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2018


Stadler, Tanja, Alexandra Gavryushkina, Rachel Warnock, Alexei J. Drummond, and Tracy A. Heath. 2018. "The fossilized birth-death model for the analysis of stratigraphic range data under different speciation concepts.". Journal of Theoretical Biology, 447:41-55. https://doi.org/10.1016/j.jtbi.2018.03.005

Zhang, Chi, Huw A. Ogilvie, Alexei J. Drummond, and Tanja Stadler. 2018. "Bayesian inference of species networks from multilocus sequence data." Molecular Biology and Evolution, Volume 35, Issue 2, Pages 504-517, https://doi.org/10.1093/molbev/msx307

Barido-Sottani, Joëlle, Veronika Bošková, Louis Du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F. Müller et al. "Taming the BEAST-A Community Teaching Material Resource for BEAST 2." 2018. Systematic biology Systematic Biology, Volume 67, Issue 1, Pages 170-174, https://doi.org/10.1093/sysbio/syx060

Ogilvie, Huw A., Timothy G. Vaughan, Nicholas J. Matzke, Graham J. Slater, Tanja Stadler, David Welch, and Alexei J. Drummond. 2018. "Infering species trees using integrative models of species evolution". bioRxiv doi: http://dx.doi.org/10.1101/242875

Duchene, Sebastian, Remco Bouckaert, David A. Duchene, Tanja Stadler, and Alexei J. Drummond. 2018. "Phylodynamic model adequacy using posterior predictive simulations". bioRxiv doi: http://dx.doi.org/10,1101/255596

Toth, C.A., A.W. Santure, G.I. Holwell, D.E. Pattemore and S. Parsons. 2018. "Courtship behaviour and display-site sharing appears conditional on body size in a lekking bat". Animal Behaviour 136:13-19. https://doi.org.10.1016/j.anbehav.2017.12.007

 

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2017


Stapley, J., Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja. 2017. "Variation in recombination frequency and districution across eukaryotes: patterns and processes". Philosophical Transactions of the Royal Society B doi: 10.1098/rstb.2016.0455

Stapley, J., Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja. 2017. "Recombination: the good, the bad and the variable". Philosophical Transactions of the Royal Society B doi: 10.1098/rstb.2017.0279

Wu Chen, Victoria G. Twort, Ross N. Crowhurst, Richard D. Newcomb and Thomas R. Buckley. 2017. "Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction". BMC Genomics 8(1): 884  https://doi.org/10.1186/s12864-017-4245-x

Wu Chen, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens and Thomas R. Buckley. 2017. "Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution". BMC Genomics 18(1): 795  https://doi.org/10.1186/s12864-017-4197-1

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

Carter Jr, Charles W. and Peter R. Wills. 2017. "Interdependence, reflexivity, fidelity, impedance matching, and the evolution of genetic coding". Molecular Biology and Evolution.  https://doi.org/10.1093/molbev/msx265

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 114(14): E8822-E8829 doi: 10.1073/pnas.1700388114

Maurits, Luke, Robert Forkel, Gereon A. Kaiping and Quentin D. Atkinson. 2017. "BEASTling: A software tool for linguistic phylogenetics using BEAST 2". PLoS One 12(8) https://doi.org/10.1371/journal.pone.0180908

Twort, Victoria G., Alice B. Dennis, Duckchul Park, Kathryn F. Lomas, Richard D. Newcomb and Thomas R. Buckley. 2017. "Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina)". PLoS ONE https://doi.org/10.1371/journal.pone.0188147

Gray, Russell D. and Joseph Watts. 2017 "Cultural macroevoluation matters". Proceedings of the National Academy of Sciences of the United States of America 114(30): 7846-7852 doi:10.1073/pnas.1620746114 

Dearden, Peter K., Neil J Gemmell, Ocean R. Mercier, Philip J. Lester, Maxwell J. Scott, Richard D. Newcomb, Thomas R. Buckley, Jeanne M. E. Jacobs, Stephen G Goldson and David R. Penman. 2017. "The potential for the use of gene drives for pest control in New Zealand: a perspective". Journal of the Royal Society of New Zealand https://doi.org/10.1080/03036758.2017.1385030

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

Painting, Christina J., Shelley Myers, Gregory I. Holwell and Thomas R. Buckley. 2017. "Phylogeography of the New Zealand giraffe weevil Lasiorhynchus barbicornis (Coleoptera: Brentidae): A comparison of biogeographic boundaries". Biological Journal of the Linnean Society 122(1): 13-28   https://doi.org/10.1093/biolinnean/blx051

Holdaway, Robert J., Jamie R. Wood, Ian A. Dickie, Kate H. Orwin, Peter J. Bellingham, Sarah J. Richardson, Phil O’B Lyver, Puke Timoti and Thomas R. Buckley. 2017. "Using DNA metabarcoding to assess New Zealand’s terrestrial biodiversity". New Zealand Journal of Ecology 41(2): 251-262 

Myers, Shelley S., Gregory I. Holwell and Thomas R. Buckley. 2017. "Genetic and morphometric data demonstrate alternative consequences of secondary contact in Clitarchus stick insects". Journal of Biogeography doi: 10.1111/jbi.13004

Carlos A. Botero, Luke J. Harmon and Quentin Atkinson. 2017. "The promise and limits of eco-evolutionary studies of human culture". Religion, Brain & Behavior 7(2): 153-155 https://doi.org/10.1080/2153599X.2015.1132249

Bordewich Magnus, Simone Linz and Charles Semple. "Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks". Journal of Theoretical Biology 423: 1-12 https://doi.org/10.1016/j.jtbi.2017.03.032

Vaughan, Timothy G., David Welch, Alexei J. Drummond, Patrick J. Biggs, Tessy George, Nigel P. French. 2017. “Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.” Genetics 205(2): 857–70. https://doi.org/10.1534/genetics.116.193425

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

Atkinson, Quentin D. 2017. "Religion and expanding the cooperative sphere in Kastom and Christian villages on Tanna, Vanuatu". Religion, Brain & Behavior. https://doi.org/10.1080/2153599X.2016.1267028

Benjamin Grant Purzycki, Joseph Henrich, Coren Apicella, Quentin D Atkinson, Adam Baimel, Emma Cohen, Rita Anne McNamara, Aiyana K Willard, Dimitris Xygalatas and Ara Norenzayan. 2017. "The evolution of religion and morality: a synthesis of ethnographic and experimental evidence from eight societies". Religion, Brain & Behavior https://doi.org/10.1080/2153599X.2016.1267027

Bryant Christopher, Mareike Fischer, Simone Linz and Charles Semple. 2017. "On the quirks of maximum parsimony and likelihood on phylogenetic networks". Journal of Theoretical Biology 417: 100-108 https://doi.org/10.1016/j.jtbi.2017.01.013

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)

White, Daniel J., Corinne Watts, Julia Allwood, Diana Prada, Ian Stringer, Danny Thornburrow and Thomas R. Buckley. 2017. "Population history and genetic bottlenecks in translocated Cook Strait giant weta, Deinacrida rugosa: recommendations for future conservation management".Conservation Genetics 18(2) 411-422 https://doi.org/10.1007/s10592-016-0916-4

Gavryushkina, Alexandra, Tracy A. Heath, Daniel T. Ksepka, Tanja Stadler, David Welch, Alexei J. Drummond. 2017. “Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.” Systematic Biology 66(1): 57–73.  https://doi.org/10.1093/sysbio/syw060

 

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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