"Stochastic Models for the Inference of Life Evolution"

Center for Interdisciplinary Research in Biology (CIRB)
Collège de France
11, place Marcelin Berthelot
75231 PARIS Cedex 05
Tel : +33 1 44 27 13 91

Email: amaury.lambert — a t —

"Stochastic Models for the Inference of Life Evolution"

Institut de Biologie de
l’École Normale Supérieure (IBENS)
École Normale Supérieure
46, rue d'Ulm
75230 PARIS Cedex 05
Tel : +33 1 44 27 85 69

Email: amaury.lambert — a t —


Some information and links

- Position(s)

- Research interests

A. Ecology, genetics and evolution: phylogenetics, macro-evolution, speciation, population genetics, molecular evolution, somatic evolution
B. Probability and stochastic processes: branching processes, coalescent theory, excursion theory, Lévy processes, measure-valued processes

- Courses under my responsibility

- PhD students

- For more information, see webpage of SMILE

A handful of movies...

Pop science

- June 10, 2022 - Podcast Holobiont
Stochastic models of evolution

- July 3, 2021 - TimeWorld Conference, Conservatoire National des Arts & Métiers
Le cancer est-il une affaire de malchance ?

- March 29, 2019 - Step'Up Closing Conference, Institut de Physique du Globe
Do our genes evolve?

- Feb 15, 2018 - École Normale Supérieure
Ils font l'ENS : Hélène Morlon et Amaury Lambert

- May 24, 2014 - Les Ernests
Déchiffrer les lois de l’Évolution : l’autre secret de l’ADN

- Dec 6, 2013 - Collège de France
The SMILE video

Research talks

- Oct 9, 16 and 23, 2020 - IICD (Columbia U)
Three lectures on "Evolutionary processes and patterns of biodiversity"

- Jun 18, 2020 - One World Probability Seminar
Probabilistic models related to the SARS-CoV-2 pandemic

- Feb 14, 2017 - Banff International Research Station
The split-and-drift random graph

- Aug 1, 2016 - Casa Matematica Oaxaca
A non exchangeable coalescent arising in phylogenetics

- Jun 17, 2015 - Centre International de Rencontres Mathématiques
A non exchangeable coalescent arising in phylogenetics

- Apr 30, 2014 - Simons Institute (U.C. Berkeley)
From individual-based population models to phylogenies

- Jun 5, 2013 - Journée "Mathématiques en Mouvement" (FSMP, U. Paris-Descartes)
Prédire le passé : mathématiques, hasard et évolution

- Jan 12, 2011 - Centre d'Alembert (U. Paris-Sud)
Modèles mathématiques probabilistes de l’évolution du vivant : deux approches complémentaires


-Gamblin, J., Gandon, S., Blanquart, F., Lambert, A. (2022)
Bottlenecks can constrain and channel evolutionary paths

-Freund, F., Kerdoncuff, E., Matuszewski, S., Lapierre, M., Hildebrandt, M., Jensen, J.D., Ferretti, L., Lambert, A., Sackton, T.B., Achaz, G. (2022)
Interpreting the pervasive observation of U-shaped Site Frequency Spectra

-Johnston, S.G.G., Lambert, A. (2022)
The coalescent structure of branching processes: A unifying Poissonisation approach

-Lambert, A., Uribe Bravo, G. (2022) 
Totally ordered measured trees and splitting trees with infinite variation II: Prolific skeleton decomposition

-Foutel-Rodier*, F., Blanquart, F., Courau, P., Czuppon, P., Duchamps, J., Gamblin, J., Kerdoncuff, E., Kulathinal, R., Régnier, L., Vuduc, L., Lambert**, A., Schertzer**, E. (2022)
From individual-based epidemic models to McKendrick-von Foerster PDEs: A guide to modeling and inferring COVID-19 dynamics
J. Math. Biol. (in press)

-Behdenna, A., Petot, P., Pothier, J., Nous, C., Lambert, A., Achaz, G. (2022)
A minimal yet flexible likelihood framework to assess correlated evolution
Systematic Biology (in press)

-Bienvenu, F., Lambert, A., Steel, M. (2022)
Combinatorial and stochastic properties of ranked tree-child networks
Rand. Struct. Algo. 60(4) 653-689

-Lambert, A. (2021)
A mathematical assessment of the efficiency of quarantining and contact tracing in curbing the COVID-19 epidemic
Math. Mod. Nat. Phen. 16 (53)

-Foutel-Rodier, F., Lambert, A., Schertzer, E. (2021) 
Exchangeable coalescents, ultrametric spaces, nested interval-partitions: A unifying approach
Ann. Appl. Prob.
31(5) 2046-2090

-Lambert, A., Miro Pina, V., Schertzer, E. (2021) 
Chromosome painting:
how recombination mixes ancestral colors
Ann. Appl. Prob.
31(2) 826-864

-Lambert, A. (2020)
L'Évolution face au hasard
In:  Le hasard, le calcul et la vie - colloque de Cerisy, Grandcolas, P., Maurel, M.C. &
Pomerol, J.C., (eds)

-Manceau*, M., Marin*, J., Morlon, H., Lambert, A. (2020)
Model-based inference of punctuated molecular evolution
Mol. Biol. Evol. 37(11) 3308-3323

-Marin, J., Achaz, G., Crombach, A., Lambert, A. (2020)
The genomic view of diversification
J. Evol. Biol. 33 1387-1404

-Cluzel, N., Lambert, A., Maday, Y., Turinici, G., Danchin, A. (2020)
Biochemical and statistical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare
C.R. Acad. Sci. Biologies 343(2) 177-209

-Kerdoncuff, E., Lambert, A., Achaz, G. (2020)
Testing for population decline using maximal linkage disequilibrium blocks
Theoret. Popul. Biol. 134 171-181

-Doulcier, G., Lambert, A., De Monte, S. Rainey, P.B. (2020)
Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity
eLife 9:e53433

-Day, T., Parsons, T.L., Lambert, A., Gandon, S. (2020)
The Price equation and evolutionary epidemiology
Philosophical Transactions B 375: 20190357

-Foutel-Rodier, F., Lambert, A., Schertzer, E. (2020)
Kingman's coalescent with erosion
Elec. J. Prob. 25 (56)

-Đinh, K.D., Jaksik, R., Kimmel, M., Lambert, A., Tavaré, S. (2020)
Statistical inference for the evolutionary history of cancer genomes
Stat. Sci. 35(1), 129-144

-Lambert, A., Schertzer, E. (2020) 
Coagulation-transport equations and the nested coalescents
Probab. Theory Relat. Fields
176(1), 77-147

Read it online

-Anciaux, Y., Lambert, A., Ronce, O., Roques, L., Martin, G. (2019) 
Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis
73(8) 1517-1532

-Bienvenu, F., Débarre, F., Lambert, A. (2019)
The split-and-drift random graph, a null model for speciation

Stoch. Proc. Appl. 129(6) 2010-2048

-Lambert, A., Schertzer, E. (2019)
Recovering the Brownian coalescent point process from the Kingman coalescent by conditional sampling
Bernoulli  25(1) 148-173

-Manceau, M., Lambert, A. (2019)
The species problem from the modeler's point of view

Bull. Math Biol. 81(3) 878-898
Read it online

-Achaz, G., Lambert, A., Schertzer, E. (2018)
The sequential loss of allelic diversity

Adv. Appl. Prob. 50(A) 13-29
[Festschrift in honor of Peter Jagers]

Read it online

-Lambert, A., Uribe Bravo, G. (2018)
Totally ordered measured trees and splitting trees with infinite variation

Elec. J. Prob. 23(120) 1-41

-Parsons, T.L., Lambert, A., Day, T., Gandon, S. (2018)
Pathogen evolution in finite populations: slow and steady spreads the best

J. Roy. Soc. Interface 15 (147) 20180135

-Maliet, O., Gascuel, F., Lambert, A. (2018)
Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity
Systematic Biology 67(6) 1025–1040

-Dávila Felipe, M., Lambert, A. (2018)
Branching processes seen from their extinction time via path decompositions of reflected Lévy processes

Elec. J. Prob.
23(98) 1-30

-Blancas, A., Duchamps, J.J., Lambert, A., Siri-Jégousse, A. (2018) 
Trees within trees: Simple nested coalescents

Elec. J. Prob. 23(94) 1-27

-Duchamps, J.J., Lambert, A. (2018)
Mutations on a random binary tree with measured boundary
Ann. Appl. Prob. 28(4) 2141-2187

-Aguilée*, R., Gascuel*, F., Lambert**, A., Ferrière**, R. (2018)
Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates
Nature Communications 9 3013

-Lambert, A. (2018)
The coalescent of a sample from a binary branching process
[Festschrift in the memory of Paul Joyce]
Theoret. Popul. Biol. 122 30-35

-Lambert, A. (2018)
Random ultrametric trees and applications

ESAIM: Proceedings & Surveys 60 70-89

-Lambert, A. (2017)
Probabilistic models for the (sub)Tree(s) of Life

Brazil. J. Probab. Statist. 31(3) 415-475

-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

-Manceau, M., Lambert, A., Morlon, H. (2017)
A unifying comparative phylogenetic framework including traits coevolving across interacting lineages
Systematic Biology 66(4) 551–568

-Lapierre, M., Lambert, A., Achaz, G. (2017)
Accuracy of demographic inferences from Site Frequency Spectrum: The case of the Yoruba population
Genetics 206(1) 439-449

-Lambert, A., Uribe Bravo, G. (2017)
The comb representation of compact ultrametric spaces

p-Adic Numb. Ultrametric Anal. Appl. 9(1) 22-38

-Lapierre, M., Blin, C., Lambert, A., Achaz, G., Rocha, E.P.C. (2016)
The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography
Mol. Biol. Evol. 33(7) 1711-1725

-Behdenna, A., Pothier, J., Abby, S., Lambert, A., Achaz, G. (2016)
Testing for independence between evolutionary processes
Systematic Biology 65 (5) 812-823

-Delaporte, C., Achaz, G., Lambert, A. (2016)
Mutational pattern of a sample from a critical branching population
J. Math. Biol. 73(3) 627-664
Read it online

-Alexander, H.K., Lambert, A., Stadler, T. (2016)
Quantifying age-dependent extinction from species phylogenies
Systematic Biology 65(1) 35-50

-Dávila Felipe, M., Lambert, A. (2015)
Time-reversal dualities for some random forests
ALEA, Lat. Am. J. Probab. Math. Stat. 12(1) 399-426

-Lambert, A., Ma, C. (2015)
The coalescent in peripatric metapopulations

J. Appl. Prob. 52(2) 538-557

-Gascuel, F., Ferrière, R., Aguilée, R., Lambert, A. (2015)
How ecology and landscape dynamics shape phylogenetic trees
Systematic Biology 64(4) 590-607

-Régnier, C.*, Achaz, G.*, Lambert, A., Cowie, R.H., Bouchet, P., Fontaine, B. (2015)
Mass extinction in poorly known taxa
PNAS 112(25) 7761-7766

-Manceau, M., Lambert, A., Morlon, H. (2015)
Phylogenies support out-of-equilibrium models of biodiversity
Ecology Letters 18(4) 347-356

-Lambert, A., Simatos, F. (2015)
Asymptotic behavior of local times of compound Poisson processes with drift in the infinite variance case 
J. Theoret. Probab. 28(1) 41-91

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

-Lambert, A., Morlon, H., Etienne, R.S. (2015)
The reconstructed tree in the lineage-based model of protracted speciation 
J. Math. Biol. 70(1) 367-397

-Etienne, R.S., Morlon, H., Lambert, A. (2014)
Estimating the duration of speciation from phylogenies
Evolution 68(8) 2430-2440

-Lambert, A. (2014)
Vers une approche formelle des origines évolutives de la simplexité
In:  Complexité-Simplexité, Berthoz, A. & Petit, J.L. (eds)

-Lambert, A., Simatos, F. (2014)
The weak convergence of regenerative processes using some excursion path decompositions 
Ann. Inst. Henri Poincaré 50(2) 492-511

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

-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

-Bansaye, V., Lambert, A. (2013)
New approaches to source–sink metapopulations decoupling demography and dispersal

Theoret. Popul. Biol. 88 31-46

-Lambert, A., Simatos, F., Zwart, B. (2013)
Scaling limits via excursion theory: Interplay between Crump-Mode-Jagers branching processes and Processor-Sharing queues 
Ann. Appl. Prob. 23(6) 2357-2381

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

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

-Lambert, A., Trapman, P. (2013)
Splitting trees stopped when the first clock rings and Vervaat's transformation

J. Appl. Prob. 50(1) 208-227

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

-Chapron, G., Wielgus, R., Lambert, A. (2013)
Overestimates of maternity and population growth rates in multi-annual breeders
Eur. J. Wildlife Res. 59 237–243

-Lambert, A., Popovic, L. (2013)
The coalescent point process of branching trees
Ann. Appl. Prob.  23(1) 99–144

-Champagnat, N., Lambert, A., Richard, M. (2012)
Birth and death processes with neutral mutations
Int. J. Stoch. Anal. Article ID 569081

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

-Puillandre, N., Lambert, A., Brouillet, S., Achaz, G. (2012)
ABGD, Automatic Barcode Gap Discovery for primary species delimitation
Mol. Ecol.
21(8) 1864-1877

-Aguilée, A., Lambert, A., Claessen, D. (2011)
Ecological speciation in dynamic landscapes
J. Evol. Biol. 24 2663-2677

-Tully,T., Lambert, A. (2011)
The evolution of post-reproductive lifespan as an insurance against developmental indeterminacy
Evolution 65 3013–3020

-Aguilée, A., de Becdelièvre, B., Lambert, A., Claessen, D. (2011)
Under which conditions is character displacement a likely outcome of secondary contact?
J. Biol. Dyn. 5 135-146

-Lambert, A. (2011)
Species abundance distributions in neutral models with immigration or mutation and general lifetimes
J. Math. Biol. 63 57-72

-Lambert, A. (2010)
Population genetics, ecology and the size of populations
J. Math. Biol. 60 469-472

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

-Caballero, M.E., Lambert, A., Uribe Bravo, G. (2009)
Proof(s) of the Lamperti representation of continuous-state branching processes 
Probab. Surveys 6 62-89

-Lambert, A. (2009)
The allelic partition for coalescent point processes 
Markov Proc. Relat. Fields. 15 359-386

-Cattiaux, P., Collet, P., Lambert, A., Martinez, S., Méléard, S., San Martin, J. (2009)
Quasi-stationary distributions and diffusion models in population dynamics 
Ann. Probab. 37 1926-1969

-Aguilée, R., Claessen, D., Lambert, A. (2009)
Allele fixation in a dynamic metapopulation: Founder effects vs refuge effects
Theoret. Pop. Biol. 76 105-117

-Champagnat, N., Lambert, A. (2008)
Adaptive dynamics in logistic branching populations 
Banach Center Publ. 80 235-244

-Lambert, A. (2008)
Population Dynamics and Random Genealogies 
Stoch. Models 24 45-163

-Raquin, A.L., F. Depaulis, A. Lambert, N. Galic, P. Brabant and I. Goldringer (2008)
Experimental estimation of mutation rates in a wheat population with a gene genealogy approach 
Genetics 179 2195-2211

-Gonzalez, A., Lambert, A., Ricciardi, A. (2008)
When does ecosystem engineering cause invasion and species replacement? 
Oikos 117 1247-1257

-Chapron, G., Miquelle, D.G., Lambert, A., Goodrich, J. M., Legendre, S., Clobert, J. (2008)
The impact on tigers of poaching versus prey depletion
J. Appl. Ecology. 45 1667-1674

-Champagnat, N., Lambert, A. (2007)
Evolution of discrete populations and the canonical diffusion of adaptive dynamics 
Ann. Appl. Prob. 17 102-155

-Lambert, A. (2007)
Quasistationary distributions and the continuous-state branching process conditioned to be never extinct 
Elec. J. Prob. 12 420-446

-Lambert, A. (2007)
Processus de branchement, génétique des populations et généalogies aléatoires 
Habilitation à diriger des recherches, Université Pierre et Marie Curie (Univ Paris 06)

-Lambert, A. (2006)
Probability of fixation under weak selection: a branching process unifying approach 
Theoret. Pop. Biol. 69 419-441

-Lambert, A. (2005)
The branching process with logistic growth 
Ann. Appl. Prob. 15 1506-1535
Initial manuscript

-Lambert, A. (2003)
Coalescence times for the branching process 
Adv. Appl. Prob. 35 1071-1089

-Lambert, A. (2002)
The genealogy of continuous-state branching processes with immigration 
Probab. Theory Relat. Fields 122 42-70

-Lambert, A. (2001)
The joint law of ages and residual lifetimes for two schemes of regenerative sets
Elec. J. Prob. 6 1-23

-Lambert, A. (2001)
Arbres, excursions et processus de Lévy complètement asymétriques
PhD dissertation, Université Pierre et Marie Curie

-Lambert, A. (2000)
Completely asymmetric Lévy processes confined in a finite interval 
Ann. Inst. H. Poincaré 36 251-274

...And for those who read Russian...

- Chapron, G, Miquelle, D.G., Goodrich, J. M., Lambert, A., Legendre, S., Clobert, J. (2005)
The effect of poaching on tigers in the Russian Far East
Chapter 25 pp.191-195 in Tigers of Sikhote-Alin Zapovednik: ecology and conservation, by Miquelle, D.G., J.G. Goodrich, and E.N. Smirnov (eds.)