ABCday: Approximate Bayesian Computation in one day (and a half)

- POSTPONED -
 

The technological revolution that the discipline of genetics has been going through for the past 10 years now allows to obtain information on the genome on a large scale. A direct application of these developments is the possibility of studying the evolution of the diversity of life for organisms other than historical models (mouse, Drosophila, nematode, yeast, human).

This revolution comes at a time when evolutionary biology has also accumulated a wealth of theoretical expectations to address questions related (1) to diversity within species (why are some species more polymorphic than others? what is the role of demography? the role of life history traits?); or (2) related to the evolution of reproductive barriers between species (are two given species genetically connected? partially connected? Or completely isolated?).

The objective of this one-day workshop is to teach to participants how from molecular data can be compared across alternative scenarios of evolution in biology using:

  1. A review of the theory linking molecular data and inferential statistics. What are the signatures that demographic events, i.e. population decline/expansion, genetic exchanges by migration, let in current genomes?
  2. A review of existing methods to study the demographic history of species from sequencing data. The focus will be on their methodological differences.
  3. Practical work to learn how to manipulate recent tools to study demographic history from high throughput data, taking into account the effects of linked selection. The focus will be on issues related to the theme of speciation to test whether two different lineages are genetically connected by gene flow and to detect which regions of their genome are linked to species barriers.

The practical component of the workshop will provide an opportunity to show how, in a single day, it is possible to carry out complete analyses from sequencing data, leading to probabilities of the scenarios studied. Importantly, it will be taught how to procede to a statistical evaluation of the power of the analysis. While the current methods will be reviewed, the participants will mainly work with a powerful and robust method: ABC for Approximate Bayesian Computation. The practical work can be carried out directly on the data sets of the participants that address the questions mentioned above, or on a large whole genome sequencing data set already available for the Latin American butterfly Heliconius.

Target audience

The ABCday workshop will be of primary interest to students and researchers with questions relating to statistical inferences of historical events from genomic data. Participants will need familiarity with the command line interface and to bring their own laptops with software pre-installed.

Program

Thursday March 10th

9am-12pm: What is ABC? (ABC easy as 1,2,3)

  1. Why comparing models in evolutionary biology?
  2. Follow an example of Bayesian inferences: let’s roll some dice.
  3. Evolution of species is a bit more complicated than dice, but ABC is easy. 
  4. ABC with dices

1pm-4pm: The ABC approach to study demographic history - Simulating data

  1. What is demographic history? Coalescence theory.
  2. What ABC simulators are available? And limitations and advantages of each.
  3. Simulating complex evolutionary scenarios.
  4. What summary statistics are useful?

Friday March 11th

9am-2:30pm: Statistical comparison between simulations and real data

The aim of this last half-day is to learn how to use the simulations produced to compare models and estimate the parameters of a given model. It will include a break at 11am for Camille's seminar and return for the final hour at 1:30pm after lunch.

  1. Classify simulated models according to their ability to easily produce the   observed data or not
  2. How to classify alternative models to compare them?        
  3. Estimate parameters from ABC approach    
  4. Tools available for forward-simulations (Bernd Gruber, UC)
  5. Example of ABC: invasion history of an invasive weed (Francisco Encinas-Viso, CSIRO)

 

Camille Roux was born in Étretat, France in 1983. He obtained a master's degree in plant biochemistry in 2007 at the University of Paris-Saclay, and then caught the evolutionary virus during a PhD in Lille with Xavier Vekemans and Vincent Castric to study speciation within the genus Arabidopsis. Then, a first post-doc in Sète with Nicolas Bierne and Nicolas Galtier to study genetic exchanges in the Mytilus mussel, and in Ciona intestinalis. A second post-doc in Lausanne with John Pannell to study sex determinism and polyploidy in Mercurialis. Since 2017, he is a prime investigator at the CNRS, in Lille, working on computational methods to analyse genomic variations of introgression during the process of speciation.

Camille's visit to Canberra is funded by the Centre for Biodiversity Analysis. Hosts: Francisco Encinas-VisoRobert Godfree (Australian National Herbarium, CSIRO) and Bernd Gruber (Centre for Conservation Ecology and Genomics, University of Canberra).