Publications for Simon Ho 2016


Publications for Simon Ho


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="

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=" 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="

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=""

>[More Information]</a>

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

Current Biology , 26(10), 399-402. <a href="

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=""

>[More Information]</a>

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="">[

More Information]</a>


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="">[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=""

>[More Information]</a>

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=""

>[More Information]</a>

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="

.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="

2-6">[More Information]</a>

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="

5">[More Information]</a>

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=""

>[More Information]</a>

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="">[M ore Information]</a>

Thornhill, A., Ho, S., Kulheim, C., Crisp, M.

Publications for Simon Ho

(2015). Interpreting the modern distribution of

Myrtaceae using a dated molecular phylogeny.

Molecular Phylogenetics and Evolution , 93,

29-43. <a href="

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

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

Bioinformatics , 31(13), 2061-2065. <a href=" 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=""

>[More Information]</a>

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="

4-3">[More Information]</a>

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


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="">[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="">[

More Information]</a>

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="

8-1">[More Information]</a>

Molak, M., Ho, S. (2015). Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA. PeerJ , 3, 1-16. <a href="">[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="

">[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="

0">[More Information]</a>

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="

24">[More Information]</a>

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="

">[More Information]</a>

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="

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

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=""

>[More Information]</a>

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="">[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="

2">[More Information]</a>


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="">[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=""

>[More Information]</a>

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

499-501. <a href="">[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=" t665">[More Information]</a>

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

BĚ€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. <a href="

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="">[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:

Publications for Simon Ho

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="

6-1">[More Information]</a>

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=""

>[More Information]</a>

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


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="

023">[More Information]</a>

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="

">[More Information]</a>

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="

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

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

5947-5965. <a href="">[M ore Information]</a>

Martin, M., Ho, S., Wales, N., Ristaino, J.,

Gilbert, M. (2014). Persistence of the

Mitochondrial Lineage Responsible for the Irish

Publications for Simon Ho

Potato Famine in Extant New World

Phytophthora infestans. Molecular Biology and

Evolution , 31(6), 1414-1420. <a href=""

>[More Information]</a>

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="">[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="

0">[More Information]</a>

Ho, S. (2014). The changing face of the molecular evolutionary clock. Trends in Ecology and Evolution , 29(9), 496-503. <a href="

4">[More Information]</a>

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="

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

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="

5722">[More Information]</a>

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="

5410">[More Information]</a>

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="

">[More Information]</a>

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="

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

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="

">[More Information]</a>


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=""

>[More Information]</a>

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="">[

More Information]</a>

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="

1">[More Information]</a>

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="">[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="">[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="">[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="">[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="

4754">[More Information]</a>

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="">[

More Information]</a>

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=""

>[More Information]</a>

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=""

>[More Information]</a>

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="

4428">[More Information]</a>

Martin, M., Cappellini, E., Samaniego, J.,

Zepeda, M., Campos, P., Seguin-Orlando, A.,

Wales, N., Orlando, L., Ho, S., Dietrich, F., et al

Publications for Simon Ho

(2013). Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications , 4, 1-7. <a href="">[

More Information]</a>

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="

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

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="">[

More Information]</a>

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

101-105. <a href="">[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="

3912">[More Information]</a>

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="

1814">[More Information]</a>

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="

5336">[More Information]</a>


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="

5">[More Information]</a>

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="

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

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=""

>[More Information]</a>

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="

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=""

>[More Information]</a>

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="

6-9">[More Information]</a>

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="

9">[More Information]</a>

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. <a href=""

>[More Information]</a>

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="

Publications for Simon Ho

10.010">[More Information]</a>

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="">[

More Information]</a>

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. <a href=""

>[More Information]</a>


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=""

>[More Information]</a>

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="">

[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=""

>[More Information]</a>

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="

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="

11.023">[More Information]</a>

Vilstrup, J., Ho, S., Foote, A., Morin, P., Kreb,

D., Krutzen, M., Parra, G., Robertson, K., de

Stephanis, R., Verborgh, P., et al (2011).

Publications for Simon Ho

Mitogenomic phylogenetic analyses of the

Delphinidae with an emphasis on the

Globicephalinae. BMC Evolutionary Biology ,

11(1), 65-1-65-10. <a href="

5">[More Information]</a>

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="

3">[More Information]</a>

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="

4">[More Information]</a>

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="

8">[More Information]</a>

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="

1.00480.x">[More Information]</a>

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

Resources , 11(3), 423-434. <a href="

1.02988.x">[More Information]</a>

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="">[

More Information]</a>

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="

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

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="

1.05178.x">[More Information]</a>

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=""

>[More Information]</a>


Ho, S., Gilbert, M. (2010). Ancient mitogenomics. Mitochondrion , 10(1), 1-11. <a href="

05">[More Information]</a>

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="

494727">[More Information]</a>

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="

7">[More Information]</a>

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="

42">[More Information]</a>

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="

0.02379.x">[More Information]</a>

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="">

[More Information]</a>

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="

005">[More Information]</a>


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=""

>[More Information]</a>

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

Systematic Biology , 58(3), 367-380. <a href="">

[More Information]</a>

Ho, S. (2009). An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters , 5(3), 421-424. <a href=""

>[More Information]</a>

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=""

>[More Information]</a>

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="

9">[More Information]</a>

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="

6">[More Information]</a>

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="

9.04134.x">[More Information]</a>

Steeman, M., Hebsgaard, M., Fordyce, R., Ho,

Publications for Simon 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="">

[More Information]</a>

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="

9.04163.x">[More Information]</a>

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="

00198">[More Information]</a>


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

Evaluation of Human Mitochondrial Substitution

Rates. American Journal of Human Genetics ,

82(4), 895-902. <a href="

19">[More Information]</a>

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="

">[More Information]</a>

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=""

>[More Information]</a>

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="">[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="

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

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="

5">[More Information]</a>

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="

14">[More Information]</a>

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="

1615">[More Information]</a>

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. <a href="

">[More Information]</a>

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="

">[More Information]</a>

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

Journal of Avian Biology , 38(4), 409-414. <a href="

7.04168.x">[More Information]</a>

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=""

>[More Information]</a>

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="

5401">[More Information]</a>

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=""

>[More Information]</a>

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="

6.03130.x">[More Information]</a>

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.


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="

718">[More Information]</a>

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

22(2), 79-83. <a href="

">[More Information]</a>

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

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

0699-0710. <a href="

0088">[More Information]</a>

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="

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


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=""

>[More Information]</a>

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="

0241">[More Information]</a>

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=""

>[More Information]</a>


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.


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.