Unleashing the power of full genome polymorphism data for inference:
new developments of the Ancestral Recombination Graph

Developing and applying population genetics models to genome data is challenging, in particular for species undergoing sexual reproduction as the process of recombination has to be accounted for. Coalescent theory offers a general analytical framework to model the common ancestry of a sample of sequences, given a demographic model. This framework can be extended to incorporate recombination, but the complexity of the underlying ancestry, represented by the so-called Ancestral Recombination Graph (ARG) prevents its application to a large number of loci, in particular to data sets produced by complete genome sequencing. Approximations to the coalescent with recombination process have therefore been developed in order to apply population genetics models at the genome scale. The most commonly used heuristic is the Sequentially Markov Coalescent (SMC) process, which models only certain types of recombination events, at the expense of ignoring others. While not being equivalent to the genuine coalescent with recombination, the SMC has the practical property of begin Markovian along the genome, enabling efficient algorithms for the estimation of the ARG. So far the SMC approach has been developed as the multiple SMC method (MSMC), which has been mainly used and benchmarked to infer past demographic events of model organisms (human, primates, Arabidopsis).

Objectives of this workshop

(1) to promote population models of genome evolution accounting for recombination.

We will discuss the current limitations of the SMC/MSMC model, in particular regarding its application to a broader range of species with life history traits differing from model organisms. In particular, we will discuss more general demographic models, such as seed-bank scenarios, and the possible extensions to varying parameters along the genome, such as recombination rates. Another topic will be the impact of strong selection and skewed offspring distributions, which are common characteristics of plant and animal pathogen species. We wish to initiate the convergence between the SMC model and multiple merger coalescent models.

(2) to discuss possible applications of the ARG in order to answer novel biological questions.

The ARG, whether it is directly measured or indirectly reconstructed, contains a lot of historical and spatial (along the genome) information of biological relevance, but generally not extracted by current approaches. We will discuss approaches to infer parameters from a given ARG, as well as statistical approaches enabling the efficient accounting of the ARG in population genomics analyses. The development of ARG/SMC models with multiple merger coalescent or seed banks will find important applications in data analysis and allow to answer novel biological questions.


Registration of participants is free but mandatory by email to Julien Dutheil, before July 15th.
Early registration is welcome.


Scientific programme is expected to start September 27th at 9am and last until September 27th at 5pm.
The invited speakers are

  • Carsten Wiuf (Department of Mathematical Sciences, University of Copenhagen): Recombination in a birth-death type ancestral process
  • Aurélien Tellier (Technical University of Munich): When evolution slows down: inferring seed banking in plants using the SMC
  • Stephan Schiffels (Max Planck Institute for the Science of Human History, Jena): Reconstructing human history from modern and ancient genome sequences.
  • Sebastian Probst (Group of Biomathematics and Theoretical Bioinformatics, University of Bielefeld): Infer recombination parameters with the help of nonlinear programming (SQP)
  • Fabian Freund (Institute of Plant Breeding, Seed Science and Population Genetics, Hohenheim): Beyond the site-frequency spectrum: Low-dimensional statistics to distinguish between coalescent models
  • Bjarki Eldon (Museum für Naturkunde Berlin): TBA
  • Gustavo Barroso (MPI for Evolutionary Biology): The Spatially Non-homogeneous Sequentially Markov Coalescent

Location, travel and hosting

The workshop will take place at

Max Planck institute for Evolutionary Biology
August-Thienemann-Str. 2
24306 Plön.

The city of Plön is accessible by train from Kiel and Lübeck. The closest airport is in Hambourg (1 hour train from Lübeck). Detailed information on how to access the institute can be found here.

Possible hotels in Plön:

If there are any questions, please don't hesitate to ask the organisers

We are looking forward to see you in Plön.


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