To introduce and develop sequence similarity networks as a promising complement to the phylogenetic framework to study evolutionary biology.
The comparison of molecular sequences from organisms, environmental samples and mobile genetic elements is fundamental in evolutionary biology to study genes, genomes and species evolution. Although phylogenetic methods play a major role in these analyses, through the inference of phylogenetic trees or networks based on families of homologous sequences, many data remained underexplored as the number of molecular sequences, especially from microbial genomes and environmental projects, grows exponentially, with typical environmental samples containing thousands of species represented by millions of sequences. In order to further enhance the evolutionary comparison of molecular sequences, we will develop a promising complementary approach, the use of large complex similarity networks (typically a few million nodes and tens of millions of edges), adapted to evolutionary biology questions. Such networks, inspired by the studies on social and regulatory networks, allow for fast inclusive comparative analyses of both (highly) divergent and conserved sequences, fully or partly similar.
improve the statistical framework to compare similarity networks.
We expect that our findings will provide an additional comparative framework for evolutionary studies, new methods of detection of environmental/genomic sequences of medical and biological interest, and a novel description of the structure of genetic diversity on Earth, unraveling the main partnerships and barriers to the exchange of sequences of DNA between genes, genomes, species and environments.
01/01/18 to 28/02/18: Dr. Diego Javier Zea officially joins the team as a post-doctoral fellow to study the evolution of domain architecture, using networks.
01/12/17 to 31/12/17: Dr. Jananan Pathmanathan works as a post-doctoral fellow for the EVOLUNET project.
04/09/17 to 27/12/17: We welcome Dr. Diego Javier Zea (from the Structural Bioinformatics Units of the Leloir Institute Foundation, Argentina), with whom we will develop networks to study the evolution of protein architectures.
03/05/2017: Mr. Eduard Ocaña (PhD student in the Ruiz-Trillo lab) in training for 3 months in the EVOLUNET team to learn network methods.
15/04/2017: Dr. Guillaume Bernard (post-doctoral fellow) joined the EVOLUNET team. Dr. Guillaume Bernard will develop a statistical framework for network comparisons.
01/10/2016: Dr. Andrew Watson (post-doctoral fellow) and Mr. Romain Lannès (PhD student) joined the EVOLUNET team. Dr. Watson will develop network methods to search for genetic public goods. Mr. Lannes will develop methods to detect divergent environmental genes and microbes.
01/07/2016-31/06/2017: EVOLUNET welcomes Pr. François-Joseph Lapointe (U. Montréal, Canada) for a one year sabbatical in Paris.
18/01/2016: EVOLUNET welcomes its first Master 2 student: Mr. Adrien Danzon, and a visiting scientist: Mr. Alexander Jaffe (visiting scientist). Both investigate environmental genetic diversity using networks.
15/07/2015: EVOLUNET welcomes Mr. Sukithar Kochappi Rajan to start studies of environmental genetic diversity for 4 months.
01/01/2015: Dr. Mattis List, eminent historical linguist, joined the lab to develop network methods, applied to language evolution.
24/11/2014: Dr. Shijulal Nelson-Sathi and Pr. William Martin visit the EVOLUNET team to consider collaborations on reticulate evolution.
01/11/2014: A new post-doctoral fellow, Dr. Eduardo Corel, joins the team EVOLUNET to work on gene and genome networks.
01/07/2014-06/07/2014: The lab welcomes Pr. François-Joseph Lapointe to develop collaborations on sequence similarity networks. To know more about FJL's multiple talents, check this.
01/06/2014: A post-doctoral position (starting in November 2014) is available. Applications are welcome.
21. Méheust R, Watson AK, Lapointe FJ, Papke RT, Lopez P, Bapteste E. Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Genome Biol. 2018 Jun 7;19(1):75. doi: 10.1186/s13059-018-1454-9.
20. Bapteste E, Huneman P. Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory. BMC Biol. 2018 May 29;16(1):56. doi: 10.1186/s12915-018-0531-6.
19.Vigliotti C, Bicep C, Bapteste E, Lopez P, Corel E. Tracking the Rules of Transmission and Introgression with Networks. Microbiol Spectr. 2018 Apr;6(2). doi: 10.1128/microbiolspec.MTBP-0008-2016.
17. Corel E, Méheust R, Watson AK, McInerney JO, Lopez P, Bapteste E. Bipartite network analysis of gene sharings in the microbial world. Mol Biol Evol. 2018 Jan 15. doi: 10.1093/molbev/msy001.
16. Pathmanathan JS, Lopez P, Lapointe FJ, Bapteste E. CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection. Mol Biol Evol. 2018 Jan 1;35(1):252-255. doi: 10.1093/molbev/msx283.
13. Lord E, Le Cam M, Bapteste É, Méheust R, Makarenkov V, Lapointe FJ. BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts. PLoS One. 2016 Aug 31;11(8):e0161474.
12. List JM, Pathmanathan JS, Lopez P, Bapteste E. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics. Biol Direct. 2016 Aug 20;11:39. doi: 10.1186/s13062-016-0145-2.
10. Méheust R, Zelzion E, Bhattacharya D, Lopez P, Bapteste E. Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3579-84. doi: 10.1073/pnas.1517551113. Epub 2016 Mar 14.
7. Bapteste E. (2015) Conflits Intérieurs. Fable Scientifique, Collection « Essais », Les éditions Matériologiques (268 pages).
6. Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E. (2015) Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biol. Feb 24;13(1):16.
3. Bapteste E. (2014) Pluralisme et évolution réticulée en microbiologie évolutive in PRÉCIS DE PHILOSOPHIE DE LA BIOLOGIE, sous la direction de F. Merlin et T. Hoquet, Collection « Philosophie des sciences » dirigée par Thierry Martin, Vuibert (321 pages).
22/02/2018: Dr. Michael Macey (The Open University, UK) gave a talk on: Analogues and Simulants – Investigations into the potential of life outside of Earth.
09/12/2016: Pr. Eugene Koonin (Senior Investigator, NCBI, USA) gave a talk on "Evolution of the virus world and antivirus defense: a tangled web"
29/04/2016: Pr. Martin Embley (Institute for Cell and Molecular Biosciences, Newcastle University, England) gave a talk on "The tangled origin of eukaryotes"
08/04/2015: Pr. Christopher Lane (U. Rhodes Island, USA) gave a talk on: "Falling in and out of parasitism: What can genomic data tell us about life history transitions?"
18/03/2015: Pr. James McInerney (U. Maynooth, Ireland) gave a talk on: "Eukaryotic origins"
24/11/2014: Pr. William Martin (U. Duesseldorf, Germany) gave a public talk on:"Major gene fluxes in early microbial evolution"
07/10/2014: Dr. Rafal Mostowy (Imperial College, UK) gave a public talk on: "The role of horizontal DNA exchange in the evolution of pneumococcal capsules".
16/06/2014: Pr. Debashish Bhattacharya (Rutgers University, USA) gave a public talk on : "Exploring the evolution of microbial eukaryotes using single cell genomics".
A challenge for network studies: exploiting data from single cell genomics to better understand protist ecology and evolution.
We plan to teach and share our methods on sequence similarity networks during two one-week European classes, each open to 10 motivated European master and PhD students in Station Biologique de Roscoff (France).
First class occurred in July 2016.
Second class occurred in June 2018.
Third class will occurr in June 2019.