Course abstracts - Bromham

Course: Reconstructing the past: Phylogenies and dates from DNA and languages

Instructor: Lindell Bromham (Australian National University), Simon Greenhill (Max Planck Institute for the Science of Human History)

Description:  Phylogenies are making an increasingly large impact in linguistics, with genetic phylogenies providing a timescale for human migration and settlement, and linguistic phylogenies tracking the diversification of languages. How are these phylogenies constructed? What assumptions do they rely on? Can we accurately date events in human history from genes or languages? Can we trust phylogenies to give us the true history? This course will provide a general background in phylogeny estimation, with an aim of giving you the intellectual tools to consider and evaluate the contribution of phylogenies to our understanding of language evolution.  The workshop will be discussion based, focussing on the ideas and assumptions surrounding historical inference. There will be a chance to put what you have learned into practise in the final class which will include a practical introduction to one of the most common software packages for inferring phylogenies.

Topics

Classes 1 & 2: Molecular phylogenetics (LB): When we conduct a phylogenetic analysis, we are using assumptions about processes of change to come up with a plausible story for how the world we observe today came to be. As methods get more sophisticated we must make increasingly complex assumptions about the way that genomes or languages evolve. In particular, dates estimated from phylogenies are strongly shaped by the assumptions made. We will examine the challenges in inferring phylogenies and dates, but also how useful phylogenies can be in examining the patterns and processes of evolution, whether for species or for languages.

Classes 3 & 4: Language phylogenies (SG): We will review the troubled history of quantitative and computational methods in historical linguistics, and describe some of the long-standing issues with these methods. We will then move on to discuss the theoretical background of Bayesian Phylogenetic methods and to demonstrate how many of the shortcomings are solved by this set of approaches. Finally, students will be taken through a hands-on tutorial on how to run BEAST2, one of the most advanced phylogenetic software packages available, and learn how to analyse their own data.

Background reading:

  • Greenhill, Simon J. (2015) "Evolution and Language: Phylogenetic Analyses." International Encyclopedia of the Social & Behavioral Sciences (Second Edition), 370-377. Elsevier.
  • Bromham Lindell (2015) An Introduction to Molecular Evolution and Phylogenetics. Oxford University Press.
  • Australian Government
  • The University of Queensland
  • Australian National University
  • The University of Melbourne
  • Western Sydney University