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Harnessing Phylogenetic Variation Among Genetic Loci to Unravel Species Phylogenies, Lateral Gene Transfer, and Recombination Hotspots

Applicant Dessimoz Christophe
Number 150654
Funding scheme SNSF Professorships
Research institution
Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Centre Intégratif de Génomique Université de Lausanne
Institution of higher education University of Lausanne - LA
Main discipline Genetics
Start/End 01.09.2015 - 31.08.2019
Approved amount 1'540'725.00
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All Disciplines (6)

Discipline
Genetics
Information Technology
Mathematics
Zoology
Molecular Biology
Methods of Epidemiology and Preventive Medicine

Keywords (15)

High performance computing; Lateral gene transfer; Gene evolution; Computational Biology; Phylogenomics; Endosymbiosis; Mixture model; Influenza evolution; Phylogenetics; Molecular Evolution; Tree of Life; Parasitic worms; Statistical modelling; Recombination; Bioinformatics

Lay Summary (French)

Lead
L'histoire évolutive des gènes est souvent modélisée à l'aide d'arbres. Or, même si l'on considère un groupe d'espèces fixe, les arbres induits pour chaque famille de gène peuvent varier considérablement. Ce projet cherche à mieux caractériser cette hétérogénéité par le développement de nouvelles méthodes statistiques et computationnelles. Ces avancées seront utilisées pour éclairer des questions ouvertes sur l'origine des espèces, sur les transfers de gènes latéraux, et sur les points chauds de recombinaison.
Lay summary

Les arbres phylogénetiques sont utilisés à travers tous les domaines du vivant pour représenter des relations évolutives entres espèces et gènes. Ils jouent un rôle important non seulement en biologie évolutive, mais aussi en génomique fonctionnelle, biologie développementale, oncologie, ou encore en épidémiologie. Cependant, les caractères moléculaires des génomes ne découlent pas nécessairement tous d'un arbre unique, à cause de duplication de gènes, recombinaison, assortiment incomplet des espèces, transfert de gène latéraux, etc. Sous le paradigme actuel, ces différences sont souvent ignorées, ce qui peut conduire à des estimations d'arbres incomplètes, biaisées, ou excessivement confiantes. Ce projet a pour but de mieux modéliser cette hétérogénéité, afin d'élucider des questions portant sur l'histoire évolutives des gènes et des espèces (en particulier les questions proches des origines de la vie sur terre), de détecter des séquences contaminées dans des échantillons d'ADN, d'identifier des transferts de gènes latéraux entres espèces, et de caractériser des évènements de réassortiments dans les virus.

Direct link to Lay Summary Last update: 28.03.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
New genome assembly of the barn owl (Tyto alba alba)
Ducrest Anne Lyse, Neuenschwander Samuel, Schmid-Siegert Emanuel, Pagni Marco, Train Clément, Dylus David, Nevers Yannis, Warwick Vesztrocy Alex, San-Jose Luis M., Dupasquier Mélanie, Dessimoz Christophe, Xenarios Ioannis, Roulin Alexandre, Goudet Jérôme (2020), New genome assembly of the barn owl (Tyto alba alba), in Ecology and Evolution, 10(5), 2284-2298.
Assigning confidence scores to homoeologs using fuzzy logic
Glover Natasha M., Altenhoff Adrian, Dessimoz Christophe (2019), Assigning confidence scores to homoeologs using fuzzy logic, in PeerJ, 6231.
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Kaleb Klara, Vesztrocy Alex Warwick, Altenhoff Adrian, Dessimoz Christophe (2019), Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python, in F1000Research, 8, 42-42.
iHam and pyHam: visualizing and processing hierarchical orthologous groups
Train Clément-Marie, Pignatelli Miguel, Altenhoff Adrian, Dessimoz Christophe (2019), iHam and pyHam: visualizing and processing hierarchical orthologous groups, in Bioinformatics, 35(14), 2504-2506.
Inferring Orthology and Paralogy
Altenhoff Adrian M., Glover Natasha M., Dessimoz Christophe (2019), Inferring Orthology and Paralogy, Springer, New York, 149-175.
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria
Philippe Hervé, Poustka Albert J., Chiodin Marta, Hoff Katharina J., Dessimoz Christophe, Tomiczek Bartlomiej, Schiffer Philipp H., Müller Steven, Domman Daryl, Horn Matthias, Kuhl Heiner, Timmermann Bernd, Satoh Noriyuki, Hikosaka-Katayama Tomoe, Nakano Hiroaki, Rowe Matthew L., Elphick Maurice R., Thomas-Chollier Morgane, Hankeln Thomas, Mertes Florian, Wallberg Andreas, Rast Jonathan P., Copley Richard R., Martinez Pedro, Telford Maximilian J. (2019), Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria, in Current Biology, 29(11), 1818.
OMA standalone: orthology inference among public and custom genomes and transcriptomes
Altenhoff Adrian M., Levy Jeremy, Zarowiecki Magdalena, Tomiczek Bartłomiej, Vesztrocy Alex Warwick, Dalquen Daniel A., Müller Steven, Telford Maximilian J., Glover Natasha M., Dylus David, Dessimoz Christophe (2019), OMA standalone: orthology inference among public and custom genomes and transcriptomes, in Genome Research, 1152-1163.
Gearing up to handle the mosaic nature of life in the quest for orthologs
Forslund Kristoffer, Pereira Cecile, Capella-Gutierrez Salvador, da Silva Alan Sousa, Altenhoff Adrian, Huerta-Cepas Jaime, Muffato Matthieu, Patricio Mateus, Vandepoele Klaas, Ebersberger Ingo, Blake Judith, Fernández Breis Jesualdo Tomás, Boeckmann Brigitte, Gabaldón Toni, Sonnhammer Erik, Dessimoz Christophe, Lewis Suzanna (2018), Gearing up to handle the mosaic nature of life in the quest for orthologs, in Bioinformatics, 34(2), 323-329.
RecPhyloXML - a format for reconciled gene trees
Duchemin Wandrille, Gence Guillaume, Chifolleau Anne-Muriel Arigon, Arvestad Lars, Bansal Mukul S, Berry Vincent, Boussau Bastien, Chevenet Françcois, Comte Nicolas, Davín Adrián A, Dessimoz Christophe, Dylus David, Hasic Damir, Mallo Diego, Planel Rémi, Posada David, Scornavacca Celine, Szöllősi Gergely, Zhang Louxin, Éric Tannier, Daubin Vincent (2018), RecPhyloXML - a format for reconciled gene trees, in Bioinformatics, bty389.
GOATOOLS: A Python library for Gene Ontology analyses
Klopfenstein D. V., Zhang Liangsheng, Pedersen Brent S., Ramírez Fidel, Vesztrocy Alex Warwick, Naldi Aurélien, Mungall Christopher J., Yunes Jeffrey M., Botvinnik Olga, Weigel Mark, Dampier Will, Dessimoz Christophe, Flick Patrick, Tang Haibao (2018), GOATOOLS: A Python library for Gene Ontology analyses, in Scientific Reports, 8, 10872.
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Piližota Ivana, Train Clément-Marie, Altenhoff Adrian, Redestig Henning, Dessimoz Christophe (2018), Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome, in Bioinformatics.
Prioritising candidate genes causing QTL using hierarchical orthologous groups
Warwick Vesztrocy Alex, Dessimoz Christophe, Redestig Henning (2018), Prioritising candidate genes causing QTL using hierarchical orthologous groups, in Bioinformatics, 34(17), 612-619.
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
Altenhoff Adrian M., Glover Natasha M., Train Clément-Marie, Kaleb Klara, Warwick Vesztrocy Alex, Dylus David, de Farias Tarcisio M., Zile Karina, Stevenson Charles, Long Jiao, Redestig Henning, Gonnet Gaston H., Dessimoz Christophe (2018), The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces, in Nucleic Acids Research, 46, D477-D485.
Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.
Suchan Tomasz, Espíndola Anahí, Rutschmann Sereina, Emerson Brent C, Gori Kevin, Dessimoz Christophe, Arrigo Nils, Ronikier Michał, Alvarez Nadir (2017), Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study., in Molecular phylogenetics and evolution, 114, 189-198.
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.
Train Clément-Marie, Glover Natasha M, Gonnet Gaston H, Altenhoff Adrian M, Dessimoz Christophe (2017), Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference., in Bioinformatics (Oxford, England), 33(14), 75-82.
Comparative genomics reveals contraction in olfactory receptor genes in bats.
Tsagkogeorga Georgia, Müller Steven, Dessimoz Christophe, Rossiter Stephen J (2017), Comparative genomics reveals contraction in olfactory receptor genes in bats., in Scientific reports, 7(1), 259-259.
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Jeffares Daniel C, Jolly Clemency, Hoti Mimoza, Speed Doug, Shaw Liam, Rallis Charalampos, Balloux Francois, Dessimoz Christophe, Bähler Jürg, Sedlazeck Fritz J (2017), Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast., in Nature communications, 8, 14061-14061.
The Gene Ontology Handbook
Dessimoz Christophe, Škunca Nives (2017), The Gene Ontology Handbook, Springer, New York.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Yuxiang, Oron Tal Ronnen, Clark Wyatt T, Bankapur Asma R, D'Andrea Daniel, Lepore Rosalba, Funk Christopher S, Kahanda Indika, Verspoor Karin M, Ben-Hur Asa, Koo Da Chen Emily, Penfold-Brown Duncan, Shasha Dennis, Youngs Noah, Bonneau Richard, Lin Alexandra, Sahraeian Sayed M E, Martelli Pier Luigi, Profiti Giuseppe, Casadio Rita, Cao Renzhi, Zhong Zhaolong, Cheng Jianlin, Altenhoff Adrian, Skunca Nives, Dessimoz Christophe, Dogan Tunca, Hakala Kai, Kaewphan Suwisa, Mehryary Farrokh, Salakoski Tapio, Ginter Filip, Fang Hai, Smithers Ben, Oates Matt, Gough Julian, Törönen Petri, Koskinen Patrik, Holm Liisa, Chen Ching-Tai, Hsu Wen-Lian, Bryson Kevin, Cozzetto Domenico, Minneci Federico, Jones David T, Chapman Samuel, Bkc Dukka, Khan Ishita K, Kihara Daisuke, Ofer Dan, Rappoport Nadav, Stern Amos, Cibrian-Uhalte Elena, Denny Paul, Foulger Rebecca E, Hieta Reija, Legge Duncan, Lovering Ruth C, Magrane Michele, Melidoni Anna N, Mutowo-Meullenet Prudence, Pichler Klemens, Shypitsyna Aleksandra, Li Biao, Zakeri Pooya, ElShal Sarah, Tranchevent Léon-Charles, Das Sayoni, Dawson Natalie L, Lee David, Lees Jonathan G, Sillitoe Ian, Bhat Prajwal, Nepusz Tamás, Romero Alfonso E, Sasidharan Rajkumar, Yang Haixuan, Paccanaro Alberto, Gillis Jesse, Sedeño-Cortés Adriana E, Pavlidis Paul, Feng Shou, Cejuela Juan M, Goldberg Tatyana, Hamp Tobias, Richter Lothar, Salamov Asaf, Gabaldon Toni, Marcet-Houben Marina, Supek Fran, Gong Qingtian, Ning Wei, Zhou Yuanpeng, Tian Weidong, Falda Marco, Fontana Paolo, Lavezzo Enrico, Toppo Stefano, Ferrari Carlo, Giollo Manuel (2016), An expanded evaluation of protein function prediction methods shows an improvement in accuracy., in Genome biology, 17(1), 184-184.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Jiang Yuxiang, Oron Tal Ronnen, Clark Wyatt T., Bankapur Asma R., D’Andrea Daniel, Lepore Rosalba, Funk Christopher S., Kahanda Indika, Verspoor Karin M., Ben-Hur Asa, Koo Da Chen Emily, Penfold-Brown Duncan, Shasha Dennis, Youngs Noah, Bonneau Richard, Lin Alexandra, Sahraeian Sayed M. E., Martelli Pier Luigi, Profiti Giuseppe, Casadio Rita, Cao Renzhi, Zhong Zhaolong, Cheng Jianlin, Altenhoff Adrian, et al. (2016), An expanded evaluation of protein function prediction methods shows an improvement in accuracy, in Genome Biology, 17(1), 184.
Compensation of dosage-sensitive genes on the chicken Z chromosome
Zimmer Fabian, Harrison Peter W., Dessimoz Christophe, Mank Judith E. (2016), Compensation of dosage-sensitive genes on the chicken Z chromosome, in Genome Biol Evol, 075-075.
Homoeologs: What Are They and How Do We Infer Them?
Glover Natasha M., Redestig Henning, Dessimoz Christophe (2016), Homoeologs: What Are They and How Do We Infer Them?, in Trends in Plant Science, 21(7), 609-621.
Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life
Victor Sojo, Dessimoz Christophe, Pomiankowski Andrew, Lane Nick (2016), Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life, in Mol Biol Evol, 164-164.
Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web
Robinson Oscar, Dylus David, Dessimoz Christophe (2016), Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web, in Mol Biol Evol, 080-080.
Standardized benchmarking in the quest for orthologs
Altenhoff Adrian M, Boeckmann Brigitte, Capella-Gutierrez Salvador, Dalquen Daniel A, DeLuca Todd, Forslund Kristoffer, Huerta-Cepas Jaime, Linard Benjamin, Pereira Cécile, Pryszcz Leszek P, Schreiber Fabian, da Silva Alan Sousa, Szklarczyk Damian, Train Clément-Marie, Bork Peer, Lecompte Odile, von Mering Christian, Xenarios Ioannis, Sjölander Kimmen, Jensen Lars Juhl, Martin Maria J, Muffato Matthieu, Gabaldón Toni, Lewis Suzanna, Thomas Paul (2016), Standardized benchmarking in the quest for orthologs, in Nature Methods, 13, 425-430.
Clustering genes of common evolutionary history.
Gori Kevin, Suchan Tomasz, Alvarez Nadir, Goldman Nick, Dessimoz Christophe, Clustering genes of common evolutionary history., in Molecular biology and evolution, msw038.

Collaboration

Group / person Country
Types of collaboration
Dr. Nick Goldman, EMBL-EBI Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Nick Lane, University College London Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Ioannis Xenarios, Vital-IT, Swiss Institute of Bioinformatics and UNIL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Manuel Gil, University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Nadir Alvarez, DEE, UNIL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
BaselLife/BC2 EMBO Young Investigator Workshop on Evolutionary and Computational Biology Talk given at a conference Fast, large-scale methods for phylogenetic tree inference & phylogenetic profiling 09.09.2019 Basel, Switzerland Dessimoz Christophe;
ISMB/ECCB 2019 Talk given at a conference Challenges and rewards of benchmarking – how to cope with a biased, incomplete, or even entirely missing ground truth 21.07.2019 Basel, Switzerland Khalili Bita; Dylus David; Dessimoz Christophe;
JOBIM 2019 Talk given at a conference Big Data: opportunities, pitfalls, and remedies 02.07.2019 Nantes, France Dessimoz Christophe;
Willi Hennig Annual Meeting Talk given at a conference Large-scale inference of gene and species phylogenies 17.09.2018 Barcelona, Spain Dessimoz Christophe;
Belgrade BioInformatics Conference 2018 Talk given at a conference Spectral signature of gene family trees 22.06.2018 Belgrade, Serbien De Oliveira Martins Leonardo;
Center for Advanced Modeling Science Day Talk given at a conference Big Data Comparative Genomics 17.11.2017 Lausanne, Switzerland Dessimoz Christophe;
Annual debate of the Linnaean Society of London Talk given at a conference Debate on Big Data 16.11.2017 London, Great Britain and Northern Ireland Dessimoz Christophe;
BC2 conference Talk given at a conference Spectral signature of gene family tree 13.09.2017 Basel, Switzerland De Oliveira Martins Leonardo; Dessimoz Christophe;
Life in Numbers 3 Talk given at a conference Integrating genomes via fine-grained orthology 31.08.2017 Wädenswil, Switzerland Dessimoz Christophe;
ISMB/ECCB Talk given at a conference OMA algorithm 2.0:
more robust to asymmetric evolutionary rates 
and more scalable hierarchical orthologous group inference 25.07.2017 Prague, Czech Republic Train Clément; Glover Natasha; Dessimoz Christophe;
SMBE Symposium on Evolution of Gene Families Talk given at a conference Relating genes and their functions across many species:
Going whole HOG 07.06.2017 Los Angeles, United States of America Glover Natasha; Dessimoz Christophe;
Departmental seminar Individual talk Making the most of noisy, 
low-quality genomes 19.04.2017 Tokyo, Japan Dessimoz Christophe;
Departmental Seminar Individual talk Gene Ontology:
biases, pitfalls, remedies 14.04.2017 Kobe, Japan Dessimoz Christophe;
ECCB 2016 Talk given at a conference Automated filtering of multiple sequence alignments frequently worsens phylogenetic inference 06.09.2016 The Hague, Netherlands Dessimoz Christophe;
C3BI seminar series, Institut Pasteur, Paris (F) Individual talk Hierarchical Orthologous Groups: a unifying and scalable framework for large-scale gene evolution 12.05.2016 Paris, France Dessimoz Christophe;
RECOMB Comparative Genomics Talk given at a conference Hierarchical Orthologous Groups a unifying and scalable framework for large-scale gene evolution 05.10.2015 Frankfurt, Germany Dessimoz Christophe;


Self-organised

Title Date Place
1st Lausanne Computational Biology meeting 03.05.2016 Lausanne, Switzerland
8th Fisher Centre meeting 21.03.2016 London, Great Britain and Northern Ireland
7th Fisher Centre meeting 12.11.2015 London, Great Britain and Northern Ireland

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Votre ADN peut-il être hacké? We Demain International 2018
Media relations: print media, online media 'Adversarial DNA' breeds buffer overflow bugs in PCs The Register International 2017
Media relations: radio, television Journal du matin RTS Radio 1ère Western Switzerland 2017
Media relations: radio, television La Méthode Scientifique France Culture International 2017
Media relations: print media, online media L'ADN, clé USB de demain? Québec Science International 2017
Media relations: print media, online media L'ADN, une nouvelle arme pour les pirates informatiques? Le Temps Western Switzerland 2017
Media relations: print media, online media Quand l'ADN se transforme en disque dur Le Figaro International 2017

Awards

Title Year
ISCB Overton Prize 2019
Sentinel of Science Award (awarded by Publons for top 1% of peer reviewers in the field of Biochemistry, Genetics and Molecular Biology) 2017
EMBO Young Investigator 2016

Associated projects

Number Title Start Funding scheme
136461 The Million Protein, Thousand Species Tree(s) of Life 01.09.2011 Fellowships for advanced researchers
199775 In the light of evolution 01.05.2021 Agora
186397 An integrated evolutionary and functional characterisation of the Drosophila immune peptidic secretome 01.07.2019 Sinergia
183723 Embracing Phylogenetic Incongruence Among Genetic Loci 01.09.2019 SNSF Professorships

Abstract

Phylogenetic trees are used throughout biology to represent evolutionary relationships among species and genes. They play an important role well beyond the field of evolutionary biology, such as in functional genomics, in developmental biology, in oncology or in epidemiology. However, the molecular characters of genomes do not necessary all share a single tree, e.g., due to duplication, recombination, incomplete lineage sorting, lateral gene transfer, etc. In the current paradigm, these potential phylogenetic differences are often ignored, which can result in incomplete, biased, and overconfident inference.In this project, we want to embrace this phylogenetic variation to elucidate long-standing questions on species phylogenies (in particular, ones close to the origins of life), to identify contaminants in DNA samples, to uncover lateral gene transfer between parasitic worms and their hosts, and to identify reassortment events in flu viruses.To these ends, a substantial portion of our efforts will be directed toward the development of new methods and software tools for inferring the nature and extent of phylogenetic variation underlying multiple genetic loci. Focal point of the project is a new method that simultaneously solves the problems of partitioning genetic loci into clusters having common evolutionary histories, and of inferring these histories. This will require progress in statistical modelling, computational optimisation, benchmarking, and visualisation tools.Given the pervasiveness of phylogenetic trees across all of biosciences, this project will yield tools and advances that impact a broad community of researchers worldwide, and strengthen Switzerland's standing in phylogenomics.
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