SMILE

Stochastic Models for the Inference of Life Evolution

Presentation

SMILE is an interdisciplinary research group gathering probabilists, statisticians, bio-informaticians and biologists.
SMILE is affiliated to the Stochastics and Biology group of LPSM (Lab of Probability, Statistics and Modeling) at Sorbonne Université (ex Université Pierre et Marie Curie Paris 06).
SMILE is hosted within the CIRB (Center for Interdisciplinary Research in Biology) at Collège de France.
SMILE is supported by Collège de France and CNRS.
Visit also our homepage at CIRB.

Recent contributions of the SMILE group related to SARS-Cov2 and COVID-19.

Directions

SMILE is hosted at Collège de France in the Latin Quarter of Paris. To reach us, go to 11 place Marcelin Berthelot (stations Luxembourg or Saint-Michel on RER B).
Our working spaces are rooms 107, 121 and 122 on first floor of building B1 (ask us for the code). Building B1 is facing you upon exiting the traversing hall behind Champollion's statue.

Contact

You can reach us by email (amaury.lambert - at - upmc.fr) or (smile - at - listes.upmc.fr).

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Publication

2019

The species problem from the modeler’s point of view

How to define and delineate species is a long-standing question sometimes called the species problem. In modern systematics, species should be groups of individuals sharing characteristics inherited from a common ancestor which distinguish them from other such groups. A good species definition should thus satisfy the following three desirable properties: (A) Heterotypy between species, (B) Homotypy within species and (E) Exclusivity, or monophyly, of each species. In practice, systematists seek to discover the very traits for which these properties are satisfied, without the a priori knowledge of the traits which have been responsible for differentiation and speciation nor of the true ancestral relationships between individuals. Here to the contrary, we focus on individual-based models of macro-evolution, where both the differentiation process and the population genealogies are explicitly modeled, and we ask: How and when is it possible, with this significant information, to delineate species in a way satisfying most or all of the three desirable properties (A), (B) and (E)? Surprisingly, despite the popularity of this modeling approach in the last two decades, there has been little progress or agreement on answers to this question. We prove that the three desirable properties are not in general satisfied simultaneously, but that any two of them can. We show mathematically the existence of two natural species partitions: the finest partition satisfying (A) and (E) and the coarsest partition satisfying (B) and (E). For each of them, we propose a simple algorithm to build the associated phylogeny. We stress that these two procedures can readily be used at a higher level, namely to cluster species into monophyletic genera. The ways we propose to phrase the species problem and to solve it should further refine models and our understanding of macro-evolution.

Publication

2016

The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.

Upcoming seminars

Resources

Planning des salles du Collège de France.
Intranet du Collège de France.