ModelFinder: fast model selection for accurate phylogenetic estimates

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1. OMA standalone: orthology inference among public and custom genomes and transcriptomes
   Adrian Altenhoff, Jeremy Levy, Magdalena Zarowiecki, Bartłomiej Tomiczek, Alex Warwick Vesztrocy, Daniel A. Dalquen, Steven Müller, Maximilian J. Telford, Natasha M. Glover, David Dylus et al. · 2019 · Genome Research
2. Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies
   Aleš Buček, Jan Šobotník, Shulin He, Mǎng Shī, Dino Peter McMahon, Edward Charles Holmes, Yves Roisin, Nathan C. Lo, Thomas Bourguignon · 2019 · Current Biology
3. Characterization of the First “ Candidatus Nitrotoga” Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria
   Katharina Kitzinger, Hanna Koch, Sebastian Lücker, Christopher J. Sedlacek, Craig William Herbold, Jasmin Schwarz, Anne Daebeler, Anna J. Mueller, Michael Lukumbuzya, Stefano Romano et al. · 2018 · mBio
4. The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis
   Fengchao Jiang, Junhuan Zhang, Sen Wang, Li Yang, Yingfeng Luo, Shenghan Gao, Meiling Zhang, Shuangyang Wu, Songnian Hu, Haoyuan Sun et al. · 2019 · Horticulture Research
5. An ancestral function of strigolactones as symbiotic rhizosphere signals
   Kyoichi Kodama, Mélanie K. Rich, Akiyoshi Yoda, Shota Shimazaki, Xiaonan Xie, Kohki Akiyama, Yohei Mizuno, Aino Komatsu, Yi Luo, Hidemasa Suzuki et al. · 2022 · Nature Communications
6. V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity
   Junxian Ou, Zhonghua Zhou, Ruixue Dai, Jing Zhang, Shan Zhao, Xiaowei Wu, Wendong Lan, Yi Ren, Lilian Cui, Qiaoshuai Lan et al. · 2021 · Journal of Virology
7. Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics
   Catherine S. McFadden, Leen P. van Ofwegen, Andrea M. Quattrini · 2022 · Bulletin of the Society of Systematic Biologists
8. The evolution and clinical impact of hepatitis B virus genome diversity
   Peter A. Revill, Thomas Tu, Hans Jürgen Netter, Lilly K. W. Yuen, STEPHEN A LOCARNINI, Margaret Littlejohn · 2020 · Nature Reviews Gastroenterology & Hepatology
9. Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites
   R. W. Briddon, Darren Patrick Martin, Philippe Roumagnac, Jesús Navas‐Castillo, Elvira Fiallo‐Olivé, Enrique Moriones, Jean‐Michel Lett, Francisco Murilo Zerbini Júnior, Arvind Varsani · 2018 · Archives of Virology
10. A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error
    Jesús A. Ballesteros, Prashant P. Sharma · 2019 · Systematic Biology
11. Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae)
    Claudia L. Henriquez, Abdullah Abdullah, Ibrar Ahmed, Mónica M. Carlsen, Alejandro Zuluaga, Thomas Bernard Croat, Michael R. McKain · 2020 · Genomics
12. The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion
    Huamei Xiao, Xin-Hai Ye, Hong-Xing Xu, Yang Mei, Yi Yang, Xi Chen, Ya-Jun Yang, Tao Liu, Yongyi Yu, Wei-Fei Yang et al. · 2020 · Molecular Ecology Resources
13. Rooting the Animal Tree of Life
    Li, Yuanning, Shen, Xing-Xing, Evans, Benjamin, Dunn, Casey W, Rokas, Antonis · 2021 · Molecular Biology and Evolution
14. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation
    Ola Brønstad Brynildsrud, Caitlin S. Pepperell, Philip Noël Suffys, Louis Grandjean, Johana Monteserin, Nadia Debech, Jon Bohlin, Kristian Alfsnes, John H.‐O. Pettersson, Ingerid Ørjansen Kirkeleite et al. · 2018 · Science Advances
15. Widespread endogenization of giant viruses shapes genomes of green algae
    Mohammad Moniruzzaman, Alaina Weinheimer, Carolina A. Martínez-Gutiérrez, Frank O. Aylward · 2020 · Nature
16. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm
    Stephen R. Doyle, Alan Tracey, Roz Laing, Nancy E. Holroyd, David J. Bartley, Wojtek Bazant, Helen L. Beasley, Robin N. Beech, Collette Britton, Karen L. Brooks et al. · 2020 · Communications Biology
17. Fungal Planet description sheets: 1284–1382
    Pedro Willem Crous, E R Osieck, Ž Jurjević, Jannes Boers, A.L. van Iperen, Mieke Starink-Willemse, Bálint Dima, Sergey V. Balashov, Timur S. Bulgakov, Peter R. Johnston et al. · 2021 · Persoonia - Molecular Phylogeny and Evolution of Fungi
18. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas
    Pablo Vinuesa, Luz Edith Ochoa-Sánchez, Bruno Contreras‐Moreira · 2018 · Frontiers in Microbiology
19. Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce
    Tong Wei, R. van Treuren, Xinjiang Liu, Zhaowu Zhang, Jiongjiong Chen, Yang Liu, Shanshan Dong, Peinan Sun, Tianming Lan, Tianming Lan et al. · 2021 · Nature Genetics
20. Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding
    Redmond, Anthony K., McLysaght, Aoife · 2021 · Nature Communications
21. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes
    Julien Guglielmini, Anthony C. Woo, Mart Krupovìč, Patrick Forterre, Morgan Gaïa · 2019 · Proceedings of the National Academy of Sciences
22. Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle in the United States
    Thao-Quyen Nguyen, Carl R. Hutter, Alexey Markin, Megan N. Thomas, Kristina Lantz, Mary Lea Killian, Garrett M. Janzen, Sriram Vijendran, Sanket Wagle, Blake Inderski et al. · 2025 · Science
23. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
    Zheng‐Shuang Hua, Yulin Wang, Paul N. Evans, Yan-Ni Qu, Kian Mau Goh, Yang-Zhi Rao, Yan-Ling Qi, Yu-Xian Li, Min‐Jun Huang, Jian‐Yu Jiao et al. · 2019 · Nature Communications
24. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria
    Jian‐Yu Jiao, Li Fu, Zheng‐Shuang Hua, Lan Liu, Nimaichand Salam, Pengfei Liu, Ai-Ping Lv, Geng Wu, Wen-Dong Xian, Qiyun Zhu et al. · 2021 · The ISME Journal
25. Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism
    Disa Bäckström, Natalya Yutin, Steffen L. Jørgensen, Jennah E. Dharamshi, Félix Homa, Katarzyna Zaremba-Niedźwiedzka, Anja Spang, Yuri I. Wolf, Eugene V. Koonin, Thijs J. G. Ettema · 2019 · mBio
26. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution
    Yong-Zhi Yang, Pengchuan Sun, Leke Lv, Donglei Wang, Da-Fu Ru, Ying Li, Tao Ma, Lei Zhang, Xing-Xing Shen, Fan-Bo Meng et al. · 2020 · Nature Plants
27. Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
    Sarah R. Smith, Christopher L. Dupont, James K. McCarthy, Jared T. Broddrick, Miroslav Obornı́k, Aleš Horák, Zoltán Füssy, Jaromír Cihlář, Sabrina Kleeßen, Hong Zheng et al. · 2019 · Nature Communications
28. Characterizing gene tree conflict in plastome-inferred phylogenies
    Joseph F. Walker, Gregory W. Stull, Nathanael Walker‐Hale, Oscar M. Vargas, Drew A. Larson · 2019 · PeerJ
29. Incomplete lineage sorting and phenotypic evolution in marsupials
    Shaohong Feng, Ming Bai, Iker Rivas-González, Cai Li, Shiping Liu, Yijie Tong, Haidong Yang, Guangji Chen, Duo Xie, Karen E. Sears et al. · 2022 · Cell
30. The critically endangered vaquita is not doomed to extinction by inbreeding depression
    Jacqueline A. Robinson, Christopher C. Kyriazis, Sergio F. Nigenda‐Morales, Annabel C. Beichman, Lorenzo Rojas‐Bracho, Kelly M. Robertson, Michaël C. Fontaine, Robert K. Wayne, Kirk E. Lohmueller, Barbara L. Taylor et al. · 2022 · Science
31. Non-photosynthetic predators are sister to red algae
    Gawryluk, Ryan M. R., Tikhonenkov, Denis V., Hehenberger, Elisabeth, Husnik, Filip, Mylnikov, Alexander P., Keeling, Patrick J. · 2019 · Nature
32. Extensive Diversity of RNA Viruses in Australian Ticks
    Erin Harvey, Karrie A. Rose, John‐Sebastian Eden, Nathan Lo, Thilanka Abeyasuriya, Mǎng Shī, Stephen Lindsay Doggett, Edward Charles Holmes · 2018 · Journal of Virology
33. Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)
    Kshitij Tandon, Chih-Ying Lu, Pei‐Wen Chiang, Naohisa Wada, Shan‐Hua Yang, Ya‐Fan Chan, Ping-Yun Chen, Hsiao-Yu Chang, Yu‐Jing Chiou, Ming-Shean Chou et al. · 2020 · The ISME Journal
34. Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans
    Daehan Lee, Stefan Zdraljevic, Lewis Stevens, Ye Wang, Robyn E. Tanny, Timothy A. Crombie, Daniel E. Cook, Amy K. Webster, Rojin Chirakar, L. Ryan Baugh et al. · 2021 · Nature Ecology & Evolution
35. Glacier ice archives nearly 15,000-year-old microbes and phages
    Zhi-Ping Zhong, Funing Tian, Simon Roux, María Consuelo Gazitúa, Natalie Solonenko, Yueh-Fen Li, M. E. Davis, James L. Van Etten, Ellen Mosley‐Thompson, Virginia I. Rich et al. · 2021 · Microbiome
36. Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: Comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae
    Iram Shahzadi, Abdullah Abdullah, Furrukh Mehmood, Zain Ali, Ibrar Ahmed, Bushra Mirza · 2019 · Genomics
37. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae)
    Claudia L. Henriquez, Abdullah Abdullah, Ibrar Ahmed, Mónica M. Carlsen, Alejandro Zuluaga, Thomas Bernard Croat, Michael R. McKain · 2020 · Planta
38. Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus
    Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, Christian Schröck, Paul Lamkowski, Jeremy Schmutz, Adam L. Healey, Bryan Thomas Piatkowski, A. Jonathan Shaw, David J. Weston et al. · 2021 · Molecular Biology and Evolution
39. Evolution of asexual and sexual reproduction in the aspergilli
    M. Ojeda-López, Wanping Chen, Carly E. Eagle, Gabriel Gutiérrez, Lili Jia, Sameira S. Swilaiman, Z. Huang, Hyo‐Sang Park, J.-H. Yu, David Cánovas et al. · 2018 · Studies in Mycology
40. Cell-Fusing Agent Virus Reduces Arbovirus Dissemination in Aedes aegypti Mosquitoes In Vivo
    Artem Baidaliuk, Elliott F. Miot, Sébastian Lequime, Isabelle Moltini-Conclois, Fanny Delaigue, Stéphanie Dabo, Laura B. Dickson, Fabien Aubry, Sarah Hélène Merkling, Van‐Mai Cao‐Lormeau et al. · 2019 · Journal of Virology
41. Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond
    Laura M. Carroll, Rachel A. Cheng, Martin Wiedmann, Jasna Kovač · 2021 · Critical Reviews in Food Science and Nutrition
42. Fungal Planet description sheets: 1182–1283
    Pedro Willem Crous, Don Arthur Cowan, Gillian Maggs‐Kölling, Neriman Yılmaz, R. Thangavel, Michael J. Wingfield, Machiel Evert Noordeloos, Bálint Dima, Tor Erik Brandrud, Gerrit Maarten Jansen et al. · 2021 · Persoonia - Molecular Phylogeny and Evolution of Fungi
43. Timing the evolution of antioxidant enzymes in cyanobacteria
    Joanne Sarah Boden, Kurt O. Konhauser, Leslie J. Robbins, Patricia Sánchez‐Baracaldo · 2021 · Nature Communications
44. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences
    Daqi Yu, Yandong Ren, Masahiro Uesaka, Alan J. S. Beavan, Matthieu Muffato, Jieyu Shen, Yongxin Li, Iori Sato, Wenting Wan, James Clark et al. · 2024 · Nature Ecology & Evolution
45. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
    Feng Liu, Jiantao Zhao, Honghe Sun, Cheng Xiong, Xuepeng Sun, Xin Wang, Zhongyi Wang, Robert L. Jarret, Jin Wang, Bingqian Tang et al. · 2023 · Nature Communications
46. Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains
    Fabien Aubry, Sofie Jacobs, Maïlis Darmuzey, Sébastian Lequime, Leen Delang, Albin Fontaine, Natapong Jupatanakul, Elliott F. Miot, Stéphanie Dabo, Caroline Manet et al. · 2021 · Nature Communications
47. Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae
    Furrukh Mehmood, Abdullah Abdullah, Iram Shahzadi, Ibrar Ahmed, Mohammad Tahir Waheed, Bushra Mirza · 2019 · Genomics
48. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes
    Yunxia Li, LI Zhang-hai, André Schuiteman, Mark W. Chase, Jianwu Li, Wei‐Chang Huang, Arief Hidayat, Shasha Wu, Xiaohua Jin · 2019 · Molecular Phylogenetics and Evolution
49. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins
    2019
50. The Mosaic Genome of Indigenous African Cattle as a Unique Genetic Resource for African Pastoralism
    Kim, Kwondo, Kwon, Taehyung, Dessie, Tadelle, Yoo, DongAhn, Mwai, Okeyo Ally, Jang, Jisung, Sung, Samsun, Lee, SaetByeol, Salim, Bashir, Jung, Jaehoon et al. · 2020 · Nature Genetics
51. Phylogenomics from low‐coverage whole‐genome sequencing
    Feng Zhang, Yinhuan Ding, Chao‐Dong Zhu, Xin Yu Zhou, Michael C. Orr, Stefan Scheu, Yun‐Xia Luan · 2019 · Methods in Ecology and Evolution
52. Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths
    Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, Emil Karpinski, Dirk Hackenberger, Paul Szpak, Jorge G. Martínez, Jim I. Mead, H. Gregory McDonald, R. D. E. MacPhee et al. · 2019 · Current Biology
53. Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses
    Dinah Henritzi, Philipp P. Petric, Nicola S. Lewis, Annika Graaf, Alberto Pessia, Elke Starick, Angele Breithaupt, Günter Strebelow, Christine Luttermann, Larissa Mareike Kristin Parker et al. · 2020 · Cell Host & Microbe
54. Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)
    Tianlong Cai, Alice Cibois, Per Alström, Robert G. Moyle, Jonathan D. Kennedy, Shimiao Shao, Ruiying Zhang, Martin Irestedt, Per G. P. Ericson, Magnus Gelang et al. · 2018 · Molecular Phylogenetics and Evolution
55. Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
    Tamara Villaverde, Lisa Pokorny, Sanna Olsson, Mario Rincón Barrado, Matthew G. Johnson, Elliot M. Gardner, Norman J. Wickett, Julià Molero, Ricarda Riina, Isabel Sanmartín · 2018 · New Phytologist
56. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida
    Jesús Lozano-Fernández, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani · 2019 · Nature Communications
57. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts
    Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, David Alejandro Duchêne, Lara Puetz, Tom O. Delmont, Harald Sveier, Louise von Gersdorff Jørgensen, Kim Præbel, Michael D. Martin, Anders Miki Bojesen et al. · 2021 · Communications Biology
58. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
    Jakub Barylski, François Enault, Bas E. Dutilh, Margo B. P. Schuller, Robert Alan Edwards, Annika Gillis, Jochen Klumpp, Petar Knežević, Mart Krupovìč, Jens H. Kuhn et al. · 2019 · Systematic Biology
59. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas
    Adrián Cazares, Matthew Moore, James P. J. Hall, Laura L. Wright, Macauley Grimes, Jean-Guillaume Emond-Rhéault, Pisut Pongchaikul, Pitak Santanirand, Roger C. Lévesque, Joanne L. Fothergill et al. · 2020 · Nature Communications
60. Redefining species limits in the Fusarium fujikuroi species complex
    Neriman Yılmaz, Marcelo Sandoval‐Denis, L. Lombard, Cobus M. Visagie, Brenda Diana Wingfield, Pedro Willem Crous · 2021 · Persoonia - Molecular Phylogeny and Evolution of Fungi
61. The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families
    Sophie de Vries, Janine M. R. Fürst‐Jansen, Iker Irisarri, Amra Dhabalia Ashok, Till Ischebeck, Kirstin Feussner, Ilka Nacif Abreu, Maike Petersen, Ivo Feußner, Jan de Vries · 2021 · The Plant Journal
62. The evolution of insect biodiversity
    Erik Tihelka, Chenyang Cai, Mattia Giacomelli, Jesús Lozano-Fernández, Omar Rota‐Stabelli, Diying Huang, Michael S. Engel, Philip C. J. Donoghue, Davide Pisani · 2021 · Current Biology
63. Increased fidelity of protein synthesis extends lifespan
    Victoria Eugenia Martinez-Miguel, Celia Lujan, Tristan Espie-Caullet, Daniel Martínez‐Martínez, Saul Moore, Cassandra Backes, Suam Gonzalez, Evgeniy R. Galimov, André EX Brown, Mario Halić et al. · 2021 · Cell Metabolism
64. A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
    Jacob Lucas Steenwyk, Xing‐Xing Shen, Abigail Lind, Gustavo Henrique Goldman, Antonis Rokas · 2019 · mBio
65. Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets
    Martin Ross Smith · 2019 · Biology Letters
66. The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization
    Suvi Sutela, Marco Forgia, Eeva J. Vainio, Marco Chiapello, Stefania Daghino, Marta Vallino, Elena Miranda De Martino, Mariangela Girlanda, Silvia Perotto, Massimo Turina · 2020 · Virus Evolution
67. A ligand-independent origin of abscisic acid perception
    Yufei Sun, Ben Harpazi, Akila Wijerathna Yapa, Ebe Merilo, Jan de Vries, Daphna Michaeli, Maayan Gal, Andrew C. Cuming, Hannes Kollist, Assaf Mosquna · 2019 · Proceedings of the National Academy of Sciences
68. Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous
    Ava Ghezelayagh, Richard C. Harrington, Edward D. Burress, Matthew A. Campbell, Janet C. Buckner, Prosanta Chakrabarty, Jessica R. Glass, W. Tyler McCraney, Peter J. Unmack, Christine E. Thacker et al. · 2022 · Nature Ecology & Evolution
69. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
    Migun Shakya, Sanaa A. Ahmed, Karen W. Davenport, Mark Flynn, Chien‐Chi Lo, Patrick Chain · 2020 · Scientific Reports
70. An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion
    Yang Liu, Zhen Zeng, Yanmei Zhang, Qian Li, Xing‐Mei Jiang, Zhen Jiang, Ji-Hong Tang, Dijun Chen, Qiang Wang, Jian‐Qun Chen et al. · 2021 · Molecular Plant
71. The evolutionary origins of the cat attractant nepetalactone in catnip
    Benjamin R. Lichman, Grant T. Godden, John P. Hamilton, Lira Palmer, Mohamed Omar Kamileen, Dongyan Zhao, Brieanne Vaillancourt, Joshua C. Wood, Miao Sun, Taliesin J. Kinser et al. · 2020 · Science Advances
72. Genome Evolution of the Obligate Endosymbiont Buchnera aphidicola
    Rebecca A. Chong, Hyun-Jin Park, Nancy A. Moran · 2019 · Molecular Biology and Evolution
73. Joining the club: First detection of African swine fever in wild boar in Germany
    Carola Sauter‐Louis, Jan Hendrik Forth, Carolina Probst, Christoph Staubach, Andreas Hlinak, Annett Rudovsky, Diana Holland, Patricia Schlieben, Melanie Göldner, Juliane Schatz et al. · 2020 · Transboundary and Emerging Diseases
74. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae)
    Liming Cai, Brian Arnold, Zhenxiang Xi, Danielle E. Khost, Niki Patel, Claire B. Hartmann, M. Sugumaran, Sawitree Sasirat, Lachezar A. Nikolov, Sarah Mathews et al. · 2021 · Current Biology
75. Clade I mpox virus genomic diversity in the Democratic Republic of the Congo, 2018–2024: Predominance of zoonotic transmission
    Eddy Kinganda-Lusamaki, Adrienne Amuri-Aziza, Nicolas Fernandez, Jean-Claude Makangara-Cigolo, Catherine B. Pratt, Emmanuel Hasivirwe Vakaniaki, Nicole A. Hoff, Gradi Luakanda-Ndelemo, Prince Akil-Bandali, Sabin Sabiti Nundu et al. · 2024 · Cell
76. Multiple independent origins of apicomplexan-like parasites
    Mathur, Varsha, Kolísko, Martin, Hehenberger, Elisabeth, Irwin, Nicholas A.T., Leander, Brian S., Kristmundsson, Árni, Freeman, Mark A., Keeling, Patrick J. · 2019 · Current Biology
77. COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses
    Zhiyuan Chen, Joseph L.-H. Tsui, Bernardo Gutiérrez, Simon Busch‐Moreno, Louis du Plessis, Xiaowei Deng, Jun Cai, Sumali Bajaj, Marc A. Suchard, Oliver G. Pybus et al. · 2024 · Science
78. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria
    Muñoz-Gómez, Sergio A., Susko, Edward, Williamson, Kelsey, Eme, Laura, Slamovits, Claudio H., Moreira, David, López-García, Purificación, Roger, Andrew J. · 2022 · Nature Ecology & Evolution
79. Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli
    Yong Wang, Jiao‐Mei Huang, Yingli Zhou, Alexandre Almeida, Robert D. Finn, Antoine Danchin, Lisheng He · 2020 · BMC Genomics
80. Mirusviruses link herpesviruses to giant viruses
    Gaïa, Morgan, Meng, Lingjie, Pelletier, Eric, Forterre, Patrick, Vanni, Chiara, Fernandez-Guerra, Antonio, Jaillon, Olivier, Wincker, Patrick, Ogata, Hiroyuki, Krupovic, Mart et al. · 2023 · Nature
81. Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update
    Pablo Cruz‐Morales, Camila A. Orellana, George Moutafis, Glenn Moonen, Gonzalo Rincón, Lars Keld Nielsen, Esteban Marcellin · 2019 · Genome Biology and Evolution
82. The complete sequence and comparative analysis of ape sex chromosomes
    Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris, Gabrielle A. Hartley, Monika Čechová, Karol Pál, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar et al. · 2024 · Nature
83. Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
    Soo Jen Low, Mária Džunková, Pierre-Alain Chaumeil, Donovan H. Parks, Philip Hugenholtz · 2019 · Nature Microbiology
84. Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes
    Xue-Bing Ni, Xiaoming Cui, Jinyue Liu, Run‐Ze Ye, Yuqian Wu, Jia-Fu Jiang, Yi Eve Sun, Qian Wang, Marcus Ho-Hin Shum, Qiao‐Cheng Chang et al. · 2023 · Nature Microbiology
85. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
    Xuehuan Feng, Jinfang Zheng, Iker Irisarri, Huihui Yu, Bo Zheng, Zahin Mohd Ali, Sophie de Vries, Jean Keller, Janine M. R. Fürst‐Jansen, Armin Dadras et al. · 2024 · Nature Genetics
86. QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution
    Bùi Quang Minh, Cuong Cao Dang, Vinh Sy Le, Robert Lanfear · 2021 · Systematic Biology
87. Genome and transcriptome mechanisms driving cephalopod evolution
    Caroline B. Albertin, Sofía Medina-Ruiz, Therese Mitros, Hannah Schmidbaur, Gustavo Sánchez, Z. Yan Wang, Jane Grimwood, Joshua J. C. Rosenthal, Clifton W. Ragsdale, Oleg Simakov et al. · 2022 · Nature Communications
88. Evidence for contemporary plant mitoviruses
    Max L. Nibert, Minh Vong, Karen Klotz Fugate, Humberto Debat · 2018 · Virology
89. Evolution on the backbone: Apocynaceae phylogenomics and new perspectives on growth forms, flowers, and fruits
    Mark Fishbein, Tatyana Livshultz, Shannon C. K. Straub, André Olmos Simões, Julien Boutte, Angela McDonnell, Abbey Foote · 2018 · American Journal of Botany
90. Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling
    Jesús Lozano-Fernández, Mattia Giacomelli, James F. Fleming, Albert Chen, Jakob Vinther, Philip Francis Thomsen, Henrik Glenner, Ferran Palero, Legg David, Thomas M. Iliffe et al. · 2019 · Genome Biology and Evolution
91. Chloranthus genome provides insights into the early diversification of angiosperms
    Xing Guo, Dongming Fang, Sunil Kumar Sahu, Shuai Yang, Xuanmin Guang, Ryan A. Folk, Stephen A. Smith, André S. Chanderbali, Sisi Chen, Min Liu et al. · 2021 · Nature Communications
92. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants
    Danyan Su, Lingxiao Yang, Xuan Shi, Xiaoya Ma, Xiaofan Zhou, S. Blair Hedges, Bojian Zhong · 2021 · Molecular Biology and Evolution
93. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
    Timothy G. Stephens, Raúl A. González‐Pech, Yuanyuan Cheng, Amin R. Mohamed, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan · 2020 · BMC Biology
94. Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa
    Jorge A. Moura de Sousa, Eugen Pfeifer, Marie Touchon, Eduardo P. C. Rocha · 2021 · Molecular Biology and Evolution
95. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil
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96. The evolutionary history of bees in time and space
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