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Embracing Phylogenetic Incongruence Among Genetic Loci

English title Embracing Phylogenetic Incongruence Among Genetic Loci
Applicant Dessimoz Christophe
Number 183723
Funding scheme SNSF Professorships
Research institution
Department of Computational Biology Falculty of Biology and Medicine University of Lausanne
Université de Lausanne Centre Integratif de Génomique Génopode - RM4030
Institution of higher education University of Lausanne - LA
Main discipline Genetics
Start/End 01.09.2019 - 31.08.2021
Approved amount 587'696.00
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All Disciplines (6)

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

Keywords (12)

Molecular Evolution; Mixture model; Phylogenetics; Bioinformatics; Recombination; Computational Biology; Phylogenomics; Gene evolution; High performance computing; Homoeology; Statistical modelling; Tree of Life

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. Cette extension de projet continue à chercher à mieux comprendre cette hétérogénéité par le développement de nouvelles méthodes statistiques et computationnelles, avec des applications à la reconstruction de l'Arbre de la Vie, et à une caractérisation des phénomènes d'hybridization dans les plantes domestiquées.
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 incongruités sont souvent ignorées, ce qui peut conduire à des estimations d'arbres incomplètes, biaisées, ou excessivement confiantes.

Dans le cadre de cette extension de projet, nous continuerons à développer des méthodes d'inférence phylogénétique en présence de signaux incongrus, et nous utiliserons ces avancées pour résoudre des problèmes biologiques de longue date, compliqués par de multiples sources d'incongruence phylogénétique. Plus précisément, nous (1) améliorerons l'évolutivité, l'utilisabilité et l'interprétabilité de notre nouvel outil logiciel "treesignal", qui modélise l'incongruité en utilisant un cadre d'apprentissage machine ; (2) contribuerons à la résolution de l'arbre de vie aviaire en utilisant des méthodes qui évitent l'assemblage et l'annotation du génome et qui sont robustes à multiples sources d'incongruité (en particulier le triage incomplet des lignées et les artefacts d'annotation du génome) ; (3) étudier les conséquences fonctionnelles de l'allopolyploïdisation (hybridisation suivie par duplication complète du génome) en génomique végétale, avec un intérêt particulier sur le coton Upland.
Direct link to Lay Summary Last update: 02.10.2019

Responsible applicant and co-applicants

Employees

Publications

Publication
Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism.
Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, Glover N (2021), Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism., in Genome Biol Evol, evab010.
Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs.
Glover N, Sheppard S, Dessimoz C (2021), Homoeolog inference methods requiring bidirectional best hits or synteny miss many pairs., in Genome Biol Evol, evab077.
ISMB/ECCB 2021 proceedings
Dessimoz C, Przytycka TM (2021), ISMB/ECCB 2021 proceedings, in Bioinformatics (Oxford, England), 37(1), i7-i8.
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
Rossier Victor, Vesztrocy Alex Warwick, Robinson-Rechavi Marc, Dessimoz Christophe (2021), OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, in Bioinformatics, btab219.
Ten years of collaborative progress in the Quest for Orthologs.
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Consortium QFO, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I (2021), Ten years of collaborative progress in the Quest for Orthologs., in Mol Biol Evol, msab098.
Want to track pandemic variants faster? Fix the bioinformatics bottleneck
Hodcroft EB, De Maio N, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C (2021), Want to track pandemic variants faster? Fix the bioinformatics bottleneck, in NATURE, 591(7848), 30-33.
A generalized Robinson-Foulds distance for labeled trees
Briand S, Dessimoz C, El-Mabrouk N, Lafond M, Lobinska G (2020), A generalized Robinson-Foulds distance for labeled trees, in BMC Genomics, 21, 779.
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 3 approved]
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Farias Tarcisio Mendes de (2020), A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL [version 2; peer review: 3 approved], in F1000Research, 21027.
A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor
Benton Richard, Dessimoz Christophe, Moi David (2020), A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor, in eLife, 9, e62507.
Benchmarking gene ontology function predictions using negative annotations
Warwick Vesztrocy A, Dessimoz C (2020), Benchmarking gene ontology function predictions using negative annotations, in Bioinformatics (Oxford, England), 36(1), 210-218.
Identifying orthologs with OMA: A primer
Zahn-Zabal Monique, Dessimoz Christophe, Glover Natasha M. (2020), Identifying orthologs with OMA: A primer, in F1000Research, 9, 27-27.
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Dylus D, Pillonel T, Opota O, Wuethrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbie V, Dessimoz C, Greub G, Lebrand A (2020), NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test, in FRONTIERS IN MICROBIOLOGY, 11(ARTN 59109), 591093.
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff AM, Train C-M, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova H-S, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C (2020), OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more., in Nucleic Acids Res, 49(D1), D373-D379.
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence
Zile Karina, Dessimoz Christophe, Wurm Yannick, Masel Joanna (2020), Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence, in Genome Biology and Evolution, 12(8), 1355-1366.
Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference
FernándezR, GabaldonT, DessimozChristophe (2020), Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference, in Delsuc F, Galtier N, Scornavacca C (ed.), No commercial publisher | Authors open access book, France, 2.4:1-2.4:14.
Parallel and scalable precise clustering
Byma S, Dhasade A, Altenhoff A, Dessimoz C, Larus JR (2020), Parallel and scalable precise clustering, in Parallel Architectures and Compilation Techniques - Conference Proceedings, PACT, 217-228, ACM, New York, NY, USA217-228.
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Moi D, Kilchoer L, Aguilar PS, Dessimoz C (2020), Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes, in PLOS COMPUTATIONAL BIOLOGY, 16(7), e1007553.
The phylogenetic range of bacterial and viral pathogens of vertebrates
Shaw Liam P., Wang Alethea D., Dylus David, Meier Magda, Pogacnik Grega, Dessimoz Christophe, Balloux Françcois (2020), The phylogenetic range of bacterial and viral pathogens of vertebrates, in Molecular Ecology, 15463.
The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, for Orthologs Consortium Quest, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C (2020), The Quest for Orthologs benchmark service and consensus calls in 2020., in Nucleic Acids Res, 48(W1), W538-W545.

Collaboration

Group / person Country
Types of collaboration
BASF CropScience Belgium (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Alexandre Roulin, UNIL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Max Telford, University College London Great Britain and Northern Ireland (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
EMBL PhD Symposium Talk given at a conference Big Data: Opportunities, challenges and some solutions 26.11.2019 Heidelberg, Germany Dessimoz Christophe;


Awards

Title Year
Award for outstanding achievements in doctoral education, Faculty of Biology and Medicine, University of Lausanne 2021
Optimus Agora Prize 2021

Associated projects

Number Title Start Funding scheme
167276 Efficient and accurate comparative genomics to make sense of high volume low quality data in biology 01.04.2017 NRP 75 Big Data
150654 Harnessing Phylogenetic Variation Among Genetic Loci to Unravel Species Phylogenies, Lateral Gene Transfer, and Recombination Hotspots 01.09.2015 SNSF Professorships
199775 In the light of evolution 01.05.2021 Agora
205085 Reconstructing ancestral microsyntenies across the tree of life, and inferring their impact on gene function and species adaptation 01.10.2021 Project funding (Div. I-III)
167149 Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data 01.04.2017 NRP 75 Big Data

Abstract

Phylogenetic trees depict evolutionary relationships among biological entities, such as genes, individuals, and species. They are fundamental to evolutionary biology, and their relevance extends to all of biology, including epidemiology, comparative genomics, oncology, developmental biology, host-pathogen interactions.One major complication arises whenever the characters making up an entity do not all share a common evolutionary history-a phenomenon referred to as phylogenetic incongruence. For example, phylogenetic incongruence arises when, among the loci used to infer species phylogenies, there is presence of incomplete lineage sorting, hybridization, introgression, lateral gene transfer, duplication and losses, etc.In this SNSF professorship extension project, we will continue to develop process-agnostic, general-purpose phylogenetic inference methods, and we will use these advances to tackle long-standing biological questions complicated by multiple sources of phylogenetic incongruence. Specifically, we will (1) improve the scalability, usability, and interpretability of our emerging software tool treesignal, which models incongruence using a machine learning framework; (2) contribute toward resolution of the Avian Tree of Life by employing methods that side-step genome assembly and annotation and cope with multiple sources of incongruence (in particular incomplete lineage sorting and genome annotation artifacts); (3) investigate the functional consequences of allopolyploidization (hybridization followed by whole genome duplication) in crop genomics, with a special focus on upland cotton.If successful, the project could resolve highly contended phylogenies, and shed light on genes related through hybridisation, many of which have been neglected to date due to methodological limitations. Ultimately, we believe that process-agnostic analysis of incongruence among loci has the potential to become a routine step in phylogenetic analyses.
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