• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Live Online Course – 1st Edition

Bayesian phylogenetic inference with BEAST2

July 10th-21st, 2023

Live sessions will be recorded

Bayesian phylogenetic inference is a powerful tool for reconstructing phylogenies while accounting for complex evolutionary dynamics. It allows prior knowledge to be integrated into the inference, and also provides a detailed picture of the uncertainty present in the dataset. However, the number and complexity of the available models and options can be daunting for users, and can make it difficult to apply inference tools effectively in practice.
In this workshop, participants will learn the theoretical concepts underlying the different models involved in Bayesian phylogenetic inference, and get hands-on experience using these models in BEAST2. Particular attention will be given to more complex tree models, such as the fossilized birth-death model used to integrate past information into phylogenies, as well as rate-heterogeneous models which allow for variations in evolutionary dynamics across clades. Finally, the course will give practical information on setting up and troubleshooting analyses in BEAST2.

Participants are encouraged to bring their own dataset, as the schedule will include time for applying the concepts discussed in the workshop to their own research questions.

Participants should be familiar with Bayesian phylogenetic inference or watch the Phyloseminar introduction series by Paul Lewis (about 4h in total) before the course:
Phyloseminar #76: Primer part 1
Phyloseminar #77: Primer part 2
Phyloseminar #78: Primer part 3a
Phyloseminar #79: Primer part 3b

  • General introductions and practical information
    • Lecture on Bayesian inference and the BEAST2 software
    • Tutorial introduction to BEAST2
    • Tutorial on substitution model averaging
  • Lecture on tree priors in BEAST2
    • Tutorial on tree priors with time-dependent variations
    • Lecture and tutorial on priors and how to set them
  • Lecture and tutorial on the fossilized birth-death process
    • Lecture and tutorial on multi-species coalescent models (StarBEAST)
  • Lecture on rate-heterogeneous birth-death models
    • Tutorial on 3 different heterogeneous models, BDMM, MSBD and ClaDS
  • Lecture and tutorial on troubleshooting and practical tips
    • Final Q&A session
    • Free time for additional tutorials or setting up an analysis with the participants’ own dataset

Graduate or postgraduate degree in Biology (including palaeontologists regardless of degree).

Participants should be familiar with Bayesian phylogenetic inference or watch the Phyloseminar introduction series by Paul Lewis (about 4h in total) before the course:
Phyloseminar #76: Primer part 1
Phyloseminar #77: Primer part 2
Phyloseminar #78: Primer part 3a
Phyloseminar #79: Primer part 3b

A good internet connection is required. The use of webcam and headphones is strongly recommended.

Joëlle Barido-Sottani instructor for Transmitting Science

Dr. Joëlle Barido-Sottani

Ecole Normale Supérieure de Paris

Bethany Allen instructor for Transmitting Science

Dr. Bethany Allen

ETH Zurich

Dates & Schedule

July 10th-21st, 2023

13:00-16:00 & 17:00- 20:00 (Madrid time zone)

Online live sessions on the 10th, 12th, 17th, 20th, and 21st of July, 13:00-16:00 and 17:00-20:00 (Madrid time zone).

Total course hours: 35

30 hours of online live lessons, plus 5 of participants working by their own.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.



This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom and tasks to be completed in between live sessions on the Slack platform.

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.


Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science

Fees & Discounts

  • Course Fee
  • Early bird (until May 31st, 2023):
  • 546 €
    (436.8 € for Ambassador Institutions)
  • Regular (after May 31st, 2023):
  • 665 €
    (532 € for Ambassador Institutions)
  • Prices include VAT
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.


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