ma G, Damiani A, East ML, Lawrenz A, Hofer H, & Osterrieder         N (2012) Current Biology, 22: 1727-1731.

67    Statistical guidelines for detecting past population shifts using ancient DNA
        Mourier T, Ho SYW, Gilbert MTP, Willerslev E, & Orlando L (2012) Molecular Biology and Evolution, 29: 2241–2251.

66    Rethinking dog domestication by integrating genetics, archeology, and biogeography
        Larson G, Karlsson E, Perri A, Webster MT, Ho SYW, Peters J, Stahl PW, Piper PJ, Lingaas F, Fredholm M, Comstock KE,         Modiano JF, Schelling C, Agoulnik AI, Leegwater P, Dobney K, Vigne J-D, Vilà C, Andersson L, Lindblad-Toh K (2012)         Proceedings of the National Academy of the USA, 109: 8878-8883.

65    PartitionFinder: new methods and software to select partitioning schemes for phylogenetic analyses
        Lanfear R, Calcott B, Ho SYW, & Guindon S (2012) Molecular Biology and Evolution, 29: 1695-1701.

64    Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using         Myrtaceae
        Thornhill AH, Popple LW, Carter RJ, Ho SYW, & Crisp MD (2012) Molecular Phylogenetics and Evolution, 63: 15-27.

63    Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of Nothofagus         (Fagales)
        Sauquet H*, Ho SYW* (equal first authors), Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK,         Carpenter RJ, Lee DM, Murphy DJ, Sniderman JMK, & Udovicic F (2012) Systematic Biology, 61: 289-313.

62    Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA
        Gongora J, Swan AB, Chong AY, Ho SYW, Damayantia CS, Kolomyjec S, Grant T, Miller E, Blair D, Furlan E, & Gust N (2012)         Journal of Zoology, 286: 110-119.

61    Phylogenetic analysis of ancient DNA sequences using BEAST
        Ho SYW (2012) Methods in Molecular Biology, 840: 229-241.


2011

60    Evaluating the impact of post-mortem damage in ancient DNA: A theoretical approach
        Molak M, & Ho SYW (2011) Journal of Molecular Evolution, 73: 244-255.

59    Species-specific responses of Late Quaternary megafauna to climate and humans
        Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R,         Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli K-P, Froese D, Zazula G,         Stafford Jr TW, Aaris-Sørensen K, Batra P, Haywood AM, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL,         Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS,         Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, &         Willerslev E (2011) Nature, 479: 359-364.

58    Vertebrate palaeontology of Australasia into the twenty-first century
        Nguyen JMT, Molak M, Black KH, Fitzgerald EMG, Travouillon KJ, & Ho SYW (2011) Biology Letters, 7: 804-806.

57    The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left         low-lying deserts genetically depauperate
        Pepper MR, Ho SYW, Fujita MK, & Keogh JS (2011) Molecular Phylogenetics and Evolution, 61: 750-759.

56    Time-dependent rates of molecular evolution
        Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, & Cooper A (2011) Molecular Ecology, 20: 3087-3101.

55    Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artioactyla)
        Gongora J, Cuddahee RE, do Nascimento FF, Palgrave CJ, Lowden S, Ho SYW, Simond D, Damayanti CS, White DJ, Randi E,         Klingel H, Rodrigues-Zarate CJ, Allen K, Moran C, & Larson G (2011) Zoologica Scripta, 40: 327-335.

54    Reply to Englund: Molecular evolution and diversification - Counting species is better than counting nodes when the         phylogeny is unknown
        Lanfear R, Bromham L, & Ho SYW (2011) Proceedings of the National Academy of Sciences of the USA, 108: E85-E86.

53    Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses
        Li W, Shi W, Qiao H, Ho SYW, Luo A, Zhang Y, Zhu C (2011) Virology Journal, 8: 183.

52    Bayesian estimation of substitution rates from ancient DNA sequences with low information content
        Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis S-O, & Shapiro B (2011) Systematic Biology, 60: 366-375.

51    Skyline-plot methods for estimating demographic history from nucleotide sequences
        Ho SYW, & Shapiro B (2011) Molecular Ecology Resources, 11: 423–434.

50    Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae
        Vilstrup J, Ho SYW, Foote AD, Morin PA, Kreb D, Krützen M, Parra GJ, Robertson KM, de Stephanis R, Verborgh P, Willerslev E,         Orlando L, & Gilbert MTP (2011) BMC Evolutionary Biology, 11: 65.

49    Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals
        Luo A, Zhang A, Ho SYW, Xu W, Zhang Y, Shi W, Cameron SL, & Zhu C (2011) BMC Genomics, 12: 84.

48    Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species
        Davison J, Ho SYW, Bray S, Korsten M, Vulla E, Hindrikson M, Østbye K, Østbye E, Lauritzen S-E, Austin J, Cooper A, & Saarma         U (2011) Quaternary Science Reviews, 30: 418-430.

47    A Bayesian method to estimate unknown sequence ages in a phylogenetic context
        Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, & Rambaut A (2011) Molecular Biology and Evolution, 28: 879-887.

46    Disulfide bond acquisition through eukaryotic protein evolution
        Wong JWH, Ho SYW, & Hogg PJ (2011) Molecular Biology and Evolution, 28: 327-334.


2010

Cover of "Systematic Biology", December 2010

45    Mutation rate is linked to diversification in birds
        Lanfear R, Ho SYW, Love D, & Bromham L (2010) Proceedings of the National Academy of         Sciences of the USA, 107: 20423-20428.

44    Phylogeographic analyses of domestic and wild yaks based on mitochondrial DNA: new data         and reappraisal
        Wang Z, Shen X, Liu B, Su J, Yonezawa T, Yu Y, Guo S, Ho SYW, Vilà C, Hasegawa M, & Liu J         (2010) Journal of Biogeography, 37: 2332-2344.

43    Tracing the temporal and spatial origins of island endemics in the Mediterranean region: A         case study from the citrus family (Ruta L., Rutaceae)
        Salvo G, Ho SYW, Rosenbaum G, Ree R, & Conti E (2010) Systematic Biology, 59: 705-722.

42    Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed         clocks
        Ho SYW, & Lanfear R (2010) Mitochondrial DNA, 21: 138-146.

41    Performance of criteria for selecting evolutionary models in phylogenetics: A comprehensive study based on simulated         data sets
        Luo A, Qiao H, Zhang Y, Shi W, Ho SYW, Xu W, Zhang A, & Zhu C (2010) BMC Evolutionary Biology, 10: 242.

40    Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and Modern         Human origins
        Endicott P, Ho SYW, & Stringer C (2010) Journal of Human Evolution, 59: 87-95.

39    Ancient mitogenomics
        Ho SYW, & Gilbert MTP (2010) Mitochondrion, 10: 1-11.


2009

38    The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis
        Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SYW, Shapiro B, Pybus O, Allain JP, & Hatzakis A (2009) PLOS Medicine, 6:         e1000198.

37    Radiation of extant cetaceans driven by restructuring of the oceans
        Steeman ME, Hebsgaard MB, Fordyce RE, Ho SYW, Rabosky DL, Nielsen R, Rahbek C, Glenner H, Sørensen MV, & Willerslev E         (2009) Systematic Biology, 58: 573-585.

36    Estimating the phylogeny and divergence times of primates using a supermatrix approach
        Chatterjee HJ*, Ho SYW*, Barnes I*, & Groves C* (equal first authors) (2009) BMC Evolutionary Biology, 9: 259.

35    Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
        Ho SYW, & Phillips MJ (2009) Systematic Biology, 58: 367-380.

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

33    Analysis of complete mitochondrial genome 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, & Schuster SC (2009) BMC Evolutionary Biology, 9: 95.

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

31    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, Pahn B, Vulla E, Roht M, Tumanov IL, Kojola I, Andersone-Lilley Z, Ozolins J, Pilot M, Mertzanis         Y, Giannakopoulos A, Vorobiev AA, Markov NI, Saveljev AP, Lyapunova EA, Abramov AV, Männil P, Valdmann H, Pazetnov SV,         Pazetnov VS, Rõkov AM, & Saarma U (2009) Molecular Ecology, 18: 1963-1979.

30    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, & Cooper A (2009) Molecular Ecology, 18: 1668-1677.

29    Accommodating the effect of ancient DNA damage on inferences of demographic histories
        Rambaut A, Ho SYW, Drummond AJ, & Shapiro B (2009) Molecular Biology and Evolution, 26: 245-248.


2008

28    The crucial role of calibration in molecular date estimates for the peopling of the Americas
        Ho SYW, & Endicott P (2008) American Journal of Human Genetics, 83: 142-146.

27    Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
        Ho SYW, Larson G, Edwards CJ, Heupink TH, Holland PWH, & Shapiro B (2008) Biology Letters, 4: 370-374.

26    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, &         Schuster SC (2008) Proceedings of the National Academy of Sciences of the USA, 105: 8327-8332.

25    A Bayesian evaluation of human mitochondrial substitution rates
        Endicott P, & Ho SYW (2008) American Journal of Human Genetics, 82: 895-902.

24    The molecular clock and estimating species divergence
        Ho SYW (2008) Nature Education.

23    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, & Rao VR (2008) American Journal of Physical Anthropology, 136: 19-27.

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

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

20    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, & Collins MJ (2008) Science         319: 33c.

        Confounding Factors in Phylogenetic Analysis
        Ho SYW (2008) 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, & Jermiin LS (2007) Molecular Phylogenetics and Evolution, 45: 792-812.

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

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

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

15    Bayesian estimation of sequence damage in ancient DNA
        Ho SYW, Heupink TH, Rambaut A, & Shapiro B (2007) 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, & Burger J (2007) 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         problem?
        Haile J, Holdaway R, Oliver K, Bunce M, Shapiro B, Gilbert MTP, Nielsen R, Munch K, Ho SYW, & Willerslev E (2007) Molecular         Biology and Evolution, 24: 982-989.

12    Mitogenetic structure of brown bears (Ursus arctos L.) in north-eastern Europe and a new time-frame for the formation of         European brown bears
        Saarma U, Ho SYW, Pybus OG, Kaljuste 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, & Rõkov AM (2007) Molecular         Ecology, 16: 401-413.


2006 and earlier

Cover of "Trends in Genetics", February 2006

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

10    Relaxed phylogenetic inference and dating with confidence
        Drummond AJ, Ho SYW, Phillips MJ, & Rambaut A (2006) 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 (2006) Genetics, 172: 733-741.

08    Molecular clocks: When times are a-changin’
        Ho SYW, & Larson G (2006) Trends in Genetics, 22: 79-83.

07    Improving the analysis of dinoflagellate phylogeny based on rDNA
        Murray S, Jørgensen MF, Ho SYW, Patterson DJ, & Jermiin LS (2005) 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, & Cooper A (2005) PLOS Biology, 3: e241.

05    Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
        Ho SYW, Phillips MJ, Cooper A, & Drummond AJ (2005) 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, & Cooper A (2005) Molecular Biology and Evolution, 22: 1355-1363.

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

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

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


Scientific commentary

(i) Calibrating mitochondrial rates in marine invertebrates
(ii) Untangling the evolutionary processes that shape plant mitochondrial genomes

Ho SYW, & Lanfear R (2012) Mitochondrial DNA, 23: 321-322.

Frozen in time: What caused the extinction of the Ice Age megafauna?
Ho SYW (2012) Australasian Science, 33: 24-26.

(i) Mitochondrial mutation rates in the water flea Daphnia pulex
(ii) Selection against pathogenic mutations in human mitogenomes
(iii) Mother's curse: Mitochondria cause problems for male flies

Lanfear R, & Ho SYW (2012) Mitochondrial DNA, 23: 153-155.

Did climate cause the extinction of the Ice Age megafauna?
Ho SYW (2011) The Conversation, article 4168.

(i) Adding insult to injury: Transmissible cancer captures host mitochondrial genomes
(ii) Evolutionary diversification of birds in the Cretaceous

Lanfear R, & Ho SYW (2011) Mitochondrial DNA, 22: 39-40.

(i) Ancient mitogenome from an unknown hominin
(ii) Population dynamics of cave bears in the Pleistocene
(iii) Mutational processes differ significantly between closely related nematodes

Ho SYW, & Lanfear R (2010) Mitochondrial DNA, 21: 147-148.

(i) Understanding the origin of doubly uniparental inheritance in bivalves
(ii) Mitogenomic sequence from an ancient polar bear

Lanfear R, Ho SYW (2010) Mitochondrial DNA, 21: 57-58.

(i) Distinctive characteristics of post-mortem damage in human mitochondrial DNA
(ii) Time-dependent molecular rates in human mitogenomes
(iii) The role of mito-nuclear interactions in F2 hybrid breakdown

Ho SYW, & Lanfear R (2010) Mitochondrial DNA, 21: 33-35.

(i) MtZoa – A new mitochondrial protein replacement matrix for metazoan phylogenetics
(ii) Evolutionary constraints on mitochondrial DNA depend on the locomotive demands of the host
(iii) Longevity, mutation rates, and the evolution of avian mitochondrial DNA
(iv) Population mitogenomics of extinct species
(v) Tracking the demographic history of seals using mitochondrial DNA

Lanfear R, & Ho SYW (2010) Mitochondrial DNA, 21: 1-4.

(i) Purifying selection in human mitochondrial DNA
(ii) Forensic analysis using mitochondrial DNA

Ho SYW (2009) Mitochondrial DNA, 20: 101-102.

(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, & Lanfear R (2009) Mitochondrial DNA, 20: 65-68.

(i) Age-related selection in mitochondrial genomes
(ii) Mitochondrial evolution in tuatara
(iii) Mitochondrial genome of the thylacine

Lanfear R, & Ho SYW (2009) Mitochondrial DNA, 20: 27-28.

(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 (2009) Mitochondrial DNA, 20: 2-6.