ModelFinder: fast model selection for accurate phylogenetic estimates

Kalyaanamoorthy, Subha, Minh, Bui Quang, Wong, Thomas K F, von Haeseler, Arndt, Jermiin, Lars S·2017·Nature Methods

DOI 10.1038/nmeth.4285

Cited by (1,026)

Items 701–800 of 1,026

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Alexey A. Kotov, Petr G. Garibian, Eugeniya I. Bekker, Derek J. Taylor, Карабанов Дмитрий Павлович · 2020 · Zoological Journal of the Linnean Society
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Matthew A. Kolmann, Lily C. Hughes, Luz Patricia Hernandez, Dahiana Arcila, Ricardo Betancur‐R, Mark Henry Sabaj, Hernán López‐Fernández, Guillermo Ortı́ · 2020 · Systematic Biology
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Barbara J. Sharanowski, Ryan D. Ridenbaugh, Patrick Piekarski, Gavin R. Broad, Gaelen R. Burke, ANDREW ROBERT DEANS, Alan R. Lemmon, Emily Claire Moriarty Lemmon, Gloria J. Diehl, James B. Whitfield et al. · 2020 · Molecular Phylogenetics and Evolution
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Rui Zhao, José Manuel Mogollón, Sophie S. Abby, Christa Schleper, Jennifer F. Biddle, Desiree L. Roerdink, Ingunn H. Thorseth, Steffen L. Jørgensen · 2020 · Proceedings of the National Academy of Sciences
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Mathu Malar C, Manuela Krüger, Claudia Krüger, Yan Wang, Jason Stajich, Jean Keller, Eric C.H. Chen, Gökalp Yildirir, Matthew Villeneuve‐Laroche, Christophe Paul Roux et al. · 2021 · Current Biology
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Eric Kuhnert, Jorge Carlos Navarro-Muñoz, Kevin Becker, Marc Stadler, Jérôme Collemare, Russell John Cox · 2021 · Studies in Mycology
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Dinesh Aggarwal, Ben Warne, Aminu S. Jahun, William L. Hamilton, Thomas Fieldman, Louis du Plessis, Verity Hill, Beth Blane, Emmeline Watkins, Elizabeth Wright et al. · 2022 · Nature Communications
Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment
Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Pausch, Hubert, Leonard, Alexander S., Crysnanto, Danang, Wang, Shikang et al. · 2023 · Genome biology
Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids
Cenci, Ugo, Sibbald, Shannon J., Curtis, Bruce A., Kamikawa, Ryoma, Eme, Laura, Moog, Daniel, Henrissat, Bernard, Maréchal, Eric, Chabi, Malika, Djemiel, Christophe et al. · 2018 · BMC Biology
Ancient co-option of an amino acid ABC transporter locus in Pseudomonas syringae for host signal-dependent virulence gene regulation
Qing Yan, Conner J. Rogan, Yin-Yuin Pang, Edward W. Davis, Jeffrey C. Anderson · 2020 · PLoS Pathogens
100-My history of bornavirus infections hidden in vertebrate genomes
Junna Kawasaki, Shohei Kojima, Yahiro Mukai, Keizō Tomonaga, Masayuki Horie · 2021 · Proceedings of the National Academy of Sciences
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Estimation of species divergence times in presence of cross-species gene flow
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Andrea M. Quattrini, Luke J. McCartin, Erin E. Easton, Jeremy Horowitz, Herman H. Wirshing, Hailey Bowers, Kenneth Mitchell, María del P. González‐García, Makiri Sei, Catherine S. McFadden et al. · 2024 · Ecology and Evolution
True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra subspinipes
Jennifer J. L. Smith, Eivind A. B. Undheim · 2018 · Toxins
Invertebrate Iridoviruses: A Glance over the Last Decade
İkbal Agah İnce, Orhan Özcan, Ayca Zeynep İlter Akülke, Erin D. Scully, Arzu Özgen · 2018 · Viruses
Botulinum Neurotoxin-Producing Bacteria. Isn’t It Time that We Called a Species a Species?
Theresa J. Smith, Charles H. D. Williamson, Karen K. Hill, Jason W. Sahl, Paul Keim · 2018 · mBio
A transcriptome-based phylogenetic study of hard ticks (Ixodidae)
N. Pierre Charrier, Axelle Hermouet, Caroline Hervet, Albert Agoulon, Stephen C. Barker, Dieter Heylen, Céline Toty, Karen D. McCoy, Olivier Plantard, Claude Rispe · 2019 · Scientific Reports
Systematic Culturomics Shows that Half of Chicken Caecal Microbiota Members can be Grown in Vitro Except for Two Lineages of Clostridiales and a Single Lineage of Bacteroidetes
Magdaléna Crhánová, Daniela Karasová, Helena Juřicová, Jitka Matiasovicova, Eva Jahodářová, Tereza Kubasová, Zuzana Seidlerová, Alois Čížek, Ivan Rychlı́k · 2019 · Microorganisms
Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements
Perry L. Wood, Xianguang Guo, Scott L. Travers, Yong‐Chao Su, Karen V. Olson, Aaron M. Bauer, L. Lee Grismer, Cameron D. Siler, Robert G. Moyle, Michael J. Andersen et al. · 2020 · Molecular Phylogenetics and Evolution
Phylogenomic Insights into the Origin of Primary Plastids
Iker Irisarri, Jürgen F. H. Strassert, Fabien Burki · 2021 · Systematic Biology
Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants
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Genome of Hippophae rhamnoides provides insights into a conserved molecular mechanism in actinorhizal and rhizobial symbioses
Zefeng Wu, Hongyun Chen, Ya Pan, Huan Feng, Dongming Fang, Jun Yang, Yayu Wang, Jun Mo Yang, Sunil Kumar Sahu, Jianling Liu et al. · 2022 · New Phytologist
Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants
Fei Ye, Petr Kment, Dávid Rédei, Jiuyang Luo, Yanhui Wang, Stefan Martin Kuechler, Wei‐Wei Zhang, Pingping Chen, Haoyang Wu, Yanzhuo Wu et al. · 2022 · Cladistics
Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil
Felipe Gomes Naveca, Valdinete Alves do Nascimento, Victor Costa de Souza, André de Lima Guerra Corado, Fernanda Nascimento, George Silva, Matilde Mejía, Maria Júlia Brandão, Ágatha Costa, Débora Duarte et al. · 2022 · Microbiology Spectrum
Prokaryotic Argonaute Proteins as a Tool for Biotechnology
Ekaterina Kropocheva, Lidiya Lisitskaya, Aleksei Agapov, A. A. Musabirov, Andrey V. Kulbachinskiy, Daria Esyunina · 2022 · Molecular Biology
Highly pathogenic avian influenza A (H5N1) virus infections in wild carnivores connected to mass mortalities of pheasants in Finland
Niina Tammiranta, Marja Isomursu, Alice Fusaro, Minna Nylund, Tiina Nokireki, Edoardo Giussani, Bianca Zecchin, Calogero Terregino, Tuija Gadd · 2023 · Infection Genetics and Evolution
De novoAssembly and Comparative Analyses of Mitochondrial Genomes in Piperales
Runxian Yu, Xudong Chen, Lingjie Long, Matthias Jost, Ran Zhao, Lumei Liu, Jeffrey P. Mower, Claude W. dePamphilis, Stefan Wanke, Yuannian Jiao · 2023 · Genome Biology and Evolution
Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020–2022
Alexander M. P. Byrne, Joe James, Benjamin C. Mollett, Stephanie M. Meyer, Tom Lewis, Magdalena Czepiel, Amanda H. Seekings, Sahar Mahmood, Saumya S. Thomas, Craig S. Ross et al. · 2023 · Microbiology Spectrum
Convergent resistance to GABA receptor neurotoxins through plant–insect coevolution
Lei Guo, Xiaomu Qiao, Diler Haji, Tian-Hao Zhou, Zhihan Liu, Noah Kerness Whiteman, Jia Huang · 2023 · Nature Ecology & Evolution
Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation
Feyza Yilmaz, Charikleia Karageorgiou, Kwondo Kim, Petar Pajic, Kendra Scheer, Christine R. Beck, Ann‐Marie Torregrossa, Charles Lee, Ömer Gökçümen, Peter A. Audano et al. · 2024 · Science
Acquisition of virulence genes by a carrier strain gave rise to the ongoing epidemics of meningococcal disease in West Africa
Ola Brønstad Brynildsrud, Vegard Eldholm, Jon Bohlin, Kennedy Uadiale, Stephen Obaro, Dominique A. Caugant · 2018 · Proceedings of the National Academy of Sciences
Antarctic Streptomyces fildesensis So13.3 strain as a promising source for antimicrobials discovery
Kattia Núñez-Montero, Claudio Lamilla, Michel Abanto, Fumito Maruyama, Milko Alberto Jorquera, Andrés Santos, Jaime Martínez-Urtaza, Leticia Barrientos · 2019 · Scientific Reports
The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)
Maarten P. M. Vanhove, Andrew G. Briscoe, Michiel W. P. Jorissen, D. Timothy J. Littlewood, Tine Huyse · 2018 · BMC Genomics
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Emre İnak, Yasin Nazım Alpkent, Sultan Çobanoğlu, Wannes Dermauw, Thomas Van Leeuwen · 2019 · Experimental and Applied Acarology
Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway
Bryan Thomas Piatkowski, Karn Imwattana, Erin A. Tripp, David J. Weston, Adam L. Healey, Jeremy Schmutz, A. Jonathan Shaw · 2020 · Molecular Phylogenetics and Evolution
Genetic diversity of soil invertebrates corroborates timing estimates for past collapses of the West Antarctic Ice Sheet
Gemma E Collins, Ian D. Hogg, Peter Convey, Leopoldo G. Sancho, Don Arthur Cowan, W. Berry Lyons, Byron J. Adams, Diana H. Wall, T. G. Allan Green · 2020 · Proceedings of the National Academy of Sciences
Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis
Hui Qi Loh, Vincent Hervé, Andreas Brune · 2021 · Frontiers in Microbiology
Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers
Fiona Valerie Franklin‐Alming, Håkon Pedersen Kaspersen, Marit Andrea Klokkhammer Hetland, Ragna Bakksjø, Live Lingaas Nesse, Thongpan Leangapichart, Iren Høyland Löhr, Amar Anandrao Telke, Marianne Sunde · 2021 · Frontiers in Microbiology
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Picchianti, Lorenzo, Sánchez de Medina Hernández, Víctor, Zhan, Ni, Irwin, Nicholas AT, Groh, Roan, Stephani, Madlen, Hornegger, Harald, Beveridge, Rebecca, Sawa‐Makarska, Justyna, Lendl, Thomas et al. · 2023 · The EMBO Journal
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Laure Nicolas Annick Ries, Lakhansing Arun Pardeshi, Zhiqiang Dong, Kaeling Tan, Jacob Lucas Steenwyk, Ana Cristina Colabardini, Jaire Alves Ferreira Filho, Patrícia Alves de Castro, Lilian Pereira Silva, Nycolas Willian Preite et al. · 2020 · PLoS Pathogens
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Wenpan Dong, Yanlei Liu, Chao Xu, Yongwei Gao, Qingjun Yuan, Zhili Suo, Zhixiang Zhang, Jiahui Sun · 2021 · BMC Genomics
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Anne E. Thomas, Javier Igea, Heidi M. Meudt, Dirk C. Albach, William G. Lee, Andrew J. Tanentzap · 2021 · American Journal of Botany
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Jadranka Rota, Victoria Twort, Andrea Chiocchio, Carlos Peña, Christopher West Wheat, Lauri Kaila, Niklas Wahlberg · 2022 · Systematic Entomology
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Ian M. Rambo, Marguerite V. Langwig, Pedro Leão, Valerie De Anda, Brett J. Baker · 2022 · Nature Microbiology
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Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans
Mustafa O. Jibrin, Neha Potnis, Sujan Timilsina, Gerald V. Minsavage, Gary Edward Vallad, Pamela D. Roberts, Jeffrey B. Jones, Erica M. Goss · 2018 · Applied and Environmental Microbiology
Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species
Xiaoqin Li, Yunjuan Zuo, Xinxin Zhu, Shuai Liao, Jinshuang Ma · 2019 · International Journal of Molecular Sciences
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Osvaldo Ulloa, Carlos Henríquez‐Castillo, Salvador Ramírez‐Flandes, Álvaro M. Plominsky, Alejandro A. Murillo, Connor Morgan‐Lang, Steven Hallam, Ramūnas Stepanauskas · 2021 · Proceedings of the National Academy of Sciences
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Wenpan Dong, Yanlei Liu, Enze Li, Chao Xu, Jiahui Sun, Wenying Li, Shiliang Zhou, Zhixiang Zhang, Zhili Suo · 2021 · Molecular Phylogenetics and Evolution
Morphological phylogeny of Megachilini and the evolution of leaf-cutter behavior in bees (Hymenoptera: Megachilidae)
Víctor H. González, Grey T. Gustafson, Michael S. Engel · 2019 · Journal of Melittology
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Mengyue Guo, Xiaohui Pang, Yanqin Xu, Wenjun Jiang, Baosheng Liao, Jingsheng Yu, Jiang Xu, Jingyuan Song, Shilin Chen · 2021 · Journal of Advanced Research
Origin and Evolution of Nitrogen Fixation in Prokaryotes
Hong‐Wei Pi, Jinn-Jy Lin, Chi‐An Chen, Po‐Hsiang Wang, Yin‐Ru Chiang, Chieh‐Chen Huang, Chiu‐Chung Young, Wen‐Hsiung Li · 2022 · Molecular Biology and Evolution
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Md Mamun Monir, Mohammad Tarequl Islam, Razib Mazumder, Dinesh Mondal, Kazi Sumaita Nahar, Marzia Sultana, Masatomo Morita, Makoto Ohnishi, Anwar Huq, Haruo Watanabe et al. · 2023 · Nature Communications
New and Interesting Fungi. 6
Pedro Willem Crous, Alexander Akulov, Sergey V. Balashov, Jannes Boers, Uwe Braun, José Joaquín Domínguez-del-Castillo, M.A. Delgado, Sandra Denman, A Erhard, Giorgio Gusella et al. · 2023 · Fungal Systematics and Evolution
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Viral potential to modulate microbial methane metabolism varies by habitat
Zhi-Ping Zhong, Jingjie Du, Stephan Köstlbacher, Petra Pjevac, Sandi Orlić, Matthew B. Sullivan · 2024 · Nature Communications
Phylogenomic Insights into the Evolution and Origin of Nematoda
Xue Qing, Yuanmeng Miles Zhang, Sidi Sun, Mohammed Ismail Ahmed, Wen‐Sui Lo, Wim Bert, Oleksandr V. Holovachov, Hongmei Li · 2024 · Systematic Biology
PHAB toxins: a unique family of predatory sea anemone toxins evolving via intra-gene concerted evolution defines a new peptide fold
Bruno Madio, Steve Peigneur, Yanni K.‐Y. Chin, Brett R. Hamilton, Sónia Troeira Henriques, Jennifer J. L. Smith, Ben Cristofori‐Armstrong, Zoltan Dekan, Berin A. Boughton, Paul F. Alewood et al. · 2018 · Cellular and Molecular Life Sciences
Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family
Zachary L. Reitz, Clifford D. Hardy, Jaewon Suk, Jean Bouvet, Alison Butler · 2019 · Proceedings of the National Academy of Sciences
Deceleration of morphological evolution in a cryptic species complex and its link to paleontological stasis
José Cerca, Christian Meyer, Dave Stateczny, Dominik Siemon, Jana Wegbrod, Günter Purschke, Dimitar Dimitrov, Torsten H. Struck · 2019 · Evolution
High diversity of coralline algae in New Zealand revealed: Knowledge gaps and implications for future research
Brenton A. Twist, Kate F. Neill, Jaret Bilewitch, So Young Jeong, Judy E. Sutherland, Wendy A. Nelson · 2019 · PLoS ONE
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Changjun Peng, Jin‐Long Ren, Cao Deng, Dechun Jiang, Jichao Wang, Jiangyong Qu, Jiang Chang, Chaochao Yan, Ke Jiang, Robert W. Murphy et al. · 2020 · Molecular Biology and Evolution
Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
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Systematic Redefinition of the Hypotricha (Alveolata, Ciliophora) Based on Combined Analyses of Morphological and Molecular Characters
Thiago da Silva Paiva · 2020 · Protist
Paralogs and Off-Target Sequences Improve Phylogenetic Resolution in a Densely Sampled Study of the Breadfruit Genus ( Artocarpus , Moraceae)
Elliot M. Gardner, Matthew G. Johnson, Joan T. Pereira, Aida Shafreena Ahmad Puad, Deby Arifiani, Sahromi, Norman J. Wickett, Nyree J. C. Zerega · 2020 · Systematic Biology
Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida <i>class nov.</i>, with Extreme Apicoplast Genome Reduction
Mathur, Varsha, Kwong, Waldan K, Husnik, Filip, Irwin, Nicholas A T, Kristmundsson, Árni, Gestal, Camino, Freeman, Mark, Keeling, Patrick J · 2021 · Genome Biology and Evolution
Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species
Natalia Álvarez-Santullano, Pamela Villegas, Mario Sepúlveda Mardones, Roberto E. Durán, Raúl A. Donoso, Angela González, Claudia Sanhueza, Rodrigo Navia, Francisca Acevedo, Danilo R. Pérez-Pantoja et al. · 2021 · Microorganisms
Solving the Coral Species Delimitation Conundrum
Catalina Ramírez‐Portilla, Andrew H. Baird, Peter F. Cowman, Andrea M. Quattrini, Saki Harii, Frédéric Sinniger, Jean‐François Flot · 2021 · Systematic Biology
The Chalcidoidea bush of life – a massive radiation blurred by mutational saturation
Astrid Cruaud, Jean–Yves Rasplus, Junxia Zhang, Roger A. Burks, Gérard Delvare, Lucian Fusu, ALEX V. GUMOVSKY, John Huber, Petr Janšta, Mircea‐Dan Mitroiu et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
An evolutionary path to altered cofactor specificity in a metalloenzyme
Anna Barwinska‐Sendra, Yuritzi M. Garcia, Kacper M. Sendra, Arnaud Baslé, Eilidh Sohini Mackenzie, Emma Tarrant, Patrick Card, Leandro C. Tabares, Cédric Bicep, Sun Un et al. · 2020 · Nature Communications
Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)
Michelle Zavala‐Paez, Leila do Nascimento Vieira, Valter A. Baura, Eduardo Balsanelli, Emanuel Maltempi de Souza, Marco Cerna, Mark W. Chase, Eric de Camargo Smidt · 2020 · Frontiers in Plant Science
Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil
Marcelo Henrique Santos Paiva, Duschinka Ribeiro Duarte Guedes, Cássia Docena, Matheus Filgueira Bezerra, Filipe Zimmer Dezordi, Laís Ceschini Machado, Larissa Krokovsky, Elisama Helvécio, Alexandre Freitas da Silva, Luydson Richardson Silva Vasconcelos et al. · 2020 · Viruses
Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae
Devin P. Bendixsen, Noah Gettle, Ciaran Gilchrist, Zebin Zhang, Rike Bahati Stelkens · 2021 · Genome Biology and Evolution
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Daniel Tamarit, Eva Caceres, Mart Krupovìč, Reindert Nijland, Laura Eme, Nicholas P. Robinson, Thijs J. G. Ettema · 2022 · Nature Microbiology
The leaf beetle Chelymorpha alternans propagates a plant pathogen in exchange for pupal protection
Aileen Berasategui, Noa Breitenbach, Marleny García-Lozano, Inès Pons, Brigitte Sailer, Christa Lanz, Viterbo E. Rodríguez, Katharina Hipp, Nadine Ziemert, Donald M. Windsor et al. · 2022 · Current Biology
A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots
Yi Chen, Ting Fang, He Su, Sifei Duan, Rui-Rui Ma, Ping Wang, Lin Wu, Wenbin Sun, Qiu-Cheng-Guang-Rong Hu, Mei-Xia Zhao et al. · 2022 · Plant Communications
Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes
David Díaz-Escandón, Gulnara M. Tagirdzhanova, Dan Vanderpool, Carmen C. G. Allen, André Aptroot, Oluna Češka, David L. Hawksworth, Alejandro Huereca, Kerry Knudsen, Jana Kocourková et al. · 2022 · Current Biology
Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance
Lei Tao, Hanning Duan, Kaifeng Tao, Yan Luo, Qingqing Li, Lu Li · 2023 · BMC Genomics
Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Aurélien Saghaï, Grace Pold, Christopher Michael Jones, Sara Hallin · 2023 · Nature Communications
The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages
Khong-Sam Chia, Jiorgos Kourelis, Albin Teulet, Martin J. Vickers, Toshiyuki Sakai, Joseph F. Walker, S. Schornack, S. Kamoun, Philip Carella · 2024 · The Plant Cell
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants
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