Simon Ho

Publications

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

In press

124 Phylogenomic analyses data of the Avian Phylogenomics Project
Jarvis ED, Mirarab S, Aberer AJ, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Wang J, Gilbert MTP, Zhang G, & The Avian Phylogenomics Consortium (in press) Gigascience.
123 Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
Duchene D, Duchene S, & Ho SYW (in press) Molecular Ecology Resources.
122 Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand
Yasaka R, Ohba K, Schwinghamer MW, Fletcher J, Ochoa Corona FM, Thomas JE, Ho SYW, Gibbs AJ, & Ohshima K (in press) Journal of General Virology.
121 Molecular-clock methods for estimating evolutionary rates and timescales
Ho SYW, & Duchene S (in press) Molecular Ecology.
120 Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Ho SYW, Duchene S, & Duchene D (in press) Molecular Ecology Resources.
119 Molecular clocks
Ho SYW (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag, Berlin-Heidelberg.
118 Molecular clocks, human evolution
Ho SYW, & Endicott P (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag, Berlin-Heidelberg.
117 Molecular clocks, relaxed variant
Ho SYW (in press) Encyclopedia of Scientific Dating Methods, eds Rink WJ, & Thompson JW. Springer-Verlag, Berlin-Heidelberg.


2015

116 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 (2015) Molecular Ecology Resources, 15: 81–86.
115 The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers
Lee TRC, Cameron SL, Evans TA, Ho SYW, & Lo N (2015) Molecular Phylogenetics and Evolution, 82: 234–244.


2014

114 Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
Li C, Zhang Y, Li J, Kong L, Hu H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SYW, Burt D, Ponting CP, Jarvis ED, Gilbert MTP, Yang H, Wang J, Lambert DM, Wang J, & Guojie Zhang (2014) Gigascience, 3: 27.
113 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 (2014) Science, 346: 1320–1331.
112 Molecular data support Orianthera: a new genus of Australian Loganiaceae
Foster CSP, Conn BJ, Henwood MJ, & Ho SYW (2014) Telopea, 16: 149–158.
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
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.
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

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 Sciences 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
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

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 diveresity
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

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.