Works matching AU Ho, Simon Y. W.

Results: 125

Combining Spatial, Genetic, and Environmental Risk Data to Define and Prioritize In Situ Conservation Units.

Published in:

Ecology & Evolution (20457758), 2025, v. 15, n. 5, p. 1, doi. 10.1002/ece3.71251

By:

McMaster, Eilish S.;
Dimon, Richard J.;
Baker, Andrew G.;
Harre, Craig;
Mallee, Justin;
Maric, Aleks;
Richards, Peter;
Wiseman, Matthew;
Ho, Simon Y. W.;
Rossetto, Maurizio

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

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods.

Published in:

Bioinformatics, 2016, v. 32, n. 22, p. 3375, doi. 10.1093/bioinformatics/btw421

By:

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

Publication type:

Article

Estimating the number and assignment of clock models in analyses of multigene datasets.

Published in:

Bioinformatics, 2016, v. 32, n. 9, p. 1281, doi. 10.1093/bioinformatics/btw005

By:

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

Publication type:

Article

Phylogenetics: Mammalian genome evolution is governed by multiple pacemakers.

Published in:

Bioinformatics, 2015, v. 31, n. 13, p. 2061, doi. 10.1093/bioinformatics/btv121

By:

Duchêne, Sebastián;
Ho, Simon Y. W.

Publication type:

Article

ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis.

Published in:

Bioinformatics, 2014, v. 30, n. 7, p. 1017

By:

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

Publication type:

Article

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data.

Published in:

Ecology & Evolution (20457758), 2020, v. 10, n. 1, p. 579, doi. 10.1002/ece3.5888

By:

Mather, Niklas;
Traves, Samuel M.;
Ho, Simon Y. W.

Publication type:

Article

EasyCodeML: A visual tool for analysis of selection using CodeML.

Published in:

Ecology & Evolution (20457758), 2019, v. 9, n. 7, p. 3891, doi. 10.1002/ece3.5015

By:

Gao, Fangluan;
Chen, Chengjie;
Arab, Daej A.;
Du, Zhenguo;
He, Yehua;
Ho, Simon Y. W.

Publication type:

Article

A simulation study of sample size for DNA barcoding.

Published in:

Ecology & Evolution (20457758), 2015, v. 5, n. 24, p. 5869, doi. 10.1002/ece3.1846

By:

Arong Luo;
Haiqiang Lan;
Cheng Ling;
Aibing Zhang;
Lei Shi;
Ho, Simon Y. W.;
Chaodong Zhu

Publication type:

Article

Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals.

Published in:

BMC Genomics, 2011, v. 12, n. 1, p. 84, doi. 10.1186/1471-2164-12-84

By:

Arong Luo;
Aibing Zhang;
Ho, Simon Y. W.;
Weijun Xu;
Yanzhou Zhang;
Weifeng Shi;
Cameron, Stephen L.;
Chaodong Zhu

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

The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus).

Published in:

Ecology & Evolution (20457758), 2024, v. 14, n. 3, p. 1, doi. 10.1002/ece3.11148

By:

Tea, Yi‐Kai;
Zhou, Yulu;
Ewart, Kyle M.;
Cheng, Guo;
Kawasaki, Kazuhiko;
DiBattista, Joseph D.;
Ho, Simon Y. W.;
Lo, Nathan;
Fan, Shaohua

Publication type:

Article

The Neotropical endemic liverwort subfamily Micropterygioideae had circum‐Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous.

Published in:

Ecology & Evolution (20457758), 2024, v. 14, n. 3, p. 1, doi. 10.1002/ece3.11066

By:

Rayos, Antonio L.;
Renner, Matthew A. M.;
Ho, Simon Y. W.

Publication type:

Article

The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0095722

By:

Jia, Fangzhi;
Lo, Nathan;
Ho, Simon Y. W.

Publication type:

Article

The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0085641

By:

Yasaka, Ryosuke;
Nguyen, Huy D.;
Ho, Simon Y. W.;
Duchêne, Sebastián;
Korkmaz, Savas;
Katis, Nikolaos;
Takahashi, Hideki;
Gibbs, Adrian J.;
Ohshima, Kazusato

Publication type:

Article

Diversification and Demography of the Oriental Garden Lizard (Calotes versicolor) on Hainan Island and the Adjacent Mainland.

Published in:

PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0064754

By:

Huang, Yong;
Guo, Xianguang;
Ho, Simon Y. W.;
Shi, Haitao;
Li, Jiatang;
Li, Jun;
Cai, Bo;
Wang, Yuezhao

Publication type:

Article

Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau

Published in:

PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0064428

By:

Jin, Qian;
Han, Huilin;
Hu, XiMin;
Li, XinHai;
Zhu, ChaoDong;
Ho, Simon Y. W.;
Ward, Robert D.;
Zhang, Ai-bing

Publication type:

Article

The Mitochondrial Genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the Evolutionary Timescale of Tachinid Flies.

Published in:

PLoS ONE, 2013, v. 8, n. 4, p. 1, doi. 10.1371/journal.pone.0061814

By:

Zhao, Zhe;
Su, Tian-juan;
Chesters, Douglas;
Wang, Shi-di;
Ho, Simon Y. W.;
Zhu, Chao-dong;
Chen, Xiao-lin;
Zhang, Chun-tian

Publication type:

Article

Turnip Mosaic Potyvirus Probably First Spread to Eurasian Brassica Crops from Wild Orchids about 1000 Years Ago.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0055336

By:

Nguyen, Huy D.;
Tomitaka, Yasuhiro;
Ho, Simon Y. W.;
Duchêne, Sebastián;
Vetten, Heinrich-Josef;
Lesemann, Dietrich;
Walsh, John A.;
Gibbs, Adrian J.;
Ohshima, Kazusato

Publication type:

Article

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology.

Published in:

PLoS ONE, 2008, v. 3, n. 2, p. 1, doi. 10.1371/journal.pone.0001615

By:

Ho, Simon Y. W.;
Saarma, Urmas;
Barnett, Ross;
Haile, James;
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

Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus).

Published in:

Systematic Biology, 2022, v. 71, n. 1, p. 1, doi. 10.1093/sysbio/syab012

By:

Tea, Yi-Kai;
Xu, Xin;
DiBattista, Joseph D;
Lo, Nathan;
Cowman, Peter F;
Ho, Simon Y W

Publication type:

Article

Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders.

Published in:

Systematic Biology, 2021, v. 70, n. 6, p. 1110, doi. 10.1093/sysbio/syaa098

By:

Xu, Xin;
Su, Yong-Chao;
Ho, Simon Y W;
Kuntner, Matjaž;
Ono, Hirotsugu;
Liu, Fengxiang;
Chang, Chia-Chen;
Warrit, Natapot;
Sivayyapram, Varat;
Aung, Khin Pyae Pyae;
Pham, Dinh Sac;
Norma-Rashid, Y;
Li, Daiqin

Publication type:

Article

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process.

Published in:

Systematic Biology, 2020, v. 69, n. 2, p. 325, doi. 10.1093/sysbio/syz038

By:

Luo, Arong;
Duchêne, David A;
Zhang, Chi;
Zhu, Chao-Dong;
Ho, Simon Y W

Publication type:

Article

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies.

Published in:

Systematic Biology, 2020, v. 69, n. 1, p. 1, doi. 10.1093/sysbio/syz032

By:

Nie, Yuan;
Foster, Charles S P;
Zhu, Tianqi;
Yao, Ru;
Duchêne, David A;
Ho, Simon Y W;
Zhong, Bojian

Publication type:

Article

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios.

Published in:

Systematic Biology, 2018, v. 67, n. 5, p. 830, doi. 10.1093/sysbio/syy011

By:

Luo, Arong;
Ling, Cheng;
Ho, Simon Y W;
Zhu, Chao-Dong

Publication type:

Article

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

Published in:

Systematic Biology, 2018, v. 67, n. 3, p. 400, doi. 10.1093/sysbio/syx076

By:

DUCHÊNE, DAVID A.;
BRAGG, JASON G.;
DUCHÊNE, SEBASTIÁN;
NEAVES, LINDA E.;
POTTER, SALLY;
MORITZ, CRAIG;
JOHNSON, REBECCA N.;
HO, SIMON Y. W.;
ELDRIDGE, MARK D. B.

Publication type:

Article

The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling.

Published in:

Systematic Biology, 2017, v. 66, n. 3, p. 413, doi. 10.1093/sysbio/syw095

By:

RITCHIE, ANDREW M.;
LO, NATHAN;
HO, SIMON Y. W.

Publication type:

Article

Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale.

Published in:

Systematic Biology, 2017, v. 66, n. 3, p. 338, doi. 10.1093/sysbio/syw086

By:

FOSTER, CHARLES S. P.;
SAUQUET, HERVÉ;
VAN DER MERWE, MARLIEN;
MCPHERSON, HANNAH;
ROSSETTO, MAURIZIO;
HO, SIMON Y. W.

Publication type:

Article

Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales).

Published in:

Systematic Biology, 2012, v. 61, n. 2, p. 289, doi. 10.1093/sysbio/syr116

By:

Sauquet, Hervé;
Ho, Simon Y. W.;
Gandolfo, Maria A.;
Jordan, Gregory J.;
Wilf, Peter;
Cantrill, David J.;
Bayly, Michael J.;
Bromham, Lindell;
Brown, Gillian K.;
Carpenter, Raymond J.;
Lee, Daphne M.;
Murphy, Daniel J.;
Sniderman, J. M. Kale;
Udovicic, Frank

Publication type:

Article

Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content.

Published in:

Systematic Biology, 2011, v. 60, n. 3, p. 366, doi. 10.1093/sysbio/syq099

By:

HO, SIMON Y. W.;
LANFEAR, ROBERT;
PHILLIPS, MATTHEW J.;
BARNES, IAN;
THOMAS, JESSICA A.;
KOLOKOTRONIS, SERGIOS-ORESTIS;
SHAPIRO, BETH

Publication type:

Article

Tracing the Temporal and Spatial Origins of Island Endemics in the Mediterranean Region: A Case Study from the Citrus Family (Ruta L., Rutaceae).

Published in:

Systematic Biology, 2010, v. 59, n. 6, p. 705, doi. 10.1093/sysbio/syq046

By:

SALVO, GABRIELE;
HO, SIMON Y. W.;
ROSENBAUM, GIDEON;
REE, RICHARD;
CONTI, ELENA

Publication type:

Article

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans.

Published in:

Systematic Biology, 2009, v. 58, n. 6, p. 573, doi. 10.1093/sysbio/syp060

By:

STEEMAN, METTE E.;
HEBSGAARD, MARTIN B.;
FORDYCE, R. EWAN;
HO, SIMON Y. W.;
RABOSKY, DANIEL L.;
NIELSEN, RASMUS;
RAHBEK, CARSTEN;
GLENNER, HENRIK;
SØRENSEN, MARTIN V.;
WILLERSLEV, ESKE

Publication type:

Article

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times.

Published in:

Systematic Biology, 2009, v. 58, n. 3, p. 367, doi. 10.1093/sysbio/syp035

By:

HO, SIMON Y. W.;
PHILLIPS, MATTHEW J.

Publication type:

Article

Evidence for Time Dependency of Molecular Rate Estimates.

Published in:

Systematic Biology, 2007, v. 56, n. 3, p. 515, doi. 10.1080/10635150701435401

By:

Ho, Simon Y. W.;
Shapiro, Beth;
Phillips, Matthew J.;
Cooper, Alan;
Drummond, Alexei J.

Publication type:

Article

The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated.

Published in:

Systematic Biology, 2004, v. 53, n. 4, p. 638, doi. 10.1080/10635150490468648

By:

Jermiin, Lars S.;
Ho, Simon Y. W.;
Ababneh, Faisal;
Robinson, John;
Larkum, Anthony W. D.

Publication type:

Article

Tracing the Decay of the Historical Signal in Biological Sequence Data.

Published in:

Systematic Biology, 2004, v. 53, n. 4, p. 623, doi. 10.1080/10635150490503035

By:

Ho, Simon Y. W.;
Jermiin, Lars S.

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

Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life.

Published in:

Insect Science, 2024, v. 31, n. 6, p. 1810, doi. 10.1111/1744-7917.13339

By:

Beasley‐Hall, Perry G.;
Kinjo, Yukihiro;
Rose, Harley A.;
Walker, James;
Foster, Charles S. P.;
Kovacs, Toby G. L.;
Bourguignon, Thomas;
Ho, Simon Y. W.;
Lo, Nathan

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