Phylogenetic analysis of ancient DNA using BEASTSimon Y W Ho
School of Biological Sciences, University of Sydney, Sydney, 2006, NSW, Australia
Methods Mol Biol 840:229-41. 2012
..A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content...
The effect of inappropriate calibration: three case studies in molecular ecologySimon Y W Ho
Department of Zoology, University of Oxford, Oxford, United Kingdom
PLoS ONE 3:e1615. 2008
..Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events...
- Elevated substitution rates estimated from ancient DNA sequences
Simon Y W Ho
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
Biol Lett 3:702-5. 2007
..Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels...
- Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity
Ross Barnett
Department of Zoology, University of Oxford, Oxford, UK
Mol Ecol 18:1668-77. 2009
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Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?James Haile
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
Mol Biol Evol 24:982-9. 2007
..Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for...
- Relaxed phylogenetics and dating with confidence
Alexei J Drummond
Department of Zoology, University of Oxford, Oxford, United Kingdom
PLoS Biol 4:e88. 2006
..From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution...
- Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
Simon Y W Ho
Department of Zoology, University of Oxford, Oxford, UK
Biol Lett 4:370-4. 2008
..The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence...
- Time dependency of molecular rate estimates and systematic overestimation of recent divergence times
Simon Y W Ho
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 22:1561-8. 2005
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- Bayesian estimation of sequence damage in ancient DNA
Simon Y W Ho
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol 24:1416-22. 2007
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- Hetero: a program to simulate the evolution of DNA on a four-taxon tree
Lars S Jermiin
School of Biological Sciences, University of Sydney, NSW, Australia
Appl Bioinformatics 2:159-63. 2003
..It has a simple user interface and output, making it equally useful in the teaching and research of phylogenetics...
- Evidence for time dependency of molecular rate estimates
Simon Y W Ho
Department of Zoology, University of Oxford, Oxford, United Kingdom
Syst Biol 56:515-22. 2007
- Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach
Martyna Molak
School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
J Mol Evol 73:244-55. 2011
..According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation...
- Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective
Jaco Weinstock
Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
PLoS Biol 3:e241. 2005
..Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species...
- Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation
Simon Y W Ho
Henry Wellcome Ancient Biomolecules Centre, Oxford, United Kingdom
Mol Biol Evol 22:1355-63. 2005
..If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates...
- Molecular clocks: when times are a-changin'
Simon Y W Ho
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
Trends Genet 22:79-83. 2006
..We conclude that many studies involving recent divergence events will need to be reconsidered...
- Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA
Isabel T Hyman
School of Biological Sciences, University of Sydney, NSW 2006, Australia
Mol Phylogenet Evol 45:792-812. 2007
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- A Bayesian evaluation of human mitochondrial substitution rates
Phillip Endicott
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
Am J Hum Genet 82:895-902. 2008
..Our results also demonstrate that human mitochondrial genomes exhibit a number of molecular evolutionary complexities that necessitate the use of sophisticated analytical models for genetic analyses...
- Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
M Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Proc Natl Acad Sci U S A 105:8327-32. 2008
..Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep...
- Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins
Phillip Endicott
Départment Hommes, Natures, sociétés, Musée de l Homme, Paris, France
J Hum Evol 59:87-95. 2010
..These results suggest that a reappraisal of key elements in the Pleistocene hominin fossil record may now be required...
- Vertebrate palaeontology of Australasia into the twenty-first century
Jacqueline M T Nguyen
School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
Biol Lett 7:804-6. 2011
..Nonetheless, further field exploration for new fossils and systematic descriptions will continue to shape our understanding of vertebrate evolution in this little-studied, but most unusual, part of the globe...
- Disulfide bond acquisition through eukaryotic protein evolution
Jason W H Wong
Prince of Wales Clinical School and Lowy Cancer Research Centre, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
Mol Biol Evol 28:327-34. 2011
..Finally, we show that the acquisition of the functionally relevant disulfide bond in domain 2 of the CD4 protein occurred independently in primates and rodents...
- Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
Jonas Binladen
Ancient DNA and Evolution Group, Centre for Ancient Genetics, Niels Bohr Institute, University of Copenhagen, Denmark
Genetics 172:733-41. 2006
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- The crucial role of calibration in molecular date estimates for the peopling of the Americas
Simon Y W Ho
Am J Hum Genet 83:142-6; author reply 146-7. 2008
- Divergence dates of libelluloid dragonflies (Odonata: Anisoptera) estimated from rRNA using paired-site substitution models
Jessica L Ware
Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, USA
Mol Phylogenet Evol 47:426-32. 2008
- Uplift of the Tibetan plateau: evidence from divergence times of glyptosternoid catfishes
Zuogang Peng
Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
Mol Phylogenet Evol 39:568-72. 2006
- Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
Mike Buckley
BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK
Science 319:33; author reply 33. 2008
..rex does not...
- Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages
Urmas Saarma
Department of Integrative Zoology, Institute of Zoology and Hydrobiology, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
Mol Ecol 16:401-13. 2007
..Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations...
- Improving the analysis of dinoflagellate phylogeny based on rDNA
Shauna Murray
The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo, 113 8657, Japan
Protist 156:269-86. 2005
..The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments...
- Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
Ceiridwen J Edwards
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
Proc Biol Sci 274:1377-85. 2007
..During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare...
