Phylogenetic Methods in Historical Linguistics
Course materials for the 11th Naxos Summer School on Diachronic Linguistics, 2026.
This course introduces phylogenetic computational methods and their application in historical linguistics, combining theoretical foundations, case studies, and hands-on applications across five lectures.
What the course is for
Quantitative phylogenetics now shapes some of the most visible claims in historical linguistics, but its methods sections are where most linguists stop reading.
The aim of this course is to change that. By the end of the week you should be able to open a paper such as Heggarty et al. (2023) on the origin of Indo-European, or Blasi et al. (2019) on the emergence of labiodental sounds, turn to the methods section, and follow the gist of it without being intimidated.
That does not mean reproducing every derivation. It means knowing what a rate matrix, a posterior distribution, a clock model and a Bayes factor are; knowing which questions these methods can and cannot answer; and knowing where the assumptions are buried, so that you can push back on them. The goal is a critical reader, not necessarily a practitioner. The three hands-on labs are there so that the machinery stops being a black box.
The five lectures
The course meets daily from Monday 20 to Friday 24 July, 14:10–14:55. Slides go up on the morning of each lecture.
- Introduction. The comparative method and the phylogenetic turn · slides
- Data and sequence comparison. Swadesh lists, Lexibank, cognate detection, PMI alignment · slides
- Probabilistic models of language change. CTMCs, substitution models, rate variation · slides
- Bayesian phylogenetic inference. MCMC, MrBayes, priors, convergence, divergence dating · slides
- Reading two methods sections. Heggarty et al. (2023) on the Indo-European homeland, Blasi et al. (2019) on labiodentals · slides
The labs
Labs 1 and 2 belong to the course: each is demonstrated at the end of its lecture and is then yours to work through. Both run in your browser, so there is nothing to install.
- Lab 1: Cognate Detection with LingPy, at the end of Lecture 2
- Lab 2: Bayesian Phylogenetics with MrBayes, at the end of Lecture 4
There is also a third lab, covering material that did not make it into the course in the end. It is not part of the programme and nothing depends on it, but it stays online for anyone curious: Lab 3: Beyond Cognacy, building a tree without a single cognate judgement.