Publications for Simon Ho 2016

Publications for Simon Ho

2016

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. <a href="http://dx.doi.org/10.1186/s12862-016-068

8-y">[More Information]</a>

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. <a href="http://dx.doi.org/10.1093/bioinformatics/bt w005">[More Information]</a>

Ritchie, A., Lo, N., Ho, S. (2016). Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker.

Organisms Diversity and Evolution . <a href="http://dx.doi.org/10.1007/s13127-016-027

5-5">[More Information]</a>

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. <a href="http://dx.doi.org/10.1093/molbev/msv241"

>[More Information]</a>

Lee, M., Ho, S. (2016). Molecular clocks.

Current Biology , 26(10), 399-402. <a href="http://dx.doi.org/10.1016/j.cub.2016.03.07

1">[More Information]</a>

Lo, N., Jun 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). <a href="http://dx.doi.org/10.1098/rspb.2015.2869"


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: an international journal of genomic and evolutionary diversity , 107(3), 199-213. <a href="http://dx.doi.org/10.1093/jhered/esv091">[

More Information]</a>

2015

Luo, A., Lan, H., Ling, C., Zhang, A., Shi, L.,

Publications for Simon Ho

Ho, S., Zhu, C. (2015). A simulation study of sample size for DNA barcoding. Ecology and

Evolution , 5(24), 5869-5879. <a href="http://dx.doi.org/10.1002/ece3.1846">[Mo re Information]</a>

Ho, S., Jun Tong, K., Foster, C., Ritchie, A., Lo,

N., Crisp, M. (2015). Biogeographic calibrations for the molecular clock. Biology Letters , 11(9),

1-7. <a href="http://dx.doi.org/10.1098/rsbl.2015.0194"


Jun 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. <a href="http://dx.doi.org/10.1126/science.aaa5460"


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. <a href="http://dx.doi.org/10.1016/j.ympev.2015.07

.010">[More Information]</a>

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. <a href="http://dx.doi.org/10.1186/s12862-015-031


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. <a href="http://dx.doi.org/10.1111/1755-0998.1229


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. <a href="http://dx.doi.org/10.1093/molbev/msv154"


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. <a href="http://dx.doi.org/10.1111/mec.13284">[M ore Information]</a>

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. <a href="http://dx.doi.org/10.1016/j.ympev.2015.07


Duchene, S., Ho, S. (2015). Mammalian genome evolution is governed by multiple pacemakers.

Bioinformatics , 31(13), 2061-2065. <a href="http://dx.doi.org/10.1093/bioinformatics/bt v121">[More Information]</a>

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. <a href="http://dx.doi.org/10.1098/rsbl.2015.0561"


Ho, S. (2015). Molecular clocks. In W. Jack

Rink, Jeroen W. Thompson (Eds.), Encyclopedia of Scientific Dating Methods , (pp. 583-588).

Dordrecht: Springer Science+Business Media. <a href="http://dx.doi.org/10.1007/978-94-007-630


Ho, S., Endicott, P. (2015). Molecular Clocks,

Human Evolution. In W. Jack Rink, Jeroen W.

Thompson (Eds.), Encyclopedia of Scientific

Dating Methods , (pp. 588-591). Dordrecht:

Springer Science+Business Media.

Ho, S. (2015). Molecular clocks, relaxed variant.

In W. Jack Rink, Jeroen W. Thompson (Eds.),

Encyclopedia of Scientific Dating Methods , (pp.

591-593). Dordrecht: Springer Science+Business

Media.

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. <a href="http://dx.doi.org/10.1111/zsc.12117">[Mo re Information]</a>

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. <a href="http://dx.doi.org/10.1099/jgv.0.000007">[


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. <a href="http://dx.doi.org/10.1186/s13742-014-003


Molak, M., Ho, S. (2015). Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA. PeerJ , 3, 1-16. <a href="http://dx.doi.org/10.7717/peerj.821">[Mor e Information]</a>

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), 1460. <a href="http://dx.doi.org/10.1126/science.aab1578

">[More Information]</a>

Ho, S., Duchene, S., Duchene, D. (2015).

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

Molecular Ecology Resources , 15(4), 688-696.

<a href="http://dx.doi.org/10.1111/1755-0998.1232


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. <a href="http://dx.doi.org/10.1016/j.virol.2015.09.0


Bally, J., Nakasugi, K., Jia, F., Jung, H., Ho, S.,

Wong, M., 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. <a href="http://dx.doi.org/10.1038/nplants.2015.165


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. <a href="http://dx.doi.org/10.1016/j.ympev.2014.09


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. <a href="http://dx.doi.org/10.1093/molbev/msv056"


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. <a href="http://dx.doi.org/10.1111/mec.13450">[M ore Information]</a>

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. <a href="http://dx.doi.org/10.1111/1755-0998.1235


2014

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. <a href="http://dx.doi.org/10.1111/evo.12469">[Mo re Information]</a>

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. <a href="http://dx.doi.org/10.1098/rspb.2014.0732"


Shapiro, B., Ho, S. (2014). Ancient hyaenas highlight the old problem of estimating evolutionary rates. Molecular Ecology , 23(3),

499-501. <a href="http://dx.doi.org/10.1111/mec.12621">[M ore Information]</a>

Duchene, S., Molak, M., Ho, S. (2014).

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics , 30(7), 1017-1019. <a href="http://dx.doi.org/10.1093/bioinformatics/bt t665">[More Information]</a>

Edwards, C., Ho, S., Barnett, R., Coxon, P.,

B̀radley, 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. <a href="http://dx.doi.org/10.1016/j.quascirev.2013.

10.015">[More Information]</a>

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. <a href="http://dx.doi.org/10.1111/zsc.12056">[Mo re Information]</a>

Ho, S., Endicott, P., Molak, M. (2014). DNA interpretation constraints in archaeology. In

Smith C. (Eds.), Encyclopedia of Global

Archaeology . (pp. 2155-2159). New York:


Springer New York LLC.

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. <a href="http://dx.doi.org/10.1007/s00251-013-074


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.

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. <a href="http://dx.doi.org/10.3201/eid2008.130910"


Ho, S., Endicott, P., Molak, M. (2014). Human evolution: Molecular timescale. In Smith C.

(Eds.), Encyclopedia of Global Archaeology .

(pp. 3511-3514). New York: Springer New York

LLC.

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. <a href="http://dx.doi.org/10.1016/j.quaint.2013.09.


Foster, C., Conn, B., Henwood, M., Ho, S.

(2014). Molecular data support Orianthera: a new genus of

Australian Loganiaceae. Telopea: Journal of

Plant Systematics , 16, 149-158. <a href="http://dx.doi.org/10.7751/telopea20147853


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.

<a href="http://dx.doi.org/10.1016/j.ympev.2014.06


Ho, S., Duchene, S. (2014). Molecular-clock methods for estimating evolutionary rates and timescales. Molecular Ecology , 23(24),

5947-5965. <a href="http://dx.doi.org/10.1111/mec.12953">[M ore Information]</a>

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. <a href="http://dx.doi.org/10.1093/molbev/msu086"


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. <a href="http://dx.doi.org/10.1111/zoj.12105">[Mo re Information]</a>

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. <a href="http://dx.doi.org/10.1186/1471-2148-14-7


Ho, S. (2014). The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution , 29(9), 496-503. <a href="http://dx.doi.org/10.1016/j.tree.2014.07.00


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. <a href="http://dx.doi.org/10.1016/j.ympev.2014.05


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. <a href="http://dx.doi.org/10.1371/journal.pone.009


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. <a href="http://dx.doi.org/10.1371/journal.pone.009


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. <a href="http://dx.doi.org/10.1186/2047-217X-3-27


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.

<a href="http://dx.doi.org/10.1016/j.ympev.2014.04


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.

<a href="http://dx.doi.org/10.1126/science.1253451


2013

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. <a href="http://dx.doi.org/10.1098/rspb.2013.1243"


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. <a href="http://dx.doi.org/10.1038/ncomms2714">[


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.

<a href="http://dx.doi.org/10.1186/1471-2156-14-9


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. <a href="http://dx.doi.org/10.1071/BT13149">[Mor e Information]</a>

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. <a href="http://dx.doi.org/10.1111/jbi.12043">[Mor e Information]</a>

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. <a href="http://dx.doi.org/10.1002/hep.26079">[Mo re Information]</a>

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. <a href="http://dx.doi.org/10.1111/mec.12462">[M ore Information]</a>

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. <a href="http://dx.doi.org/10.1371/journal.pone.006


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. <a href="http://dx.doi.org/10.1038/ncomms2656">[


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. <a href="http://dx.doi.org/10.1093/molbev/mss223"


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. <a href="http://dx.doi.org/10.1093/molbev/mss232"


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.

<a href="http://dx.doi.org/10.1371/journal.pone.006


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. <a href="http://dx.doi.org/10.1038/ncomms3172">[


Yeoh, S., Ho, S., Thornhill, A., Foley, W.

(2013). Regional population expansion in

Eucalyptus globulus. Molecular Phylogenetics and Evolution , 68(3), 498-501. <a href="http://dx.doi.org/10.1016/j.ympev.2013.04


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. <a href="http://dx.doi.org/10.1038/ncomms2836">[


Ho, S., Lo, N. (2013). The insect molecular clock. Australian Journal of Entomology , 52(2),

101-105. <a href="http://dx.doi.org/10.1111/aen.12018">[Mo re Information]</a>

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. <a href="http://dx.doi.org/10.1371/journal.pgen.100


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. <a href="http://dx.doi.org/10.1371/journal.pone.006


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. <a href="http://dx.doi.org/10.1371/journal.pone.005


2012

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. <a href="http://dx.doi.org/10.1016/j.cub.2012.07.03


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. <a href="http://dx.doi.org/10.1016/j.ympev.2011.12


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. <a href="http://dx.doi.org/10.1098/rsbl.2012.0774"


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. <a href="http://dx.doi.org/10.1111/j.1469-7998.201

1.00854.x">[More Information]</a>

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. <a href="http://dx.doi.org/10.1093/molbev/mss020"


Ho, S. (2012). Phylogenetic Analysis of Ancient

DNA using BEAST. In Beth Shapiro and

Michael Hofreiter (Eds.), Methods in Molecular

Biology, 840: Ancient DNA , (pp. 229-241). New

York: Humana Press. <a href="http://dx.doi.org/10.1007/978-1-61779-51


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 (PNAS) , 109(23), 8878-8883.

<a href="http://dx.doi.org/10.1073/pnas.120300510


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),



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. <a href="http://dx.doi.org/10.1016/j.quascirev.2012.



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. <a href="http://dx.doi.org/10.1093/sysbio/syr116">[


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),



2011

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. <a href="http://dx.doi.org/10.1093/molbev/msq262"


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. <a href="http://dx.doi.org/10.1093/sysbio/syq099">

[More Information]</a>

Wong, J., Ho, S., Hogg, P. (2011). Disulfide bond acquisition through eukaryotic protein evolution. Molecular Biology and Evolution ,

28(1), 327-334. <a href="http://dx.doi.org/10.1093/molbev/msq194"


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. <a href="http://dx.doi.org/10.1007/s00239-011-947

4-z">[More Information]</a>

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. <a href="http://dx.doi.org/10.1016/j.quascirev.2010.


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. <a href="http://dx.doi.org/10.1186/1471-2148-11-6


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. <a href="http://dx.doi.org/10.1186/1743-422X-8-18


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. <a href="http://dx.doi.org/10.1186/1471-2164-12-8


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 (PNAS) ,

108(17), E85-E86. <a href="http://dx.doi.org/10.1073/pnas.110194010


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. <a href="http://dx.doi.org/10.1111/j.1463-6409.201


Ho, S., Shapiro, B. (2011). Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology

Resources , 11(3), 423-434. <a href="http://dx.doi.org/10.1111/j.1755-0998.201


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. <a href="http://dx.doi.org/10.1038/nature10574">[


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. <a href="http://dx.doi.org/10.1016/j.ympev.2011.08


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. <a href="http://dx.doi.org/10.1111/j.1365-294X.201


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. <a href="http://dx.doi.org/10.1098/rsbl.2011.0549"


2010

Ho, S., Gilbert, M. (2010). Ancient mitogenomics. Mitochondrion , 10(1), 1-11. <a href="http://dx.doi.org/10.1016/j.mito.2009.09.0


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. <a href="http://dx.doi.org/10.3109/19401736.2010.


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 (PNAS) ,

107(47), 20423-20428. <a href="http://dx.doi.org/10.1073/pnas.100788810


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. <a href="http://dx.doi.org/10.1186/1471-2148-10-2


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. <a href="http://dx.doi.org/10.1111/j.1365-2699.201


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. <a href="http://dx.doi.org/10.1093/sysbio/syq046">


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. <a href="http://dx.doi.org/10.1016/j.jhevol.2010.04.


2009

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. <a href="http://dx.doi.org/10.1093/molbev/msn256"


Ho, S., Phillips, M. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.

Systematic Biology , 58(3), 367-380. <a href="http://dx.doi.org/10.1093/sysbio/syp035">


Ho, S. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters , 5(3), 421-424. <a href="http://dx.doi.org/10.1098/rsbl.2008.0729"


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, 1-11. <a href="http://dx.doi.org/10.1186/1471-2148-9-95"


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), 1-19. <a href="http://dx.doi.org/10.1186/1471-2148-9-25


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. <a href="http://dx.doi.org/10.1016/j.tree.2009.04.00


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. <a href="http://dx.doi.org/10.1111/j.1365-294X.200


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. <a href="http://dx.doi.org/10.1093/sysbio/syp060">


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. <a href="http://dx.doi.org/10.1111/j.1365-294X.200


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),

1-12. <a href="http://dx.doi.org/10.1371/journal.pmed.10


2008

Endicott, P., Ho, S. (2008). A Bayesian

Evaluation of Human Mitochondrial Substitution

Rates. American Journal of Human Genetics ,

82(4), 895-902. <a href="http://dx.doi.org/10.1016/j.ajhg.2008.01.0


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. <a href="http://dx.doi.org/10.1126/science.1147046


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. <a href="http://dx.doi.org/10.1098/rsbl.2008.0073"


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.

<a href="http://dx.doi.org/10.1002/ajpa.20773">[M ore Information]</a>

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. <a href="http://dx.doi.org/10.1016/j.ympev.2007.10


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

(PNAS) , 105(24), 8327-8332. <a href="http://dx.doi.org/10.1073/pnas.080231510


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. <a href="http://dx.doi.org/10.1016/j.ajhg.2008.06.0


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. <a href="http://dx.doi.org/10.1371/journal.pone.000


Ho, S. (2008). The molecular clock and estimating species divergence. Nature Education

Knowledge , 1(1), 168-168.

2007

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. <a href="http://dx.doi.org/10.1093/molbev/msm016


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. <a href="http://dx.doi.org/10.1093/molbev/msm062


Ho, S. (2007). Calibrating molecular estimates of substitution rates and divergence times in birds.

Journal of Avian Biology , 38(4), 409-414. <a href="http://dx.doi.org/10.1111/j.0908-8857.200


Ho, S., Kolokotronis, S., Allaby, R. (2007).

Elevated substitution rates estimated from ancient DNA sequences. Biology Letters , 3(6),

702-705. <a

Publications for Simon Ho href="http://dx.doi.org/10.1098/rsbl.2007.0377"


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. <a href="http://dx.doi.org/10.1080/1063515070143


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. <a href="http://dx.doi.org/10.1098/rspb.2007.0020"


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. <a href="http://dx.doi.org/10.1111/j.1365-294X.200


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.

2006

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.

<a href="http://dx.doi.org/10.1534/genetics.105.049


Ho, S., Larson, G. (2006). Molecular clocks: when times are a-changin’. Trends in Genetics ,

22(2), 79-83. <a href="http://dx.doi.org/10.1016/j.tig.2005.11.006


Drummond, A., Ho, S., Phillips, M., Rambaut,

A. (2006). Relaxed Phylogenetics and Dating with Confidence. PLoS Biology , 4(5),

0699-0710. <a href="http://dx.doi.org/10.1371/journal.pbio.004


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. <a

Publications for Simon Ho href="http://dx.doi.org/10.1016/j.ympev.2005.10


2005

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. <a href="http://dx.doi.org/10.1093/molbev/msi125"


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. <a href="http://dx.doi.org/10.1371/journal.pbio.003


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.

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. <a href="http://dx.doi.org/10.1093/molbev/msi145"


2004

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.

Ho, S., Jermiin, L. (2004). Tracing The Decay Of

The Historical Signal In Biological Sequence

Data. Systematic Biology , 53(4), 623-637.

2003

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.

Publications for Simon Ho 2016

Related documents

Products

Support

Publications for Simon Ho 2016

Related documents

Add this document to collection(s)

Add this document to saved

Suggest us how to improve StudyLib