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List of works by Simon Y. W. Ho

A Bayesian phylogenetic method to estimate unknown sequence ages

scientific article

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

scientific article published on 01 March 2020

A comparison of methods for estimating substitution rates from ancient DNA sequence data.

scientific article

A potentially fatal mix of herpes in zoos

scientific article

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

scientific article published on 07 December 2019

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

article

Accommodating the effect of ancient DNA damage on inferences of demographic histories

scientific article

Accounting for uncertainty in the evolutionary timescale of green plants through clock-partitioning and fossil calibration strategies

article

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

scientific article published on 9 March 2005

Adaptation and conservation insights from the koala genome

scientific article published on 02 July 2018

American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations

scientific article published on 01 September 2020

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates.

scientific article published in July 2014

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

scientific article published on 22 September 2017

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

scientific article (publication date: 11 May 2009)

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

scientific article

Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

scientific article

Ancient hyaenas highlight the old problem of estimating evolutionary rates.

scientific article published in February 2014

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

scientific article

Ancient mitogenomics

scientific article published on 27 September 2009

Angels in disguise: sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages

scientific article published on 05 August 2020

Assemblage accumulation curves: A framework for resolving species accumulation in biological communities using DNA sequences

scientific article published in 2019

Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

scientific article (publication date: February 2006)

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 21 October 2019

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 06 July 2020

Bayesian estimation of sequence damage in ancient DNA.

scientific article published on 29 March 2007

Bayesian estimation of substitution rates from ancient DNA sequences with low information content

scientific article published on 4 February 2011

Bayesian molecular dating: opening up the black box.

scientific article published on 15 December 2017

Biogeographic calibrations for the molecular clock

scientific article

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

scientific article published on 01 August 2019

Calibrating the genomic clock of modern birds using fossils

scientific article published on 16 September 2024

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

scientific article published on 14 November 2013

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

scientific article (publication date: 4 January 2008)

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

scientific article published in 2013

Comparison of Methods for Molecular Species Delimitation across a Range of Speciation Scenarios

scientific article published on 15 February 2018

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

article by Marju Keis et al published 28 November 2012 in Journal of Biogeography

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Correction: Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation

scientific article published on 21 July 2020

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

scientific article (publication date: 23 August 2008)

Cross-validation to select Bayesian hierarchical models in phylogenetics

scientific article published on 26 May 2016

Cryptic diversity, diversification and vicariance in two species complexes ofTomocerus(Collembola, Tomoceridae) from China

article

Dating the emergence of human pathogens

scientific article published on 01 June 2020

Dating the origin and dispersal of hepatitis B virus infection in humans and primates

scientific article

Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes.

scientific article published on 26 July 2015

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

scientific article

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

scientific article published on 26 November 2019

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

scientific article published in June 2018

Divergent evolutionary processes associated with colonization of offshore islands

scientific article published in October 2013

Early cave art and ancient DNA record the origin of European bison

scientific article

Early diversifications of angiosperms and their insect pollinators: Were they unlinked?

scientific article published on 19 November 2021

Early diversifications of angiosperms and their insect pollinators: were they unlinked?

scientific article published in May 2022

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

article

Elevated substitution rates estimated from ancient DNA sequences

scientific article (publication date: 22 December 2007)

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

scientific article

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

scientific article

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

scientific article published on 6 January 2016

Estimating the phylogeny and divergence times of primates using a supermatrix approach

scientific article published in 2009

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations

scientific article published on 10 July 2015

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

scientific article

Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach.

scientific article

Evidence for Permo-Triassic colonization of the deep sea by isopods

scientific article (publication date: 23 December 2012)

Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective

scientific article published on 28 June 2005

Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes

scientific article published on 08 January 2020

Founder-specific inbreeding depression affects racing performance in Thoroughbred horses.

scientific article published on 18 April 2018

Genetic architecture of the<i>Tetragonula carbonaria</i>species complex of Australian stingless bees (Hymenoptera: Apidae: Meliponini)

scientific article published on 05 June 2014

Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens

scientific article published on 09 October 2020

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

scientific article (publication date: February 2016)

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

scientific article published on 19 June 2015

Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae)

scientific article published on 26 June 2019

INSECT PHYLOGENOMICS. Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

scientific article published on July 2015

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

scientific article published in 2023

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

scientific article published in June 2010

Inclusion of rare taxa from Blattidae and Anaplectidae improves phylogenetic resolution in the cockroach superfamily Blattoidea

scientific article published in 2023

Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes

scientific article published on 29 July 2020

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

scientific article (publication date: 17 June 2008)

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

article by Peeter Anijalg et al published 15 November 2017 in Journal of Biogeography

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

scientific article published on 01 April 2020

Mammalian genome evolution is governed by multiple pacemakers

scientific article

Mito-communications

scientific article published in June 2011

Mito-communications

scientific article published on 16 May 2012

Mito-communications

scientific article

Mito-communications

Mito-communications

Mito-communications

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

scientific article (publication date: 7 June 2007)

Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex

scholarly article

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

scientific article

Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages

scientific article published in January 2007

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

scientific article

Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa

article

Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats

Molecular clocks

scientific article published in May 2016

Molecular data support Orianthera: a new genus of Australian Loganiaceae

scientific article (publication date: 20 October 2014)

Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)

scientific article published in 2016

Molecular systematics and biogeography of Logania R.Br. (Loganiaceae).

scientific article published on 12 June 2014

Molecular-clock methods for estimating evolutionary rates and timescales

scientific article published on 30 October 2014

Movements of southern elephant seals (Mirounga leonina) from Davis Base, Antarctica: combining population genetics and tracking data

scientific article published in 2022

Multiple evolutionary origins of Australian soil-burrowing cockroaches driven by climate change in the Neogene

scientific article published in February 2016

Mutation rate is linked to diversification in birds

scientific article

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

scientific article

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity

scientific article

One hundred twenty years of koala retrovirus evolution determined from museum skins

scientific article

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

scientific article published on 19 July 2018

Parallel evolution of mound-building and grass-feeding in Australian nasute termites.

scientific article published in February 2017

Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world phytophthora infestans

scientific article published on 27 February 2014

PhyloMAd: efficient assessment of phylogenomic model adequacy

scientific article published on 01 July 2018

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

scientific article

Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.

scientific article published on 3 October 2012

Phylogenomic analyses data of the avian phylogenomics project

scientific article

Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal

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

scholarly article by Timothy R. C. Lee published in 2013

Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity

scientific article

Phylogeography of the iconic Australian red-tailed black-cockatoo (Calyptorhynchus banksii) and implications for its conservation

scientific article published on 12 May 2020

Phylogeography, Genetic Diversity, and Management Units of Hawksbill Turtles in the Indo-Pacific.

scientific article published on 27 November 2015

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)

scientific article published on 25 May 2018

Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

scientific article

Radiation of extant cetaceans driven by restructuring of the oceans

scientific article

Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction

scientific article published on 09 October 2019

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

scientific article

Relaxed phylogenetics and dating with confidence

scientific article

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

scientific article published on September 2015

Rethinking dog domestication by integrating genetics, archeology, and biogeography

scientific article

Rethinking the evolution of extant sub-Saharan African suids (Suidae, Artiodactyla)

scientific article (publication date: 14 June 2011)

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

scientific article

Sexual selection, body mass and molecular evolution interact to predict diversification in birds

scientific article published on 01 March 2019

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

scientific article published on 12 September 2014

Skyline-plot methods for estimating demographic history from nucleotide sequences

scientific article published on 06 February 2011

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

scientific article (publication date: 2 November 2011)

Statistical guidelines for detecting past population shifts using ancient DNA.

scientific article

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

scientific article published on 25 September 2017

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

scientific article published in May 2009

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

scientific article published in April 2018

Taller plants have lower rates of molecular evolution

scientific article published on January 2013

Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome

scientific article

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

scientific article (publication date: 4 December 2012)

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales).

scientific article

The Genome as an Evolutionary Timepiece

scientific article

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

scientific article

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data

scientific article

The Recovery, Interpretation and Use of Ancient Pathogen Genomes

scientific article published on 01 October 2020

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus

scientific article

The effect of inappropriate calibration: three case studies in molecular ecology

scientific article (publication date: 20 February 2008)

The evolutionary history and global spatio-temporal dynamics of potato virus Y

scientific article published on 01 July 2020

The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data

scientific article published on 21 September 2017

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

scientific article

The impact of calibration and clock-model choice on molecular estimates of divergence times

scientific article published on 6 June 2014

The impacts of drift and selection on genomic evolution in insects

scientific article published on 27 April 2017

The influence of rate heterogeneity among sites on the time dependence of molecular rates

scientific article published on 21 May 2012

The origins and radiation of Australian Coptotermes termites: from rainforest to desert dwellers.

scientific article published on 6 October 2014

The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus

scientific article

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

scientific article (publication date: July 2005)

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

scientific article published in December 2015

Time-dependent rates of molecular evolution

scientific article published on 08 July 2011

Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences.

scientific article

Transoceanic dispersal and plate tectonics shaped global cockroach distributions: evidence from mitochondrial phylogenomics.

scientific article published on 6 February 2018

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

scientific article published on 16 December 2014

Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago.

scientific article

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data

scientific article

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

scientific article published in 2021

Vertebrate palaeontology of Australasia into the twenty-first century

scientific article (publication date: 23 December 2011)

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

Zebra Alphaherpesviruses (EHV-1 and EHV-9): Genetic Diversity, Latency and Co-Infections

scientific article published on 20 September 2016

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