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Dr. Daniele Silvestro

Place and date of birth: Turin (Italy), September 28, 1984
E-mail: silvestro.daniele@gmail.com
Website: http://antonelli-lab.net/index.php


February 2012
PhD in Natural Sciences at the Senckenberg Research Institute and University of Frankfurt/M, Germany, with summa com laude (defended Feb 27, 2012).
Supervisors: G. Zizka, K. Schulte.

July 2008
MSc in Evolutionary Biology at the University of Turin, Italy, with summa cum laude, honorific mention, and press dignity.
Supervisor: M. Meregalli.

July 2006
BSc in Natural Sciences at the University of Turin, Italy, with summa cum laude. Supervisor: M. Meregalli.

Professional experience

August 2013 – present
Postdoc at the University of Gothenburg, Sweden (Antonelli Lab).
Guest scientist at University of Lausanne, Switzerland (Computational Phylogenetics group, N. Salamin).

March 2012 – July 2013
Postdoc at the Senckenberg Research Institute in Frankfurt/M, Germany.

August – December 2012
Postdoc at the University of Lausanne, Switzerland and Swiss Institute of Bioinformatics (Computational
Phylogenetics group, N. Salamin).

January 2011, May 2012
Guest researcher at Australian Tropical Herbarium, James Cook University, Cairns, Australia (K. Schulte, D. M. Crayn).

Awards and grants

2015 - (March) Submitted application to the Swedish Research Council for a 4-year Project Research Grant for Junior Researchers to be developed at Gothenburg University.

2012 - (December) 1-year postdoctoral grant of the Wenner-Gren Foundation, Sweden for the period August 2013 to July 2014. Project title: “Integrating Molecular and Fossil data to investigate patterns and dynamics of species diversification”. Applicants: Alexandre Antonelli, Daniele Silvestro. Total amount: 34,100 €.

2012 - (December) “Wolfgang Strutz” PhD thesis award granted by the Senckenberg Nature Research Society, Germany. Awarded amount: 10,000 €.

2012 - (November) 2-year postdoctoral grant of the Carl Tryggers Foundation, Sweden, first year declined in favor of the Wenner-Gren grant. Project title: “A New Bayesian Approach to Understand the Evolution of Biodiversity Hotspots”. Applicants: Alexandre Antonelli, Daniele Silvestro. Total amount: 62,000 €.

2012 - (May) Freunde und Förderer grant of the Goethe University, Frankfurt, Germany for a 2-week research stay at the James Cook University in Cairns (Australia). Total amount: 1,300 €.

2012 - (March) Leibniz-DAAD Research Fellowship funding a 1-year postdoctoral project titled: “A neglected wealth in phylogenies: the analysis of speciation and extinction rates”. Total amount: 22,080 €.

2011 - (July) Willkomm-Stiftung grant of the Goethe University, Frankfurt, Germany and funds from the Deutsche Bromeliengesellschaft (German Bromeliads Society) supporting the participation to the XVIII International Botanical Congress in Melbourne (Australia). Total amount: 1,400 €.

2011 - (January) BiKF Outgoing grant (Frankfurt, Germany) for a 4-week research stay at the Australian Tropical Herbarium in Cairns (Australia). Total amount: 2,000 €.

2011 - (June) Optime Award for best graduated students at the University and Polytechnic of Turin (Italy) from Club Optime, Unione Industriale Torino.

2011 - (January) Scientific collaborator grant from University of Turin, Italy (Prof. E. Balletto). Total amount: 4,000 €.

Invited talks

2015 - Biogeographic analysis of fossil lineages

June 26, Guarujá, Sao Paulo, Brazil, Evolution meeting (SSE symposium on “Frontiers in Parametric Biogeography”; J. Albert, A. Antonelli).

June 24, University of Sao Paulo, Brazil (2nd meeting on “The regulators of biodiversity in deep time”; T. Ezard, T. B. Quental, M. Benton).

2014 - Rise and fall of canid clades inferred from the fossil record

October 8, University of Uppsala, Sweden (Martin Ryberg).

Opportunities and challenges to estimating plant diversification from fossils

June 14, University of Zurich, Switzerland (Evolutionary Plant Radiations Meeting; C. Hughes, P. Linder).

Estimation of speciation and extinction from fossil data using PyRate

September 11, University of Southampton, United Kingdom (1st meeting on “The regulators of biodiversity in deep time”; T. Ezard, T. B. Quental, M. Benton).

May 6, University of Leipzig, Germany (J. Schnitzler, A. Mulch).

April 8, University of Sao Paulo, Brazil (T. B. Quental).

Phylogenetic comparative methods without phylogeny (using the fossil record)

February 20, University of Lyon, France (N. Lartillot).

February 10, University of Gothenburg, Sweden (B. Oxelman).

2013 - Bayesian Inference of Speciation and Extinction Rates using the Fossil Record

September 23, University of California – Berkeley, USA (H. Morlon, T. B. Quental, C. Marshall).

September 16, University of Montreal, Canada (Mathematics for an Evolving Biodiversity; N. Lartillot, A. Lambert).

September 4, University of Stockholm, Sweden (A. Humphreys, C. Rydin).

February 15, Centre for Ecological and Evolutionary Synthesis – Oslo, Norway (L. H. Liow, N. C. Stenseth).

2012 - Bayesian inference of macroevolutionary processes using the fossil record.

October 22, Collège de France – Paris, France. (Phylogenetic approaches to diversification; A. Lambert, H. Morlon).

Key innovations in Bromeliads.

October 4, Federal University of Pernambuco – Recife, Brazil. (Forum of Ecology and Evolution; D. Astúa de Moraes).

Testing the effect of evolutionary key innovations using a Bayesian approach.

June 11, University of Leipzig, Germany. (Alexandra Muellner).

February 9, Biodiversity and Climate Research Centre, Frankfurt, Germany. (Steffen Paul).

2011 - Testing hypotheses on species diversification: A Bayesian framework.

December 12, University of Zurich, Switzerland. (J. de Vos, C. Hughes, P. Linder).

December 7, University of Gothenburg, Sweden. (A. Antonelli).

Teaching experience

(February–July) Supervision of Mariia Korolyuk, master student in Complex System science at the Chalmers University of Technology (Gothenburg, Sweden) for a project (20 credits) titled: Modeling continuous trait evolution in the absence of phylogenetic information.

(April 6) 1-day workshop on Estimating speciation and extinction rates from the fossil record using PyRate at the University of São Paulo, Brazil.

(January 31) 1-day workshop on Historical biogeography using Lagrange and BioGeoBEARS at the University of Gothenburg, Sweden (F. Condamine, C. D. Bacon).

(August 28) 1-day workshop on Diversification rate estimation: Theory and practice at the University of Gothenburg, Sweden.

(September 24 – October 5) Lecturer at the Recife Winter School on Phylogeny, Biogeography, and Spatial Modeling: Theoretical and Practical basis at the Federal University of Pernambuco, Recife, Brazil (A. Benko-Iseppon, J. Schnitzler).

(June 7–8) Lectures with practical computer work on Bayesian modeling of speciation within the Doctoral course on Bayesian Statistics and Applications for Phylogenetics at the University of Lausanne, Switzerland (N. Salamin, N. Lartillot).

(May 31) 1-day workshop on Testing hypotheses on species diversification using novel Bayesian approaches at James Cook University, Cairns, Australia.

(Spring term) Lectures on Molecular Evolution and Phylogenetic Inference with practical computer work for Bachelor and Master students at Goethe University, Frankfurt, Germany (G. Zizka).

(January 27) 1-day workshop on Diversification in space: Parametric approaches for historical biogeography at James Cook University, Cairns, Australia.

(January 25) 1-day workshop on Diversification through time: Inferring speciation and extinction rates from phylogenies at James Cook University, Cairns, Australia.

Lectures on theoretical cladistics and phylogenetic inference during a course on Systematics and Taxonomy at the University of Turin, Italy (M. Meregalli).


Python program to estimate speciation, extinction, and preservation rates from fossils using a Bayesian framework. Over 300 downloads, cited in 12 articles since March 2014. Available at http://dsilvestro.github.io/PyRate/.

Bayesian estimation of diversification rates through time from dated phylogenies using Markov chain Monte Carlo. The program is written in Python and R. Over 1,400 downloads worldwide, cited in 33 articles as of August 2015. Available at http://sourceforge.net/projects/bayesrate/.

A graphical front-end for RAxML. Selected as official partner by M. Miller among the softwares that will feature REST services from the CIPRES platform. Over 22,700 downloads worldwide, cited in 519 articles as of August 2015. Available at http://sourceforge.net/projects/raxmlgui/

R package to analyze inter- and intraspecific trait evolution with a hierarchical Bayesian model (main developer: A. Kostikova). Available at https://github.com/trollius/jive.

Python package for easy and fast coding of species into user-defined operational units (main developer: M. Töpel). Available at https://github.com/mtop/speciesgeocoder.

Computer program to estimate molecular coevolution based on an alignment and a phylogeny using maximum likelihood or MCMC (main developer: L. Dib). Available at: http://www2.unil.ch/phylo/bioinformatics/coev.html.

Python and R scripts to estimate the rates of state transition through time based on stochastic character mapping.

Reviewer for:

Nature Communications, Proceedings of the National Academy of Sciences USA, PLOS Biology, Journal of Biogeography, Systematic Biology, New Phytologist, Evolution, Functional Ecology, Global Ecology and Biogeography, Bioinformatics, Biological Reviews, Taxon, Zoological Journal of Linnean Society.

Additional skills

Extensive experience in Bayesian computational methods and algorithms, and computer analysis especially in the field of macroevolution, phylogenetics, historical biogeography, stochastic processes. Strong Python and R programming skills (in particular numerical and scientific libraries). Fluent English, basic Portuguese, Italian native speaker.

2015 |  2014 |  2013 | 

Bacon C.D., Silvestro D., Jaramillo C., Smith B.T., Chakrabarty P., Antonelli A., 2015. Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Sciences of the United States of America 112(19) pp. 6110-6115. [DOI] [Web of Science] [Pubmed]
Bacon C.D., Silvestro D., Jaramillo C., Smith B.T., Chakrabarty P., Antonelli A., 2015. Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases. Proceedings of the National Academy of Sciences of the United States of America 112(43) pp. E5767-E5768. [DOI] [Web of Science] [Pubmed]
Pires M.M., Silvestro D., Quental T.B., 2015. Continental faunal exchange and the asymmetrical radiation of carnivores. Proceedings of the Royal Society B Biological Sciences 282(1817) p. 20151952. [DOI] [Web of Science] [Pubmed]
Silvestro D., Antonelli A., Salamin N., Quental T.B., 2015. The role of clade competition in the diversification of North American canids. Proceedings of the National Academy of Sciences of the United States of America 112(28) pp. 8684-8689. [DOI] [Web of Science] [Pubmed]
Silvestro D., Kostikova A., Litsios G., Pearman P.B., Salamin N., 2015. Measurement Errors Should Always Be Incorporated in Phylogenetic Comparative Analysis. Methods in Ecology and Evolution 6(3) pp. 340-346. [DOI] [Web of Science]
Dib L., Silvestro D., Salamin N., 2014. Evolutionary footprint of coevolving positions in genes. Bioinformatics 30(9) pp. 1241-1249. [DOI] [Web of Science] [Pubmed]
Masters J.C., Genin F., Silvestro D., Lister A.M., DelPero M., 2014. The red island and the seven dwarfs: body size reduction in Cheirogaleidae. Journal of Biogeography 41(10) pp. 1833-1847. [DOI] [Web of Science]
Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N., 2014. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology 63(3) pp. 349-367. [DOI] [Web of Science] [Pubmed]
Masters J.C., Silvestro D., Génin F., Delpero M., 2013. Seeing the Wood through the Trees: The Current State of Higher Systematics in the Strepsirhini. Folia Primatologica 84(3-5) pp. 201-219. [DOI] [Web of Science] [Pubmed]


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