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

2018

Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity

Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology of the species tree and on the distribution of its branch lengths. However, the rate of decrease of PD strongly depends on the relative depths of the nodes in the tree and on the order in which species become extinct. We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying topology, clade relative depths and clade relative extinction risks. This model can be seen as an extension to Aldous' one parameter splitting model (\$$\beta\$$, which controls for tree balance) with two additional parameters: a new parameter \$$\alpha\$$ quantifying the correlation between the richness of a clade and its relative depth, and a parameter \$$\eta\$$ quantifying the correlation between the richness of a clade and its frequency (relative abundance or range), taken herein as a proxy for its overall extinction risk. We show on simulated phylogenies that loss of PD depends on the combined effect of all three parameters, \$$\beta\$$, \$$\alpha\$$ and \$$\eta\$$. In particular, PD may decrease as fast as species diversity when high extinction risks are clustered within small, old clades, corresponding to a parameter range that we term the `thin ice zone' (\$$\beta<-1\$$ or \$$\alpha<0\$$; \$$\eta>1\$$). Besides, when high extinction risks are clustered within large clades, the loss of PD can be higher in trees that are more balanced (\$$\beta>0\$$), in contrast to the predictions of earlier studies based on simpler models. We propose a Monte-Carlo algorithm, tested on simulated data, to infer all three parameters. Applying it to a real dataset comprising 120 bird clades (class Aves) with known range sizes , we show that parameter estimates precisely fall close to close to a 'thin ice zone': the combination of their ranking tree shape and non-random extinctions risks makes them prone to a sudden collapse of PD.

Publication

2016

Fidelity of parent-offspring transmission and the evolution of social behavior in structured populations

The theoretical investigation of how spatial structure affects the evolution of social behavior has mostly been done under the assumption that parent-offspring strategy transmission is perfect, ie, for genetically transmitted traits, that mutation is very weak or absent. Here, we investigate the evolution of social behavior in structured populations under arbitrary mutation probabilities. We consider populations of fixed size N, structured such that in the absence of selection, all individuals have the same probability of reproducing or dying (neutral reproductive values are the all same). Two types of individuals, A and B, corresponding to two types of social behavior, are competiting; the fidelity of strategy transmission from parent to offspring is tuned by a parameter μ. Social interactions have a direct effect on individual fecundities. Under the assumption of small phenotypic differences (weak selection), we provide a formula for the expected frequency of type A individuals in the population, and deduce conditions for the long-term success of one strategy against another. We then illustrate this result with three common life-cycles (Wright-Fisher, Moran Birth-Death and Moran Death-Birth), and specific population structures (graph-structured populations). Qualitatively, we find that some life-cycles (Moran Birth-Death, Wright-Fisher) prevent the evolution of altruistic behavior, confirming previous results obtained with perfect strategy transmission. We also show that computing the expected frequency of altruists on a regular graph may require knowing more than just the graph{\textquoteright}s size and degree.

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Resources

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