Computational Phylogenetics
... Molecular Data, Evolutionary Modeling and Computational Tools

Daniele Silvestro

Daniele is working at the Antonelli Lab (University of Gothenburg, Sweden). His main research focus is developing Bayesian approaches to estimate macroevolutionary rates from fossil data and phylogenetic trees.
Daniele also develops the programs PyRate, BayesRate, and raxmlGUI.

Funding: Carl Tryggers post-doctoral research fellowship, University of Gothenburg, Sweden.

Papers

(Google scholar’s list)

Silvestro D., Antonelli A., Salamin N., Quental T. B, 2015. The role of competition in evolutionary replacements of North American canids. Proceedings of the National Academy of Sciences USA, 112:8684–8689.

Pires M. M., Silvestro D., Quental T. B, 2015. Continental Faunal Exchange and the Asymmetrical Radiation of Carnivores. Proceedings of the Royal Society B, 282: 20151952.

Bacon C. D., Silvestro D., Jaramillo C. A., Smith B. T., Chakrabarty P., Antonelli A, 2015. Reply to Lessios and to Marko et al.: An early and progressive biotic interchange across the Isthmus of Panama is robust to missing data and biases. Proceedings of the National Academy of Sciences USA, doi: 10.1073/pnas.1515451112

Serrano-Serrano M., Perret M., Guignard M., Chautems A., Silvestro D., and Salamin N, 2015. Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae. Accepted in BMC Evolutionary Biology.

Kostikova A.*, Silvestro D.*, Pearman P. B., Salamin N, 2015. Bridging inter- and intraspecific trait evolution with a hierarchical Bayesian approach. Accepted in Systematic Biology. *Equal contributions.

Silvestro D., Cascales-Miñana B., Bacon C. D., Antonelli A, 2015. Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. New Phytologist, 207:425–436.

Bacon C. D., Silvestro D., Jaramillo C. A., 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 USA,112:6110–6115. Featured as Highlight in Science 348:770.

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, 6:340–346.

Antonelli A., Zizka A., Silvestro D., Scharn R., Cascales-Miñana B., Bacon C. D, 2015. An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics. Frontiers in Genetics, 6:130.

Silvestro D., Salamin N., Schnitzler J., 2014. PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution, doi:10.1111/2041-210X.12263.

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, 63:349–367.

Dib L., Silvestro D., Salamin N., 2014. Evolutionary footprint of coevolving positions in genes. Bioinformatics, doi: 10.1093/bioinformatics/btu012.

Silvestro D., Zizka G., Schulte K., 2014 Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68:163–175.

Louzada R. B., Schulte K., Wanderley M. G. L., Silvestro D., Zizka G., Barfuss M.H.J., Palma-Silva C., 2014. Molecular phylogeny of Orthophytum (Bromeliaceae) elucidates infrageneric relationships and demonstrates the taxonomic significance of the inflorescence type. Molecular Phylogenetics and Evolution, 77:54-64.

Masters C. J., Génin F., Silvestro D., Lister A. M., DelPero M., 2014. The Red Island and the seven dwarfs: Body size reduction in Cheirogaleidae. Journal of Biogeography, doi: 10.1111/jbi.12327.

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, 84:201–219.

Wagner N., Silvestro D., Brie D., Ibisch P. L., Zizka G., Weising K., Schulte K., 2013. Spatiotemporal evolution of Fosterella (Bromeliaceae) in the Central Andean biodiversity hotspot. Journal of Biogeography, 40:869–880.

Silvestro D., Michalak I., 2012. RaxmlGUI: A graphical front-end for RAxML. Organisms Diversity and Evolution, 12:335–337.

Silvestro D., Schnitzler J., Zizka G., 2011. A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11:311.

Picone B., Masters J., Silvestro D., Sineo L., Del Pero M., 2011. A Phylogenetic Analysis of Human Syntenies revealed by Chromosome Painting in Euarchontoglires Orders. Journal of Mammalian Evolution, 18:131–146.

Schulte K., Silvestro D., Kiehlmann E., Vesely S., Novoa P., Zizka G. 2010. Detection of recent hybridization between sympatric Chilean Puya species (Bromeliaceae) using AFLP markers and reconstruction of complex relationships. Molecular Phylogenetics and Evolution, 57(3):1105–1119.

Tirelli T., Silvestro D., Pessani D. and Tudge C.,  2010. Description of the male reproductive system of Paguristes eremita (Anomura, Diogenidae) and its placement in a phylogeny of diogenid species based on spermatozoal and spermatophore ultrastructure. Zoologischer Anzeiger, 248(4):299–312

Meregalli M. & Silvestro D., 2008. Assessing relationships between Mediterranean and Afrotropical taxa of Cleonini (Coleoptera: Curculionidae: Lixinae): a survey based on Bayesian analysis and lineage geohistory reconstruction. Biogeographia, vol. XXIX:117–132.

Tirelli T., Campantico E., Pessani D.,  Silvestro D. and Tudge C., 2008. Reproductive biology of Mediterranean Hermit crabs: fine structure of spermatophores and spermatozoa of Diogenes pugilator (Decapoda: Anomura) and its bearing on a sperm phylogeny of the Diogenidae. Journal of Crustacean Biology, 28(3):534–542.

 

Written on Sunday October 6, 2013