Simon Ho


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


202 Evolutionary rates are correlated between cockroach symbiont and mitochondrial genomes
Arab DA, Bourguignon T, Wang Z, Ho SYW, Lo N
bioRxiv, doi:10.1101/542241
201 Linking branch lengths across loci provides the best fit for phylogenetic inference
Duchene DA, Tong KJ, Foster CSP, Duchene S,Lanfear R, Ho SYW
bioRxiv, doi:10.1101/467449

In press

200 A simulation-based evaluation of tip-dating under the fossilized birth-death process
Luo A, Duchêne DA, Zhang C, Zhu C-D, Ho SYW
Systematic Biology
199 Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families
Ritchie AM, Ho SYW
Journal of Language Evolution
198 Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies
Nie Y, Foster CSP, Zhu T, Yao R, Duchêne DA, Ho SYW, Zhong B
Systematic Biology
197 Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
van der Merwe M, Yap S, Bragg JG, Cristofolini C, Foster CSP, Ho SYW, Rossetto M
Methods in Ecology and Evolution
196 Dating methods: Genetic
Ho SYW, Endicott P
Encyclopedia of Global Archaeology, 2nd edition, ed. Smith C. Springer, Cham


195 EasyCodeML: A visual tool for analysis of selection using CodeML
Gao F, Chen C, Arab DA, Du Z, He Y, Ho SYW
Ecology and Evolution, 9: 3891–3898
194 Sexual selection, body mass, and molecular evolution interact to predict diversification in birds
Iglesias-Carrasco M, Jennions MD, Ho SYW, Duchêne D
Proceedings of the Royal Society of London B, 286: 20190172
193 Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa
Knapp M, Thomas JE, Haile J, Prost S, Ho SYW, Dussex N, Cameron-Christie S, Kardailsky O, Barnett R, Bunce M, Gilbert MTP, Scofield RP
Molecular Phylogenetics and Evolution, 134: 122–128
192 Revisiting the genetic diversity and population structure of the critically endangered leatherback turtles in the Southwest Atlantic Ocean: Insights for species conservation
Vargas SM, Lins LSF, Molfetti E, Ho SYW, Monteiro D, Barreto J, Colman L, Vila-Verde L, Baptistotte C, Thome JCA, Santos FR
Journal of the Marine Biological Association of the UK, 99: 34–41
191 Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea: Malacostraca)
Van Der Wal C, Ahyong ST, Ho SYW, Lins LSF, Lo N
Invertebrate Systematics, 33: 89–100
190 Molecular clock
Van Der Wal C, Ho SYW
Encyclopedia of Bioinformatics and Computational Biology, eds Ranganathan S, Gribskov M, Nakai K, Schönbach C. Elsevier, Amsterdam. Volume 2, pp 719–726


189 The molecular clock and evolutionary timescales
Luo A, Ho SYW
Biochemical Society Transactions, 46: 1183–1190
188 Europe was a hub for the global spread of potato virus S in the 19th century
Duan G, Zhan F, Du Z, Ho SYW, Gao F
Virology, 525: 200–204
187 Rapid evolutionary dynamics of pepper mild mottle virus
Guan X, Yang C, Fu J, Du Z, Ho SYW, Gao F
Virus Research, 256: 96–99
186 Comparison of methods for molecular species delimitation across a range of speciation scenarios
Luo A, Ling C, Ho SYW*, Zhu C* (*equal last authors)
Systematic Biology, 67: 830–846
185 Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive Para C Lineage for millennia
Zhou Z, Lundstrom I, Tran-Dien A, Duchêne S, Alikhan N-F, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenoien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill F-X, Ho SYW, Gilbert MTP, Achtman M
Current Biology, 28: 2420–2428
184 Adaptation and conservation insights from the koala genome
Johnson RN, O'Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O'Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AYY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Marshall Graves JA, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K
Nature Genetics, 50: 1102–1111
183 PhyloMAd: Efficient assessment of phylogenomic model adequacy
Duchêne DA, Ho SYW, Duchêne S
Bioinformatics, 34: 2300–2301
182 Differences in performance among test statistics for assessing phylogenomic model adequacy
Duchêne DA, Duchêne S, Ho SYW
Genome Biology and Evolution, 10: 1375–1388
181 Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)
Foster CSP, Henwood MJ, Ho SYW
Molecular Phylogenetics and Evolution, 127: 156–167
180 A comparison of methods for estimating substitution rates from ancient DNA sequence data
Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW
BMC Evolutionary Biology, 18: 70
179 Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing
Lee C, Moroldo M, Perdomo-Sabogal A, Mach N, Marthey S, Lecardonnel J, Wahlberg P, Chong AY, Estelle J, Ho SYW, Rogel-Gaillard C, Gongora J
Immunogenetics, 70: 401–417
178 Founder-specific inbreeding depression affects racing performance in Thoroughbred horses
Todd ET, Ho SYW, Thomson PC, Ang RA, Velie BD, Hamilton NA
Scientific Reports, 8: 6167
177 Analysis of phylogenomic tree space resolves relationships among marsupial families
Duchêne DA, Bragg JG, Duchêne S, Neaves LE, Potter S, Moritz C, Johnson RN, Ho SYW*, Eldridge MDB* (*equal last authors)
Systematic Biology, 67: 400–412
176 Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events
Frantz LAF, Rudzinski A, Surya Nugraha AM, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease E, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire J, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G
Proceedings of the Royal Society of London B, 285: 20172566
175 Bayesian molecular dating: Opening up the black box
Bromham L*, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW* (*equal first authors)
Biological Reviews, 93: 1165–1191
174 Transoceanic dispersal and plate tectonics shaped global cockroach distributions: Evidence from mitochondrial phylogenomics
Bourguignon T, Tang Q, Ho SYW, Juna F, Wang Z, Arab DA, Cameron SL, Walker J, Rentz D, Evans TA, Lo N
Molecular Biology and Evolution, 35: 970–983
173 Large-scale migrations of brown bears in Eurasia and to North America during the Late Pleistocene
Anijalg P, Ho SYW, Davison J, Keis M, Tammeleht E, Bobowik K, Tumanov IL, Saveljev AP, Lyapunova EA, Vorobiev AA, Markov NI, Kryukov AP, Kojola I, Swenson JE, Hagen SB, Eiken HG, Paule L, Saarma U
Journal of Biogeography, 45: 394–405
172 Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles
Hudjashov G, Endicott P, Post H, Nagle N, Ho SYW, Lawson DJ, Reidla M, Karmin M, Rootsi S, Metspalu E, Saag L, Villems R, Cox MP, Mitchell RJ, Garcia-Bertrand RL, Metspalu M, Herrera RJ
Scientific Reports, 8: 1823


171 An evolutionary timescale for terrestrial isopods and a lack of molecular support for the monophyly of Oniscidea (Crustacea:Isopoda)
Lins LSF, Ho SYW, Lo N
Organisms Diversity & Evolution, 17: 831–820.
170 Strategies for partitioning clock models in phylogenomic dating: Application to the angiosperm evolutionary timescale
Foster CSP, Ho SYW
Genome Biology and Evolution, 9: 2752–2763
169 The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data
Van Der Wal C, Ahyong ST, Ho SYW, Lo N
PeerJ, 5: e3844
168 The timescale of emergence and spread of turnip mosaic potyvirus
Yasaka R, Fukagawa H, Ikematsu M, Soda H, Korkmaz S, Golnaraghi A, Katis N, Ho SYW, Gibbs AJ, Ohshima K
Scientific Reports, 7: 4240
167 Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences
Li X, Liu H, Liu L, Feng Y, Kalish ML, Ho SYW, Shao Y
Scientific Reports, 7: 4024
166 Purifying selection and concerted evolution of RNA-sensing Toll-like receptors in migratory waders
Raven N, Lisovski S, Klaassen M, Lo N, Madsen T, Ho SYW, Ujvari B
Infection, Genetics and Evolution, 53: 135–145
165 Ecological diversification of the Australian Coptotermes termites and the evolution of mound building
Lee TRC, Evans TA, Cameron SL, Hochuli DF, Ho SYW, Lo N
Journal of Biogeography, 44: 1405–1417
164 New statistical criteria detect phylogenetic bias caused by compositional heterogeneity
Duchêne DA, Duchêne S, Ho SYW
Molecular Biology and Evolution, 34: 1529–1534
163 The impacts of drift and selection on genomic evolution in insects
Tong KJ, Duchêne S, Lo N, Ho SYW
PeerJ, 5: e3241
162 A review of the status of Coptotermes (Isoptera : Rhinotermitidae) species in Australia with the description of two new small termite species from Northern and Eastern Australia
Lee TRC, Evans TA, Cameron SL, Ho SYW, Namyatova AA, Lo N
Invertebrate Systematics, 31: 180–190
161 The impact of the tree prior on molecular dating of mixed inter- and intraspecies data sets
Ritchie AM, Lo N, Ho SYW
Systematic Biology, 66: 413–425
160 Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale
Foster CSP, Sauquet H, van der Merwe M, McPherson H, Rossetto M, Ho SYW
Systematic Biology, 66: 338–351
159 Mitochondrial phylogenomics resolves the global spread of higher termites, ecosystem engineers of the tropics
Bourguignon T, Lo N, Sobotnik J, Ho SYW, Iqbal N, Coissac E, Lee M, Jendryka M, Sillam-Dusses D, Krizkova B, Roisin Y, Evans TA
Molecular Biology and Evolution, 34: 589-597
158 Parallel evolution of mound-building and grass-feeding in Australian nasute termites
Arab DA, Namyatova A, Evans TA, Cameron SL, Yeates DK, Ho SYW, Lo N
Biology Letters, 13: 20160665


157 Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)
Foster CSP, Cantrill DJ, James EA, Syme AE, Jordan R, Douglas R, Ho SYW, Henwood MJ
Australian Systematic Botany, 29: 185–196
156 Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods
Duchêne S, Geoghegan J, Holmes EC, Ho SYW
Bioinformatics, 32: 3375–3379
155 Reconstructing evolutionary timescales using phylogenomics
Tong KJ, Lo N, Ho SYW
Zoological Systematics, 41: 343–351
154 Early cave art and ancient DNA record the origin of European bison
Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SYW, Kosintsev P, Lee MSY, Baryshnikov G, Bollongino R, Bover P, Burger J, Chival D, Cregut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T, Hofman-Kaminska E, Immel A, Julien M-A, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne J-D, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A
Nature Communications, 7: 13158
153 The genome as an evolutionary timepiece
Ho SYW, Chen AXY, Lins LSF, Duchêne DA, Lo N
Genome Biology and Evolution, 8: 3006–3010
152 Mitochondrial rate variation among lineages of passerine birds
Nguyen JMT, Ho SYW
Journal of Avian Biology, 47: 690–696
151 Zebra alphaherpesviruses (EHV-1 and EHV-9): genetic diversity, latency and co-infections
Abdelgawad A, Damiani A, Ho SYW, Strauss G, Szentiks CA, East ML, Osterrieder N, Greenwood AD
Viruses, 8: 262
150 Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker
Ritchie AM, Lo N, Ho SYW
Organisms Diversity & Evolution, 16: 467–480
149 Mitogenomics of the extinct cave lion, Panthera spelaea (Goldfuss, 1810), resolve its position within the Panthera cats
Barnett R, Zepeda Mendoza ML, Soares AER, Ho SYW, Zazula G, Yamaguchi N, Shapiro B, Kirillova IV, Larson G, Gilbert MTP
Open Quaternary, 2: 4
148 Cross-validation to select Bayesian hierarchical models in phylogenetics
Duchêne S, Duchêne DA, Di Giallonardo F, Eden J-S, Geoghegan JL, Holt KE, Ho SYW, Holmes EC
BMC Evolutionary Biology, 16: 115
147 Molecular clocks
Current Biology, 26: R399-R402
146 Estimating the number and assignment of clock models in analyses of multigene data sets
Duchêne S, Foster CSP, Ho SYW
Bioinformatics, 32: 1281–1285
145 Ancient mitochondrial DNA provides high-resolution timescale of the peopling of the Americas
Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S, Rohland N, Nordenfelt S, Valdiosera C, Richards SM, Rohrlach A, Romero MIB, Espinoza IF, Cagigao ET, Jiménez LW, Makowski K, Reyna ISL, Lory JM, Torrez JAB, Rivera MA, Burger RL, Ceruti MC, Reinhard J, Wells RS, Politis G, Santoro CM, Standen VG, Smith C, Reich D, Ho SYW, Cooper A, Haak W
Science Advances, 2: e1501385
144 Phylogeography, genetic diversity, and management units of hawksbill turtles in the Indo-Pacific
Vargas SM, Jensen MP, Ho SYW, Mobaraki A, Broderick D, Mortimer JA, Whiting S, Miller J, Prince RIT, Bell IP, Hoenner X, Limpus CJ, Santos FR, FitzSimmons NN
Journal of Heredity, 107: 199–213
143 Multiple evolutionary origins of Australian soil-burrowing cockroaches driven by climate change in the Neogene
Lo N, Tong KJ, Rose HA, Ho SYW, Beninati T, Lowe D, Matsumoto T, Maekawa K
Proceedings of the Royal Society of London B, 283: 20152869
142 Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans
Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M, Seguin-Orlando A, Ristaino JB, Gilbert MTP
Molecular Biology and Evolution, 33: 478–491
141 Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome
Ohshima K, Matsumoto K, Yasaka R, Nishiyama M, Soejima K, Korkmaz S, Ho SYW, Gibbs AJ, Takeshita M
Virology, 487: 188–197


140 A simulation study of sample size for DNA barcoding
Luo A, Lan H, Ling C, Zhang A, Ho SYW, Zhu C
Ecology and Evolution, 5: 5869–5879
139 Time-dependent estimates of molecular evolutionary rates: Evidence and causes
Ho SYW, Duchêne S, Molak M, Shapiro B
Molecular Ecology, 24: 6007–6012
138 The extremophile Nicotiana benthamiana has traded viral defence for early vigour
Bally J, Nakasugi K, Jia F, Jung H, Ho SYW, Wong M, Paul CM, Naim F, Wood CC, Crowhurst RN, Hellens RP, Dale JL, Waterhouse PM
Nature Plants, 1: 15165
137 Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance
Alexander M, Ho SYW, Molak M, Carlborg O, Dorshorst B, Honaker C, Besnier F, Wahlberg P, Dobney K, Siegel P, Andersson L, Larson G
Biology Letters, 11: 20150561
136 Evaluating the adequacy of molecular-clock models using posterior predictive simulations
Duchêne D, Duchêne S, Holmes EC, Ho SYW
Molecular Biology and Evolution, 32: 2986–2995
135 Response to Comment on "Whole genome analyses resolve early branches in the tree of life of modern birds"
Cracraft J*, Houde P*, Ho SYW* (*equal first authors), Mindell DP, Fjeldsa J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MTP, Zhang G, Braun EL, Jarvis ED
Science, 349: 1460
134 Biogeographic calibrations for the molecular clock
Ho SYW, Tong KJ, Foster CSP, Ritchie AM, Lo N, Crisp MD
Biology Letters, 11: 20150194
133 Molecular phylogeny and the underestimated species diversity of the endemic white-bellied rat (Rodentia: Muridae: Niviventer) in Southeast Asia and China
Lu L, Ge D, Chester D, Ho SYW, Ma Y, Li G, Wen Z, Wu Y, Wang J, Xia L, Liu J, Guo T, Zhang X, Zhu C, Yang Q, Liu Q
Zoologica Scripta, 44: 475–494
132 Comment on "Phylogenomics resolves the timing and pattern of insect evolution"
Tong KJ, Duchêne S, Ho SYW, Lo N
Science, 349: 487b
131 Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes
Paraskevis D*, Angelis K*, Magiorkinis G, Kostaki E, Ho SYW*, Hatzakis A* (*equal first authors)
Molecular Phylogenetics and Evolution, 93: 44–54
130 Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny
Thornhill AH, Külheim C, Ho SYW, Crisp MD
Molecular Phylogenetics and Evolution, 93: 29–43
129 Geographic and temporal dynamics of a global radiation and diversification in the killer whale
Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis G, Ferguson SH, Ford JK, Ford M, Garilao C, Gilbert MTP, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SYW, Foote AD
Molecular Ecology, 24: 3964–3979
128 Molecular clocks, relaxed variant
Encyclopedia of Scientific Dating Methods, eds Rink WJ, Thompson JW. Springer-Verlag, Berlin-Heidelberg. pp 591–593
127 Molecular clocks, human evolution
Ho SYW, Endicott P
Encyclopedia of Scientific Dating Methods, eds Rink WJ, Thompson JW. Springer-Verlag, Berlin-Heidelberg. pp 588–591
126 Molecular clocks
Encyclopedia of Scientific Dating Methods, eds Rink WJ, Thompson JW. Springer-Verlag, Berlin-Heidelberg. pp 583–588
125 Mammalian genome evolution is governed by multiple pacemakers
Duchêne S, Ho SYW
Bioinformatics, 31: 2061-2065
124 The performance of the date-randomisation test in phylogenetic analyses of time-structured virus data
Duchêne S, Duchêne D, Holmes EC, Ho SYW
Molecular Biology and Evolution, 32: 1895-1906
123 Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences
Duchêne D, Duchêne S, Ho SYW
Molecular Ecology Resources, 15: 785–794
122 Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Ho SYW, Duchêne S, Duchêne D
Molecular Ecology Resources, 15: 688–696
121 Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
Duchêne S, Ho SYW, Holmes EC
BMC Evolutionary Biology, 15: 36
120 Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA
Molak M, Ho SYW
PeerJ, 3: e821
119 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
Journal of General Virology, 96: 701–713
118 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
Gigascience, 4: 4
117 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
Molecular Ecology Resources, 15: 81–86
116 The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers
Lee TRC, Cameron SL, Evans TA, Ho SYW, Lo N
Molecular Phylogenetics and Evolution, 82: 234–244


115 Molecular-clock methods for estimating evolutionary rates and timescales
Ho SYW, Duchêne S
Molecular Ecology, 23: 5947–5965
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, Zhang G
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
Science, 346: 1320–1331
112 Molecular data support Orianthera: a new genus of Australian Loganiaceae
Foster CSP, Conn BJ, Henwood MJ, Ho SYW
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
Evolution, 68: 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
Biological Journal of the Linnean Society, 113: 149–161
109 The changing face of the molecular evolutionary clock
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
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
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
Quaternary Science Reviews, 96: 131–139
105 Molecular systematics and biogeography of Logania R.Br. (Loganiaceae)
Foster CSP, Ho SYW, Conn BJ, Henwood MJ
Molecular Phylogenetics and Evolution, 78: 324–333
104 The impact of calibration and clock-model choice on molecular estimates of divergence times
Duchêne S, Lanfear R, Ho SYW
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
Zoologica Scripta, 43: 393–404
102 Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
Duchêne S, Holmes EC, Ho SYW
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
Molecular Biology and Evolution, 31: 1414–1420
100 Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
Duchêne S, Ho SYW
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
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
BMC Evolutionary Biology, 14: 70
097 ClockstaR: Choosing the number of relaxed-clock models in molecular phylogenetic analysis
Duchêne S*, Molak M, Ho SYW* (*equal first authors)
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
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)
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, Duchêne S, Korkmaz S, Katis N, Takahashi H, Gibbs AJ, Ohshima K
PLOS ONE, 9: e85641
093 Human evolution: Molecular timescale
Ho SYW, Endicott P, Molak M
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
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
Immunogenetics, 66: 53–65


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
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
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
Molecular Ecology, 22: 5205–5220
087 Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens
Langford S SM, Kraitsek S, Baskerville B, Ho SYW, Gongora J
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
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
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
PLOS ONE, 8: e64754
083 Regional population expansion in Eucalyptus globulus
Yeoh SH, Ho SYW, Thornhill AH, Foley WJ
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
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
Nature Communications, 4: 1879
080 The insect molecular clock
Ho SYW, Lo N
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 C, 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
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
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
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
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
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
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
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
Molecular Biology and Evolution, 30: 253–262


071 Evidence for Permo-Triassic colonization of the deep sea by isopods
Lins LSF, Ho SYW, Wilson GDF, Lo N
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
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
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
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
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
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
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
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
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
Journal of Zoology, 286: 110–119
061 Phylogenetic analysis of ancient DNA sequences using BEAST
Methods in Molecular Biology, 840: 229–241


060 Evaluating the impact of post-mortem damage in ancient DNA: A theoretical approach
Molak M, Ho SYW
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
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
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
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
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
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
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
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
Systematic Biology, 60: 366–375
051 Skyline-plot methods for estimating demographic history from nucleotide sequences
Ho SYW, Shapiro B
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
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
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
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
Molecular Biology and Evolution, 28: 879–887
046 Disulfide bond acquisition through eukaryotic protein evolution
Wong JWH, Ho SYW, Hogg PJ
Molecular Biology and Evolution, 28: 327–334


045 Mutation rate is linked to diversification in birds
Lanfear R, Ho SYW, Love D, Bromham L
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
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
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
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
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
Journal of Human Evolution, 59: 87–95
039 Ancient mitogenomics
Ho SYW, Gilbert MTP
Mitochondrion, 10: 1–11


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
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
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)
BMC Evolutionary Biology, 9: 259
035 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
Ho SYW, Phillips MJ
Systematic Biology, 58: 367–380
034 Evaluating the mitochondrial timescale of human evolution
Endicott P, Ho SYW, Metspalu M, Stringer C
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
BMC Evolutionary Biology, 9: 95
032 An examination of phylogenetic models of substitution rate variation among lineages
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
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
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
Molecular Biology and Evolution, 26: 245–248


028 The crucial role of calibration in molecular date estimates for the peopling of the Americas
Ho SYW, Endicott P
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
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
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
American Journal of Human Genetics, 82: 895–902
024 The molecular clock and estimating species divergence
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
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
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
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
Science 319: 33c
  Confounding Factors in Phylogenetic Analysis
VDM Verlag, Saarbrücken, Germany. 87 pages. ISBN 978-3-639-04610-6


019 Molecular phylogeny of Australian Helicarionidae, Euconulidae, and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
Hyman IT, Ho SYW, Jermiin LS
Molecular Phylogenetics and Evolution, 45: 792–812
018 Elevated substitution rates estimated from ancient DNA
Ho SYW, Kolokotronis S-O, Allaby RG
Biology Letters, 3: 702–705
017 Calibrating molecular estimates of substitution rates and divergence times in birds
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
Systematic Biology, 56: 515–522
015 Bayesian estimation of sequence damage in ancient DNA
Ho SYW, Heupink TH, Rambaut A, Shapiro B
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
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
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
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
Molecular Phylogenetics and Evolution, 39: 568–572 (2006)
010 Relaxed phylogenetic inference and dating with confidence
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A
PLOS Biology, 4: e88 (2006)
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
Genetics, 172: 733–741 (2006)
008 Molecular clocks: When times are a-changin'
Ho SYW, Larson G
Trends in Genetics, 22: 79–83 (2006)
007 Improving the analysis of dinoflagellate phylogeny based on rDNA
Murray S, Jørgensen MF, Ho SYW, Patterson DJ, Jermiin LS
Protist, 156: 269–286 (2005)
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, Lai X, Cooper A
PLOS Biology, 3: e241 (2005)
005 Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
Ho SYW, Phillips MJ, Cooper A, Drummond AJ
Molecular Biology and Evolution, 22: 1561–1568 (2005)
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
Molecular Biology and Evolution, 22: 1355–1363 (2005)
003 The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD
Systematic Biology, 53: 638–643 (2004)
002 Tracing the decay of the historical signal in biological sequence data
Ho SYW, Jermiin LS
Systematic Biology, 53: 623–637 (2004)
001 Hetero: A program to simulate the evolution of DNA on four-taxon trees
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD
Applied Bioinformatics, 2: 159–163 (2003)

Scientific commentary

The Big Bang of bird evolution
Australasian Science, 36: 29-32 (2015)

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

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

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

(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
Mitochondrial DNA, 23: 153-155 (2012)

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

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

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

(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
Mitochondrial DNA, 21: 147-148 (2010)

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

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

(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
Mitochondrial DNA, 21: 33-35 (2010)

(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
Mitochondrial DNA, 21: 1-4 (2010)

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

Mitochondrial DNA, 20: 101-102 (2009)

(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
Mitochondrial DNA, 20: 65-68 (2009)

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

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

(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

Mitochondrial DNA, 20: 2-6 (2009)