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) |
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| 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 |
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| 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) |
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| 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) |
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| 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) |
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| 17:45 |
Workshop committee
| Affiliation | Organizing committee | Speaker / Instructor | Teaching Assistant | Logistics | |
| Joëlle Barido Sottani | Ecole Normale Supérieure | ||||
| Yindi Cao | Chinese Academy of Sciences | ||||
| Meijing Chang | Chinese Academy of Sciences | ||||
| Minghao Du | Ecole Normale Supérieure | ||||
| Louis du Plessis | ETH Zürich | ||||
| Sasha Gavryushkina | University of Adelaide | ||||
| Simon Ho | University of Sydney | ||||
| Eva (Yutong) Li | University of Auckland | ||||
| Xue'er Liu | Chinese Academy of Sciences | ||||
| Arong Luo | Chinese Academy of Sciences | ||||
| Zhaohui Pan | Chinese Academy of Sciences | ||||
| Sophie Seidel | University of Washington | ||||
| Yutai Shi | Chinese Academy of Sciences | ||||
| Timothy Vaughn | ETH Zürich | ||||
| Rachel Warnock | Friedrich-Alexander Universität | ||||
| Walter (Dong) Xie | University of Auckland | ||||
| Jiabao Xing | Fudan University | ||||
| Xing Xu | Chinese Academy of Sciences | ||||
| Yuan Xu | University of Auckland | ||||
| Xiao Yao | University of Auckland | ||||
| Robert (Haobo) Yuan | ETH Zürich | ||||
| Chi Zhang | Chinese Academy of Sciences | ||||
| Rong Zhang | Duke-NUS Medical School | ||||
| Yinan Zhang | Chinese 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
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.
- Location in Google maps
- Location in Baidu maps
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
- Paul Lewis’ Phyloseminar Phylogenetics 101 primer is an excellent introduction to the topic (4 hours of content):
- Decoding Genomes: From Sequences to Phylodynamics, Tanja Stadler, Carsten Magnus, Timothy Vaughan, Joëlle Barido-Sottani, Veronika Bošková, Jana S. Huisman, Jūlija Pečerska (PDF available free of charge from the website)
- Bayesian Evolutionary Analysis with BEAST, Alexei J. Drummond, Remco R. Bouckaert
- Molecular Evolution: A Statistical Approach, Ziheng Yang
- Inferring Phylogenies, Joseph Felsenstein
Statistics and Bayesian inference
- Information Theory, Inference and Learning Algorithms, David MacKay (PDF available free of charge from the website)
- Ziheng Yang’s statistics primer gives a short overview of the topic (excluding Bayesian inference).
- Richard McElreath’s Statistical Rethinking course uses Bayesian inference to teach data analysis.
Questions
Please contact the organizing committee at ttb.beijing@ivpp.ac.cn.
