In this workshop, participants will gain a deeper understanding of the theoretical background and practical applications of both morphological and genomic data in modern evolutionary studies.

The workshop covers the collection of morphometric data using microCT scans and explores its relevance in macroevolutionary studies. Additionally, participants will learn how to integrate this data into molecular analysis to infer speciation times, morphological rates of evolution, and ancestral character reconstructions.

Led by two leading experts in the field, Emma Sherratt (The University of Adelaide) and Mario Dos Reis (Queen Mary University of London, CSIRO visitor), this workshop includes two seminars and two practical sessions.

This is an opportunity to enhance your knowledge and skills in generating and integrating morphological and genomic data in phylogenetic studies.

Target audience

Seminars: Open to the general public with interest in evolutionary biology.

Practical sessions: Students, researchers and general public interested in analyzing morphometric data and interested in timing species diversifications. Please register here. Registrations close 26 April.

Workshop participants are encouraged to attend both seminars before the practical sessions.

Practical sessions

Mon 1 May: A practical guide to collecting and analysing morphometric data

Emma Sherratt and Damien Esquerré

This activity will cover the whole process of a morphometric study, from data collection to analysis and visualization. Data collection will be discussed, with a mix of practical and video demonstrations, because several different software exist, and each is specific to different structures. The tpsDIG2 software will be used for practice. Data analysis will be practical learning using code scripts written in the R programming language, utilizing the geomorph and Morpho packages.

Aims: Theory of shape analysis and hands-on tutorial on collecting and analyzing morphometric data. Specific topics will include:

1. How to collect landmark coordinates
2. The theory of shape analysis
3. Statistical analyses for multivariate data
4. Visualisation of landmark shape changes
5. Intro to Phylogenetic comparative methods with multivariate data

The files for the morphometrics part are all available here to download before the workshop.

Tue 2 May: Species divergence time inference using morphometric and genomic data

Mario dos Reis and Hermes Escalona

This activity will cover the use of our mcmc3r and MCMCTree software packages for Bayesian inference of species divergence times using genomic and morphometric data.

Aims: Hands-on tutorial on Bayesian molecular clock dating with the software MCMCTree (PAML). Specific topics will include:

1. How to use mcmc3r to prepare morphometric data for MCMC analysis
2. Joint MCMC analysis of morphometric and genomic data to infer speciation timings using MCMCtree
3. Visualization of results in R
4. Inference of morphological and molecular evolutionary rates among lineages
5. Ancestral reconstruction of morphology across the phylogeny

Software & background knowledge

Attendees will need to bring their own laptops with the following software installed:

• R and RStudio, including the following R packages: geomorph, Morpho, mcmc3r, ape and their dependencies.
• PAML http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz (please set your PATH variable as explained here. Please DO NOT install PAML X).

Please install and test the software before the workshop so you have time to get in touch if you have any questions. During the workshop, time to help attendees with software installation issues will be very limited.

Attendees are expected to already know basic principles of phylogenetics (for example, they may have used a tree inference software package such as IQ-TREE or RAxML), know how to use R, and be familiar working with the command line. If you are a complete beginner, you can also download this quick guide. We'd also like to recommend the e-book: The Art of R Programming.

Schedule