July 14, 2025-July 18, 2025

Preliminary Programme

(subject to change)

Invited talks Lectures Tutorials Interactive
Sunday
2025/07/13
Monday
2025/07/14
Tuesday
2025/07/15
Wednesday
2025/07/16
Thursday
2025/07/17
Friday
2025/07/18
08:45 Arrival Welcome Housekeeping Housekeeping Housekeeping Housekeeping
09:00 Joëlle Barido-Sottani
Introduction to Bayesian phylogenetics
Simon Ho
TBA (link)
Sasha Gavryushkina
Birth-death models for estimating speciation and epidemiological parameters (link)
Xing Xu
Morphology-based phylogenetic analysis: Taxon sampling, character formulation and coding (link)
Arong Luo
Molecular data and their use in macroevolutionary studies (link)
09:15
09:30
09:45
10:00 Break Break Break Break Break
10:15 Chi Zhang
First steps in BEAST2 and setting priors
Walter Xie
LinguaPhylo and LPhyBEAST
Rachel Warnock
Divergence time estimation and total evidence dating
Joëlle Barido-Sottani
Structured models in phylodynamics
Sophie Seidel
Single-cell phylogenetics for developmental biology
10:30
10:45
11:00
11:15 Introduction to BEAST2
(tutorial)
Analysing Time-Stamped Data with LinguaPhylo and BEAST
(tutorial)
Dating species divergences with the fossilized birth-death process
(tutorial)
Modelling macro-evolution with BDMM-prime
(tutorial)
Estimating single-cell trees from lineage tracing data with TiDeTree
(tutorial)
11:30
11:45 Visualizing BEAST2 results in R
(tutorial)
Modelling pathogen spread with MASCOT
(tutorial)
12:00
12:15 Lunch
IVPP
Lunch
IVPP
Free afternoon Lunch
IVPP
Lunch
IVPP
12:30
12:45
13:00
13:15 Simon Ho
Molecular clock dating and modelling rate variation
Rong Zhang
Inference using continuous traits
Chi Zhang
Species tree inference and the multispecies coalescent
Rachel Warnock
Morphological models and total-evidence dating
13:30
13:45
14:00
14:15 Prior selection and clock calibration
(tutorial)
Modelling continuous trait evolution in BEAST2
(tutorial)
Estimating species trees using StarBEAST3
(tutorial)
Modelling morphological evolution in BEAST2
(tutorial)
14:30
14:45
15:00
15:15 Break Break Break Break
15:30 Chi Zhang
Tree priors
Joëlle Barido-Sottani
Troubleshooting & practical tips
Robert Yuan
Model selection & model averaging
Free Q&A session and wrap-up
(optional)
15:45
16:00
16:15
16:30 Inference of past population dynamics using skyline models
(BEAST2 tutorial ,LPhyBEAST tutorial)
BEAST2 initialization
(tutorial)
Clock model selection
(tutorial)
16:45
17:00 BEAST2 convergence
(tutorial)
Model selection with nested sampling
(tutorial)
Departure
17:15
17:30 BEAST Clinic & Tutorial catch-up
(optional)
BEAST Clinic & Tutorial catch-up
(optional)
BEAST Clinic & Tutorial catch-up
(optional)
17:45

Workshop committee

AffiliationOrganizing committeeSpeaker / InstructorTeaching AssistantLogistics
Joëlle Barido SottaniEcole Normale Supérieure
Yindi CaoChinese Academy of Sciences
Meijing ChangChinese Academy of Sciences
Minghao DuEcole Normale Supérieure
Louis du PlessisETH Zürich
Sasha GavryushkinaUniversity of Adelaide
Simon HoUniversity of Sydney
Eva (Yutong) LiUniversity of Auckland
Xue'er LiuChinese Academy of Sciences
Arong LuoChinese Academy of Sciences
Zhaohui PanChinese Academy of Sciences
Sophie SeidelUniversity of Washington
Yutai ShiChinese Academy of Sciences
Timothy VaughnETH Zürich
Rachel WarnockFriedrich-Alexander Universität
Walter (Dong) XieUniversity of Auckland
Jiabao XingFudan University
Xing XuChinese Academy of Sciences
Yuan XuUniversity of Auckland
Xiao YaoUniversity of Auckland
Robert (Haobo) YuanETH Zürich
Chi ZhangChinese Academy of Sciences
Rong ZhangDuke-NUS Medical School
Yinan ZhangChinese Academy of Sciences

Required Software

Please ensure the following software is installed prior to the start of the workshop.

  • BEAST 2: BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. We will be using this software to perform analyses on the data brought to the workshop. We will be using BEAST v2.7 for the workshop (download).
  • FigTree: FigTree is a graphical viewer of phylogenetic trees, specifically designed to display summarised and annotated trees produced by BEAST (download).
  • Tracer: Tracer is a program for analysing the trace files generated by Bayesian MCMC runs. It can be used to check mixing, ESS, parameter correlations, etc. (download).
  • BEAGLE (optional): BEAGLE is a high-performance library that can perform the core calculations in BEAST2 (and many other phylogenetics packages) much faster. BEAGLE isn’t necessary for the workshop, but it will speed up your analyses (download).
  • R: R is a free software environment that provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques, and is highly extensible (download).
  • RStudio (optional): RStudio provides a friendly front-end for R (download).

Venue and travel information

IVPP outside
IVPP inside

The workshop will take place at the Institute for Vertebrate Paleontology and Paleoanthropology (中国科学院古脊椎动物与古人类研究所) in Beijing, China. Participants are expected to book their own accommodation Beijing. The workshop organisers are not responsible for organising daily travel to and from the IVPP.

Travellers from many countries are able to visit China without needing to apply for a visa. Please see here and here for further details. The SMBE 2025 website has list of practical information and tips for travelling to Beijing this July.

Additional resources

There are a lot of great resources for brushing up or deepening your knowledge of the models used in BEAST2. This is a selection of resources that we consider especially useful, several of which are freely available on the internet. It is not expected that you’ve worked through any of these before the workshop!

Phylogenetics and phylodynamics

Statistics and Bayesian inference

Questions

Please contact the organizing committee at ttb.beijing@ivpp.ac.cn.


Sponsors of the Beijing workshop