Introduction

References cited

Boyd, R., M. Borgerhoff-Mulder, W. Durham, and P. Richerson. Are Cultural Phylogenies Possible? In Human by Nature, Between Biology and the Social Sciences, edited by P. Weingart, P. Richerson, S.D. Mithcell, and S. Maasen, 355–86. Mahwah, NJ: Lawrence Erlbaum Assoicates, 1997. [Link]

Foster, Jacob G. Culture and Computation: Steps to a Probably Approximately Correct Theory of Culture. Poetics 68 (1 June 2018): 144–54. [Link]

Gjesfjeld, Erik, Daniele Silvestro, Jonathan Chang, Bernard Koch, Jacob G. Foster, and Michael E. Alfaro. A Quantitative Workflow for Modeling Diversification in Material Culture. PLOS ONE 15, no. 2 (6 February 2020): e0227579. [Link]

Gray, Russell D., Alexei J. Drummond, and Simon J. Greenhill. Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement. Science 323, no. 5913 (2009): 479–483. [Link]

Koch, Bernard, Daniele Silvestro, and Jacob G. Foster. n.d. The Evolutionary Dynamics of Cultural Change (as Told Through the Birth and Brutal, Blackened Death of Metal Music). SocArXiv. osf.io/preprints/socarxiv/659bt. [Link]

Mesoudi, Alex. Pursuing Darwin's Curious Parallel: Prospects for a Science of Cultural Evolution. Proceedings of the National Academy of Sciences 114, no. 30 (2017): 7853–7860. [Link]

Mesoudi, Alex, Andrew Whiten, and Kevin N. Laland. Towards a Unified Science of Cultural Evolution. Behavioral and Brain Sciences 29, no. 4 (August 2006): 329–47. [Link]

Raup, David M., Stephen Jay Gould, Thomas J. M. Schopf, and Daniel S. Simberloff. Stochastic Models of Phylogeny and the Evolution of Diversity. The Journal of Geology 81, no. 5 (1 September 1973): 525–42. [Link]

Silvestro, Daniele, Nicolas Salamin, Alexandre Antonelli, and Xavier Meyer. Improved Estimation of Macroevolutionary Rates from Fossil Data Using a Bayesian Framework. Paleobiology 45, no. 4 (2019): 546–70. [Link]

Sperber, Dan. Explaining Culture: A Naturalistic Approach. Oxford: Blackwell, 1996.


Tutorial 1
Diversity and Diversification

References cited

Abernathy, William. The Productivity Dilemma: Roadblock to Innovation in the Automobile Industry. Baltimore ; London: Johns Hopkins University Press, 1978.

Foster, Jacob G. ‘Culture and Computation: Steps to a Probably Approximately Correct Theory of Culture’. Poetics 68 (1 June 2018): 144–54. [Link]

Gjesfjeld, Erik, Daniele Silvestro, Jonathan Chang, Bernard Koch, Jacob G. Foster, and Michael E. Alfaro. ‘A Quantitative Workflow for Modeling Diversification in Material Culture’. PLOS ONE 15, no. 2 (6 February 2020): e0227579. [Link]

Leonard, Robert D, and George T Jones, eds. Quantifying Diversity in Archaeology. Cambridge University Press Cambridge, 1989.

Stirling, Andy. ‘A General Framework for Analysing Diversity in Science, Technology and Society’. Journal of the Royal Society Interface 4, no. 15 (2007): 707–719. [Link]


Tutorial 2
Introduction to Birth-Death Processes and LiteRate

References cited

Crawford, Forrest W., Vladimir N. Minin, and Marc A. Suchard. ‘Estimation for General Birth-Death Processes’. Journal of the American Statistical Association 109, no. 506 (3 April 2014): 730–47. [Link]

Green, Peter J. ‘Reversible Jump Markov Chain Monte Carlo Computation and Bayesian Model Determination’. Biometrika 82, no. 4 (1 December 1995): 711–32. [Link]

Keiding, Niels. ‘Maximum Likelihood Estimation in the Birth-and-Death Process’. The Annals of Statistics 3, no. 2 (March 1975): 363–72. [Link]

Kendall, David G. ‘On the Generalized “Birth-and-Death” Process’. The Annals of Mathematical Statistics 19, no. 1 (March 1948): 1–15. [Link]

Novozhilov, Artem S., Georgy P. Karev, and Eugene V. Koonin. ‘Biological Applications of the Theory of Birth-and-Death Processes’. Briefings in Bioinformatics 7, no. 1 (1 March 2006): 70–85. [Link]

Silvestro, Daniele, Nicolas Salamin, Alexandre Antonelli, and Xavier Meyer. ‘Improved Estimation of Macroevolutionary Rates from Fossil Data Using a Bayesian Framework’. Paleobiology 45, no. 4 (2019): 546–70. [Link]

Silvestro, Daniele, Nicolas Salamin, and Jan Schnitzler. ‘PyRate: A New Program to Estimate Speciation and Extinction Rates from Incomplete Fossil Data’. Methods in Ecology and Evolution 5, no. 10 (2014): 1126–1131. [Link]

Silvestro, Daniele, Jan Schnitzler, Lee Hsiang Liow, Alexandre Antonelli, and Nicolas Salamin. ‘Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data’. Systematic Biology 63, no. 3 (2014): 349–367. [Link]


Tutorial 3
Interpreting LiteRate Results

References cited

Kahn-Harris, Keith. Extreme Metal: Music and Culture on the Edge. Berg Publishers, Oxford 2006.

Kass, Robert E., and Adrian E. Raftery. 'Bayes Factors’. Journal of the American Statistical Association 90, no. 430 (1995): 773–795.

Silvestro, Daniele, Nicolas Salamin, Alexandre Antonelli, and Xavier Meyer. ‘Improved Estimation of Macroevolutionary Rates from Fossil Data Using a Bayesian Framework’. Paleobiology 45, no. 4 (2019): 546–70. [Link]

METAL PAPER


Tutorial 4
Modeling Evolutionary Mechanisms in Diversification Rates

References cited

Bourdieu, Pierre. The Rules of Art: Genesis and Structure of the Literary Field. Stanford University Press, Palo Alto 1996.

Gjesfjeld, Erik, Daniele Silvestro, Jonathan Chang, Bernard Koch, Jacob G. Foster, and Michael E. Alfaro. ‘A Quantitative Workflow for Modeling Diversification in Material Culture’. PLOS ONE 15, no. 2 (6 February 2020): e0227579. [Link]

Kahn-Harris, Keith. Extreme Metal: Music and Culture on the Edge. Berg Publishers, Oxford 2006.


Tutorial 5
Cultural Phylogenies

References cited

Boyd, R., and P.J. Richerson. Culture and the Evolutionary Process. Chicago: University of Chicago Press, 1985.

Dunn, Michael. ‘Language Phylogenies’. In The Routledge Handbook of Historical Linguistics, edited by Claire Bowern and Bethwyn Evans, 208–29. London: Routledge, 2015. [Link]

Gjesfjeld, Erik, and Peter Jordan. ‘Contributions of Bayesian Phylogenetics to Exploring Patterns of Macroevolution in Archaeological Data’. In Handbook of Evolutionary Research in Archaeology, edited by Anna Marie Prentiss, 161–82. Cham: Springer International Publishing, 2019. [Link]

Gray, Russell D., Alexei J. Drummond, and Simon J. Greenhill. ‘Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement’. Science 323, no. 5913 (2009): 479–483. [Link]

Gray, Russell D., and Fiona M. Jordan. ‘Language Trees Support the Express-Train Sequence of Austronesian Expansion’. Nature 405, no. 6790 (2000): 1052–1055. [Link]

Greenhill, Simon J., and Russell D. Gray. ‘Austronesian Language Phylogenies: Myths and Misconceptions about Bayesian Computational Methods’. In Austronesian Historical Linguistics and Culture History: A Festschrift for Robert Blust., edited by A. Adelaar and A. Pawley, 1–23. Pacific Linguistics, 2009.

Harmon, Luke. Phylogenetic Comparative Methods · Learning from Trees, 2018. [Link]

Lewis, Paul O. ‘A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data’. Systematic Biology 50, no. 6 (2001): 913–925. [Link]

Lipo, C., M. Collard, M. O’Brien, and S. Shennan, eds. Mapping Our Ancestors: Phylogenetic Approaches in Anthropology and Prehistory. New Brunswick, NJ: Aldine Transactions, 2006. [Link]

Mace, Ruth, Mark Pagel, John R. Bowen, Keith F. Otterbein, Mark Ridley, Thomas Schweizer, and Eckart Voland. ‘The Comparative Method in Anthropology [and Comments and Reply]’. Current Anthropology 35, no. 5 (1 December 1994): 549–64. [Link]

Mulder, Monique Borgerhoff, Charles L. Nunn, and Mary C. Towner. ‘Cultural Macroevolution and the Transmission of Traits’. Evolutionary Anthropology: Issues, News, and Reviews 15, no. 2 (2006): 52–64. [Link]

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O’Brien, Michael J., R. Lee Lyman, Youssef Saab, Elias Saab, John Darwent, and Daniel S. Glover. ‘Two Issues in Archaeological Phylogenetics: Taxon Construction and Outgroup Selection’. Journal of Theoretical Biology 215, no. 2 (2002): 133–150. [Link]

Pagel, Mark. ‘Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters’. Proc. R. Soc. Lond. B 255 (1994): 37–45. [Link]

Raup, David M., Stephen Jay Gould, Thomas J. M. Schopf, and Daniel S. Simberloff. ‘Stochastic Models of Phylogeny and the Evolution of Diversity’. The Journal of Geology 81, no. 5 (1 September 1973): 525–42. [Link]

Tehrani, J., and M. Collard. ‘Investigating Cultural Evolution through Biological Phylogenetic Analyses of Turkmen Textiles’. Journal of Anthropological Archaeology 21, no. 4 (2000): 443–63. [Link]

Tëmkin, Ilya, and Niles Eldredge. ‘Phylogenetics and Material Cultural Evolution’. Current Anthropology 48, no. 1 (1 February 2007): 146–54. [Link]

Watts, Joseph, Oliver Sheehan, Quentin D. Atkinson, Joseph Bulbulia, and Russell D. Gray. ‘Ritual Human Sacrifice Promoted and Sustained the Evolution of Stratified Societies’. Nature 532, no. 7598 (April 2016): 228–31. [Link]

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