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2017


Wills, P. R. and Charles W. Carter Jr. 2017. "Insuperable problems of the genetic code initially emerging in an RNA world". Biosystems https://doi.org/10.1016/j.biosystems.2017.09.006

Greenhill, S. J., Chieh-Hsi Wu Xia Hua, Michael Dunn, Stephen C. Levenison and Russell D. Gray. 2017. "Evolutionary dynamics of language systems". Proceedings of the National Academy of Sciences of the United States of America 201700388 doi: 10.1073/pnas.1700388114

Bouckaert, Remco R., and Alexei J. Drummond. 2017. “bModelTest: Bayesian Phylogenetic Site Model Averaging and Model Comparison.” BMC evolutionary biology 17(1): 42.

Gavryushkina, Alexandra et al. 2017. “Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.” Systematic Biology 66(1): 57–73.

Vaughan, Timothy G. et al. 2017. “Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.” Genetics 205(2): 857–70.

Ogilvie, Huw A., Bouckaert, Remco R., and Alexei J. Drummond. 2017. "StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates." Molecular Biology and Evolution msx126 doi:https://doi.org/10.1093/molbev/msx126

Matschiner, Michael, Zuzana Musilová, Julia MI Barth, Zuzana Starostová, Walter Salzburger, Mike Steel and Remco Bouckaert. 2017. "Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes." Systematic Biology 66(1):3-22 doi: https://doi.org/10.1093/sysbio/syw076

Vaughan, Timothy G., Gabriel E Leventhal, David A Rasmussen, Alexei J Drummond, David Welch and Tanja Stadler. 2017. "Directly Estimating Epidemic Curves From Genomic Data." bioRxiv doi: https://doi.org/10.1101/142570

Stadler, Tanja, Alexandra Gavryushkina, Rachel Warnock, Alexei J Drummond, Tracy A Heath. 2017. "The Fossilized Birth-Death Model for the Analysis of Stratigraphic Range Data under Different Speciation Concepts." arXiv preprint arXiv:1706.10106

Barido-Sottani, Joëlle, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F Müller, Jūlija Pečerska, David A Rasmussen, Chi Zhang, Alexei J Drummond, Tracy A Heath, Oliver G Pybus, Timothy G Vaughan and Tanja Stadler. 2017. "Taming the BEAST – A Community Teaching Material Resource for BEAST 2." Systematic Biology syx060 doi:https://doi.org/10.1093/sysbio/syx060

Vaughan, Timothy G. 2017. "IcyTree: Rapid Browser-Based Visualization for Phylogenetic Trees and Network." Bioinformatics btx155

Gray, Russell, Quentin Atkinson, Colin Renfrew. 2017. "Dating and Placing Indo-European: Anatolia, 9,000 Years BP." Annual Reivew of Linguistics 3(1)

 

2016


Drummond, A. J., & Stadler, T. 2016. “Bayesian Phylogenetic Estimation of Fossil Ages.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 371(1699).

Gavryushkin, A., & Drummond, A. J. 2016. “The Space of Ultrametric Phylogenetic Trees.” Journal of Theoretical Biology 403: 197–208.

Kühnert, D., Stadler, T., Vaughan, T. G., & Drummond, A. J. 2016. “Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.” Molecular Biology and Evolution 33(8): 2102–16.

Ogilvie, H. A., Heled, J., Xie, D., & Drummond, A. J. 2016. “Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods.” Systematic Biology 65(3): 381–96.

Watts, J., Bulbulia, J. Gray, R.D., Atkinson, Q.D. 2016 "Clarity and causality needed in claims about Big Gods" The Behavioral and Brain Sciences 39(27) doi: 10.1017/S0140525X15000576

Galla, S.J., Buckley, T.R., Elshire, R., Hale, M.L., Knapp, M., McCallum, J., Moraga, R., Santure, A.W., Wilcox, P., Steeves, T.E. 2016 "Building storng relationships between conservation genetics and primary industry leeds to mutually beneficial genomic advances" Molecular Ecology 25(21):5267-5281

Santure, A. 2016 "An ecological model organism flies into the genomics era" Molecular Ecology Resources 4(2):379-381

Matthews, L., Passmore, S., Richard, P. M., Gray, R. D., Atkinson, Q. D. 2016 "Shared cultural history as a predictor of political and economic changes among nation states" PLoS ONE 11(4):e0152979  doi:10.1371/journal.pone.0152979

Watts, J., Sheehan, O., Atkinson, Q.D., Bulbulia, J., Gray, R.D. 2016 "Ritual human sacrifice promoted and sustained the evolution of stratiied societies" Nature 532(7598):228-231 

Gray, R., Atkinson, Q., Renfew, C., 2016 "Dating and placing Indo-European: Anatolia, 9,000 years BP" Annual Review of Linguistics 3(1)

Guindon, S., Guo, H., Welch, D. 2016 "Demographic inference under the coalescent in a spatial continuum" bioRxiv 042135

Matsciner, M., Zuzana Musilova., Barth, J.M.I., Starastova, Z., Salzburger, W., Steel, M., Bouckaert, R. 2016 "Bayesian node dating based on probabiliites of fossil sampling supports trans-atlantic dispersal of cichlid fishes" bioRxiv 038455

Csordas, A. and Bouckaert, R. 2016 "Bayesia analysis of normal mouse cell lineage trees allowing intra-individual cell population specific mutation rates" bioRxiv 040733

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2015


Popinga, Alex, Tim Vaughan, Tanja Stadler, and Alexei J. Drummond. 2015. “Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models.”Genetics 199 (2): 595–607. http://doi.org/10.1534/genetics.114.172791.

Drummond, Alexei J., and Remco R. Bouckaert. 2015. Bayesian Evolutionary Analysis ; with BEAST . Cambridge, United Kingdom: Cambridge University Press.

Drummond, Alexei J., Richard D. Newcomb, Thomas R. Buckley, Dong Xie, Andrew Dopheide, Benjamin Cm Potter, Joseph Heled, et al. 2015. “Evaluating a Multigene Environmental DNA Approach for Biodiversity Assessment.” GigaScience 4: 46. http://doi.org/10.1186/s13742-015-0086-1.

Stadler, Tanja, Timothy G. Vaughan, Alex Gavryushkin, Stephane Guindon, Denise Kühnert, Gabriel E. Leventhal, and Alexei J. Drummond. 2015. “How Well Can the Exponential-Growth Coalescent Approximate Constant-Rate Birth–death Population Dynamics?” Proceedings of the Royal Society of London B: Biological Sciences 282 (1806): 20150420.http://rspb.royalsocietypublishing.org/content/282/1806/20150420.abstract.

Guindon, Stephane. 2015. “On the Interpretation of Results Returned by Branch-Site Models.”https://peerj.com/preprints/944/.

Privault, Nicolas, and Stéphane Guindon. 2015. “Closed Form Modeling of Evolutionary Rates by Exponential Brownian Functionals.” Journal of Mathematical Biology, 1–23.http://link.springer.com/article/10.1007/s00285-015-0863-6.

Muto, Yoshinori, Stéphane Guindon, Toshiaki Umemura, László K\Hohidai, and Hiroshi Ueda. 2015. “Adaptive Evolution of Formyl Peptide Receptors in Mammals.” Journal of Molecular Evolution 80 (2): 130–41.http://link.springer.com/article/10.1007/s00239-015-9666-z.

 

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2014


Gavryushkina, Alexandra, David Welch, Tanja Stadler, and Alexei J. Drummond. 2014. “Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration.” PLoS Computational Biology 10 (12): e1003919. http://doi.org/10.1371/journal.pcbi.1003919.

Gavruskin, Alex, and Alexei J. Drummond. 2014. “The Space of Ultrametric Phylogenetic Trees.”arXiv:1410.3544 [math, Stat], October. http://arxiv.org/abs/1410.3544.

Kühnert, Denise, Tanja Stadler, Timothy G. Vaughan, and Alexei J. Drummond. 2014. “Simultaneous Reconstruction of Evolutionary History and Epidemiological Dynamics from Viral Sequences with the Birth–death SIR Model.” Journal of The Royal Society Interface 11 (94): 20131106.http://doi.org/10.1098/rsif.2013.1106.

Opie, Christopher, Quentin D. Atkinson, Robin I. M. Dunbar, and Susanne Shultz. 2014. “Reply to Lukas and Clutton-Brock: Infanticide Still Drives Primate Monogamy.” Proceedings of the National Academy of Sciences 111 (17): E1675–E1675. http://doi.org/10.1073/pnas.1403165111.

Vaughan, Timothy G., Denise Kühnert, Alex Popinga, David Welch, and Alexei J. Drummond. 2014. “Efficient Bayesian Inference under the Structured Coalescent.” Bioinformatics, April, btu201.http://doi.org/10.1093/bioinformatics/btu201.

Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, and Alexei J. Drummond. 2014. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLoS Comput Biol 10 (4): e1003537. http://doi.org/10.1371/journal.pcbi.1003537.

Vrancken, Bram, Andrew Rambaut, Marc A. Suchard, Alexei Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, and Philippe Lemey. 2014. “The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates.” PLoS Comput Biol 10 (4): e1003505.http://doi.org/10.1371/journal.pcbi.1003505.

Bulbulia, Joseph, Quentin Atkinson, Russell Gray, and Simon Greenhill. 2014. “Why Do Religious Cultures Evolve Slowly? The Cultural Evolution of Cooperative Calling and the Historical Study of Religions.” Inhttp://universitypublishingonline.org/acumen/chapter.jsf?bid=CBO9781844657346&cid=CBO9781844657346A021. Acumen Publishing.https://digitalcollections.anu.edu.au/handle/1885/11569.

Davies, Neil, Dawn Field, Linda Amaral-Zettler, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, et al. 2014. “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.” Standards in Genomic Sciences 9 (3). http://doi.org/10.4056/431.

Davies, Neil, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, et al. 2014. “The Founding Charter of the Genomic Observatories Network.” GigaScience 3 (March): 2.http://doi.org/10.1186/2047-217X-3-2.

Shultz, Susanne, Christopher Opie, Emma Nelson, Q. D. Atkinson, and R. I. M. Dunbar. 2014. Lucy to Language: The Benchmark Papers: Evolution of Primates Social Systems: Implications for Hominin Social Evolution. Oxford University Press.

Kamilar, Jason M., and Quentin D. Atkinson. 2014. “Cultural Assemblages Show Nested Structure in Humans and Chimpanzees but Not Orangutans.” Proceedings of the National Academy of Sciences 111 (1): 111–15. http://doi.org/10.1073/pnas.1313318110.

Ranjard, Louis, David Welch, Marie Paturel, and Stéphane Guindon. 2014. “Modelling Competition and Dispersal in a Statistical Phylogeographic Framework.” Systematic Biology, syu040.http://sysbio.oxfordjournals.org/content/early/2014/06/13/sysbio.syu040.short.

Long, Jennifer, Niki Harré, and Quentin D. Atkinson. 2014. “Understanding Change in Recycling and Littering Behavior Across a School Social Network.” American Journal of Community Psychology, 1–13.http://doi.org/10.1007/s10464-013-9613-3.

Kamilar, Jason M., and Quentin D. Atkinson. 2014. “Patterns of Cultural Nestedness in Humans, Chimpanzees, and Orangutans.” In AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, 153:154–55. WILEY-BLACKWELL 111 RIVER ST, HOBOKEN 07030-5774, NJ USA.

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2013


Opie, Christopher, Quentin D. Atkinson, Robin I. M. Dunbar, and Susanne Shultz. 2013. “Reply to Dixson: Infanticide Triggers Primate Monogamy.” Proceedings of the National Academy of Sciences 110 (51): E4938–E4938. http://doi.org/10.1073/pnas.1319662110.

Leache, A., M. Fujita, V. Minin, and R. Bouckaert. 2013. “Species Delimitation Using Genome-Wide SNP Data.” 001172. http://biorxiv.org/lookup/doi/10.1101/001172.

Heled, Joseph, and Alexei J. Drummond. 2013. “Calibrated Birth-Death Phylogenetic Time-Tree Priors for Bayesian Inference.”  arXiv:1311.4921 [q-Bio], November. http://arxiv.org/abs/1311.4921.

Lu, Ashley, and Stéphane Guindon. 2013. “Performance of Standard and Stochastic Branch-Site Models for Detecting Positive Selection among Coding Sequences.” Molecular Biology and Evolution, November.http://doi.org/10.1093/molbev/mst198.

Gray, R. D., S. J. Greenhill, and Q. D. Atkinson. 2013. Cultural Evolution: Society, Technology, Language, and Religion: Three New Questions. MIT Press.

Gavryushkina, Alexandra, David Welch, and Alexei J. Drummond. 2013. “Recursive Algorithms for Phylogenetic Tree Counting.” Algorithms for Molecular Biology 8 (1): 26. http://doi.org/10.1186/1748-7188-8-26.

Heled, Joseph, and Remco R. Bouckaert. 2013. “Looking for Trees in the Forest: Summary Tree from Posterior Samples.” BMC Evolutionary Biology 13 (1): 221. http://doi.org/10.1186/1471-2148-13-221.

Cheng, Yan, Stephane Guindon, Allen Rodrigo, Lin Ying Wee, Masafumi Inoue, Alex J V Thompson, Stephen Locarnini, and Seng Gee Lim. 2013. “Cumulative Viral Evolutionary Changes in Chronic Hepatitis B Virus Infection Precedes Hepatitis B E Antigen Seroconversion.” Gut 62 (9): 1347–55.http://doi.org/10.1136/gutjnl-2012-302408.

Bahl, Justin, Scott Krauss, Denise Kühnert, Mathieu Fourment, Garnet Raven, S. Paul Pryor, Lawrence J. Niles, et al. 2013. “Influenza A Virus Migration and Persistence in North American Wild Birds.” Edited by Raul Andino. PLoS Pathogens 9 (8): e1003570. http://doi.org/10.1371/journal.ppat.1003570.

Pagel, Mark, Quentin D. Atkinson, Andreea S. Calude, and Andrew Meade. 2013. “Reply to Mahowald and Gibson and to Heggarty: No Problems with Short Words, and No Evidence Provided.” Proceedings of the National Academy of Sciences 110 (35): E3255–E3255. http://doi.org/10.1073/pnas.1309838110.

Pagel, Mark, Quentin D. Atkinson, Andreea S. Calude, and Andrew Meade. 2013. “Reply to Mahowald and Gibson and to Heggarty: No Problems with Short Words, and No Evidence Provided.” Proceedings of the National Academy of Sciences 110 (35): E3255–E3255. http://doi.org/10.1073/pnas.1309838110.

Kühnert, Denise, Tanja Stadler, Timothy G. Vaughan, and Alexei J. Drummond. 2013. “Simultaneous Reconstruction of Evolutionary History and Epidemiological Dynamics from Viral Sequences with the Birth-Death SIR Model.” arXiv:1308.5140 [math, Q-Bio, Stat], August. http://arxiv.org/abs/1308.5140.

Opie, Christopher, Quentin D. Atkinson, Robin I. M. Dunbar, and Susanne Shultz. 2013. “Male Infanticide Leads to Social Monogamy in Primates.” Proceedings of the National Academy of Sciences 110 (33): 13328–32. http://doi.org/10.1073/pnas.1307903110.

Gavin, Michael C., Carlos A. Botero, Claire Bowern, Robert K. Colwell, Michael Dunn, Robert R. Dunn, Russell D. Gray, et al. 2013. “Toward a Mechanistic Understanding of Linguistic Diversity.” BioScience 63 (7): 524–35. http://doi.org/10.1525/bio.2013.63.7.6.

Vaughan, Timothy G, and Alexei J Drummond. 2013. “A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics.” Molecular Biology and Evolution 30 (6): 1480–93.http://doi.org/10.1093/molbev/mst057.

Pagel, Mark, Quentin D. Atkinson, Andreea S. Calude, and Andrew Meade. 2013. “Ultraconserved Words Point to Deep Language Ancestry across Eurasia.” Proceedings of the National Academy of Sciences 110 (21): 8471–76. http://doi.org/10.1073/pnas.1218726110.

Ross, Robert M., Simon J. Greenhill, and Quentin D. Atkinson. 2013. “Population Structure and Cultural Geography of a Folktale in Europe.” Proceedings of the Royal Society B: Biological Sciences 280 (1756): 20123065. http://doi.org/10.1098/rspb.2012.3065.

Atkinson, Quentin D. 2013. “The Descent of Words.” Proceedings of the National Academy of Sciences 110 (11): 4159–60.  http://doi.org/10.1073/pnas.1300397110.

Sanz, Crickette, Josep Call, and Christophe Boesch. 2013. Tool Use in Animals: Cognition and Ecology. Cambridge University Press.

Wu, Chieh-Hsi, Marc A Suchard, and Alexei J Drummond. 2013. “Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments.” Molecular Biology and Evolution 30 (3): 669–88.http://doi.org/10.1093/molbev/mss258.

Baele, Guy, Wai Lok Sibon Li, Alexei J. Drummond, Marc A. Suchard, and Philippe Lemey. 2013. “Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics.” Molecular Biology and Evolution 30 (2): 239–43. http://doi.org/10.1093/molbev/mss243.

Cheng, Yan, Stephane Guindon, Allen Rodrigo, and Seng Gee Lim. 2013. “Increased Viral Quasispecies Evolution in HBeAg Seroconverter Patients Treated with Oral Nucleoside Therapy.” Journal of Hepatology58 (2): 217–24. http://doi.org/10.1016/j.jhep.2012.09.017.

Taylor, Alex H., Rachael Miller, and Russell D. Gray. 2013. “Reply to Dymond et Al.: Clear Evidence of Habituation Counters Counterbalancing.” Proceedings of the National Academy of Sciences 110 (5): E337–E337. http://doi.org/10.1073/pnas.1219586110.

Taylor, Alex H., Rachael Miller, and Russell D. Gray. 2013. “Reply to Boogert et Al.: The Devil Is Unlikely to Be in Association or Distraction.” Proceedings of the National Academy of Sciences 110 (4): E274–E274.http://doi.org/10.1073/pnas.1220564110.

Stadler, Tanja, Denise Kühnert, Sebastian Bonhoeffer, and Alexei J Drummond. 2013. “Birth-Death Skyline Plot Reveals Temporal Changes of Epidemic Spread in HIV and Hepatitis C Virus (HCV).” Proceedings of the National Academy of Sciences of the United States of America 110 (1): 228–33.http://doi.org/10.1073/pnas.1207965110.

Guindon, Stéphane. 2013. “From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates along Lineages.” Systematic Biology 62 (1): 22–34.

Gray, Russell D., Simon J. Greenhill, and Quentin D. Atkinson. 2013. “Phylogenetic Models of Language Change: Three New Questions.” Https://mitpress.mit.edu/books/cultural-Evolution.https://digitalcollections.anu.edu.au/handle/1885/11537.

Bulbulia, J., A. W. Geertz, Q. D. Atkinson, E. Cohen, N. Evans, P. Francois, H. Gintis, et al. 2013. “The Cultural Evolution of Religion.”  404http://repository.ubn.ru.nl/handle/2066/122543.

Paterson, Adrian M., Graham P. Wallis, Martyn Kennedy, and Russell D. Gray. 2013. “Behavioural Evolution in Penguins Does Not Reflect Phylogeny.” Cladistics, n/a – n/a. http://doi.org/10.1111/cla.12040.

Bouckaert, Remco, Mónica V Alvarado-Mora, and João R Rebello Pinho. 2013. “Evolutionary Rates and HBV: Issues of Rate Estimation with Bayesian Molecular Methods.” Antiviral Therapy 18 (3 Pt B): 497–503.http://doi.org/10.3851/IMP2656.

Heled, Joseph, David Bryant, and Alexei J Drummond. 2013. “Simulating Gene Trees under the Multispecies Coalescent and Time-Dependent Migration.” BMC Evolutionary Biology 13: 44.http://doi.org/10.1186/1471-2148-13-44.

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