SMILE: Stochastic Models for the Inference of Life Evolution

Principal Investigator: Amaury LAMBERT, Pr. UPMC

Probabilistic models of evolution can be used to infer the historical patterns of species diversification from the knowledge of genotypes and phenotypes of contemporary species: identification of source regions of biodiversity in geographical space or in niche space, reconstruction of traits of ancestral species, inference of diversification rate shifts across paleontological time...

The approaches used in evolution modeling can be divided into: a) the top-down approach, used in phylogenetics and comparative systematics, where macro-evolutionary processes are described by simple stochastic models that have little empirical justification and are usually treated by sophisticated statistical methods (e.g., Markov chain Monte Carlo in tree space); the bottom-up approach, used in population genetics and ecology, where evolution emerges from the interaction of its microscopic components, namely organisms and their genes, which handles microscopic, measurable parameters (fecundity, survival probability, dispersal probability, mutation rate, recombination rate...), and builds models on this microscopic description.

The most used approach in data analysis is the top-down approach. It proposes simple null models of species diversification and of genotype/phenotype evolution, and rates them according to their ability to reproduce present day data. Our first line of research consists in developing mathematical and numerical techniques for the analysis of such models. Mathematical progress relies in particular on the theory of branching processes and coalescent processes. Numerical methods include likelihood computation, peeling algorithms and MCMC on trees augmented with the history of extinct lineages. This research will not only solve some current challenges in phylogenetics but also help get round computationally demanding statistical procedures, which in turn should pave the way for new ways of modeling evolution.

However, the relative good performance of a phenomenological model is rarely informative of the biological reality of evolution at the microscopic level. In addition, there is no guarantee that the model selected as the best one, indeed is a good one. In contrast, in bottom-up models, the confidence we have in the model stems from the knowledge we have of the microscopic scale and in particular from the fact that microscopic parameters are measurable. In addition, scaling limit techniques can yield macroscopic objects which emerge as the limit of the fine scale description. The standard coalescent is the best example of such a universal object, emerging from a very general class of models with large, fixed population size. Our second line of research is to contribute to push this effort further by proposing other models of macro-evolution arising as scaling limits of microscopically described biological populations. This line contributes to the utilization of possibly slightly more complex, but more reliable models for phylogenetic trees and for the evolutionary dynamics of quantitative traits. Our group focuses on the spatial structuring of populations on large time scales (dynamic landscapes) and on phenotypic evolution driven by intraspecific selection, under the assumption of rare mutations (adaptive dynamics). 

Our third line of research concerns the history of genetic sequences in the macro-evolutionary timescale. In particular, we study the evolutionary constraints governing the order in which successive mutations occur at the same locus or at different loci. We are interested in the origin of such constraints and in the subsequent predictability of evolutionary pathways in the case when they are strong and pervasive.

Our way of doing research is to promote the discussion between personalities from different research areas or from different backgrounds. This is reflected by the wealth of specialties represented in our group: probability, statistics, bio-informatics, ecology, evolutionary biology.

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Selected Publication 2010-2017

- Tomasetti, C., Durrett, R., Kimmel, M., Lambert, A., Parmigiani, G., Zauber, A. & Vogelstein, B., (2017), Role of stem-cell divisions in cancer risk. Nature 548, E13–E14. 

- Lapierre, M., Lambert, A. & Achaz, G. (2017), Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population. Genetics 206, 439–449.

- Débarre, F. (2017), Fidelity of parent-offspring transmission and the evolution of social behavior in structured populations. J. Theor. Biol. 420, 26–35.

- Manceau, M., Lambert, A. & Morlon, H. (2016), A unifying comparative phylogenetic framework including traits coevolving across interacting lineages. Syst. Biol. 

- Delaporte, C., Achaz, G. & Lambert, A. (2016), Mutational pattern of a sample from a critical branching population. J. Math. Biol. 1–38. 

- Alexander, H.K., Lambert, A. & Stadler, T. (2016), Quantifying Age-dependent Extinction from Species Phylogenies. Syst. Biol. 65, 35–50. 

- Suez, M., Behdenna, A., Brouillet, S., Graça, P., Higuet, D. & Achaz, G. (2016), MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads. Mol Ecol Resour 16, 524–533.

- Hartnett, A.T., Schertzer, E., Levin, S.A. & Couzin, I.D. (2016), Heterogeneous Preference and Local Nonlinearity in Consensus Decision Making. Phys. Rev. Lett. 116, 038701.

- Davila Felipe, M. & Lambert, A. (2015), Time Reversal Dualities for some Random Forests. ALEA Lat. Am. J. Probab. Math. Stat. 12, 399–426.

- Debarre, F., Yeaman, S. & Guillaume, F. (2015), Evolution of Quantitative Traits under a Migration-Selection Balance: When Does Skew Matter? Am. Nat. 186, S37–S47.

- Gascuel, F., Ferrière, R., Aguilée & R., Lambert, A. (2015), How Ecology and Landscape Dynamics Shape Phylogenetic Trees. Syst. Biol. 64, 590–607.

- Clémençon, S., Cousien, A., Felipe M.D. & Tran, V.C. (2015), On computer-intensive simulation and estimation methods for rare-event analysis in epidemic models. Statist. Med. 34, 3696–3713.

- Lambert, A. & Ma, C. (2015), The Coalescent in Peripatric Metapopulations. J. Appl. Probab. 52, 538–557.

- Lambert, A., Morlon, H., Etienne, R.S. (2015), The reconstructed tree in the lineage-based model of protracted speciation. J. Math. Biol. 70, 367–397.

- Massol, F., & Débarre, F. (2015), Evolution of dispersal in spatially and temporally variable environments: The importance of life cycles. Evolution 69, 1925–1937.

- Newman, C.M., Ravishankar, K. & Schertzer, E. (2015), Brownian net with killing. Stochastic Processes and their Applications 125, 1148–1194. Regnier, C., Achaz, G., Lambert, A., Cowie, R.H., Bouchet, P. & Fontaine, B. (2015), Mass extinction in poorly known taxa. Proc. Natl. Acad. Sci. U. S. A. 112, 7761–7766.

- Rolland, J., Condamine, F.L., Beeravolu, C.R., Jiguet, F. & Morlon, H. (2015), Dispersal is a major driver of the latitudinal diversity gradient of Carnivora. Global Ecology and Biogeography 24, 1059–1071.

- Suez, M., Behdenna, A., Brouillet, S., Graça, P., Higuet, D. & Achaz, G., (2015), MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads. Mol Ecol Resour n/a–n/a.

- Berdahl A., Torney C.J., Schertzer E. & Levin S.A. (2015), On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments. Evolution. 69, 1390–1405. 

- Condamine F.L., Nagalingum N.S., Marshall C.R. & Morlon H. (2015), Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol. Biol. 15, 65.

- Débarre F. (2015), Fitness costs in spatially structured environments. Evolution, 12646.

- Lambert A. & Simatos F. (2015), Asymptotic Behavior of Local Times of Compound Poisson Processes with Drift in the Infinite Variance Case. J. Theor. Probab. 28, 41-91.

- Manceau M., Lambert A. & Morlon H. (2015), Phylogenies support out-of-equilibrium models of biodiversity. Ecol Lett 18, 347–356.

- Martin G. & Lambert A. (2015), A simple, semi-deterministic approximation to the distribution of selective sweeps in large populations. Theor. Popul. Biol. 101, 40-46.

- Morlon, H., O’Connor, T.K., Bryant, J.A., Charkoudian, L.K., Docherty, K.M., Jones, E., Kembel, S.W., Green, J.L., and Bohannan, B.J.M. (2015). The Biogeography of Putative Microbial Antibiotic Production. PLoS ONE 10, e0130659.

- Regnier, C., Achaz, G., Lambert, A., Cowie, R.H., Bouchet, P., and Fontaine, B. (2015). Mass extinction in poorly known taxa. Proc. Natl. Acad. Sci. U. S. A. 112, 7761–7766.

- Reyes, E., Morlon, H., and Sauquet, H. (2015). Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae. New Phytol. 207, 401–410.

- Etienne R.S., Morlon H. & Lambert A. (2014), Estimating the duration of speciation from phylogenies. Evolution 68, 2430–2440.

- Ferretti L., Mamino M. & Bianconi G. (2014), Condensation and topological phase transitions in a dynamical network model with rewiring of the links. Phys Rev E Stat Nonlin Soft Matter Phys 89, 042810.

- Lambert A., Alexander H.K. & Stadler T. (2014), Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics. J. Theor. Biol. 352, 60–70.

- Moen D., & Morlon H. (2014), Why does diversification slow down? Trends Ecol. Evol. 29, 190–197.

- Morlon H. (2014), Phylogenetic approaches for studying diversification. Ecol. Lett. 17, 508–525.

- Rolland J., Jiguet F., Jønsson K.A., Condamine F.L. & Morlon H. (2014), Settling down of seasonal migrants promotes bird diversification. Proc. Biol. Sci. 281, 20140473.

- Champagnat N. & Lambert A. (2013), Splitting trees with neutral Poissonian mutations II: Largest and oldest families. Stoch. Proc. Appl. 123(4) 1368-1414.

- Aguilée R., Claessen D. & Lambert A. (2013) Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics. Evolution 67(5) 1291-1306.

- Bansaye V. & Lambert A. (2013) Past, growth and persistence of source-sink metapopulations. Theoret. Popul. Biol. 88 31-46.

- Lambert A. & Stadler T. (2013) Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies. Theoret. Popul. Biol. 90 113-128.

- Lambert A. & Steel M. (2013) Predicting the loss of phylogenetic diversity under non-stationary diversification models. J. Theoret. Biol. 337 111-124.

Lambert A. & Popovic .L (2013), The coalescent point process of branching trees, Annals of Applied Probability, Vol. 23, No. 1, 99-144.

- Lambert A. & Trapman P. (2013), Splitting trees stopped when the first clock rings and Vervaat's transformation, Journal of Applied Probability, Volume 50, Number 1 (2013), 208-227.

- Champagnat N. & Lambert A. (2012), Splitting trees with neutral Poissonian mutations I: Small families. Stoch. Proc. Appl. 122(3) 1003-1033.

- Mariadassou M., Bar-Hen A. & Kishino H. (2012), Taxon Influence: Assessing taxon-induced incongruities in phylogenetic inference, Systematic Biology 61 337-345.

- Morlon H., Kemps B., Plotkin J.B. & Brisson D. (2012), Explosive radiation of a bacterial species group, Evolution66: 2577-2586.

- Morlon H. (2012), Cooperative warfare in the microbial world, Science, Vol. 337 no. 6099 pp. 1184-1185.

- Stewart A.J., Parsons T.L. & Plotkin J.B. (2012), Environmental robustness and the evolvability of populations, Evolution 66 (5) 1598-1612.

- Draghi J.A., Parsons T.L. & Plotkin J.B. (2011), Epistasis increases the rate of conditionally neutral substitution in an adapting population, Genetics 187 (4): 1139-1152.

- Morlon H.,Parsons T.L., & Plotkin J.B. (2011), Reconciling molecular phylogenies with the fossil record, Proceedings of the National Academy of Sciences108: 16327-16332.

- Morlon H.,Schwilk D., Bryant J., Marquet P., Rebelo T., Tauss C., Bohannan B. & Green J. (2011), Spatial patterns of phylogenetic diversity, Ecology Letters14: 141-149.

- Puillandre N., Lambert A., Brouillet S. & Achaz G. (2011), ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Molecular Ecology 21:8 1864-1877.

- Lambert A. (2011), Species abundance distributions in neutral models with immigration or mutation and general lifetimes, Journal of Mathematical Biology 63: 57-72.

- Aguilée A., Lambert A. & Claessen D. (2011), Ecological speciation in dynamic landscapes, Journal of Evolutionary Biology 24: 2663-2677.

- Morlon H., Potts M. & Plotkin J.B. (2010), Inferring the dynamics of diversification: a coalescent approach PLoS Biology 8(9): e1000493.

- Draghi J.A., Parsons T.L., Wagner G.P. & Plotkin J.B. (2010), Mutational robustness can facilitate adaptation, Nature 463 (7279): 353-355.

- Lambert A. (2010), The contour of splitting trees is a Lévy process, Annals of Probability 38 348-395.


Group leader:
Lambert Amaury, PR, UPMC, Univ. Paris 06

Senior researchers:
Achaz Guillaume, MC HDR, UPMC
Schertzer Emmanuel, MC UPMC
Débarre Florence, CR2 CNRS
Blanquart François, CR CNRS
Kimmel Marek, PR (fév.-juin)

Postdoctoral fellows & PhD Students:
Garcia Thomas, Postdoctoral fellow
Marin Julie, Postdoctoral fellow
Miro Pina Veronica, PhD student
Manceau Marc, PhD student
Bienvenu Francois, PhD student
Duchamps Jean-Jil, PhD student
Kerdoncuff Elise, PhD student

External PhD co-supervisors:
Cazelles Bernard, UPMC
Ferrière Régis, ENS

Master Students (M1-M2):
Foutel-Rodier Félix, M2 (oct-fev)