Simon Ho

Publications

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

In press

120  Whole genome analyses resolve early branches in the tree of life of modern birds
        Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da         Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S,         Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE,         Bruford M, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV,         Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Petersen B,         Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng         Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J,         Orlando L, Barker K, Jønsson KA, Johnson W, Koepfli K-P, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR,         Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T,         Jun W, Gilbert MTP, & Zhang G (in press) Science.

119  Molecular data support Orianthera: a new genus of Australian Loganiaceae
        Foster CSP, Conn BJ, Henwood MJ, & Ho SYW (in press) Telopea.

118  Molecular-clock methods for estimating evolutionary rates and timescales
        Ho SYW, & Duchene S (in press) Molecular Ecology.

117  The origins and radiation of Australian Coptotermes termites: from rainforest to desert dwellers
        Lee TRC, Cameron SL, Evans TA, Ho SYW, & Lo N (in press) Molecular Phylogenetics and Evolution.

116  Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
        Ho SYW, Duchene S, & Duchene D (in press) Molecular Ecology Resources.

115  Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian         phylogenetic analyses of ancient DNA
        Molak M, Suchard MA, Ho SYW, Beilman DW, & Shapiro B (in press) Molecular Ecology Resources.

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

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

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


2014

111  Accounting for rate variation among lineages in comparative demographic analyses
        Hope AG, Ho SYW, Malaney JL, Cook JA, & Talbot SL (2014) Evolution, 68-69: 2689-2700.

110  Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera, Apidae,         Meliponini)
        Brito RM, Francisco FO, Ho SYW, & Oldroyd BP (2014) Biological Journal of the Linnean Society, 113: 149-161.

109  The changing face of the molecular evolutionary clock
        Ho SYW (2014) Trends in Ecology and Evolution, 29: 496-503.

108  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 (2014)
        Quaternary International, 339-340: 224-231.

107  Global and local persistence of influenza A(H5N1) virus
        Li X, Zhang Z, Yu A, Ho SYW, Carr MJ, Zheng W, Zhang Y, Zhu C, Lei F, Shi W (2014) Emerging Infectious Diseases, 20:         1287-1295.

106  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 (2014) Quaternary Science Reviews, 96: 131-139

105  Molecular systematics and biogeography of Logania R.Br. (Loganiaceae)
        Foster CSP, Ho SYW, Conn BJ, & Henwood MJ (2014) Molecular Phylogenetics and Evolution, 78: 324-333.

104  The impact of calibration and clock-model choice on molecular estimates of divergence times
        Duchene S, Lanfear R, & Ho SYW (2014) Molecular Phylogenetics and Evolution, 78: 277-289.

103  Cryptic diversity, diversification and vicariance in two species complexes of Tomocerus (Collembola, Tomoceridae)         from China)
        Zhang F, Yu D, Luo Y, Ho SYW, Wang B, & Zhu C (2014) Zoologica Scripta, 43: 393-404.

102  Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
        Duchene S, Holmes EC, & Ho SYW (2014) Proceedings of the Royal Society of London B, 281: 20140732.

101  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 (2014) Molecular Biology and Evolution, 31: 1414-1420.

100  Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
        Duchene S & Ho SYW (2014) Molecular Phylogenetics and Evolution, 77: 65-70.

099  The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and         timescales
        Jia F, Lo N, & Ho SYW (2014) PLOS ONE, 9: e95722.

098  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.

097  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.

096  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.

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

094  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.

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

092  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.

091  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

090  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.

089  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.

088  Divergent evolutionary processes associated with colonization of offshore islands
        Mart'nkova 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.

087  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.

086  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.

085  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.

084  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.

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

082  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.

081  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.

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

079  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.

078  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.

077  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.

076  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.

075  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.

074  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.

073  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.

072  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

071  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.

070  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.

069  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.

068  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.

067  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.

066  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.

065  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.

064  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.

063  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.

062  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.

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


2011

060  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.

059  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.

058  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.

057  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.

056  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.

055  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.

054  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.

053  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.

052  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.

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

050  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.

049  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.

048  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.

047  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.

046  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

045  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.

044  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.

043  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.

042  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.

041  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.

040  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.

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


2009

038  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.

037  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.

036  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.

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

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

033  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.

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

031  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.

030  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.

029  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

028  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.

027  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.

026  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.

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

024  The molecular clock and estimating species divergence
        Ho SYW (2008) Nature Education, 1: 168.

023  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.

022  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.

021  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.

020  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

019  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.

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

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

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

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

014  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.

013  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.

012  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

011  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.

010  Relaxed phylogenetic inference and dating with confidence
        Drummond AJ, Ho SYW, Phillips MJ, & Rambaut A (2006) PLOS Biology, 4: e88.

009  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.

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

007  Improving the analysis of dinoflagellate phylogeny based on rDNA
        Murray S, Jørgensen MF, Ho SYW, Patterson DJ, & Jermiin LS (2005) Protist, 156: 269-286.

006  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.

005  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.

004  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.

003  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.

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

001  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.