Reconstructing a dated tree of life using phylogenetic incongruence

Publications

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties

Author(s): Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti, Manolo Gouy, Dominique Madern
Published in: Molecular Biology and Evolution, Issue Volume 38, Issue 9, Pages 3754–3774, 2021, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab146

Nucleotide Usage Biases Distort Inferences of the Species Tree

Author(s): Rui Borges, Bastien Boussau, Gergely J Szöllősi, Carolin Kosiol
Published in: Genome Biology and Evolution, Issue Volume 14, Issue 1, evab290, 2022, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab290

The structure of the hematopoietic system can explain chronic myeloid leukemia progression.

Author(s): Pérez-Jiménez M, Derényi I, Szöllősi G.J.
Published in: Scientific Reports, Issue 13, 5411, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-32400-2

Distinguishing excess mutations and increased cell death based on variant allele frequencies

Author(s): Gergely Tibély, Dominik Schrempf, Imre Derényi , Gergely J. Szöllősi
Published in: PLoS Computational Biology, Issue 18(4): e1010048, 2022, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1010048

ATP synthase evolution on a cross-braced dated tree of life

Author(s): Tara A. Mahendrarajah, Edmund R. R. Moody, Dominik Schrempf, Lénárd L. Szánthó, Nina Dombrowski, Adrián A. Davín, Davide Pisani, Philip C. J. Donoghue, Gergely J. Szöllősi, Tom A. Williams, Anja Spang
Published in: Nature Communications, Issue 14, 2023, Page(s) 7456, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42924-w

SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss

Author(s): Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A Williams, Gergely J Szöllősi, Alexandros Stamatakis
Published in: Molecular Biology and Evolution, Issue Volume 39, Issue 2, msab365,, 2022, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab365

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

Author(s): Brogan J. Harris, James W. Clark, Dominik Schrempf, Gergely J. Szöllősi, Philip C. J. Donoghue, Alistair M. Hetherington , Tom A. Williams
Published in: Nature Ecology and Evolution, Issue 6, 1634–1643, 2022, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-022-01885-x

Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization

Author(s): Demeter M., Derényi I., Szöllősi G.J.
Published in: Nature Communications, Issue 13, 1666, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29004-1

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Author(s): Miyauchi Shingo; Kiss Enikő; Kuo Alan; Drula Elodie; Kohler Annegret; SánchezGarcía Marisol; Morin Emmanuelle; Andreopoulos Bill; Barry Kerrie W.; Bonito Gregory; Buée Marc; Carver Akiko; Chen Cindy; Cichocki Nicolas; Clum Alicia; Culley David; Crous Pedro W.; Fauchery Laure; Girlanda Mariangela; Hayes Richard D.; Kéri Zsófia; LaButti Kurt; Lipzen
Published in: Nature Communications, Issue 11, 5125, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18795-w

Divergent genomic trajectories predate the origin of animals and fungi

Author(s): Ocaña-Pallarès Eduard; Williams Tom A.; López-Escardó David ; Arroyo Alicia S. ; Pathmanathan Jananan S. ; Bapteste Eric ; Tikhonenkov Denis V. ; Keeling Patrick J. ; Szöllősi Gergely J. ; Ruiz-Trillo Iñaki
Published in: Nature, Issue 609, 747–753, 2022, ISSN 1476-4687
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-05110-4

An estimate of the deepest branches of the tree of life from ancient vertically evolving genes

Author(s): Edmund RR Moody, Tara A Mahendrarajah, Nina Dombrowski, James W Clark, Celine Petit, jean Pierre Offre, Gergely J Szöllősi, Anja Spang, Tom A Williams
Published in: eLife, Issue 66695, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.66695

Compositionally Constrained Sites Drive Long-Branch Attraction

Author(s): Lénárd L Szánthó, Nicolas Lartillot, Gergely J Szöllősi, Dominik Schrempf
Published in: Systematic Biolog, Issue Volume 72, Issue 4, Pages 767–780,, 2023, ISSN 1076-836X
Publisher: Oxford University Press
DOI: 10.1093/sysbio/syad013

Parameter Estimation and Species Tree Rooting Using ALE and GeneRax

Author(s): Tom A Williams, Adrián A Davín, Benoit Morel, Lénárd L Szánthó, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J Szöllősi
Published in: Genome Biology and Evolution, Issue Volume 15, Issue 7, evad134, 2023, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evad134

Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy

Author(s): Peter G Foster; Dominik Schrempf; Gergely J Szöllősi; Tom A Williams; Cymon J Cox; T Martin Embley
Published in: Systematic Biology, Issue Volume 72, Issue 3, Pages 723–737, 2023, ISSN 1076-836X
Publisher: Oxford University Press
DOI: 10.1093/sysbio/syac042

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Author(s): Tom A. Williams, Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, T. Martin Embley
Published in: Proceedings of the National Academy of Sciences, Issue 114/23, 2017, Page(s) E4602-E4611, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1618463114

RecPhyloXML: a format for reconciled gene trees

Author(s): 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
Published in: Bioinformatics, Issue 34/21, 2018, Page(s) 3646-3652, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty389

Genome size evolution in the Archaea

Author(s): Siri Kellner, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, Tom A. Williams
Published in: Emerging Topics in Life Sciences, Issue 2/4, 2018, Page(s) 595-605, ISSN 2397-8554
Publisher: Siri Kellner, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, Tom A. Williams
DOI: 10.1042/etls20180021

Hierarchical tissue organization as a general mechanism to limit the accumulation of somatic mutations

Author(s): Imre Derényi, Gergely J. Szöllősi
Published in: Nature Communications, Issue 8, 2017, Page(s) 14545, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms14545

Phylogenomics provides robust support for a two-domains tree of life

Author(s): Tom A. Williams, Cymon J. Cox, Peter G. Foster, Gergely J. Szöllősi, T. Martin Embley
Published in: Nature Ecology & Evolution, Issue 4/1, 2020, Page(s) 138-147, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-019-1040-x

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

Author(s): Adrián A Davín, Théo Tricou, Eric Tannier, Damien M de Vienne, Gergely J Szöllősi
Published in: Bioinformatics, Issue 36/4, 2019, Page(s) 1286-1288, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz710

Gene transfers can date the tree of life

Author(s): Adrián A. Davín, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szöllősi
Published in: Nature Ecology & Evolution, Issue 2/5, 2018, Page(s) 904-909, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-018-0525-3

Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity

Author(s): Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosiol
Published in: Molecular Biology and Evolution, Issue 36/6, 2019, Page(s) 1294-1301, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz043

IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era

Author(s): Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear
Published in: Molecular Biology and Evolution, Issue ACCEPTED MANUSCRIPT, 2020, Page(s) msaa015, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa015

Scalable empirical mixture models that account for across-site compositional heterogeneity

Author(s): Dominik Schrempf, Nicolas Lartillot, Gergely Szöllősi
Published in: Molecular Biology and Evolution, Issue accepted pending revision, 2020, ISSN 0737-4038
Publisher: Oxford University Press

A compartment size-dependent selective threshold limits mutation accumulation in hierarchical tissues

Author(s): Dániel Grajzel, Imre Derényi, Gergely J. Szöllősi
Published in: Proceedings of the National Academy of Sciences, Issue 117/3, 2020, Page(s) 1606-1611, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1913104117

Megaphylogeny resolves global patterns of mushroom evolution

Author(s): 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
Published in: Nature Ecology & Evolution, Issue 3/4, 2019, Page(s) 668-678, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-019-0834-1

GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss

Author(s): Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely J. Szöllősi
Published in: Molecular Biology and Evolution, Issue to appear, 2020, ISSN 0737-4038
Publisher: Oxford University Press

MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers

Author(s): Cédric Chauve, Akbar Rafiey, Adrián A. Davín, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J. Szöllősi, Vincent Daubin, Eric Tannier
Published in: bioRxiv, Issue 10.1101/127548, 2017, Page(s) peer-reviewed and recommended by Peer Community In Evolutionary Biology. 10.24072/pci.evolbiol.100037, ISSN 2551-668X
Publisher: Peer Community In Evolutionary Biology
DOI: 10.1101/127548

Inferring the Deep Past from Molecular Data

Author(s): Tom A Williams, Dominik Schrempf, Gergely J Szöllősi, Cymon J Cox, Peter G Foster, T Martin Embley
Published in: Genome Biology and Evolution, Issue Volume 13, Issue 5, evab067, 2021, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab067

Relative Time Constraints Improve Molecular Dating

Author(s): Gergely J Szöllõsi, Sebastian Höhna, Tom A Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau
Published in: Systematic Biology, Issue Volume 71, Issue 4, Pages 797–809, 2022, ISSN 1076-836X
Publisher: Oxford University Press
DOI: 10.1093/sysbio/syab084

A rooted phylogeny resolves early bacterial evolution

Author(s): GARETH A. COLEMAN; ADRIÁN A. DAVÍN; TARA A. MAHENDRARAJAH; LÉNÁRD L. SZÁNTHÓ; ANJA SPANG; PHILIP HUGENHOLTZ; GERGELY J. SZÖLLŐSI; TOM A. WILLIAMS;
Published in: Science, Issue Vol 372, Issue 6542, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abe0511

Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets

Author(s): László G. Nagy, Gergely Szöllősi
Published in: Fungal Phylogenetics and Phylogenomics, Issue 100, 2017, Page(s) 49-72, ISBN 9780-128132616
Publisher: Elsevier
DOI: 10.1016/bs.adgen.2017.09.008

The Sources of Phylogenetic Conflicts

Author(s): Schrempf, Dominik; Szöllősi, Gergely
Published in: Phylogenetics in the Genomic Era, eds. Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas., Issue pp.3.1:1--3.1:23, 2020
Publisher: No commercial publisher | Authors open access book

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