simonho.org

In press

2008

27     The crucial role of calibration in molecular date estimates for the peopling of the Americas
Ho SYW and Endicott P. American Journal of Human Genetics, 83: 142-146.

26     Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PWH, and Shapiro B. Biology Letters, 4: 370-374.

25     Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
Gilbert MTP, Drautz DI, Lesk AM, Ho SYW, Qi J, Ratan A, Hsu C-H, Sher A, Dalén L, Götherström A, Tomsho LP, Rendulic S, Packard M, Campos PF, Kuznetsova T, Shidlovskiy F, Tikhonov A, Willerslev E, Iacumin P, Buigues B, Ericson PGP, Germonpré M, Kosintsev P, Nikolaev V, Nowak-Kemp M, Knight JR, Irzyk GP, Perbost CS, Fredrikson KM, Harkins TT, Sheridan S, Miller W, and Schuster SC. Proceedings of the National Academy of Sciences of the USA, 105: 8327-8332.

24     A Bayesian evaluation of human mitochondrial substitution rates
Endicott P and Ho SYW. American Journal of Human Genetics, 82: 895-902.

23     Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands
Barik SS, Sahani R, Prasad BVR, Endicott P, Metspalu M, Bhattacharya S, Sarkar BN, Annapoorna PCH, Sreenath J, Sun D, Sanchez JJ, Ho SYW, Chandrasekar A, and Rao VR. American Journal of Physical Anthropology, 136: 19-27.

22     Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models
Ware JL, Ho SYW, and Kjer K. Molecular Phylogenetics and Evolution, 47: 426-432.

21     The effect of inappropriate calibration: Three case studies in molecular ecology
Ho SYW, Saarma U, Barnett R, Haile J, and Shapiro B. PLoS ONE, 3: e1615.

20     Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
Buckley M, Walker A, Ho SYW, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MTP, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, and Collins MJ. Science, 319: 33c.

2007

19     Molecular phylogeny of Australian Helicarionidae, Euconulidae, and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
Hyman IT, Ho SYW, and Jermiin LS. Molecular Phylogenetics and Evolution, 45: 792-812.

18     Elevated substitution rates estimated from ancient DNA
Ho SYW, Kolokotronis S-O, and Allaby RG. Biology Letters, 3: 702-705.

17     Calibrating molecular estimates of substitution rates and divergence times in birds
Ho SYW. Journal of Avian Biology, 38: 409-414.

16     Evidence for time dependency of molecular rate estimates
Ho SYW, Shapiro B, Phillips MJ, Cooper A, and Drummond AJ. Systematic Biology, 56: 515-522.

15     Bayesian estimation of sequence damage in ancient DNA
Ho SYW, Heupink TH, Rambaut A, and Shapiro B. Molecular Biology and Evolution, 24: 1416-1422.

14     Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne J-D, Baird JF, Larson G, Ho SYW, Heupink TH, Shapiro B, Freeman AR, Thomas MG, Arbogast R-M, Arndt B, Bartosiewicz L, Benecke N, Budja M, Chaix L, Choyke AM, Coqueugniot R, Döle H-J, Göldner H, Hartz S, Helmer D, Herzig B, Hongo H, Mashkour M, Özdogan M, Pucher E, Roth G, Schade-Lindig S, Schmölcke U, Schulting RJ, Stephan E, Uerpmann H-P, Vörös I, Voytek B, Bradley DG, and Burger J. Proceedings of the Royal Society of London B, 274: 1377-1385.

13     Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?
Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, Nielsen R, Munch K, Ho SYW, Shapiro B, and Willerslev E. Molecular Biology and Evolution, 24: 982-989.

12     Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages
Saarma U, Ho SYW, Pybus OG, Kaljust M, Tumanov IM, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann A, Lyapunova EA, Abramov AV, Männil P, Korsten M, Vulla E, Pazetnov SV, Pazetnov VS, Putchkovskiy SV, and Rõkov AM. Molecular Ecology, 16: 401-413.

2006

11     Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes
Peng Z*, Ho SYW*(equal first authors), Zhang Y, and He S. Molecular Phylogenetics and Evolution, 39: 568-572.

10     Relaxed phylogenetics and dating with confidence
Drummond AJ, Ho SYW, Phillips MJ, and Rambaut A. PLoS Biology, 4: e88.

09     Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SYW, Hansen AJ, Willerslev E. Genetics, 172: 733-741.

08     Molecular clocks: When times are a-changin'
Ho SYW and Larson G. Trends in Genetics, 22: 79-83.

2005

07     Improving the analysis of dinoflagellate phylogeny based on rRNA
Murray S, Jørgensen MF, Ho SYW, Patterson DJ, and Jermiin LS. Protist, 156: 269-286.

06     Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective
Weinstock J, Willerslev E, Sher A, Tong W, Ho SYW, Rubinstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, and Cooper A. PLoS Biology, 3: e241.

05     Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
Ho SYW, Phillips MJ, Cooper A, and Drummond AJ. Molecular Biology and Evolution, 22: 1561-1568.

04     Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
Ho SYW, Phillips MJ, Drummond AJ, and Cooper A. Molecular Biology and Evolution, 22: 1355-1363.

2004

03     The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
Jermiin LS, Ho SYW, Ababneh F, Robinson J, and Larkum AWD. Systematic Biology, 53: 638-643.

02     Tracing the decay of the historical signal in biological sequence data
Ho SYW and Jermiin LS. Systematic Biology, 53: 623-637.

2003

01     Hetero: A program to simulate the evolution of DNA on four-taxon trees
Jermiin LS, Ho SYW, Ababneh F, Robinson J, and Larkum AWD. Applied Bioinformatics, 2: 159-163