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Title / AuthorCited by Year
Relaxed phylogenetics and dating with confidence
AJ Drummond, SYW Ho, MJ Phillips, A Rambaut
PLOS Biology 4 (5), e88
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
SYW Ho, MJ Phillips, A Cooper, AJ Drummond
Molecular Biology and Evolution 22 (7), 1561-1568
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
SYW Ho, MJ Phillips
Systematic Biology 58 (3), 367-380
Molecular clocks: When times are a-changin'
SYW Ho, G Larson
Trends in Genetics 22 (2), 79-83
PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
R Lanfear, B Calcott, SYW Ho, S Guindon
Molecular Biology and Evolution 29 (6), 1695-1701
Calibrating molecular estimates of substitution rates and divergence times in birds
Journal of Avian Biology 38 (4), 409-414
Evidence for time dependency of molecular rate estimates
SYW Ho, B Shapiro, MJ Phillips, A Cooper, AJ Drummond
Systematic Biology 56 (3), 515-522
Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
CJ Edwards, R Bollongino, A Scheu, A Chamberlain, A Tresset, JD Vigne, ...
Proceedings of the Royal Society of London B 274 (1616), 1377-1385
The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
LS Jermiin, SYW Ho, F Ababneh, J Robinson, AWD Larkum
Systematic Biology 53 (4), 638-643
Species-specific responses of Late Quaternary megafauna to climate and humans
ED Lorenzen, D Nogués-Bravo, L Orlando, J Weinstock, J Binladen, ...
Nature 479 (7373), 359-364
Time‐dependent rates of molecular evolution
SYW Ho, R Lanfear, L Bromham, MJ Phillips, J Soubrier, AG Rodrigo, ...
Molecular ecology 20 (15), 3087-3101
The effect of inappropriate calibration: three case studies in molecular ecology
SYW Ho, U Saarma, R Barnett, J Haile, B Shapiro
PLOS ONE 3 (2), e1615
Radiation of extant cetaceans driven by restructuring of the oceans
ME Steeman, MB Hebsgaard, RE Fordyce, SYW Ho, DL Rabosky, ...
Systematic Biology 58 (6), 573-585
A rough guide to BEAST 1.4
AJ Drummond, SYW Ho, N Rawlence, A Rambaut
University of Auckland, New Zealand
Estimating the phylogeny and divergence times of primates using a supermatrix approach
HJ Chatterjee, SYW Ho, I Barnes, C Groves
BMC Evolutionary Biology 9 (1), 259
Tracing the decay of the historical signal in biological sequence data
SYW Ho, LS Jermiin
Systematic Biology 53 (4), 623-637
Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
SYW Ho, MJ Phillips, AJ Drummond, A Cooper
Molecular Biology and Evolution 22 (5), 1355-1363
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
MTP Gilbert, DI Drautz, AM Lesk, SYW Ho, J Qi, A Ratan, CH Hsu, A Sher, ...
Proceedings of the National Academy of Sciences of the USA 105 (24), 8327-8332
Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective
J Weinstock, E Willerslev, A Sher, W Tong, SYW Ho, D Rubenstein, ...
PLOS Biology 3 (8), e241
Skyline‐plot methods for estimating demographic history from nucleotide sequences
SYW Ho, B Shapiro
Molecular Ecology Resources 11 (3), 423-434
The global spread of hepatitis C virus 1a and 1b: A phylodynamic and phylogeographic analysis
G Magiorkinis, E Magiorkinis, D Paraskevis, SYW Ho, B Shapiro, ...
PLOS Medicine 6 (12), e1000198
Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins
P Endicott, SYW Ho, C Stringer
Journal of Human Evolution 59 (1), 87-95
Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
J Binladen, C Wiuf, MTP Gilbert, M Bunce, R Barnett, G Larson, ...
Genetics 172 (2), 733-741
Evaluating the mitochondrial timescale of human evolution
P Endicott, SYW Ho, M Metspalu, C Stringer
Trends in Ecology and Evolution 24 (9), 515-521
Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity
R Barnett, B Shapiro, I Barnes, SYW Ho, J Burger, N Yamaguchi, ...
Molecular Ecology 18 (8), 1668-1677
Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages
U Saarma, SYW Ho, OG Pybus, M Kaljuste, IL Tumanov, I Kojola, ...
Molecular Ecology 16 (2), 401-413
Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?
J Haile, R Holdaway, K Oliver, M Bunce, MTP Gilbert, R Nielsen, K Munch, ...
Molecular Biology and Evolution 24 (4), 982-989
Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of Nothofagus (Fagales)
H Sauquet, SYW Ho, MA Gandolfo, GJ Jordan, P Wilf, DJ Cantrill, ...
Systematic Biology 61 (2), 289-313
Rethinking dog domestication by integrating genetics, archeology, and biogeography
G Larson, EK Karlsson, A Perri, MT Webster, SYW Ho, J Peters, PW Stahl, ...
Proceedings of the National Academy of Sciences of the USA 109 (23), 8878-8883
A Bayesian evaluation of human mitochondrial substitution rates
P Endicott, SYW Ho
American Journal of Human Genetics 82 (4), 895-902
Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes
Z Peng, SYW Ho, Y Zhang, S He
Molecular Phylogenetics and Evolution 39 (2), 568-572
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
M Buckley, A Walker, SYW Ho, Y Yang, C Smith, P Ashton, JT Oates, ...
Science 319 (5859), 33-33
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
E Willerslev, MTP Gilbert, J Binladen, SYW Ho, PF Campos, A Ratan, ...
BMC Evolutionary Biology 9 (1), 95
Elevated substitution rates estimated from ancient DNA sequences
SYW Ho, SO Kolokotronis, RG Allaby
Biology Letters 3 (6), 702-705
Improving the analysis of dinoflagellate phylogeny based on rDNA
S Murray, M Flø Jørgensen, SYW Ho, DJ Patterson, LS Jermiin
Protist 156 (3), 269-286
An examination of phylogenetic models of substitution rate variation among lineages
Biology Letters 5 (3), 421-424
Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: A general demographic model for mammals?
M Korsten, SYW Ho, J Davison, B Pähn, E Vulla, M Roht, IL Tumanov, ...
Molecular Ecology 18 (9), 1963-1979
The crucial role of calibration in molecular date estimates for the peopling of the Americas
SYW Ho, P Endicott
American Journal of Human Genetics 83 (1), 142-146
Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
SYW Ho, G Larson, CJ Edwards, TH Heupink, KE Lakin, PWH Holland, ...
Biology Letters 4 (4), 370-374
Bayesian estimation of sequence damage in ancient DNA
SYW Ho, TH Heupink, A Rambaut, B Shapiro
Molecular Biology and Evolution 24 (6), 1416-1422
Mutation rate is linked to diversification in birds
R Lanfear, SYW Ho, D Love, L Bromham
Proceedings of the National Academy of Sciences of the USA 107 (47), 20423-20428
Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
A Luo, H Qiao, Y Zhang, W Shi, SYW Ho, W Xu, A Zhang, C Zhu
BMC Evolutionary Biology 10 (1), 242
Bayesian estimation of substitution rates from ancient DNA sequences with low information content
SYW Ho, R Lanfear, MJ Phillips, I Barnes, JA Thomas, SO Kolokotronis, ...
Systematic Biology 60 (3), 366-375
Ancient mitogenomics
SYW Ho, MTP Gilbert
Mitochondrion 10 (1), 1-11
Tracing the temporal and spatial origins of island endemics in the Mediterranean region: A case study from the citrus family (Ruta L., Rutaceae)
G Salvo, SYW Ho, G Rosenbaum, R Ree, E Conti
Systematic Biology 59 (6), 705-722
Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species
J Davison, SYW Ho, SC Bray, M Korsten, E Tammeleht, M Hindrikson, ...
Quaternary Science Reviews 30 (3), 418-430
Accommodating the effect of ancient DNA damage on inferences of demographic histories
A Rambaut, SYW Ho, AJ Drummond, B Shapiro
Molecular Biology and Evolution 26 (2), 245-248
A Bayesian phylogenetic method to estimate unknown sequence ages
B Shapiro, SYW Ho, AJ Drummond, MA Suchard, OG Pybus, A Rambaut
Molecular Biology and Evolution 28 (2), 879-887
Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands
SS Barik, R Sahani, BVR Prasad, P Endicott, M Metspalu, BN Sarkar, ...
American Journal of Physical Anthropology 136 (1), 19-27
Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals
A Luo, A Zhang, SYW Ho, W Xu, Y Zhang, W Shi, SL Cameron, C Zhu
BMC Genomics 12 (1), 84
Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae
JT Vilstrup, SYW Ho, AD Foote, PA Morin, D Kreb, M Krützen, GJ Parra, ...
BMC Evolutionary Biology 11 (1), 65
Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses
W Li, W Shi, H Qiao, SYW Ho, A Luo, Y Zhang, C Zhu
Virology Journal 8 (1), 183
Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: New data and reappraisal
Z Wang, X Shen, B Liu, J Su, T Yonezawa, Y Yu, S Guo, SYW Ho, C Vila, ...
Journal of Biogeography 37 (12), 2332-2344
Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
SYW Ho, R Lanfear
Mitochondrial DNA 21 (3-4), 138-146
Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
P Brotherton, W Haak, J Templeton, G Brandt, J Soubrier, CJ Adler, ...
Nature Communications 4, 1764
Disulfide bond acquisition through eukaryotic protein evolution
JWH Wong, SYW Ho, PJ Hogg
Molecular Biology and Evolution 28 (1), 327-334
Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae
AH Thornhill, LW Popple, RJ Carter, SYW Ho, MD Crisp
Molecular Phylogenetics and Evolution 63 (1), 15-27
Taller plants have lower rates of molecular evolution
R Lanfear, SYW Ho, TJ Davies, AT Moles, L Aarssen, NG Swenson, ...
Nature Communications 4, 1879
Dating the origin and dispersal of hepatitis B virus infection in humans and primates
D Paraskevis, G Magiorkinis, E Magiorkinis, SYW Ho, R Belshaw, ...
Hepatology 57 (3), 908-916
Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
IT Hyman, SYW Ho, LS Jermiin
Molecular Phylogenetics and Evolution 45 (3), 792-812
One hundred twenty years of koala retrovirus evolution determined from museum skins
MC Ávila-Arcos, SYW Ho, Y Ishida, N Nikolaidis, K Tsangaras, K Hönig, ...
Molecular Biology and Evolution 30 (2), 299-304
Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models
JL Ware, SYW Ho, K Kjer
Molecular Phylogenetics and Evolution 47 (1), 426-432
Hetero: A program to simulate the evolution of DNA on a four-taxon tree
LS Jermiin, SYW Ho, F Ababneh, J Robinson, AWD Larkum
Applied Bioinformatics 2, 159-164
Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago
HD Nguyen, Y Tomitaka, SYW Ho, S Duchêne, HJ Vetten, D Lesemann, ...
PLOS ONE 8 (2), e55336
Statistical guidelines for detecting past population shifts using ancient DNA
T Mourier, SYW Ho, MTP Gilbert, E Willerslev, L Orlando
Molecular Biology and Evolution 29 (9), 2241-2251
The genetic legacy of aridification: Climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate.
M Pepper, SYW Ho, MK Fujita, K JS
Molecular Phylogenetics and Evolution 61 (3), 750-759
Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north‐western Eurasia
M Keis, J Remm, SYW Ho, J Davison, E Tammeleht, IL Tumanov, ...
Journal of Biogeography 40, 915-927
Rethinking the evolution of extant sub‐Saharan African suids (Suidae, Artiodactyla)
J Gongora, RE Cuddahee, FF Nascimento, CJ Palgrave, S Lowden, ...
Zoologica Scripta 40 (4), 327-335
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
MD Martin, E Cappellini, JA Samaniego, ML Zepeda, PF Campos, ...
Nature Communications 4, 2172
A potentially fatal mix of herpes in zoos
AD Greenwood, K Tsangaras, SYW Ho, CA Szentiks, VM Nikolin, G Ma, ...
Current Biology 22, 1727-1731
Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA
J Gongora, AB Swan, AY Chong, SYW Ho, CS Damayanti, S Kolomyjec, ...
Journal of Zoology 286, 110-119
The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent
CB Mallick, FM Iliescu, M Möls, S Hill, R Tamang, G Chaubey, R Goto, ...
PLOS Genetics 9 (11), e1003912
Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts
AD Foote, K Kaschner, SE Schultze, C Garilao, SYW Ho, K Post, ...
Nature Communications 4, 1677
Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages
M Molak, ED Lorenzen, B Shapiro, SYW Ho
Molecular Biology and Evolution 30 (2), 253-262
Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles
CJ Edwards, CD Soulsbury, MJ Statham, SYW Ho, D Wall, G Dolf, G Iossa, ...
Quaternary Science Reviews 57, 95-104
The molecular clock and estimating species divergence
Nature Education 1 (1), 1-2
Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau
Q Jin, H Han, XM Hu, XH Li, CD Zhu, SYW Ho, RD Ward, A Zhang
PLOS ONE 8 (5), e64428
The influence of rate heterogeneity among sites on the time dependence of molecular rates
J Soubrier, M Steel, MSY Lee, CD Sarkissian, S Guindon, SYW Ho, ...
Molecular Biology and Evolution 29 (11), 3345-3358
Divergent evolutionary processes associated with colonization of offshore islands
N Martínková, R Barnett, T Cucchi, R Struchen, M Pascal, M Pascal, ...
Molecular Ecology 22 (20), 5205-5220
The insect molecular clock
SYW Ho, N Lo
Australian Journal of Entomology 52, 101-105
Evidence for Permo-Triassic colonization of the deep sea by isopods
LSF Lins, SYW Ho, GDF Wilson, N Lo
Biology Letters 8 (6), 979-982
Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records
JT Miller, DJ Murphy, SYW Ho, DJ Cantrill, D Seigler
Australian Journal of Botany 61 (6), 436-445
Evaluating the impact of post-mortem damage in ancient DNA: A theoretical approach
M Molak, SYW Ho
Journal of Molecular Evolution 73, 1-12
Reply to Englund: Molecular evolution and diversification—Counting species is better than counting nodes when the phylogeny is unknown
R Lanfear, L Bromham, SYW Ho
Proceedings of the National Academy of Sciences of the USA 108 (17), E85-E86
Ancient hyaenas highlight the old problem of estimating evolutionary rates
B Shapiro, SYW Ho
Molecular Ecology 23 (3), 499-501
Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex
M Stiller, M Molak, S Prost, G Rabeder, G Baryshnikov, W Rosendahl, ...
Quaternary International
Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis
R Barnett, N Yamaguchi, B Shapiro, SYW Ho, I Barnes, R Sabin, ...
BMC Evolutionary Biology 14 (1), 70
The temporal evolution and global spread of cauliflower mosaic virus, a plant pararetrovirus
R Yasaka, HD Nguyen, SYW Ho, S Duchêne, S Korkmaz, N Katis, ...
PLOS ONE 9 (1), e85641
Evolution of MHC class I in the Order Crocodylia
W Jaratlerdsiri, SR Isberg, DP Higgins, SYW Ho, J Salomonsen, K Skjodt, ...
ClockstaR: Choosing the number of relaxed-clock models in molecular phylogenetic analysis
S Duchêne, M Molak, SYW Ho
Adaptive radiation of chemosymbiotic deep-sea mussels
J Lorion, S Kiel, B Faure, M Kawato, SYW Ho, B Marshall, S Tsuchida, ...
Proceedings of the Royal Society B: Biological Sciences 280, 20131243
The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of tachinid flies
Z Zhao, T Su, D Chesters, SYW Ho, C Zhu, X Chen, C Zhang
PLOS ONE 8 (4), e61814
Vertebrate palaeontology of Australasia into the twenty-first century
JMT Nguyen, M Molak, KH Black, EMG Fitzgerald, KJ Travouillon, ...
Biology Letters 7 (6), 804-806
Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
S Duchêne, SYW Ho
Molecular Phylogenetics and Evolution 77, 65-70
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
S Duchêne, EC Holmes, SYW Ho
Proceedings of the Royal Society B: Biological Sciences 281 (1786), 20140732
Genetic architecture of the Tetragonula carbonaria species complex of Australian stingless bees (Hymenoptera: Apidae: Meliponini)
RM Brito, F O Francisco, SYW Ho, BP Oldroyd
Biological Journal of the Linnean Society
Molecular systematics and biogeography of Logania R. Br.(Loganiaceae)
CSP Foster, SYW Ho, BJ Conn, MJ Henwood
Molecular Phylogenetics and Evolution
The impact of calibration and clock-model choice on molecular estimates of divergence times
S Duchêne, R Lanfear, SYW Ho
Molecular Phylogenetics and Evolution
Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon‐date and calibration error into Bayesian phylogenetic analyses of ancient DNA
M Molak, MA Suchard, SYW Ho, DW Beilman, B Shapiro
Molecular Ecology Resources
Accounting for rate variation among lineages in comparative demographic analyses
AG Hope, SYW Ho, JL Malaney, JA Cook, SL Talbot
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