BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

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1. Dengue Virus Serotype 4 Is Responsible for the Outbreak of Dengue in East Java City of Jember, Indonesia
   Aryati Aryati, Billy Jordan Wrahatnala, Benediktus Yohan, May Fanny, Faradila Khoirun Nisa Hakim, Eka Putri Sunari, Nelly Zuroidah, Puspa Wardhani, Marsha Sinditia Santoso, Dominicus Husada et al. · 2020 · Viruses
2. Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium
   Sergey N. Gavrilov, Daria G. Zavarzina, Ivan M. Elizarov, Tamara V. Tikhonova, Natalia I. Dergousova, Vladimir O. Popov, Jonathan Richard Lloyd, David Knight, Mohamed Y. El‐Naggar, Sahand Pirbadian et al. · 2021 · Frontiers in Microbiology
3. Phylogenetic Systematics of the Millipede Family Xystodesmidae
   Jackson C. Means, Derek A. Hennen, Tsutomu Tanabe, Paul E. Marek · 2021 · Insect Systematics and Diversity
4. Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand
   Jemma L. Geoghegan, Jordan Douglas, Xiaoyun Ren, Matthew Storey, James Hadfield, Olin Silander, Nikki E. Freed, Lauren Jelley, Sarah Jefferies, Jillian Sherwood et al. · 2021 · Emerging infectious diseases
5. An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation
   Rodrigo Costa‐Araújo, José Sousa Silva, Jean P. Boubli, Rogério Vieira Rossi, Gustavo Rodrigues Canale, Fabiano Rodrigues de Melo, Fabrício Bertuol, Felipe Ennes Silva, Diego Augusto Santos Silva, Stephen D. Nash et al. · 2021 · Scientific Reports
6. Fuzzy species borders of glacial survivalists in the Carpathian biodiversity hotspot revealed using a multimarker approach
   Tomasz Mamos, Krzysztof Jaźdźewski, Zuzana Čiamporová‐Zaťovičová, FEDOR JR ČIAMPOR, Michał Grabowski · 2021 · Scientific Reports
7. Early cephalopod evolution clarified through Bayesian phylogenetic inference
   Alexander Pohle, Björn Kröger, Rachel C. M. Warnock, Andy H. King, David H. Evans, Martina Aubrechtová, Marcela Cichowolski, Xiang Min Fang, Christian Klug · 2022 · BMC Biology
8. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae
   Lei Zhao, Yingying Yang, Xiao‐Jian Qu, Hong Mā, Yi Hu, Hongtao Li, Ting‐Shuang Yi, De-Zhu Li · 2022 · Annals of Botany
9. SPREAD 4: online visualisation of pathogen phylogeographic reconstructions
   Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A. Suchard, Guy Baele, Philippe Lemey · 2022 · Virus Evolution
10. TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data
    Sophie Seidel, Tanja Stadler · 2022 · Proceedings of the Royal Society B Biological Sciences
11. A contribution to Porogramme (Polyporaceae, Agaricomycetes) and related genera
    Wei-Lin Mao, Ying-Da Wu, Honggao Liu, Yuan Yuan, Yu‐Cheng Dai · 2023 · IMA Fungus
12. An empirical guide for producing a dated phylogeny with treePL in a maximum likelihood framework
    Kévin J. L. Maurin · 2020 · arXiv (Cornell University)
13. Behavioral innovation and genomic novelty are associated with the exploitation of a challenging dietary opportunity by an avivorous bat
    Lixin Gong, Yang Geng, Zhiqiang Wang, Aiqing Lin, Huan Wu, Lei Feng, Zhenglanyi Huang, Hui Ming Wu, Jiang Feng, Tinglei Jiang · 2022 · iScience
14. Recent co-evolution of two pandemic plant diseases in a multi-hybrid swarm
    Mostafa Rahnama, Bradford J. Condon, João Paulo Ascari, Julian R. Dupuis, Emerson M. Del Ponte, Kerry F. Pedley, Sebastián Martínez, Barbara S. Valent, MARK L. FARMAN · 2023 · Nature Ecology & Evolution
15. Simulations of Sequence Evolution: How (Un)realistic They Are and Why
    Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau · 2023 · Molecular Biology and Evolution
16. Multi‐response phylogenetic mixed models: concepts and application
    Ben Halliwell, Barbara R. Holland, Luke A. Yates · 2025 · Biological reviews/Biological reviews of the Cambridge Philosophical Society
17. Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot
    Marcus Thadeu T. Santos, Rafael Félix de Magalhães, Mariana Lúcio Lyra, Fabrício Rodrigues dos Santos, Hussam Zaher, Luis Olímpio Menta Giasson, Paulo Christiano de Anchieta Garcia, Ana Carolina Carnaval, Célio F. B. Haddad · 2020 · Molecular Phylogenetics and Evolution
18. New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America
    Joyce Rodrigues do Prado, L. Lacey Knowles, Alexandre Reis Percequillo · 2020 · Molecular Phylogenetics and Evolution
19. An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas
    Flavio Augusto da Silva Coelho, Stephanie Gill, Crystal Tomlin, Timothy H. Heaton, Charlotte Lindqvist · 2021 · Proceedings of the Royal Society B Biological Sciences
20. Fifty million years of beetle evolution along the Antarctic Polar Front
    Helena P. Baird, Seunggwan Shin, Rolf G. Oberprieler, M. Hullé, Philippe Vernon, Katherine L. Moon, Richard H. Jr. Adams, Duane D. McKenna, Steven L. Chown · 2021 · Proceedings of the National Academy of Sciences
21. Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete
    Sonja Bamberger, Jie Xu, Bernhard Hausdorf · 2021 · Systematic Biology
22. Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale ): Additional species diversity and Pleistocene climate change as a major driver of diversification
    Molly M. McDonough, Adam W. Ferguson, Robert C. Dowler, Matthew E. Gompper, Jesús Eduardo Maldonado · 2020 · Molecular Phylogenetics and Evolution
23. Global invasion history of the emerging plant pathogen Phytophthora multivora
    Tetyana Tsykun, Simone Prospero, Corine N. Schoebel, Alexander J. Rea, Treena Isobel Burgess · 2022 · BMC Genomics
24. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny
    Qianshi Lin, Thomas Braukmann, Marybel Soto Gomez, Juliana Lischka Sampaio Mayer, Fábio Pinheiro, Vincent S. F. T. Merckx, Saša Stefanović, Sean W. Graham · 2022 · New Phytologist
25. The Genomic Natural History of the Aurochs
    Rossi, Conor, Sinding, Mikkel-Holger S., Mullin, Victoria E., Scheu, Amelie, Erven, Jolijn A. M., Verdugo, Marta Pereira, Daly, Kevin G., Ciucani, Marta Maria, Mattiangeli, Valeria, Teasdale, Matthew D. et al. · 2024 · Nature
26. Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea)
    Hannah Marie Wood, Jörg Wunderlich · 2023 · Systematic Biology
27. Population Dynamics and Structural Effects at Short and Long Range Support the Hypothesis of the Selective Advantage of the G614 SARS-CoV-2 Spike Variant
    Emiliano Trucchi, Paolo Gratton, Fabrizio Mafessoni, Stefano Motta, Francesco Cicconardi, Filippo Mancia, Giorgio Bertorelle, Ilda D’Annessa, Daniele Di Marino · 2020 · Molecular Biology and Evolution
28. Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past
    Héctor Tejero‐Cicuéndez, Austin H. Patton, Daniel S. Caetano, Jiřı́ Šmı́d, Luke J. Harmon, Salvador Carranza · 2021 · Systematic Biology
29. Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene
    Jordan Douglas, Alexei J. Drummond, Richard L. Kingston · 2021 · Virus Evolution
30. Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)
    Meng‐Yuan Zhou, Jing-Xia Liu, Pengfei Ma, Junbo Yang, De-Zhu Li · 2022 · Journal of Systematics and Evolution
31. The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia
    Galya V. Klink, Ksenia R. Safina, Elena Nabieva, Nikita Shvyrev, Sofya K. Garushyants, Evgeniia I. Alekseeva, Andrey B. Komissarov, Daria Danilenko, Andrei A. Pochtovyi, Elizaveta V. Divisenko et al. · 2022 · Virus Evolution
32. Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species
    Zhi‐Hui Su, Ayako Sasaki, Junko Kusumi, Po-An Chou, Hsy‐Yu Tzeng, Hongqing Li, Hui Yu · 2022 · Communications Biology
33. Rainfall and sea level drove the expansion of seasonally flooded habitats and associated bird populations across Amazonia
    André Oliveira Sawakuchi, Eduardo D. Schultz, Fabiano do Nascimento Pupim, Dailson José Bertassoli, Daniela Fonseca Melo de Souza, Diego Fontana Siqueira Cunha, Carlos Eduardo Manjon Mazoca, Manuela Pinheiro Ferreira, Carlos Henrique Grohmann, Ingo Wahnfried et al. · 2022 · Nature Communications
34. Genetic differentiation, demographic history and distribution models of high alpine endemic vicariants outline the response of species to predicted climate changes in a Central Asian biodiversity hotspot
    Lizaveta Vintsek, Ewelina Klichowska, Arkadiusz S. Nowak, Marcin Nobis · 2022 · Ecological Indicators
35. Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae)
    Lily C. Hughes, Chloe M. Nash, William T. White, Mark W. Westneat · 2022 · Systematic Biology
36. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
    Sarah Nadeau, Timothy G. Vaughan, Christiane Beckmann, Ivan Topolsky, Chaoran Chen, Emma B. Hodcroft, Tobias Schär, Ina Nissen, Natascha Santacroce, Elodie Burcklen et al. · 2022 · Science Translational Medicine
37. Putting the F into FBD analysis: tree constraints or morphological data?
    Joëlle Barido‐Sottani, Alexander Pohle, Kenneth De Baets, Duncan J. E. Murdock, Rachel C. M. Warnock · 2023 · Palaeontology
38. Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences
    Kris V. Parag, Louis du Plessis, Oliver G. Pybus · 2020 · Molecular Biology and Evolution
39. Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
    Beatriz Mello, Qiqing Tao, Jose Barba‐Montoya, Sudhir Kumar · 2020 · Molecular Ecology Resources
40. A new bat species of the genus Myotis with comments on the phylogenetic placement of M. keaysi and M. pilosatibialis
    Carlos Alberto Carrión Bonilla, Joseph Anthony Cook · 2020 · Therya
41. Formal Syntax and Deep History
    Andrea Ceolin, Cristina Guardiano, Monica Alexandrina Irimia, Giuseppe Longobardi · 2020 · Frontiers in Psychology
42. Geo-Climatic Changes and Apomixis as Major Drivers of Diversification in the Mediterranean Sea Lavenders (Limonium Mill.)
    Konstantina Koutroumpa, Ben H. Warren, Spyros Theodoridis, Mario Coiro, Maria Manuel Romeiras, Ares Jiménez, Elena Conti · 2021 · Frontiers in Plant Science
43. Complex patterns of Gondwanan biogeography revealed in a dispersal‐limited arachnid
    Shahan Derkarabetian, Caitlin M. Baker, Gonzalo Giribet · 2021 · Journal of Biogeography
44. Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini)
    Leidys Murillo‐Ramos, Nicolas Chazot, Pasi Sihvonen, Erki Õunap, Nan Jiang, Hongxiang Han, John T. Clarke, Robert Β. Davis, Toomas Tammaru, Niklas Wahlberg · 2021 · Molecular Phylogenetics and Evolution
45. Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents
    Charles Kumakamba, Fabien Roch Niama, Francisca M. Muyembe, Jean-Vivien Mombouli, Placide Mbala Kingebeni, Rock Aime Nina, Ipos Ngay Lukusa, Gerard Bounga, Frida N’Kawa, Cynthia Goma Nkoua et al. · 2021 · PLoS ONE
46. The molecular systematics and diversification of a taxonomically unstable group of Asian cicada tribes related to Cicadini Latreille, 1802 (Hemiptera : Cicadidae)
    Kathy B. R. Hill, David C. Marshall, Kiran Marathe, Maxwell S. Moulds, Young June Lee, Thai-Hong Pham, Alma B. Mohagan, Vivek Sarkar, Benjamin Wills Price, Joannes Petrus Duffels et al. · 2021 · Invertebrate Systematics
47. Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants
    Xue-Wei Wang, Ji-Hang Jiang, Shi-Liang Liu, Yusufjon Gafforov, Li-Wei Zhou · 2021 · Phytopathology
48. Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification
    Jeremy J. Kirchman, Nancy Rotzel McInerney, Thomas C. Giarla, Storrs L. Olson, Beth Slikas, Robert C. Fleischer · 2021 · The Auk
49. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada
    Carmen Lía Murall, Éric Fournier, José Héctor Gálvez, Arnaud N’Guessan, Sarah Julia Reiling, Pierre-Olivier Quirion, Sana Naderi, Anne-Marie Roy, Shu‐Huang Chen, Paul Stretenowich et al. · 2021 · Genome Medicine
50. A scalable analytical approach from bacterial genomes to epidemiology
    Xavier Didelot, Julian Parkhill · 2022 · Philosophical Transactions of the Royal Society B Biological Sciences
51. Evolutionary origins of the prolonged extant squamate radiation
    Chase Doran Brownstein, Dalton L. Meyer, Matteo Fabbri, Bhart-Anjan Singh Bhullar, Jacques A. Gauthier · 2022 · Nature Communications
52. Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda)
    Bingyu Guo, Lingfeng Kong · 2022 · Genes
53. Phylogenetics and the Cenozoic radiation of lampreys
    Chase Doran Brownstein, Thomas J. Near · 2022 · Current Biology
54. Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay
    Gladys Estigarribia, Guillermo Sequera, Sarita Aguirre, Julieta Méndez, Paulo César Pereira dos Santos, Natalie Weiler Gustafson, Margarita Godoy, Analía Ortiz, Cynthia Céspedes, Gloria Martínez et al. · 2023 · Nature Communications
55. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation
    Christian Robert Voolstra, Benjamin C. C. Hume, Eric J. Armstrong, Guinther Mitushasi, Barbara Porro, Nicolas Oury, Sylvain Agostini, Émilie Boissin, Julie Poulain, Quentin Carradec et al. · 2023 · npj Biodiversity
56. Selective Sampling of Species and Fossils Influences Age Estimates Under the Fossilized Birth–Death Model
    Michael Matschiner · 2019 · Frontiers in Genetics
57. Evolutionary History of Alzheimer Disease-Causing Protein Family Presenilins with Pathological Implications
    Ammad Aslam Khan, Raja Hashim Ali, Bushra Mirza · 2020 · Journal of Molecular Evolution
58. Evolutionary History of the Galápagos Rail Revealed by Ancient Mitogenomes and Modern Samples
    Jaime A. Chaves, Pedro J. Martinez-Torres, Emiliano A. Depino, Sebastian A. Espinoza‐Ulloa, Jefferson García Loor, Annabel C. Beichman, Martin Stervander · 2020 · Diversity
59. Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex
    Alistair R. McTaggart, Timothy Yong James, Roger Graham Shivas, A. Drenth, Brenda Diana Wingfield, Brett Anthony Summerell, Tuan Anh Duong · 2021 · Studies in Mycology
60. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae
    Carla Rodrigues, Val F. Lanza, Luísa Maria Sobreira Vieira Peixe, Teresa M. Coque, Ângela Novais · 2023 · Microbiology Spectrum
61. Unilocus delimitation methods reveal the underestimated species diversity of Thomasomys (Rodentia, Cricetidae)
    Dennisse Ruelas, Víctor Pacheco, José Pérez Z., Juan F. Díaz‐Nieto, Pierre‐Henri Fabre · 2024 · Zoologica Scripta
62. Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
    Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin, Alexei J. Drummond · 2025 · PLoS Computational Biology
63. How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles
    Teo Delić, Fabio Stoch, Špela Borko, Jean‐François Flot, Cene Fišer · 2020 · Journal of Biogeography
64. Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control
    Kimberly R. Andrews, Alida T. Gerritsen, Arash Rashed, David William Crowder, Silvia I. Rondon, Willem G. van Herk, Robert S. Vernon, Kevin W. Wanner, Cathy M. Wilson, Daniel D. New et al. · 2020 · Communications Biology
65. Heterologous arenavirus vector prime-boost overrules self-tolerance for efficient tumor-specific CD8 T cell attack
    Weldy V. Bonilla, Nicole Kirchhammer, Anna‐Friederike Marx, Sandra M. Kallert, Magdalena Anna Krzyzaniak, Min Lu, Stéphanie Darbre, Sarah Schmidt, Josipa Raguz, Ursula Berka et al. · 2021 · Cell Reports Medicine
66. The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus
    Julian F. Quintero‐Galvis, Pablo Saenz‐Agudelo, Juan Luis Celis-Diez, Guillermo Cesar Amico, Miriam Soledad Vazquez, Aaron B. A. Shafer, Roberto F. Nespolo · 2021 · Molecular Phylogenetics and Evolution
67. Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh
    Lauren A. Cowley, Mokibul Hassan Afrad, Sadia Isfat Ara Rahman, Md Mahfuz Al Mamun, Taylor Chin, Ayesha S. Mahmud, Mohammed Ziaur Rahman, Mallick Masum Billah, Manjur Hossain Khan, Sharmin Sultana et al. · 2021 · Nature Microbiology
68. Evidence for extensive hybridisation and past introgression events in feather grasses using genome-wide SNP genotyping
    Evgenii Baiakhmetov, Daria Ryzhakova, Гудкова Полина Дмитриевна, Marcin Nobis · 2021 · BMC Plant Biology
69. Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry
    Jing Zhang, Yan Wang, Tao Chen, Qing Chen, Lei Wang, Zhenshan Liu, Hao Wang, Rui Xie, Wen He, Ming Li et al. · 2021 · Frontiers in Plant Science
70. Phylogeny, biogeography and classification of Teletisoptera (Blattaria: Isoptera)
    Menglin Wang, Simon Hellemans, Jan Šobotník, Jigyasa Arora, Aleš Buček, David Sillam‐Dussès, Crystal Clitheroe, Tomer Lu, Nathan C. Lo, Michael S. Engel et al. · 2022 · Systematic Entomology
71. Deconstructing the crustacean squat lobster genus Munida to reconstruct the evolutionary history and systematics of the family Munididae (Decapoda, Anomura, Galatheoidea)
    Annie Machordom, Shane T. Ahyong, Nikos Andreakis, Keiji Baba, David Buckley, Ricardo García-Jiménez, Anna W. McCallum, Paula C. Rodríguez‐Flores, Enrique Macpherson · 2022 · Invertebrate Systematics
72. Evolutionary and Genetic Recombination Analyses of Coxsackievirus A6 Variants Associated with Hand, Foot, and Mouth Disease Outbreaks in Thailand between 2019 and 2022
    Jiratchaya Puenpa, Nutsada Saengdao, Nongkanok Khanarat, Sumeth Korkong, Jira Chansaenroj, Ritthideach Yorsaeng, Nasamon Wanlapakorn, Yong Poovorawan · 2022 · Viruses
73. Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong
    Ruopeng Xie, Kimberly M. Edwards, Dillon Charles Adam, Kathy S. M. Leung, Tim K. Tsang, Shreya Gurung, Weijia Xiong, Xiaoman Wei, Daisy Y.M. Ng, Gigi Y.Z. Liu et al. · 2023 · Nature Communications
74. The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage
    Xiaoyuan Lin, Zhou Sha, Jakob Trimpert, Dušan Kunec, Chen Jiang, Yan Xiong, Binbin Xu, Zhenglin Zhu, Weiwei Xue, Haibo Wu · 2023 · Cell Host & Microbe
75. Enzymic recognition of amino acids drove the evolution of primordial genetic codes
    Jordan Douglas, Remco Bouckaert, Charles W. Carter, Peter R. Wills · 2023 · Nucleic Acids Research
76. Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives
    Pere Renom, Toni de-Dios, Sergi Civit, Laia Llovera, Alejandro Sánchez‐Gracia, Esther Lizano, Juan Carlos Rando, Tomàs Marquès‐Bonet, Gaël J. Kergoat, Isaac Casanovas‐Vilar et al. · 2021 · Biology Letters
77. Systematic Revision of Thomasomys cinereus (Rodentia: Cricetidae: Sigmodontinae) from Northern Peru and Southern Ecuador, With Descriptions of Three New Species
    Víctor Pacheco, Dennisse Ruelas · 2023 · Bulletin of the American Museum of Natural History
78. HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
    Guy Baele, Luiz Max Carvalho, Marius Brusselmans, Gytis Dudas, Xiang Ji, John T. McCrone, Philippe Lemey, Marc A. Suchard, Andrew Rambaut · 2025 · Bioinformatics
79. Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia
    Jessica A. Oswald, Julie M. Allen, Michelle J. LeFebvre, Brian J. Stucky, Ryan A. Folk, Nancy A. Albury, Gary S. Morgan, Robert Guralnick, David W. Steadman · 2020 · Scientific Reports
80. Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation
    Andrew M. Ritchie, Xia Hua, Marcel Cardillo, Keaghan J. Yaxley, Russell Dinnage, Lindell D. Bromham · 2020 · Diversity and Distributions
81. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
    Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo B Gambacorti-Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza · 2021 · Patterns
82. Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
    Manon Ragonnet‐Cronin, Olivia Boyd, Lily Geidelberg, David Jorgensen, Fabrícia Ferreira do Nascimento, Igor A. Siveroni, Robert Johnson, Marc Baguelin, Zulma M. Cucunubá, Elita Jauneikaite et al. · 2021 · Nature Communications
83. Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review
    Maylis Layan, Simon Dellicour, Guy Baele, Simon Cauchemez, Hervé Bourhy · 2021 · PLoS neglected tropical diseases
84. Hybridization with mountain hares increases the functional allelic repertoire in brown hares
    Jaakko Pohjoismäki, Craig Michell, Riikka Levänen, Steve Smith · 2021 · Scientific Reports
85. Phylogenomics and Fossil Data Inform the Systematics and Geographic Range Evolution of a Diverse Neotropical Ant Lineage
    Shauna L. Price, Benjamin D. Blanchard, Scott Powell, Bonnie B. Blaimer, Corrie Saux Moreau · 2022 · Insect Systematics and Diversity
86. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil
    Tiago Gräf, Gonzalo Bello, Felipe Gomes Naveca, Marcelo Ferreira da Costa Gomes, Vanessa Leiko Oikawa Cardoso, Alexandre Freitas da Silva, Filipe Zimmer Dezordi, Mirleide Cordeiro dos Santos, Katia Correa de Oliveira Santos, Érika Lopes Rocha Batista et al. · 2022 · iScience
87. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
    Dawei Cai, Siqi Zhu, Mian Gong, Naifan Zhang, Jia Wen, Qiyao Liang, Weilu Sun, Xinyue Shao, Yaqi Guo, Yudong Cai et al. · 2022 · eLife
88. Climate change will redefine taxonomic, functional, and phylogenetic diversity of Odonata in space and time
    Tommaso Cancellario, Rafael Miranda, Enrique Baquero, Diego Fontaneto, Alejandro Martínez, Stefano Mammola · 2022 · npj Biodiversity
89. Cosmopolitan abyssal lineages? A systematic study of East Pacific deep-sea squat lobsters (Decapoda: Galatheoidea: Munidopsidae)
    Paula C. Rodríguez‐Flores, Charlotte A. Seid, Greg W. Rouse, Gonzalo Giribet · 2023 · Invertebrate Systematics
90. Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities
    Leo Joseph, Jon T. Merwin, Brian Tilston Smith · 2020 · Emu - Austral Ornithology
91. Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019
    Jessica C. Chen, Kane Patel, Peyton A. Smith, Eshaw Vidyaprakash, Caroline Snyder, Kaitlin A. Tagg, Hattie E. Webb, Morgan N. Schroeder, Lee S. Katz, Lori A. Rowe et al. · 2023 · Emerging infectious diseases
92. Chromosome‐level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood)
    Wen Xie, Chao He, Zhangjun Fei, Youjun Zhang · 2020 · Molecular Ecology Resources
93. Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)
    Flávia Fonseca Pezzini, Kyle Graham Dexter, Jefferson Carvalho-Sobrinho, Catherine Anne Kidner, James A. Nicholls, Luciano Paganucci de Queiroz, R. Toby Pennington · 2021 · Frontiers of Biogeography
94. New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels
    Camille Christe, Carlos G. Boluda, Darina Koubínová, Laurent Gautier, Yamama Naciri · 2021 · Molecular Phylogenetics and Evolution
95. A Virus Infecting Hibiscus rosa-sinensis Represents an Evolutionary Link Between Cileviruses and Higreviruses
    Alejandro Olmedo-Velarde, John S. Hu, Michael J. Melzer · 2021 · Frontiers in Microbiology
96. Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences
    Fuzuki Mizuno, Jun Gojobori, Masahiko Kumagai, Hisao Baba, Yasuhiro Taniguchi, Osamu Kondo, Masami Matsushita, Takayuki Matsushita, Fumihiko Matsuda, Koichiro Higasa et al. · 2021 · Scientific Reports
97. Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis
    Naizhe Li, Yun Feng, Bram Vrancken, Yuyang Chen, Lü Dong, Qiqi Yang, Moritz U. G. Kraemer, Oliver G. Pybus, Hailin Zhang, Oliver J. Brady et al. · 2021 · The Lancet Regional Health - Western Pacific
98. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim
    Fabrizio Menardo, Liliana K. Rutaihwa, Michaela Zwyer, Sònia Borrell, Iñaki Comas, Emilyn Costa Conceição, Mireia Coscollá, Helen Suzanne Cox, Moses Lutaakome Joloba, Horng-Yunn Dou et al. · 2021 · F1000Research
99. An updated subtribal classification of Compositae tribe Anthemideae based on extended phylogenetic reconstructions
    Christoph Oberprieler, Alisha Töpfer, Marco Dorfner, Miriam Stock, Robert Vogt · 2022 · Willdenowia - Annals of the Botanic Garden and Botanical Museum Berlin-Dahlem
100. An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice
     T. Brock Wooldridge, Andreas F. Kautt, Jean‐Marc Lassance, Sade McFadden, VERA S. DOMINGUES, Ricardo Mallarino, Hopi E. Hoekstra · 2022 · Proceedings of the National Academy of Sciences