Model-based species delimitation workshop

With recently developed coalescent-based analytical methods, coupled with technological advances for collecting genomic datasets across many individuals per putative species, we no longer have to worry about missing recently diverged taxa because of limited power. However, these remarkable gains have conversely given rise to a new problem – the increased resolution of genomic data makes it possible to not only detect divergent species lineages, but also population structure within them – a fractal hierarchy of divergences. Misidentification of population structure as putative species is therefore emerging as a key issue. 

The workshop will address the conceptual issues surrounding model-based inference of species boundaries, as well as provide hands-on methodological training with programs for species delimitation.

Topics will include choice of models for delimiting species; effects of gene flow on species delimitation; impacts of geographic sample design; cryptic species; integrative approach for combining phenotypic and genetic data; and a new approach of speciation-based species delimitation models, that also provides a framework for gaining insights about the speciation process itself.

The structure of the workshop will balance lecture and discussion with computer modules that will provide experience with data simulation, Bayesian inference, and interpreting the results of delimitation analyses. The workshop will focus on the challenges of model-based species delimitation and emphasise recent advances in the field. Participants are encouraged to bring their own empirical data to receive advice and work on analyses. 


  • Lacey Knowles, Robert B. Payne Collegiate Professor and Curator, Museum of Zoology, University of Michigan
  • Jeet Sukumaran, Assistant Professor, San Diego State University
  • Arnaud Becheler, Postdoctoral Fellow, University of Michigan



Wednesday 12 June
Lec 1
History of species delimitation and ramifications of accurate species delimitation
Lec 2 
The Multispecies Coalescent
Lec 3 
Challenges with species delimitation
Prac 1 
Estimating species tree and testing delimitation hypotheses
  • BPP
  • *Beast
  • simulate data under the multispecies coalescent
Thursday 13 June
Lec 4 
Speciation-based species delimitation
Prac 2 
Analyze data using DELINEATE program


Friday 14 June
Lec 5 
Limitations with genetic-based delimitation
Prac 3 
Assessing effects of sampling and performance
  • Integrative phenotypic and genetic data: run ibpp

* Lecture and practical slides will be made available to participants in a Dropbox folder.

Preparing for the workshop

Participants should familiarise themselves with some of the conceptual background and approaches that will be presented in the workshop prior to attending. This includes the following background readings and installing the following software.




Registration and attending

Places are limited and registration will close 5 June 2019. The cost for the workshop is $50* and will include morning and afternoon teas. Lunch will not be provided, however the new Kambri precinct is nearby, or there is a small kitchen with a fridge near the workshop room if you would like to bring your own. Information on parking at ANU can be found here and the closest carparks to the venue are the Sullivans Creek carpark and Union Court carpark.

*ANU participants please note: We have been advised by ANU Finance that ANU staff and students should not pay for ANU activities (which includes CBA events) using an ANU Purchase Card - you will need to request a journal transfer. Please use the Promotional Code 'ANU' at checkout (this will allow you to register without a credit card) and then email CoS Finance (or your relevant college Finance team) and ask them to do a journal transfer for your registration costs ($50) to the CBA's account (S415100201) from your chosen account.