Gerhard Jäger
Slides
- Foundations; distance-based inference
- Estimating distances, estimating trees from distances
- Maximum Parsimony
- Maximum Likelihood
- Bayesian Inference (slides by Fred Ronquist)
Additional Reading
- Overview material
- Jäger, Gerhard & Johann-Mattis List, 2016, Statistical and computational elaborations of the classical comparative method, manuscript, Tübingen and Paris.
- List, Johann-Mattis, 2014, Sequence Comparison in Historical Linguistics, Dissertations in Language and Cognition, 1 . Düsseldorf University Press, Düsseldorf.
- Nunn, Charles L., 2011, The Comparative Approach in Evolutionary Anthropology and Biology, The University of Chicago Press.
- Atkinson, Quentin D. & Russell D. Gray, 2005, Curious Parallels and Curious Connections—Phylogenetic Thinking in Biology and Historical Linguistics, Systematic Biology 54(4):513–526.
- Background reading in theoretical bioinformatics
- Chen, Ming-Hui, Lynn Kuo & Paul O. Lewis, 2014, Bayesian Phylogenetics. Methods, Algorithms and Applications. Abingdon.
- Durbin, Richard, Sean R. Eddy, Anders Krogh & Graeme Mitchison, 1998, Biological Sequence Analysis. Cambridge.
- Warren Ewens & Gregory Grant, 2005, Statistical Methods in Bioinformatics: An Introduction. Springer.
- Research highlights:
- Bouckaert, Remco, Philippe Lemey, Michael Dunn, Simon J. Greenhill, Alexander V. Alekseyenko, Alexei J. Drummond, Russell D. Gray, Marc A. Suchard & Quentin D. Atkinson, 2012, Mapping the Origins and Expansion of the Indo-European Language Family, Science 337(6097), 957-960.
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Chang, Will, Chundra Cathcart, David Hall, & Andrew Garrett, 2015, Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis, Language 9(1), 194-244.
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Pagel, Mark, Quentin D. Atkinson, Andreea S. Calude, & Andrew Meade, 2013, Ultraconserved words point to deep language ancestry across Eurasia. Proceedings of the National Academy of Sciences 110(21), 8471-8476.
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Pagel, Mark, Quentin D. Atkinson, & Andrew Meade, 2007, Frequency of word-use predicts rates of lexical evolution throughout Indo-European history. Nature 449.7163, 717-720.
- Wichmann, Søren, André Müller & Velupillai, Viveka, 2010, Homelands of the world’s language families: A quantitative approach, Diachronica 27(2), 247-276.
- Some of my own work on the topic:
- Jäger, Gerhard, 2015, Support for linguistic macrofamilies from weighted sequence alignment, Proceedings of the National Academy of Science, 112(41), 12752–12757.
- Jäger, Gerhard, 2013, Phylogenetic inference from word lists using weighted alignment with empirically determined weights, Language Dynamics and Change 3(2), 245-291.
- Jäger, Gerhard & Søren Wichmann, 2016, Inferring the world tree of languages from word lists, in Roberts S.G., Cuskley C., McCrohon L., Barceló-Coblijn L. , Feher O. & Verhoef T., eds., The Evolution of Language: Proceedings of the 11th International Conference (EVOLANG11).
Resources
- Recommended software This link is password-protected; I will give you the credentials in class.
- Data and code snippets for exercises
- Data sources: