Works by Ho, Simon Y. W.

Results: 124

Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective.

Published in:

PLoS Biology, 2005, v. 3, n. 8, p. 1373, doi. 10.1371/journal.pbio.0030241

By:

Weinstock, Jaco;
Willerslev, Eske;
Sher, Andrei;
Wenfei Tong;
Ho, Simon Y. W.;
Rubenstein, Dan;
Storer, John;
Burns, James;
Martin, Larry;
Bravi, Claudio;
Prieto, Alfredo;
Froese, Duane;
Scott, Eric;
Lai Xulong;
Cooper, Alan

Publication type:

Article

Combining morphological and molecular data resolves the phylogeny of Squilloidea (Crustacea : Malacostraca).

Published in:

Invertebrate Systematics, 2019, v. 33, n. 1, p. 89, doi. 10.1071/IS18035

By:

Van Der Wal, Cara;
Ahyong, Shane T.;
Ho, Simon Y. W.;
Lins, Luana S. F.;
Lo, Nathan

Publication type:

Article

A review of the status of Coptotermes (Isoptera : Rhinotermitidae) species in Australia with the description of two new small termite species from northern and eastern Australia.

Published in:

Invertebrate Systematics, 2017, v. 31, n. 2, p. 180, doi. 10.1071/IS16031

By:

Lee, Timothy R. C.;
Evans, Theodore A.;
Cameron, Stephen L.;
Ho, Simon Y. W.;
Namyatova, Anna A.;
Lo, Nathan

Publication type:

Article

Testing molecular date estimates using an ecological and vicariant case study in treefrogs: The Geological‐Ecological Molecular Calibration.

Published in:

Journal of Biogeography, 2024, v. 51, n. 11, p. 2136, doi. 10.1111/jbi.14971

By:

Jowers, Michael J.;
Pajares, Jesús Muñoz;
Weber, John;
Arkle, Jeanette;
Arenas‐Castro, Salvador;
Ho, Simon Y. W.;
Rivas, Gilson A.;
Murphy, John C.;
Borzée, Amaël;
Pyron, R. Alexander;
Perez‐Losada, Marcos;
De Freitas, Mayke;
Downie, J. Roger;
Moreno‐Rueda, Gregorio;
Forcina, Giovanni;
Sánchez‐Ramírez, Santiago

Publication type:

Article

Large‐scale migrations of brown bears in Eurasia and to North America during the Late Pleistocene.

Published in:

Journal of Biogeography, 2018, v. 45, n. 2, p. 394, doi. 10.1111/jbi.13126

By:

Anijalg, Peeter;
Ho, Simon Y. W.;
Davison, John;
Keis, Marju;
Tammeleht, Egle;
Bobowik, Katalina;
Tumanov, Igor L.;
Saveljev, Alexander P.;
Lyapunova, Elena A.;
Vorobiev, Alexandr A.;
Markov, Nikolai I.;
Kryukov, Alexey P.;
Kojola, Ilpo;
Swenson, Jon E.;
Hagen, Snorre B.;
Eiken, Hans Geir;
Paule, Ladislav;
Saarma, Urmas

Publication type:

Article

Ecological diversification of the Australian Coptotermes termites and the evolution of mound building.

Published in:

Journal of Biogeography, 2017, v. 44, n. 6, p. 1405, doi. 10.1111/jbi.12878

By:

Lee, Timothy R. C.;
Evans, Theodore A.;
Cameron, Stephen L.;
Hochuli, Dieter F.;
Ho, Simon Y. W.;
Lo, Nathan

Publication type:

Article

Bayesian molecular dating: opening up the black box.

Published in:

Biological Reviews, 2018, v. 93, n. 2, p. 1165, doi. 10.1111/brv.12390

By:

Bromham, Lindell;
Hua, Xia;
Duchêne, David A.;
Duchêne, Sebastián;
Ritchie, Andrew M.;
Ho, Simon Y. W.

Publication type:

Article

The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis.

Published in:

2009

By:

Magiorkinis G;
Magiorkinis E;
Paraskevis D;
Ho SY;
Shapiro B;
Pybus OG;
Allain JP;
Hatzakis A;
Magiorkinis, Gkikas;
Magiorkinis, Emmanouil;
Paraskevis, Dimitrios;
Ho, Simon Y W;
Shapiro, Beth;
Pybus, Oliver G;
Allain, Jean-Pierre;
Hatzakis, Angelos

Publication type:

journal article

The Global Spread of Hepatitis C Virus 1a and 1b: A Phylodynamic and Phylogeographic Analysis.

Published in:

PLoS Medicine, 2009, v. 6, n. 12, p. 1, doi. 10.1371/journal.pmed.1000198

By:

Magiorkinis, Gkikas;
Magiorkinis, Emmanouil;
Paraskevis, Dimitrios;
Ho, Simon Y. W.;
Shapiro, Beth;
Pybus, Oliver G.;
Allain, Jean-Pierre;
Hatzakis, Angelos

Publication type:

Article

Using phylogenetics to explore interspecies genetic rescue options for a critically endangered parrot.

Published in:

Conservation Science & Practice, 2021, v. 3, n. 9, p. 1, doi. 10.1111/csp2.483

By:

Hogg, Carolyn J.;
Morrison, Caitlin;
Dudley, Jessica S.;
Alquezar‐Planas, David E.;
Beasley‐Hall, Perry G.;
Magrath, Michael J. L.;
Ho, Simon Y. W.;
Lo, Nathan;
Johnson, Rebecca N.;
Grueber, Catherine E.

Publication type:

Article

Phylogeography and diversity of the terrestrial isopod Spherillo grossus ( Oniscidea: Armadillidae) on the Australian East Coast.

Published in:

Zoological Journal of the Linnean Society, 2014, v. 170, n. 2, p. 297, doi. 10.1111/zoj.12105

By:

Lee, Timothy R. C.;
Ho, Simon Y. W.;
Wilson, George D. F.;
Lo, Nathan

Publication type:

Article

Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north-western Eurasia.

Published in:

Journal of Biogeography, 2013, v. 40, n. 5, p. 915, doi. 10.1111/jbi.12043

By:

Keis, Marju;
Remm, Jaanus;
Ho, Simon Y. W.;
Davison, John;
Tammeleht, Egle;
Tumanov, Igor L.;
Saveljev, Alexander P.;
Männil, Peep;
Kojola, Ilpo;
Abramov, Alexei V.;
Margus, Tõnu;
Saarma, Urmas;
Phillimore, Albert

Publication type:

Article

Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal Z. F. Wang et al. Phylogeographical patterns of yaks.

Published in:

Journal of Biogeography, 2010, v. 37, n. 12, p. 2332, doi. 10.1111/j.1365-2699.2010.02379.x

By:

Zhaofeng Wang;
Xin Shen;
Bin Liu;
Jianping Su;
Yonezawa, Takahiro;
Yun Yu;
Songchang Guo;
Ho, Simon Y. W.;
Vilà, Carles;
Hasegawa, Masami;
Jianquan Liu

Publication type:

Article

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Published in:

Genome Biology & Evolution, 2024, v. 16, n. 4, p. 1, doi. 10.1093/gbe/evae064

By:

Duchêne, David A;
Duchêne, Sebastián;
Stiller, Josefin;
Heller, Rasmus;
Ho, Simon Y W

Publication type:

Article

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy.

Published in:

Genome Biology & Evolution, 2018, v. 10, n. 6, p. 1375, doi. 10.1093/gbe/evy094

By:

Duchêne, David A.;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

Strategies for Partitioning ClockModels in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2752, doi. 10.1093/gbe/evx198

By:

Foster, Charles S. P.;
Ho, Simon Y. W.

Publication type:

Article

The Genome as an Evolutionary Timepiece.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 9, p. 3006, doi. 10.1093/gbe/evw220

By:

Ho, Simon Y. W.;
Chen, Amanda X. Y.;
Lins, Luana S. F.;
Duchêne, David A.;
Lo, Nathan

Publication type:

Article

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Published in:

BMC Evolutionary Biology, 2016, v. 16, p. 1, doi. 10.1186/s12862-016-0688-y

By:

Duchêne, Sebastián;
Duchêne, David A.;
Di Giallonardo, Francesca;
Eden, John-Sebastian;
Geoghegan, Jemma L.;
Holt, Kathryn E.;
Ho, Simon Y. W.;
Holmes, Edward C.

Publication type:

Article

Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models.

Published in:

BMC Evolutionary Biology, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12862-015-0312-6

By:

Duchêne, Sebastián;
Ho, Simon Y. W.;
Holmes, Edward C.

Publication type:

Article

Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis.

Published in:

BMC Evolutionary Biology, 2014, v. 14, n. 1, p. 1, doi. 10.1186/1471-2148-14-70

By:

Barnett, Ross;
Yamaguchi, Nobuyuki;
Shapiro, Beth;
Ho, Simon Y. W.;
Barnes, Ian;
Sabin, Richard;
Werdelin, Lars;
Cuisin, Jacques;
Larson, Greger

Publication type:

Article

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae.

Published in:

BMC Evolutionary Biology, 2011, v. 11, n. 1, p. 65, doi. 10.1186/1471-2148-11-65

By:

Vilstrup, Julia T.;
Ho, Simon Y. W.;
Foote, Andrew D.;
Morin, Phillip A.;
Kreb, Danielle;
Krützen, Michael;
Parra, Guido J.;
Robertson, Kelly M.;
de Stephanis, Renaud;
Verborgh, Philippe;
Willerslev, Eske;
Orlando, Ludovic;
Gilbert, M. Thomas P.

Publication type:

Article

Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets.

Published in:

BMC Evolutionary Biology, 2010, v. 10, p. 242, doi. 10.1186/1471-2148-10-242

By:

Arong Luo;
Huijie Qiao;
Yanzhou Zhang;
Weifeng Shi;
Ho, Simon Y. W.;
Weijun Xu;
Aibing Zhang;
Chaodong Zhu

Publication type:

Article

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.

Published in:

BMC Evolutionary Biology, 2009, v. 9, p. 1, doi. 10.1186/1471-2148-9-95

By:

Willerslev, Eske;
Gilbert, M. Thomas P.;
Binladen, Jonas;
Ho, Simon Y. W.;
Campos, Paula F.;
Ratan, Aakrosh;
Tomsho, Lynn P.;
da Fonseca, Rute R.;
Sher, Andrei;
Kuznetsova, Tatanya V.;
Nowak-Kemp, Malgosia;
Roth, Terri L.;
Miller, Webb;
Schuster, Stephan C.

Publication type:

Article

Species-specific responses of Late Quaternary megafauna to climate and humans.

Published in:

Nature, 2011, v. 479, n. 7373, p. 359, doi. 10.1038/nature10574

By:

Lorenzen, Eline D.;
Nogués-Bravo, David;
Orlando, Ludovic;
Weinstock, Jaco;
Binladen, Jonas;
Marske, Katharine A.;
Ugan, Andrew;
Borregaard, Michael K.;
Gilbert, M. Thomas P.;
Nielsen, Rasmus;
Ho, Simon Y. W.;
Goebel, Ted;
Graf, Kelly E.;
Byers, David;
Stenderup, Jesper T.;
Rasmussen, Morten;
Campos, Paula F.;
Leonard, Jennifer A.;
Koepfli, Klaus-Peter;
Froese, Duane

Publication type:

Article

ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES.

Published in:

Evolution, 2014, v. 68, n. 9, p. 2689, doi. 10.1111/evo.12469

By:

Hope, Andrew G.;
Ho, Simon Y. W.;
Malaney, Jason L.;
Cook, Joseph A.;
Talbot, Sandra L.

Publication type:

Article

Genetic structure and phylogeography of platypuses revealed by mitochondrial DNA.

Published in:

Journal of Zoology, 2012, v. 286, n. 2, p. 110, doi. 10.1111/j.1469-7998.2011.00854.x

By:

Gongora, Jaime;
Swan, Amelia B.;
Chong, Amanda Y.;
Ho, Simon Y. W.;
Damayanti, Chandramaya S.;
Kolomyjec, Stephen;
Grant, Tom;
Miller, Emily;
Blair, David;
Furlan, Elise;
Gust, Nick

Publication type:

Article

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 4, p. 1202, doi. 10.1093/molbev/msz291

By:

Duchêne, David A;
Tong, K Jun;
Foster, Charles S P;
Duchêne, Sebastián;
Lanfear, Robert;
Ho, Simon Y W

Publication type:

Article

Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 4, p. 970, doi. 10.1093/molbev/msy013

By:

Bourguignon, Thomas;
Tang, Qian;
Ho, Simon Y W;
Juna, Frantisek;
Wang, Zongqing;
Arab, Daej A;
Cameron, Stephen L;
Walker, James;
Rentz, David;
Evans, Theodore A

Publication type:

Article

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 6, p. 1529, doi. 10.1093/molbev/msx092

By:

Duchêne, David A.;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

Mitochondrial Phylogenomics Resolves the Global Spread of Higher Termites, Ecosystem Engineers of the Tropics.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 3, p. 589, doi. 10.1093/molbev/msw253

By:

Bourguignon, Thomas;
Lo, Nathan;
Šobotník, Jan;
Ho, Simon Y. W.;
Iqbal, Naeem;
Coissac, Eric;
Lee, Maria;
Jendryka, Martin M.;
Sillan-Dussès, David;
Křížková, Barbora;
Roisin, Yves;
Evans, Theodore A.

Publication type:

Article

Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.

Published in:

Molecular Biology & Evolution, 2016, v. 33, n. 2, p. 478, doi. 10.1093/molbev/msv241

By:

Martin, Michael D.;
Vieira, Filipe G.;
Ho, Simon Y. W.;
Wales, Nathan;
Schubert, Mikkel;
Seguin-Orlando, Andaine;
Ristaino, Jean B.;
Gilbert, M. Thomas P.

Publication type:

Article

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 11, p. 2986, doi. 10.1093/molbev/msv154

By:

Duchêne, David A.;
Duchêne, Sebastian;
Holmes, Edward C.;
Ho, Simon Y. W.

Publication type:

Article

Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes.

Published in:

Genetics, 2006, v. 172, n. 2, p. 733, doi. 10.1534/genetics105.049718

By:

Binladen, Jonas;
Wiuf, Carsten;
Gilbert, M. Thomas P.;
Bunce, Michael;
Barnett, Ross;
Larson, Greger;
Greenwood, Alex D.;
Haile, James;
Ho, Simon Y. W.;
Hansen, Anders J.;
Willerslev, Eske

Publication type:

Article

Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae).

Published in:

Molecular Ecology, 2019, v. 28, n. 16, p. 3771, doi. 10.1111/mec.15172

By:

Tea, Yi‐Kai;
Van Der Wal, Cara;
Ludt, William B.;
Gill, Anthony C.;
Lo, Nathan;
Ho, Simon Y. W.

Publication type:

Article

Time-dependent estimates of molecular evolutionary rates: evidence and causes.

Published in:

Molecular Ecology, 2015, v. 24, n. 24, p. 6007, doi. 10.1111/mec.13450

By:

Ho, Simon Y. W.;
Duchêne, Sebastián;
Molak, Martyna;
Shapiro, Beth

Publication type:

Article

Molecular-clock methods for estimating evolutionary rates and timescales.

Published in:

Molecular Ecology, 2014, v. 23, n. 24, p. 5947, doi. 10.1111/mec.12953

By:

Ho, Simon Y. W.;
Duchêne, Sebastián

Publication type:

Article

Ancient hyaenas highlight the old problem of estimating evolutionary rates.

Published in:

Molecular Ecology, 2014, v. 23, n. 3, p. 499, doi. 10.1111/mec.12621

By:

Shapiro, Beth;
Ho, Simon Y. W.

Publication type:

Article

Divergent evolutionary processes associated with colonization of offshore islands.

Published in:

Molecular Ecology, 2013, v. 22, n. 20, p. 5205, doi. 10.1111/mec.12462

By:

Martínková, Natália;
Barnett, Ross;
Cucchi, Thomas;
Struchen, Rahel;
Pascal, Marine;
Pascal, Michel;
Fischer, Martin C.;
Higham, Thomas;
Brace, Selina;
Ho, Simon Y. W.;
Quéré, Jean‐Pierre;
O'Higgins, Paul;
Excoffier, Laurent;
Heckel, Gerald;
Rus Hoelzel, A.;
Dobney, Keith M.;
Searle, Jeremy B.

Publication type:

Article

Time-dependent rates of molecular evolution.

Published in:

Molecular Ecology, 2011, v. 20, n. 15, p. 3087, doi. 10.1111/j.1365-294X.2011.05178.x

By:

HO, SIMON Y. W.;
LANFEAR, ROBERT;
BROMHAM, LINDELL;
PHILLIPS, MATTHEW J.;
SOUBRIER, JULIEN;
RODRIGO, ALLEN G.;
COOPER, ALAN

Publication type:

Article

Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records.

Published in:

Australian Journal of Botany, 2013, v. 61, n. 6, p. 436, doi. 10.1071/BT13149

By:

Miller, Joseph T.;
Murphy, Daniel J.;
Ho, Simon Y. W.;
Cantrill, David J.;
Seigler, David

Publication type:

Article

The molecular clock and evolutionary timescales.

Published in:

Biochemical Society Transactions, 2018, v. 46, n. 5, p. 1183, doi. 10.1042/BST20180186

By:

Arong Luo;
Ho, Simon Y. W.

Publication type:

Article

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 4, p. 688, doi. 10.1111/1755-0998.12320

By:

Ho, Simon Y. W.;
Duchêne, Sebastián;
Duchêne, David

Publication type:

Article

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 4, p. 785, doi. 10.1111/1755-0998.12352

By:

Duchêne, David;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 1, p. 81, doi. 10.1111/1755-0998.12295

By:

Molak, Martyna;
Suchard, Marc A.;
Ho, Simon Y. W.;
Beilman, David W.;
Shapiro, Beth

Publication type:

Article

Skyline-plot methods for estimating demographic history from nucleotide sequences.

Published in:

Molecular Ecology Resources, 2011, v. 11, n. 3, p. 423, doi. 10.1111/j.1755-0998.2011.02988.x

By:

HO, SIMON Y. W.;
SHAPIRO, BETH

Publication type:

Article

Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates.

Published in:

Systematic Biology, 2024, v. 73, n. 3, p. 532, doi. 10.1093/sysbio/syae002

By:

Kovacs, Toby G L;
Walker, James;
Hellemans, Simon;
Bourguignon, Thomas;
Tatarnic, Nikolai J;
McRae, Jane M;
Ho, Simon Y W;
Lo, Nathan

Publication type:

Article

Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution.

Published in:

Systematic Biology, 2023, v. 72, n. 6, p. 1337, doi. 10.1093/sysbio/syad055

By:

Asar, Yasmin;
Sauquet, Hervé;
Ho, Simon Y W

Publication type:

Article

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process.

Published in:

Systematic Biology, 2023, v. 72, n. 4, p. 781, doi. 10.1093/sysbio/syad011

By:

Luo, Arong;
Zhang, Chi;
Zhou, Qing-Song;
Ho, Simon Y W;
Zhu, Chao-Dong

Publication type:

Article

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.

Published in:

Systematic Biology, 2022, v. 71, n. 3, p. 676, doi. 10.1093/sysbio/syab075

By:

Duchêne, David A;
Mather, Niklas;
Wal, Cara Van Der;
Ho, Simon Y W

Publication type:

Article

Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.

Published in:

Systematic Biology, 2022, v. 71, n. 2, p. 490, doi. 10.1093/sysbio/syab051

By:

Vankan, Mezzalina;
Ho, Simon Y W;
Duchêne, David A

Publication type:

Article