• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

Live Online Course – 2nd Edition

Bayesian phylogenetic inference with BEAST2

March 11th-22nd, 2024

Live sessions will be recorded

REGISTRATION IS CLOSED

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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

The course programme includes lectures and tutorials on the following topics:

  • General introductions and practical information
  • Bayesian inference and the BEAST2 software – Introduction to BEAST2
  • Priors and how to set them
  • Tree priors (birth-death and coalescent processes)
  • Fossilized birth-death process
  • Multi-species coalescent models (StarBEAST)
  • Rate-heterogeneous birth-death models
  • Model selection
  • Troubleshooting and practical tipsFinal 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
France

Bethany Allen instructor for Transmitting Science

Dr. Bethany Allen

ETH Zurich
Switzerland

Dates & Schedule

March 11th-22nd, 2024

Online live sessions on the 11th, 13th, 15th, 18th, 20th and 22nd of March.

15:00-18:30 (Madrid time zone)

Total course hours: 35

21 hours of online live lessons, plus 14 hours of participants working independently.

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.

Language

English

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

Places are limited to 20 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
Greece

Fees & Discounts

  • Course Fee
  • Early bird (until January 31st, 2024):
  • 546 €
    (436.8 € for Ambassador Institutions)
  • Regular (after January 31st, 2024):
  • 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.