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Reconstructing a dated tree of life using phylogenetic incongruence

Total Cost €


EC-Contrib. €






 GENECLOCKS project word cloud

Explore the words cloud of the GENECLOCKS project. It provides you a very rough idea of what is the project "GENECLOCKS" about.

reconstruct    transfer    generate    informative    tree    microbial    analysed    first    rare    fungi    parallel    limits    with    hgt    differences    dated    pattern    harness    history    sorting    sequences    clear    time    species    amounts    paucity    resolve    series    gene    phylogenies    nbsp    coexisting    size    advent    model    incongruence    instead    molecular    fossils    horizontal    events    programming    population    speciations    trees    genome    on    evolutionary    rooted    debates    life    eukaryotes    homologous    reached    timing    relationship    data    quantification    groups    complete    maximise    genomes    context    questions    position    sequencing    impasse    occur    systematically    dating    diversification    hence    formulated    phylogeny    invaluable    archaea    rate    explaining    extreme    reignited    animals    evolution    wealth    earth    answer    biologically    phylogenetic    extract    hgts    eukaryotic    answering    reconstructs    genomic    lineage   

Project "GENECLOCKS" data sheet

The following table provides information about the project.


Organization address
address: EGYETEM TER 1-3
postcode: 1053

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Hungary [HU]
 Total cost 1˙453˙542 €
 EC max contribution 1˙453˙542 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-STG
 Funding Scheme ERC-STG
 Starting year 2017
 Duration (year-month-day) from 2017-07-01   to  2022-06-30


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 


 Project objective

With the advent of genome-scale sequencing, molecular phylogeny, which reconstructs gene trees from homologous sequences, has reached an impasse. Instead of answering open questions, new genomes have reignited old debates. The problem is clear, gene trees are not species trees, each is the unique result of series of evolutionary events. If, however, we model these differences in the context of a common species tree, we can access a wealth of information on genome evolution and the diversification of species that is not available to traditional methods. For example, as horizontal gene transfer (HGT) can only occur between coexisting species, HGTs provide information on the order of speciations. When HGT is rare, lineage sorting can generate incongruence between gene trees and the dating problem can be formulated in terms of biologically meaningful parameters (such as population size), that are informative on the rate of evolution and hence invaluable to molecular dating. My first goal is to develop methods that systematically extract information on the pattern and timing of genomic evolution by explaining differences between gene trees. This will allow us to, for the first time, reconstruct a dated tree of life from genome-scale data. We will use parallel programming to maximise the number of genomes analysed. My second goal is to apply these methods to open problems, e.g.: i) to resolve the timing of microbial evolution and its relationship to Earth history, where the extreme paucity of fossils limits the use of molecular dating methods, by using HGT events as “molecular fossils”; ii) to reconstruct rooted phylogenies from complete genomes and harness phylogenetic incongruence to answer long standing questions, such as the of diversification of animals or the position of eukaryotes among archaea; and iii) for eukaryotic groups such as Fungi, where evidence of significant amounts of HGT is emerging our methods will also allow the quantification of the extent of HGT.


year authors and title journal last update
List of publications.
2020 Dániel Grajzel, Imre Derényi, Gergely J. Szöllősi
A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues
published pages: 1606-1611, ISSN: 0027-8424, DOI: 10.1073/pnas.1913104117
Proceedings of the National Academy of Sciences 117/3 2020-03-05
2020 Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
published pages: msaa015, ISSN: 0737-4038, DOI: 10.1093/molbev/msaa015
Molecular Biology and Evolution ACCEPTED MANUSCRIPT 2020-03-05
2017 Cédric Chauve, Akbar Rafiey, Adrián A. Davín, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J. Szöllősi, Vincent Daubin, Eric Tannier
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers
published pages: peer-reviewed an, ISSN: 2551-668X, DOI: 10.1101/127548
bioRxiv 10.1101/127548 2020-03-05
2020 Dominik Schrempf, Nicolas Lartillot, Gergely Szöllősi
Scalable empirical mixture models that account for across-site compositional heterogeneity
published pages: , ISSN: 0737-4038, DOI:
Molecular Biology and Evolution accepted pending revision 2020-03-05
2020 Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely J. Szöllősi
GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss
published pages: , ISSN: 0737-4038, DOI:
Molecular Biology and Evolution to appear 2020-03-05
2019 Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol
Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity
published pages: 1294-1301, ISSN: 0737-4038, DOI: 10.1093/molbev/msz043
Molecular Biology and Evolution 36/6 2020-03-05
2019 Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis
Megaphylogeny resolves global patterns of mushroom evolution
published pages: 668-678, ISSN: 2397-334X, DOI: 10.1038/s41559-019-0834-1
Nature Ecology & Evolution 3/4 2020-03-05
2020 Tom A. Williams, Cymon J. Cox, Peter G. Foster, Gergely J. Szöllősi, T. Martin Embley
Phylogenomics provides robust support for a two-domains tree of life
published pages: 138-147, ISSN: 2397-334X, DOI: 10.1038/s41559-019-1040-x
Nature Ecology & Evolution 4/1 2020-02-28
2018 Adrián A. Davín, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szöllősi
Gene transfers can date the tree of life
published pages: 904-909, ISSN: 2397-334X, DOI: 10.1038/s41559-018-0525-3
Nature Ecology & Evolution 2/5 2020-02-28
2019 Adrián A Davín, Théo Tricou, Eric Tannier, Damien M de Vienne, Gergely J Szöllősi
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
published pages: 1286-1288, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btz710
Bioinformatics 36/4 2020-02-28
2017 Imre Derényi, Gergely J. Szöllősi
Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations
published pages: 14545, ISSN: 2041-1723, DOI: 10.1038/ncomms14545
Nature Communications 8 2019-09-17
2018 Siri Kellner, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, Tom A. Williams
Genome size evolution in the Archaea
published pages: 595-605, ISSN: 2397-8554, DOI: 10.1042/etls20180021
Emerging Topics in Life Sciences 2/4 2019-09-17
2017 Tom A. Williams, Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, T. Martin Embley
Integrative modeling of gene and genome evolution roots the archaeal tree of life
published pages: E4602-E4611, ISSN: 0027-8424, DOI: 10.1073/pnas.1618463114
Proceedings of the National Academy of Sciences 114/23 2019-09-17
2018 Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Celine Scornavacca, Gergely Szöllősi, Louxin Zhang, Éric Tannier, Vincent Daubin
RecPhyloXML: a format for reconciled gene trees
published pages: 3646-3652, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty389
Bioinformatics 34/21 2019-09-17

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