JOURNAL ARTICLES
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