Journals | - Duchêne, D., Duchene, S., Stiller, J., Heller, R., Ho, S. (2024). ClockstaRX: Testing Molecular Clock Hypotheses with Genomic Data. Genome Biology and Evolution, 16(4). [More Information]
- Kovacs, T., Walker, J., Hellemans, S., Bourguignon, T., Tatarnic, N., Mcrae, J., Ho, S., Lo, N. (2024). Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates. Systematic Biology, 73(3), 532-545. [More Information]
- Warwick Dus Adams, M., Carlile, N., Hutton, I., Ho, S., Lo, N., Walker, J., Rose, H., Jones, B., Zwick, A., Yang, H., et al (2024). Plio-Pleistocene decline of mesic forest underpins diversification in a clade of Australian Panesthia cockroaches. Systematic Entomology. [More Information]
- Beasley-Hall, P., Kinjo, Y., Rose, H., Walker, J., Foster, C., Kovacs, T., Bourguignon, T., Ho, S., Lo, N. (2024). Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life. Insect Science. [More Information]
- Jowers, M., Pyron, R., Perez-Losada, M., De Freitas, M., Downie, J., Moreno-Rueda, G., Forcina, G., Sánchez-Ramírez, S., Pajares, J., Weber, J., Ho, S., et al (2024). Testing molecular date estimates using an ecological and vicariant case study in treefrogs: The Geological-Ecological Molecular Calibration. Journal of Biogeography. [More Information]
- Tea, Y., Zhou, Y., Ewart, K., Cheng, G., Kawasaki, K., DiBattista, J., Ho, S., Lo, N., Fan, S. (2024). The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus). Ecology and Evolution, 14(3). [More Information]
- Asar, Y., Sauquet, H., Ho, S. (2023). Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution. Systematic Biology, 72(6), 1337-1356. [More Information]
- Van Der Wal, C., Ahyong, S., Warwick Dus Adams, M., Ewart, K., Ho, S., Lo, N. (2023). Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Molecular Phylogenetics and Evolution, 178. [More Information]
- Luo, A., Zhang, C., Zhou, Q., Ho, S., Zhu, C. (2023). Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating under the Fossilized Birth-Death Process. Systematic Biology, 72(4), 781-801. [More Information]
- Deng, W., Luo, X., Ho, S., Liao, S., Wang, Z., Che, Y. (2023). Inclusion of rare taxa from Blattidae and Anaplectidae improves phylogenetic resolution in the cockroach superfamily Blattoidea. Systematic Entomology, 48(1), 23-39. [More Information]
- Asar, Y., Ho, S., Sauquet, H. (2022). Early diversifications of angiosperms and their insect pollinators: were they unlinked? Trends in Plant Science, 27(9), 858-869. [More Information]
- Vankan, M., Ho, S., Duchene, D. (2022). Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. Systematic Biology, 71(2), 490-500. [More Information]
- Duchêne, D., Mather, N., Van Der Wal, C., Ho, S. (2022). Excluding Loci with Substitution Saturation Improves Inferences from Phylogenomic Data. Systematic Biology, 71(3), 676-689. [More Information]
- Chua, M., Ho, S., McMahon, C., Jonsen, I., de Bruyn, M. (2022). Movements of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: combining population genetics and tracking data. Polar Biology, 45(7), 1163-1174. [More Information]
- Tea, Y., Xu, X., DiBattista, J., Lo, N., Cowman, P., Ho, S. (2022). Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus). Systematic Biology, 71(1), 1-12. [More Information]
- Van Der Wal, C., Ahyong, S., Lo, N., Ho, S., Mccormack, R. (2022). Redescription of Euastacus clydensis Riek, 1969 (Crustacea: Parastacidae), a valid species of spiny crayfish from southern New South Wales, Australia. Zootaxa, 5222 (3), 285-297. [More Information]
- Kawakubo, S., Tomitaka, Y., Tomimura, K., Koga, R., Matsuoka, H., Uematsu, S., Yamashita, K., Ho, S., Ohshima, K. (2022). The recombinogenic history of turnip mosaic potyvirus reveals its introduction to Japan in the 19th century. Virus Evolution, 8(2). [More Information]
- Tims, A., Unmack, P., Ho, S. (2021). A fossil-calibrated time-tree of all Australian freshwater fishes. Molecular Phylogenetics and Evolution, 161, 1-7. [More Information]
- Kawakubo, S., Gao, F., Li, S., Tan, Z., Huang, Y., Adkar-Purushothama, C., Gurikar, C., Maneechoat, P., Chiemsombat, P., Aye, S., Ho, S., et al (2021). Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road. Proceedings of the National Academy of Sciences of the United States of America, 11(12). [More Information]
- Larena, M., Sánchez-Quinto, F., Sjödin, P., McKenna, J., Ebeo, C., Reyes, R., Casel, O., Huang, J., Hagada, K., Guilay, D., Ho, S., et al (2021). Multiple migrations to the Philippines during the last 50,000 years. Proceedings of the National Academy of Sciences of the United States of America, 118(13), e2026132118. [More Information]
- Xu, X., Su, Y., Ho, S., Kuntner, M., Ono, H., Liu, F., Chang, C., Warrit, N., Sivayyapram, V., Aung, K., et al (2021). Phylogenomic analysis of ultraconserved elements resolves the evolutionary and biogeographic history of segmented trapdoor spiders". Systematic Biology, 70(6), 1110-1122. [More Information]
- Hogg, C., Morrison, C., Dudley, J., Alquezar-Planas, D., Beasley-Hall, P., Magrath, M., Ho, S., Lo, N., Johnson, R., Grueber, C. (2021). Using phylogenetics to explore interspecies genetic rescue options for a critically endangered parrot. Conservation Science and Practice, 3(9), 1-10. [More Information]
- Mather, N., Traves, S., Ho, S. (2020). A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data. Ecology and Evolution, 10(1), 579-589. [More Information]
- Luo, A., Duchene, D., Zhang, C., Zhu, C., Ho, S. (2020). A Simulation-Based Evaluation of Tip-Dating under the Fossilized Birth-Death Process. Systematic Biology, 69(2), 325-344. [More Information]
- Nie, Y., Foster, C., Zhu, T., Yao, R., Duchene, D., Ho, S., Zhong, B. (2020). Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies. Systematic Biology, 69(1), 1-16. [More Information]
- Karpinski, E., Hackenberger, D., Zazula, G., Widga, C., Duggan, A., Golding, G., Kuch, M., Klunk, J., Jass, C., Groves, P., Ho, S., et al (2020). American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations. Nature Communications, 11(1), 4048. [More Information]
- Tea, Y., Hobbs, J., Vitelli, F., DiBattista, J., Ho, S., Lo, N. (2020). Angels in disguise: sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages. Proceedings of the Royal Society B: Biological Sciences, 287(1932), 20201459. [More Information]
- Duchêne, S., Lemey, P., Stadler, T., Ho, S., Duchene, D., Dhanasekaran, V., Baele, G. (2020). Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations. Molecular Biology and Evolution, 37(11), 3363-3379. [More Information]
- Ho, S., Duchene, S. (2020). Dating the emergence of human pathogens. Science, 368(6497), 1310-1311. [More Information]
- Arab, D., Bourguignon, T., Wang, Z., Ho, S., Lo, N. (2020). Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes. Biology Letters, 16(1), 20190702. [More Information]
- Barnett, R., Westbury, M., Sandoval-Velasco, M., Vieira, F., Jeon, S., Zazula, G., Martin, M., Ho, S., Mather, N., Gopalakrishnan, S., et al (2020). Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens. Current Biology, 30(24), 5018-5025. [More Information]
- Bourguignon, T., Kinjo, Y., Villa-Martín, P., Coleman, N., Tang, Q., Arab, D., Wang, Z., Tokuda, G., Hongoh, Y., Ohkuma, M., Ho, S., Lo, N., et al (2020). Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes. Current Biology, 30(19), 3848-3855.e4. [More Information]
- Duchene, D., Tong, K., Foster, C., Duchene, S., Lanfear, R., Ho, S. (2020). Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference. Molecular Biology and Evolution, 37(4), 1202-1210. [More Information]
- Xu, X., Kuntner, M., Bond, J., Ono, H., Ho, S., Liu, F., Yu, L., Li, D. (2020). Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands. Molecular Phylogenetics and Evolution, 151, 106900. [More Information]
- Ewart, K., Lo, N., Ogden, R., Joseph, L., Ho, S., Frankham, G., Eldridge, M., Schodde, R., Johnson, R. (2020). Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation. Heredity, 125(3), 85-100. [More Information]
- Gao, F., Kawakubo, S., Ho, S., Ohshima, K. (2020). The evolutionary history and global spatio-temporal dynamics of potato virus y. Virus Evolution, 6(2), 1-10. [More Information]
- Duchene, S., Ho, S., Carmichael, A., Holmes, E., Poinar, H. (2020). The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Current Biology, 30(19), R1215-R1231. [More Information]
- Zhang, L., Chen, F., Zhang, X., Li, Z., Zhao, Y., Lohaus, R., Chang, X., Dong, W., Ho, S., Liu, X., et al (2020). The water lily genome and the early evolution of flowering plants. Nature, 577(7788), 79-84. [More Information]
- Che, Y., Bai, Q., Deng, W., Liao, S., He, J., Ho, S., Wang, Z. (2020). Uplift-driven diversification revealed by the historical biogeography of the cockroach Cryptocercus Scudder (Blattodea: Cryptocercidae) in eastern Asia. Systematic Entomology, 45(1), 60-72. [More Information]
- Van Der Merwe, M., Yap, J., Bragg, J., Cristofolini, C., Foster, C., Ho, S., Rossetto, M. (2019). Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using chloroplast DNA sequences. Methods in Ecology and Evolution, 10(7), 971-981. [More Information]
- Tea, Y., Van Der Wal, C., Ludt, W., Gill, A., Lo, N., Ho, S. (2019). Boomeranging around Australia: Historical biogeography and population genomics of the anti-equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae). Molecular Ecology, 28(16), 3771-3785. [More Information]
- Van Der Wal, C., Ahyong, S., Ho, S., Lins, L., Lo, N. (2019). Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea: Malacostraca). Invertebrate Systematics, 33(1), 89-100. [More Information]
- Thomas, J., Carvalho, G., Haile, J., Rawlence, N., Martin, M., Ho, S., Sigfússon, A., Jósefsson, V., Frederiksen, M., Linnebjerg, J., et al (2019). Demographic reconstruction from ancient DNA supports rapid extinction of the great auk. eLife, 8, 1-35. [More Information]
- Gao, F., Chen, C., Arab, D., Du, Z., He, Y., Ho, S. (2019). EasyCodeML: A visual tool for analysis of selection using CodeML. Ecology and Evolution, 9(7), 3891-3898. [More Information]
- Fahey, M., Rossetto, M., Wilson, P., Ho, S. (2019). Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae). Heredity, 123(4), 532-548. [More Information]
- Ritchie, A., Ho, S. (2019). Influence of the tree prior and sampling scale on Bayesian phylogenetic estimates of the origin times of language families. Journal of Language Evolution, 4(2), 108-123. [More Information]
- Knapp, M., Thomas, J., Haile, J., Prost, S., Ho, S., Dussex, N., Cameron-Christie, S., Kardailsky, O., Barnett, R., et al (2019). Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa. Molecular Phylogenetics and Evolution, 134, 122-128. [More Information]
- Montagna, M., Tong, K., Magoga, G., Strada, L., Tintori, A., Ho, S., Lo, N. (2019). Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction. Proceedings of the Royal Society B: Biological Sciences, 286(1912), 1-9. [More Information]
- Vargas, S., Lins, L., Molfetti, E., Ho, S., Monteiro, D., Barreto, J., Colman, L., Vila-Verde, L., Baptistotte, C., Alciata Thome, J., et al (2019). Revisiting the genetic diversity and population structure of the critically endangered leatherback turtles in the South-west Atlantic Ocean: insights for species conservation. Journal of the Marine Biological Association of the United Kingdom, 99(1), 31-41. [More Information]
- Iglesias-Carrasco, M., Jennions, M., Ho, S., Duchene, D. (2019). Sexual selection, body mass and molecular evolution interact to predict diversification in birds. Proceedings of the Royal Society B: Biological Sciences, 286(1899), 1-7. [More Information]
- Tong, K., Duchene, D., Duchene, S., Geoghegan, J., Ho, S. (2018). A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evolutionary Biology, 18(1), 1-10. [More Information]
- Johnson, R., O'Meally, D., Chen, Z., Etherington, G., Ho, S., Nash, W., Grueber, C., Cheng, Y., Whittington, C., Dennison, S., Peel, E., Brandies, P., Hogg, C., Govendir, M., Jones, E., Wright, B., Belov, K., et al (2018). Adaptation and conservation insights from the koala genome. Nature Genetics, 50(8), 1102-1111. [More Information]
- Duchene, D., Bragg, J., Duchene, S., Neaves, L., Potter, S., Moritz, C., Johnson, R., Ho, S., Eldridge, M. (2018). Analysis of phylogenomic tree space resolves relationships among marsupial families. Systematic Biology, 67(3), 400-412. [More Information]
- Bromham, L., Duchene, S., Hua, X., Ritchie, A., Duchene, D., Ho, S. (2018). Bayesian molecular dating: opening up the black box. Biological Reviews, 93(2), 1165-1191. [More Information]
- Luo, A., Ling, C., Ho, S., Zhu, C. (2018). Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios. Systematic Biology, 67(5), 830-846. [More Information]
- Duchene, D., Duchene, S., Ho, S. (2018). Differences in performance among test statistics for assessing phylogenomic model adequacy. Genome Biology and Evolution, 10(6), 1375-1388. [More Information]
- Duan, G., Zhan, F., Du, Z., Ho, S., Gao, F. (2018). Europe was a hub for the global spread of potato virus S in the 19th century. Virology, 525, 200-204. [More Information]
- Todd, E., Ho, S., Thomson, P., Ang, R., Velie, B., Hamilton (Ellis), N. (2018). Founder-specific inbreeding depression affects racing performance in Thoroughbred horses. Scientific Reports, 8(1), 1-10. [More Information]
- Lee, C., Moroldo, M., Perdomo Sabogal, A., Mach, N., Marthey, S., Lecardonnel, J., Wahlberg, P., Chong, A., Estelle, J., Ho, S., Gongora, J., et al (2018). Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing. Immunogenetics, 70(6), 401-417. [More Information]
- Hudjashov, G., Endicott, P., Post, H., Nagle, N., Ho, S., Lawson, D., Reidla, M., Karmin, M., Rootsi, S., Metspalu, E., et al (2018). Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Scientific Reports, 8(1), 1-12. [More Information]
- Anijalg, P., Ho, S., Davison, J., Keis, M., Tammeleht, E., Bobowik, K., Tumanov, I., Saveljev, A., Lyapunova, E., Vorobiev, A., et al (2018). Large-scale migrations of brown bears in Eurasia and to North America during the Late Pleistocene. Journal of Biogeography, 45(2), 394-405. [More Information]
- Zhou, Z., Lundstrom, I., Tran-Dien, A., Duchene, S., Alikhan, N., Sergeant, M., Langridge, G., Fotakis, A., Nair, S., Ho, S., et al (2018). Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Current Biology, 28(15), 2420-2428.e10. [More Information]
- Duchene, D., Duchene, S., Ho, S. (2018). PhyloMAd: Efficient assessment of phylogenomic model adequacy. Bioinformatics, 34(13), 2300-2301. [More Information]
- Foster, C., Henwood, M., Ho, S. (2018). Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea). Molecular Phylogenetics and Evolution, 127, 156-167. [More Information]
- Guan, X., Yang, C., Fu, J., Du, Z., Ho, S., Gao, F. (2018). Rapid evolutionary dynamics of pepper mild mottle virus. Virus Research, 256, 96-99. [More Information]
- Frantz, L., Rudzinski, A., Nugraha, A., Evin, A., Burton, J., Hulme-Beaman, A., Linderholm, A., Barnett, R., Vega, R., Irving-Pease, E., Ho, S., et al (2018). Synchronous diversification of sulawesi's iconic artiodactyls driven by recent geological events. Proceedings of the Royal Society B: Biological Sciences, 285(1876), 1-8. [More Information]
- Luo, A., Ho, S. (2018). The molecular clock and evolutionary timescales. Biochemical Society Transactions, 46(5), 1183-1190. [More Information]
- Bourguignon, T., Tang, Q., Ho, S., Juna, F., Wang, Z., Arab, D., Cameron, S., Walker, J., Rentz, D., Evans, T., Lo, N. (2018). Transoceanic dispersal and plate tectonics shaped global cockroach distributions: Evidence from mitochondrial phylogenomics. Molecular Biology and Evolution, 35(4), 970-983. [More Information]
- Lee, T., Evans, T., Cameron, S., Ho, S., Namyatova, A., Lo, N. (2017). 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. Invertebrate Systematics, 31(2), 180-190. [More Information]
- Lins, L., Ho, S., Lo, N. (2017). An evolutionary timescale for terrestrial isopods and a lack of molecular support for the monophyly of Oniscidea (Crustacea: Isopoda). Organisms Diversity and Evolution, 17(4), 813-820. [More Information]
- Lee, T., Evans, T., Cameron, S., Hochuli, D., Ho, S., Lo, N. (2017). Ecological diversification of the Australian Coptotermes termites and the evolution of mound building. Journal of Biogeography, 44, 1405-1417. [More Information]
- Foster, C., Sauquet, H., Van Der Merwe, M., McPherson, H., Rossetto, M., Ho, S. (2017). Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale. Systematic Biology, 66(3), 338-351. [More Information]
- Bourguignon, T., Lo, N., Sobotnik, J., Ho, S., Iqbal, N., Coissac, E., Lee, M., Jendryka, M., Sillam-Dusses, D., Krizkova, B., et al (2017). Mitochondrial Phylogenomics Resolves the Global Spread of Higher Termites, Ecosystem Engineers of the Tropics. Molecular Biology and Evolution, 34(3), 589-597. [More Information]
- Duchene, D., Duchene, S., Ho, S. (2017). New statistical criteria detect phylogenetic bias caused by compositional heterogeneity. Molecular Biology and Evolution, 34(6), 1529-1534. [More Information]
- Arab, D., Namyatova, A., Evans, T., Cameron, S., Yeates, D., Ho, S., Lo, N. (2017). Parallel evolution of mound-building and grass-feeding in Australian nasute termites. Biology Letters, 13(2), 1-5. [More Information]
- Raven, N., Lisovski, S., Klaassen, M., Lo, N., Madsen, T., Ho, S., Ujvari, B. (2017). Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders. Infection, Genetics and Evolution, 53, 135-145. [More Information]
- Foster, C., Ho, S. (2017). Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale. Genome Biology and Evolution, 9(10), 2752-2763. [More Information]
- Van Der Wal, C., Ahyong, S., Ho, S., Lo, N. (2017). The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data. PeerJ, 2017 (9), 1-17. [More Information]
- Ritchie, A., Lo, N., Ho, S. (2017). The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling. Systematic Biology, 66(3), 413-425. [More Information]
- Tong, K., Duchene, S., Lo, N., Ho, S. (2017). The impacts of drift and selection on genomic evolution in insects. PeerJ, 5(4), 1-16. [More Information]
- Yasaka, R., Fukagawa, H., Ikematsu, M., Soda, H., Korkmaz, S., Golnaraghi, A., Katis, N., Ho, S., Gibbs, A., Ohshima, K. (2017). The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus. Scientific Reports, 7(1), 1-14. [More Information]
- Li, X., Liu, H., Liu, L., Feng, Y., Kalish, M., Ho, S., Shao, Y. (2017). Tracing the epidemic history of HIV-1 CRF01-AE clusters using near-complete genome sequences. Scientific Reports, 7, 1-11. [More Information]
- Llamas, B., Fehren-Schmitz, L., Valverde, G., Soubrier, J., Mallick, S., Rohland, N., Nordenfelt, S., Valdiosera, C., Richards, S., Rohrlach, A., Ho, S., et al (2016). Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Science Advances, 2(4), 1-10. [More Information]
- Duchene, S., Duchene, D., Di Giallonardo, F., Eden, J., Geoghegan, J., Holt, K., Ho, S., Holmes, E. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC Evolutionary Biology, 16(1), 1-8. [More Information]
- Soubrier, J., Gower, G., Chen, K., Richards, S., Llamas, B., Mitchell, K., Ho, S., Kosintsev, P., Lee, M., Baryshnikov, G., et al (2016). Early cave art and ancient DNA record the origin of European bison. Nature Communications, 7, 1-7. [More Information]
- Duchene, S., Geoghegan, J., Holmes, E., Ho, S. (2016). Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics, 32(22), 3375-3379. [More Information]
- Duchene, S., Foster, C., Ho, S. (2016). Estimating the number and assignment of clock models in analyses of multigene datasets. Bioinformatics, 32(9), 1281-1285. [More Information]
- Ritchie, A., Lo, N., Ho, S. (2016). Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker. Organisms Diversity and Evolution, 16(3), 467-480. [More Information]
- Martin, M., Vieira, F., Ho, S., Wales, N., Schubert, M., Seguin-Orlando, A., Ristaino, J., Gilbert, M. (2016). Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans. Molecular Biology and Evolution, 33(2), 478-491. [More Information]
- Nguyen, J., Ho, S. (2016). Mitochondrial rate variation among lineages of passerine birds. Journal of Avian Biology, 47(5), 690-696. [More Information]
- Barnett, R., Mendoza, M., Soares, A., Ho, S., Zazula, G., Yamaguchi, N., Shapiro, B., Kirillova, I., Larson, G., Gilbert, M. (2016). Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats. Open Quaternary, 2(4), 1-11. [More Information]
- Lee, M., Ho, S. (2016). Molecular clocks. Current Biology, 26(10), 399-402. [More Information]
- Foster, C., Cantrill, D., James, E., Syme, A., Jordan, R., Douglas, R., Ho, S., Henwood, M. (2016). Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae). Australian Systematic Botany, 29, 185-196. [More Information]
- Lo, N., Tong, K., Rose, H., Ho, S., Beninati, T., Low, D., Matsumoto, T., Maekawa, K. (2016). Multiple evolutionary origins of Australian soil-burrowing cockroaches driven by climate change in the Neogene. Proceedings of the Royal Society B: Biological Sciences, 283(1825), 1-8. [More Information]
- Vargas, S., Jensen, M., Ho, S., Mobaraki, A., Broderick, D., Mortimer, J., Whiting, S., Miller, J., Prince, R., Bell, I., et al (2016). Phylogeography, Genetic Diversity, and Management Units of Hawksbill Turtles in the Indo-Pacific. Journal of Heredity, 107(3), 199-213. [More Information]
- Tong, K., Lo, N., Ho, S. (2016). Reconstructing evolutionary timescales using phylogenomics. Zoological Systematics, 41(4), 343-351. [More Information]
- Ho, S., Chen, A., Lins, L., Duchene, D., Lo, N. (2016). The Genome as an Evolutionary Timepiece. Genome Biology and Evolution, 8(9), 3006-3010. [More Information]
- Abdelgawad, A., Damiani, A., Ho, S., Strauss, G., Szentiks, C., East, M., Osterrieder, N., Greenwood, A. (2016). Zebra Alphaherpesviruses (EHV-1 and EHV-9): Genetic Diversity, Latency and Co-Infections. Viruses, 8(9), 1-13. [More Information]
- Luo, A., Lan, H., Ling, C., Zhang, A., Shi, L., Ho, S., Zhu, C. (2015). A simulation study of sample size for DNA barcoding. Ecology and Evolution, 5(24), 5869-5879. [More Information]
- Ho, S., Tong, K., Foster, C., Ritchie, A., Lo, N., Crisp, M. (2015). Biogeographic calibrations for the molecular clock. Biology Letters, 11(9), 1-7. [More Information]
- Tong, K., Duchene, S., Ho, S., Lo, N. (2015). Comment on "Phylogenomics resolves the timing and pattern of insect evolution". Science, 349(6427), 487-487. [More Information]
- Paraskevis, D., Angelis, K., Magiorkinis, G., Kostaki, E., Ho, S., Hatzakis, A. (2015). Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes. Molecular Phylogenetics and Evolution, 93, 44-54. [More Information]
- Duchene, S., Ho, S., Holmes, E. (2015). Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models. BMC Evolutionary Biology, 15(1), 1-10. [More Information]
- Molak, M., Suchard, M., Ho, S., Bellman, D., Shapiro, B. (2015). Empirical calibrated radiocarbon sampler: A tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA. Molecular Ecology Resources, 15(1), 81-86. [More Information]
- Duchene, D., Duchene, S., Holmes, E., Ho, S. (2015). Evaluating the adequacy of molecular clock models using posterior predictive simulations. Molecular Biology and Evolution, 32(11), 2986-2995. [More Information]
- Morin, P., Parsons, K., Archer, F., Avila-Arcos, M., Barrett-Lennard, L., Dalla Rosa, L., Duchene, S., Durban, J., Ellis, G., Ferguson, S., Ho, S., et al (2015). Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Molecular Ecology, 24(15), 3964-3979. [More Information]
- Thornhill, A., Ho, S., Kulheim, C., Crisp, M. (2015). Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny. Molecular Phylogenetics and Evolution, 93, 29-43. [More Information]
- Duchene, S., Ho, S. (2015). Mammalian genome evolution is governed by multiple pacemakers. Bioinformatics, 31(13), 2061-2065. [More Information]
- Alexander, M., Ho, S., Molak, M., Barnett, R., Carlborg, O., Dorshorst, B., Honaker, C., Besnier, F., Wahlberg, P., Dobney, K., et al (2015). Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance. Biology Letters, 11(10), 1-4. [More Information]
- Lu, L., Ge, D., Chesters, D., Ho, S., Ma, Y., Li, G., Wen,, Z., Wu, Y., Wang, J., Xia, L., et al (2015). Molecular phylogeny and the underestimated species diversity of the endemic white-bellied rat (Rodentia: Muridae: Niviventer) in Southeast Asia and China. Zoologica Scripta, 44(5), 475-494. [More Information]
- Yasaka, R., Ohba, K., Schwinghame, M., Fletcher, J., Ochoa-Corona, F., Thomas, J., Ho, S., Gibbs, A., Ohshima, K. (2015). Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand. Journal of General Virology, 96(3), 701-713. [More Information]
- Jarvis, E., Mirarab, S., Aberer, A., Li, B., Houde, P., Li, C., Ho, S., Faircloth, B., Nabholz, B., Howard, J., et al (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4, 1-9. [More Information]
- Molak, M., Ho, S. (2015). Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA. PeerJ, 3, 1-16. [More Information]
- Cracraft, J., Houde, P., Ho, S., Mindel, D., Fjeldså, J., Lindow, B., Edwards, S., Rahbek, C., Mirarab, S., Warnow, T., et al (2015). Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science, 349(6255), 1-3. [More Information]
- Ho, S., Duchene, S., Duchene, D. (2015). Simulating and detecting autocorrelation of molecular evolutionary rates among lineages. Molecular Ecology Resources, 15(4), 688-696. [More Information]
- Ohshima, K., Matsumoto, K., Yasaka, R., Nishiyama, M., Soejima, K., Korkmaz, S., Ho, S., Gibbs, A., Takeshita, M. (2015). Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology, 487(2016), 188-197. [More Information]
- Bally, J., Nakasugi, K., Jia, F., Jung, H., Ho, S., Wong, C., Paul, C., Naim, F., Wood, C., Crowhurst, R., Waterhouse, P., et al (2015). The extremophile Nicotiana benthamiana has traded viral defence for early vigour. Nature Plants, 1, 1-6. [More Information]
- Lee, T., Cameron, S., Evans, T., Ho, S., Lo, N. (2015). The origins and radiation of Australian Coptotermes termites: From rainforest to desert dwellers. Molecular Phylogenetics and Evolution, 82(PA), 234-244. [More Information]
- Duchene, S., Duchene, D., Holmes, E., Ho, S. (2015). The performance of the date-randomization test in
phylogenetic analyses of time-structured virus data. Molecular Biology and Evolution, 32(7), 1895-1906. [More Information]
- Ho, S., Duchene, S., Molak, M., Shapiro, B. (2015). Time-dependent estimates of molecular evolutionary rates: evidence and causes. Molecular Ecology, 24(24), 6007-6012. [More Information]
- Duchene, D., Duchene, S., Ho, S. (2015). Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences. Molecular Ecology Resources, 15(4), 785-794. [More Information]
- Hope, A., Ho, S., Malaney, J., Cook, J., Talbot, S. (2014). Accounting for rate variation among lineages in comparative demographic analyses. Evolution, 68(9), 2689-2700. [More Information]
- Duchene, S., Holmes, E., Ho, S. (2014). Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society B: Biological Sciences, 281(1786), 1-7. [More Information]
- Shapiro, B., Ho, S. (2014). Ancient hyaenas highlight the old problem of estimating evolutionary rates. Molecular Ecology, 23(3), 499-501. [More Information]
- Duchene, S., Molak, M., Ho, S. (2014). ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics, 30(7), 1017-1019. [More Information]
- Edwards, C., Ho, S., Barnett, R., Coxon, P., BÌ€radley, D., Lord, T., O'Connor, T. (2014). Continuity of brown bear maternal lineages in northern England through the Last-glacial period. Quaternary Science Reviews, 96, 131-139. [More Information]
- Zhang, F., Yu, D., Luo, Y., Ho, S., Wang, B., Zhu, C. (2014). Cryptic diversity, diversification and vicariance in two species complexes of Tomocerus (Collembola, Tomoceridae) from China. Zoologica Scripta, 43(4), 393-404. [More Information]
- Jaratlerdsiri, W., Isberg, S., Higgins, D., Ho, S., Salomonsen, J., Skjodt, K., Miles, L., Gongora, J. (2014). Evolution of MHC class i in the Order Crocodylia. Immunogenetics, 66(1), 53-65. [More Information]
- Brito, R., Fransisco, F., Ho, S., Oldroyd, B. (2014). Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera: Apidae: Meliponini). Biological Journal of the Linnean Society, 113(1), 149-161. [More Information]
- Li, X., Zhang, Z., Yu, A., Ho, S., Carr, M., Zheng, W., Zhang, Y., Zhu, C., Lei, F., Shi, W. (2014). Global and local persistence of influenza A(H5N1) virus. Emerging Infectious Diseases, 20(8), 1287-1295. [More Information]
- Stiller, M., Molak, M., Prost, S., Rabeder, G., Baryshnikov, G., Rosendahl, W., Münzel, S., Bocherens, H., Grandal d'Anglade, A., Hilpert, B., Ho, S., et al (2014). Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quaternary International, 339-340, 224-231. [More Information]
- Foster, C., Conn, B., Henwood, M., Ho, S. (2014). Molecular data support Orianthera: a new genus of
Australian Loganiaceae. Telopea, 16, 149-158. [More Information]
- Foster, C., Ho, S., Conn, B., Henwood, M. (2014). Molecular systematics and biogeography of Logania R.Br. (Loganiaceae). Molecular Phylogenetics and Evolution, 78(2014), 324-333. [More Information]
- Ho, S., Duchene, S. (2014). Molecular-clock methods for estimating evolutionary rates and timescales. Molecular Ecology, 23(24), 5947-5965. [More Information]
- Martin, M., Ho, S., Wales, N., Ristaino, J., Gilbert, M. (2014). Persistence of the Mitochondrial Lineage Responsible for the Irish Potato Famine in Extant New World Phytophthora infestans. Molecular Biology and Evolution, 31(6), 1414-1420. [More Information]
- Lee, T., Ho, S., Wilson, G., Lo, N. (2014). Phylogeography and diversity of the terrestrial isopod Spherillo grossus (Oniscidea: Armadillidae) on the Australian East Coast. Zoological Journal of the Linnean Society, 170(2), 297-309. [More Information]
- Barnett, R., Yamaguchi, N., Shapiro, B., Ho, S., Barnes, I., Sabin, R., Werdelin, L., Cuisin, J., Larson, G. (2014). Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evolutionary Biology, 14(1), 1-11. [More Information]
- Ho, S. (2014). The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution, 29(9), 496-503. [More Information]
- Duchene, S., Lanfear, R., Ho, S. (2014). The impact of calibration and clock-model choice on molecular estimates of divergence times. Molecular Phylogenetics and Evolution, 78(1), 277-289. [More Information]
- Jia, F., Lo, N., Ho, S. (2014). The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales. PloS One, 9(5), 1-8. [More Information]
- Yasaka, R., Nguyen, H., Ho, S., Duchene, S., Korkmaz, S., Katis, N., Takahashi, H., Gibbs, A., Ohshima, K. (2014). The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus. PloS One, 9(1), 1-12. [More Information]
- Li, C., Zhang, Y., Li, J., Kong, L., Hu, H., Pan, H., Xu, L., Deng, Y., Li, Q., Ho, S., et al (2014). Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. GigaScience, 3(27), 1-15. [More Information]
- Duchene, S., Ho, S. (2014). Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data. Molecular Phylogenetics and Evolution, 77(2014), 65-70. [More Information]
- Jarvis, E., Mirarab, S., Aberer, A., Li, B., Houde, P., Li, C., Ho, S., Faircloth, B., Nabholz, B., Howard, J., et al (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331. [More Information]
- Lorion, J., Kiel, S., Faure, B., Kawato, M., Ho, S., Marshall, B., Tsuchida, S., Miyazaki, J., Fujiwara, Y. (2013). Adaptive radiation of chemosymbiotic deep-sea mussels. Proceedings of the Royal Society B: Biological Sciences, 280(1770), 1-10. [More Information]
- Foote, A., Kaschner, K., Schultze, S., Garilao, C., Ho, S., Post, K., Higham, T., Stokowska, C., Van Der Es, H., Embling, C., et al (2013). Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature Communications, 4, 1-7. [More Information]
- Langford, S., Kraitsek, S., Baskerville, B., Ho, S., Gongora, J. (2013). Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens. BMC Genetics, 14(2), 1-8. [More Information]
- Miller, J., Murphy, D., Ho, S., Cantrill, D., Seigler, D. (2013). Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany, 61(6), 436-445. [More Information]
- Keis, M., Remm, J., Ho, S., Davison, J., Tammeleht, E., Tumanov, I., Saveljev, A., Mannil, P., Kojola, I., Abramov, A., et al (2013). Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia. Journal of Biogeography, 40(5), 915-927. [More Information]
- Paraskevis, D., Magiorkinis, G., Magiorkinis, E., Ho, S., Belshaw, R., Allain, J., Hatzakis, A. (2013). Dating the origin and dispersal of hepatitis B virus infection in humans and primates. Hepatology, 57(3), 908-916. [More Information]
- Martinkova, N., Barnett, R., Cucchi, T., Struchen, R., Pascal, M., Pascal, M., Fischer, M., Higham, T., Brace, S., Ho, S., et al (2013). Divergent evolutionary processes associated with colonization of offshore islands. Molecular Ecology, 22(20), 5205-5220. [More Information]
- Huang, Y., Guo, X., Ho, S., Shi, H., Li, J., Li, J., Cai, B., Wang, Y. (2013). Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland. PloS One, 8(6), 1-13. [More Information]
- Brotherton, P., Haak, W., Templeton, J., Brandt, G., Soubrier, J., Adler, C., Richards, S., Der Sarkissian, C., Ganslmeier, R., Friedrich, S., Ho, S., et al (2013). Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications, 4, 1-11. [More Information]
- Avila-Arcos, M., Ho, S., Ishida, Y., Nikolaidis, N., Tsangaras, K., Honig, K., Medina, R., Rasmussen, M., Fordyce, S., Calvignac-Spencer, S., et al (2013). One hundred twenty years of koala retrovirus evolution determined from museum skins. Molecular Biology and Evolution, 30(2), 299-304. [More Information]
- Molak, M., Lorenzen, E., Shapiro, B., Ho, S. (2013). Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages. Molecular Biology and Evolution, 30(2), 253-262. [More Information]
- Jin, Q., Han, H., Hu, X., Li, X., Zhu, C., Ho, S., Ward, R., Zhang, A. (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One, 8(5), 1-13. [More Information]
- Martin, M., Cappellini, E., Samaniego, J., Zepeda, M., Campos, P., Seguin-Orlando, A., Wales, N., Orlando, L., Ho, S., Dietrich, F., et al (2013). Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 4, 1-7. [More Information]
- Yeoh, S., Ho, S., Thornhill, A., Foley, W. (2013). Regional population expansion in Eucalyptus globulus. Molecular Phylogenetics and Evolution, 68(3), 498-501. [More Information]
- Lanfear, R., Ho, S., Jonathan, D., Moles, A., Aarssen, L., Swenson, N., Warman, L., Zanne, A., Allen, A. (2013). Taller plants have lower rates of molecular evolution. Nature Communications, 4, 1-7. [More Information]
- Ho, S., Lo, N. (2013). The insect molecular clock. Australian Journal of Entomology, 52(2), 101-105. [More Information]
- Basu Mallick, C., Mircea Iliescu, F., Mols, M., Hill, S., Tamang, R., Chaubey, G., Goto, R., Ho, S., Gallego Romero, I., Crivellaro, F., et al (2013). The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genetics, 9(11), 1-13. [More Information]
- Zhao, Z., Su, T., Chesters, D., Wang, S., Ho, S., Zhu, C., Chen, X., Zhang, C. (2013). The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies. PloS One, 8(4), 1-15. [More Information]
- Nguyen, H., Tomitaka, Y., Ho, S., Duchene, S., Vetten, H., Lesemann, D., Walsh, J., Gibbs, A., Ohshima, K. (2013). Turnip mosaic potyvirus probably first spread to Eurasian Brassica crops from wild orchids about 1000 years ago. PloS One, 8(2), 1-13. [More Information]
- Greenwood, A., Tsangaras, K., Ho, S., Szentkis, C., Nikolin, V., Ma, G., Damiani, A., East, M., Lawrenz, A., Hofer, H., et al (2012). A Potentially Fatal Mix of Herpes in Zoos. Current Biology, 22, 1727-1731. [More Information]
- Thornhill, A., Popple, L., Carter, R., Ho, S., Crisp, M. (2012). Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Molecular Phylogenetics and Evolution, 63(1), 15-27. [More Information]
- Dos Santos Ferreira Lins, L., Ho, S., Wilson, G., Lo, N. (2012). Evidence for Permo-Triassic colonization of the deep sea by isopods. Biology Letters, 8(6), 979-982. [More Information]
- Gongora, J., Swan, A., Chong, A., Ho, S., Damayanti, C., Kolomyjec, S., Grant, T., Miller, E., Blair, D., Furlan, E., et al (2012). Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA. Journal of Zoology, 286, 110-119. [More Information]
- Lanfear, R., Calcott, B., Ho, S., Guindon, S. (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701. [More Information]
- Larson, G., Karlsson, E., Perri, A., Webster, M., Ho, S., Peters, J., Stahl, P., Piper, P., Lingaas, F., Fredholm, M., et al (2012). Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proceedings of the National Academy of Sciences of the United States of America, 109(23), 8878-8883. [More Information]
- Mourier, T., Ho, S., Gilbert, M., Willerslev, E., Orlando, L. (2012). Statistical guidelines for detecting past population shifts using ancient DNA. Molecular Biology and Evolution, 29(9), 2241-2251. [More Information]
- Edwards, C., Soulsbury, C., Statham, M., Ho, S., Wall, D., Dolf, G., Lossa, G., Baker, P., Harris, S., Sacks, B., et al (2012). Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles. Quaternary Science Reviews, 57, 95-104. [More Information]
- Sauquet, H., Ho, S., Gondolfo, M., Jordan, G., Wilf, P., Cantrill, D., Bayly, M., Bromham, L., Brown, G., Carpenter, R., et al (2012). Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of nothofagus (Fagales). Systematic Biology, 61(2), 289-313. [More Information]
- Soubrier, J., Steel, M., Lee, M., Der Sarkissian, C., Guindon, S., Ho, S., Cooper, A. (2012). The influence of rate heterogeneity among sites on the time dependence of molecular rates. Molecular Biology and Evolution, 29(11), 3345-3358. [More Information]
- Shapiro, B., Ho, S., Drummond, A., Suchard, M., Pybus, O., Rambaut, A. (2011). A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. Molecular Biology and Evolution, 28(2), 879-887. [More Information]
- Ho, S., Lanfear, R., Phillips, M., Barnes, I., Thomas, J., Kolokotronis, S., Shapiro, B. (2011). Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology, 60(3), 1-10. [More Information]
- Wong, J., Ho, S., Hogg, P. (2011). Disulfide bond acquisition through eukaryotic protein evolution. Molecular Biology and Evolution, 28(1), 327-334. [More Information]
- Molak, M., Ho, S. (2011). Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach. Journal of Molecular Evolution, 73(3-4), 244-255. [More Information]
- Davison, J., Ho, S., Bray, S., Korsten, M., Tammeleht, E., Hindrikson, M., Ostbye, K., Ostbye, E., Lauritzen, S., Austin, J., et al (2011). Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews, 30(3-4), 418-430. [More Information]
- Vilstrup, J., Ho, S., Foote, A., Morin, P., Kreb, D., Krutzen, M., Parra, G., Robertson, K., de Stephanis, R., Verborgh, P., et al (2011). Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evolutionary Biology, 11(1), 65-1-65-10. [More Information]
- Li, W., Shi, W., Qiao, H., Ho, S., Luo, A., Zhang, Y., Zhu, C. (2011). Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virology Journal, 8, 1-9. [More Information]
- Luo, A., Zhang, A., Ho, S., Xu, W., Zhang, Y., Shi, W., Cameron, S., Zhu, C. (2011). Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals. BMC Genomics, 12, 1-13. [More Information]
- Lanfear, R., Bromham, L., Ho, S. (2011). Reply to Englund: Molecular evolution and diversification - Counting species is better than counting nodes when the phylogeny is unknown. Proceedings of the National Academy of Sciences of the United States of America, 108(17), E85-E86. [More Information]
- Gongora, J., Cuddahee, R., do Nascimento, F., Palgrave, C., Lowden, S., Ho, S., Simond, D., Damayanti, C., White, D., Tay, W., Rodrigues-Zarate, C., Moran, C., et al (2011). Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla). Zoologica Scripta, 40(4), 327-335. [More Information]
- Ho, S., Shapiro, B. (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources, 11(3), 423-434. [More Information]
- Lorenzen, E., Nogues-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K., Ugan, A., Borregaard, M., Gilbert, M., Nielsen, R., Ho, S., et al (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479(7373), 359-364. [More Information]
- Pepper, M., Ho, S., Fujita, M., Keogh, S. (2011). The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate. Molecular Phylogenetics and Evolution, 61(3), 750-759. [More Information]
- Ho, S., Lanfear, R., Bromham, L., Phillips, M., Soubrier, J., Rodrigo, A., Cooper, A. (2011). Time-dependent rates of molecular evolution. Molecular Ecology, 20(15), 3087-3101. [More Information]
- Nguyen, J., Molak, M., Black, K., Fitzgerald, E., Travouillon, T., Ho, S. (2011). Vertebrate palaeontology of australasia into the twenty-first century. Biology Letters, 7(6), 804-806. [More Information]
- Ho, S., Gilbert, M. (2010). Ancient mitogenomics. Mitochondrion, 10(1), 1-11. [More Information]
- Ho, S., Lanfear, R. (2010). Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA, 21(3-4), 138-146. [More Information]
- Lanfear, R., Ho, S., Love, D., Bromham, L. (2010). Mutation rate is linked to diversification in birds. Proceedings of the National Academy of Sciences of the United States of America, 107(47), 20423-20428. [More Information]
- Luo, A., Qiao, H., Zhang, Y., Shi, W., Ho, S., Xu, W., Zhang, A., Zhu, C. (2010). Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evolutionary Biology, 10(242), 1-13. [More Information]
- Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S., Vila, C., Hasegawa, M., et al (2010). Phylogeographic analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal of Biogeography, 37(12), 2332-2344. [More Information]
- Salvo, G., Ho, S., Rosenbaum, G., Ree, R., Conti, E. (2010). Tracing the temporal and spatial origins of island endemics in the Mediterranean region: A case study from the citrus family (Ruta L., Rutaceae). Systematic Biology, 59(6), 705-722. [More Information]
- Endicott, P., Ho, S., Stringer, C. (2010). Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and Modern Human origins. Journal of Human Evolution, 59(1), 87-95. [More Information]
- Rambaut, A., Ho, S., Drummond, A., Shapiro, B. (2009). Accommodating the effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution, 26(2), 245-248. [More Information]
- Ho, S., Phillips, M. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58(3), 367-380. [More Information]
- Ho, S. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters, 5(3), 421-424. [More Information]
- Willerslev, E., Gilbert, M., Binladen, J., Ho, S., Campos, P., Ratan, A., Tomsho, L., da Fonseca, R., Sher, A., Kuznetsova, T., et al (2009). Analysis of complete mitochondrial genome from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evolutionary Biology, 9(1), 95. [More Information]
- Chatterjee, H., Ho, S., Barnes, I., Groves, C. (2009). Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evolutionary Biology, 9(1), 259. [More Information]
- Endicott, P., Ho, S., Metspalu, M., Stringer, C. (2009). Evaluating the mitochondrial timescale of human evolution. Trends in Ecology and Evolution, 24(9), 515-521. [More Information]
- Barnett, R., Shapiro, B., Barnes, I., Ho, S., Burger, J., Yamaguchi, N., Higham, T., Wheeler, H., Rosendahl, W., Sher, A., et al (2009). Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Molecular Ecology, 18(8), 1668-1677. [More Information]
- Steeman, M., Hebsgaard, M., Fordyce, R., Ho, S., Rabosky, D., Nielsen, R., Rahbek, C., Glenner, H., Sorensen, M., Willerslev, E. (2009). Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58(6), 573-585. [More Information]
- Korsten, M., Ho, S., Davison, J., Pahn, B., Vulla, E., Roht, M., Tumanov, I., Kojola, I., Andersone-Lilley, Z., Ozolins, J., et al (2009). Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Molecular Ecology, 18(9), 1963-1979. [More Information]
- Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Ho, S., Shapiro, B., Pybus, O., Allain, J., Hatzakis, A. (2009). The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis. PLoS Medicine, 6(12), 1000198. [More Information]
- Endicott, P., Ho, S. (2008). A Bayesian Evaluation of Human Mitochondrial Substitution Rates. American Journal of Human Genetics, 82(4), 895-902. [More Information]
- Buckley, M., Walker, A., Ho, S., Yang, Y., Smith, C., Ashton, P., Oates, J., Cappellini, E., Koon, H., Penkman, K., et al (2008). Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science, 319(5859), 33-33. [More Information]
- Ho, S., Larson, G., Edwards, C., Heupink, T., Lakin, K., Holland, P., Shapiro, B. (2008). Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biology Letters, 4(4), 370-374. [More Information]
- Barik, S., Sahani, R., Prasad, B., Endicott, P., Metspalu, M., Sarkar, B., Bhattacharya, S., Annapoorna, P., Sreenath, J., Sun, D., et al (2008). Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. American Journal of Physical Anthropology, 136(1), 19-27. [More Information]
- Ware, J., Ho, S., Kjer, K. (2008). Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models. Molecular Phylogenetics and Evolution, 47(1), 426-432. [More Information]
- Gilbert, M., Drautz, D., Lesk, A., Ho, S., Qi, J., Ratan, A., Hsu, C., Sher, A., Dalen, L., Gotherstrom, A., et al (2008). Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America, 105(24), 8327-8332. [More Information]
- Ho, S., Endicott, P. (2008). The crucial role of calibration in molecular date estimates for the peopling of the Americas. American Journal of Human Genetics, 83(1), 142-146. [More Information]
- Ho, S., Saarma, U., Barnett, R., Haile, J., Shapiro, B. (2008). The effect of inappropriate calibration: Three case studies in molecular ecology. PloS One, 3(2), 1-8. [More Information]
- Ho, S. (2008). The molecular clock and estimating species divergence. Nature Education Knowledge, 1(1), 168-168.
- Haile, J., Holdaway, R., Oliver, K., Bunce, M., Gilbert, M., Nielsen, R., Munch, K., Ho, S., Shapiro, B., Willerslev, E. (2007). Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution, 24(4), 982-989. [More Information]
- Ho, S., Heupink, T., Rambaut, A., Shapiro, B. (2007). Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution, 24(6), 1416-1422. [More Information]
- Ho, S. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology, 38(4), 409-414. [More Information]
- Ho, S., Kolokotronis, S., Allaby, R. (2007). Elevated substitution rates estimated from ancient DNA sequences. Biology Letters, 3(6), 702-705. [More Information]
- Ho, S., Shapiro, B., Phillips, M., Cooper, A., Drummond, A. (2007). Evidence for time dependency of molecular rate estimates. Systematic Biology, 56(3), 515-522. [More Information]
- Edwards, C., Bollongino, R., Scheu, A., Chamberlain, A., Tresset, A., Vigne, J., Baird, J., Larson, G., Ho, S., Heupink, T., et al (2007). Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proceedings of the Royal Society B: Biological Sciences, 274(1616), 1377-1385. [More Information]
- Saarma, U., Ho, S., Pybus, O., Kaljuste, M., Tumanov, I., Kojola, I., Vorobiev, A., Markov, N., Saveljev, A., Valdmann, H., et al (2007). Mitogenetic structure of brown bears (Ursus arctos L.) in north-eastern Europe and a new time-frame for the formation of European brown bears. Molecular Ecology, 16(2), 401-413. [More Information]
- Hyman, I., Ho, S., Jermiin, L. (2007). Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Molecular Phylogenetics and Evolution, 45(3), 792-812. [More Information]
- Binladen, J., Wiuf, C., Gilbert, M., Bunce, M., Barnett, R., Larson, G., Greenwood, A., Haile, J., Ho, S., Hansen, A., et al (2006). Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172(2), 733-741. [More Information]
- Ho, S., Larson, G. (2006). Molecular clocks: when times are a-changin'. Trends in Genetics, 22(2), 79-83. [More Information]
- Drummond, A., Ho, S., Phillips, M., Rambaut, A. (2006). Relaxed Phylogenetics and Dating with Confidence. PLoS Biology, 4(5), 0699-0710. [More Information]
- Peng, Z., Ho, S., Zhang, Y., He, S. (2006). Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Molecular Phylogenetics and Evolution, 39(2), 568-572. [More Information]
- Ho, S., Phillips, M., Drummond, A., Cooper, A. (2005). Accuracy of rate estimation using relaxed clock models, with a critical focus on the early metazoan radiation. Molecular Biology and Evolution, 22(5), 1355-1363. [More Information]
- Weinstock, J., Willerslev, E., Sher, A., Tong, W., Ho, S., Rubenstein, D., Storer, J., Burns, J., Martin, L., Bravi, C., et al (2005). Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective. PLoS Biology, 3(8), e241 - 1373-e241 - 1379. [More Information]
- Murray, S., Flo Jorgensen, M., Ho, S., Patterson, D., Jermiin, L. (2005). Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist, 156(3), 269-286. [More Information]
- Ho, S., Phillips, M., Cooper, A., Drummond, A. (2005). Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution, 22(7), 1561-1568. [More Information]
- Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2004). The Biasing Effect Of Compositional Heterogeneity On Phylogenetic Estimates May Be Underestimated. Systematic Biology, 53(4), 638-643. [More Information]
- Ho, S., Jermiin, L. (2004). Tracing The Decay Of The Historical Signal In Biological Sequence Data. Systematic Biology, 53(4), 623-637. [More Information]
- Jermiin, L., Ho, S., Ababneh, F., Robinson, J., Larkum, A. (2003). Hetero: a program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics, 2(3), 159-163.
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