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

2015

How Ecology and Landscape Dynamics Shape Phylogenetic Trees

Whether biotic or abiotic factors are the dominant drivers of clade diversification is a long-standing question in evolutionary biology. The ubiquitous patterns of phylogenetic imbalance and branching slowdown have been taken as supporting the role of ecological niche filling and spatial heterogeneity in ecological features, and thus of biotic processes, in diversification. However, a proper theoretical assessment of the relative roles of biotic and abiotic factors in macroevolution requires models that integrate both types of factors, and such models have been lacking. In this study, we use an individual-based model to investigate the temporal patterns of diversification driven by ecological speciation in a stochastically fluctuating geographic landscape. The model generates phylogenies whose shape evolves as the clade ages. Stabilization of tree shape often occurs after ecological saturation, revealing species turnover caused by competition and demographic stochasticity. In the initial phase of diversification (allopatric radiation into an empty landscape), trees tend to be unbalanced and branching slows down. As diversification proceeds further due to landscape dynamics, balance and branching tempo may increase and become positive. Three main conclusions follow. First, the phylogenies of ecologically saturated clades do not always exhibit branching slowdown. Branching slowdown requires that competition be wide or heterogeneous across the landscape, or that the characteristics of landscape dynamics vary geographically. Conversely, branching acceleration is predicted under narrow competition or frequent local catastrophes. Second, ecological heterogeneity does not necessarily cause phylogenies to be unbalanced--short time in geographical isolation or frequent local catastrophes may lead to balanced trees despite spatial heterogeneity. Conversely, unbalanced trees can emerge without spatial heterogeneity, notably if competition is wide. Third, short isolation time causes a radically different and quite robust pattern of phylogenies that are balanced and yet exhibit branching slowdown. In conclusion, biotic factors have a strong and diverse influence on the shape of phylogenies of ecologically saturating clades and create the evolutionary template in which branching slowdown and tree imbalance may occur. However, the contingency of landscape dynamics and resource distribution can cause wide variation in branching tempo and tree balance. Finally, considerable variation in tree shape among simulation replicates calls for caution when interpreting variation in the shape of real phylogenies.

Publication

2018

The genomic view of diversification

Evolutionary relationships between species are traditionally represented in the form of a tree, called the species tree. The reconstruction of the species tree from molecular data is hindered by frequent conflicts between gene genealogies. A standard way of dealing with this issue is to postulate the existence of a unique species tree where disagreements between gene trees are explained by incomplete lineage sorting (ILS) due to random coalescences of gene lineages inside the edges of the species tree. This paradigm, known as the multi-species coalescent (MSC), is constantly violated by the ubiquitous presence of gene flow revealed by empirical studies, leading to topological incongruences of gene trees that cannot be explained by ILS alone. Here we argue that this paradigm should be revised in favor of a vision acknowledging the importance of gene flow and where gene histories shape the species tree rather than the opposite. We propose a new, plastic framework for modeling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees. As an illustration, we implement this framework in a mathematical model called the genomic diversification (GD) model based on coalescent theory, with four parameters tuning replication, genetic differentiation, gene flow and reproductive isolation. We use it to evaluate the amount of gene flow in two empirical data-sets. We find that in these data-sets, gene tree distributions are better explained by the best fitting GD model than by the best fitting MSC model. This work should pave the way for approaches of diversification using the richer signal contained in genomic evolutionary histories rather than in the mere species tree.

Publication

2015

The reconstructed tree in the lineage-based model of protracted speciation

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne and Rosindell in Syst Biol 61(2):204–213, (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed by Lambert in Ann Probab 38(1):348–395, (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable.

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