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Relaxed Phylogenetics and Dating with Confidence

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Cited by:

  1. Yao-Tsun Li & Hui-Ying Ko & Joseph Hughes & Ming-Tsan Liu & Yi-Ling Lin & Katie Hampson & Kirstyn Brunker, 2024. "From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  2. Joanne S. Boden & Juntao Zhong & Rika E. Anderson & Eva E. Stüeken, 2024. "Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  3. Alice M. Clement & Richard Cloutier & Michael S. Y. Lee & Benedict King & Olivia Vanhaesebroucke & Corey J. A. Bradshaw & Hugo Dutel & Kate Trinajstic & John A. Long, 2024. "A Late Devonian coelacanth reconfigures actinistian phylogeny, disparity, and evolutionary dynamics," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  4. Sayaka Miura & Koichiro Tamura & Qiqing Tao & Louise A Huuki & Sergei L Kosakovsky Pond & Jessica Priest & Jiamin Deng & Sudhir Kumar, 2020. "A new method for inferring timetrees from temporally sampled molecular sequences," PLOS Computational Biology, Public Library of Science, vol. 16(1), pages 1-24, January.
  5. Mercedes M Burns & Marshal Hedin & Jeffrey W Shultz, 2013. "Comparative Analyses of Reproductive Structures in Harvestmen (Opiliones) Reveal Multiple Transitions from Courtship to Precopulatory Antagonism," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-11, June.
  6. Dinesh Aggarwal & Ben Warne & Aminu S. Jahun & William L. Hamilton & Thomas Fieldman & Louis Plessis & Verity Hill & Beth Blane & Emmeline Watkins & Elizabeth Wright & Grant Hall & Catherine Ludden & , 2022. "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  7. Rebecca L. Kordas & Samraat Pawar & Dimitrios-Georgios Kontopoulos & Guy Woodward & Eoin J. O’Gorman, 2022. "Metabolic plasticity can amplify ecosystem responses to global warming," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
  8. Lokman Galal & Frédéric Ariey & Meriadeg Ar Gouilh & Marie-Laure Dardé & Azra Hamidović & Franck Letourneur & Franck Prugnolle & Aurélien Mercier, 2022. "A unique Toxoplasma gondii haplotype accompanied the global expansion of cats," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  9. Bethany L Dearlove & Simon D W Frost, 2015. "Measuring Asymmetry in Time-Stamped Phylogenies," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-16, July.
  10. Qiqi Yang & Ben Wang & Phillipe Lemey & Lu Dong & Tong Mu & R. Alex Wiebe & Fengyi Guo & Nídia Sequeira Trovão & Sang Woo Park & Nicola Lewis & Joseph L.-H. Tsui & Sumali Bajaj & Yachang Cheng & Luoju, 2024. "Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  11. Nico Neureiter & Peter Ranacher & Nour Efrat-Kowalsky & Gereon A. Kaiping & Robert Weibel & Paul Widmer & Remco R. Bouckaert, 2022. "Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-14, December.
  12. Idrissa Nonmon Sanogo & Claire Guinat & Simon Dellicour & Mohamed Adama Diakité & Mamadou Niang & Ousmane A Koita & Christelle Camus & Mariette Ducatez, 2024. "Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa," Post-Print hal-04498485, HAL.
  13. Annefleur C. Langedijk & Bram Vrancken & Robert Jan Lebbink & Deidre Wilkins & Elizabeth J. Kelly & Eugenio Baraldi & Abiel Homero Mascareñas de Los Santos & Daria M. Danilenko & Eun Hwa Choi & María , 2024. "The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  14. Michael D Nowak & Andrew B Smith & Carl Simpson & Derrick J Zwickl, 2013. "A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-13, June.
  15. Jonathon D. Gass & Nichola J. Hill & Lambodhar Damodaran & Elena N. Naumova & Felicia B. Nutter & Jonathan A. Runstadler, 2023. "Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016–Early 2022," IJERPH, MDPI, vol. 20(11), pages 1-17, June.
  16. Niklas Wikström & Kent Kainulainen & Sylvain G Razafimandimbison & Jenny E E Smedmark & Birgitta Bremer, 2015. "A Revised Time Tree of the Asterids: Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-26, May.
  17. Andrew F Magee & Sebastian Höhna & Tetyana I Vasylyeva & Adam D Leaché & Vladimir N Minin, 2020. "Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts," PLOS Computational Biology, Public Library of Science, vol. 16(10), pages 1-23, October.
  18. Lu Lu & Reina S. Sikkema & Francisca C. Velkers & David F. Nieuwenhuijse & Egil A. J. Fischer & Paola A. Meijer & Noortje Bouwmeester-Vincken & Ariene Rietveld & Marjolijn C. A. Wegdam-Blans & Paulien, 2021. "Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  19. Stéphane Aris-Brosou, 2007. "Dating Phylogenies with Hybrid Local Molecular Clocks," PLOS ONE, Public Library of Science, vol. 2(9), pages 1-8, September.
  20. Renzo F. Balboa & Laura D. Bertola & Anna Brüniche-Olsen & Malthe Sebro Rasmussen & Xiaodong Liu & Guillaume Besnard & Jordi Salmona & Cindy G. Santander & Shixu He & Dietmar Zinner & Miguel Pedrono &, 2024. "African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  21. Alexandra Gavryushkina & David Welch & Tanja Stadler & Alexei J Drummond, 2014. "Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-15, December.
  22. Dai, Ning & Jones, Galin L., 2017. "Multivariate initial sequence estimators in Markov chain Monte Carlo," Journal of Multivariate Analysis, Elsevier, vol. 159(C), pages 184-199.
  23. Matheus Pontes-Nogueira & Marcio Martins & Laura R V Alencar & Ricardo J Sawaya, 2021. "The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-18, September.
  24. Cristian R Altaba, 2009. "Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-13, February.
  25. Mekala Sundaram & Janna R Willoughby & Nathanael I Lichti & Michael A Steele & Robert K Swihart, 2015. "Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.
  26. David G Haskell & Anupam Adhikari, 2009. "Darwin's Manufactory Hypothesis Is Confirmed and Predicts the Extinction Risk of Extant Birds," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-6, May.
  27. Haogao Gu & Ruopeng Xie & Dillon C. Adam & Joseph L.-H. Tsui & Daniel K. Chu & Lydia D. J. Chang & Sammi S. Y. Cheuk & Shreya Gurung & Pavithra Krishnan & Daisy Y. M. Ng & Gigi Y. Z. Liu & Carrie K. C, 2022. "Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
  28. Matthew Hall & Mark Woolhouse & Andrew Rambaut, 2015. "Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set," PLOS Computational Biology, Public Library of Science, vol. 11(12), pages 1-36, December.
  29. Nan Song & Ai-Ping Liang, 2013. "A Preliminary Molecular Phylogeny of Planthoppers (Hemiptera: Fulgoroidea) Based on Nuclear and Mitochondrial DNA Sequences," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-11, March.
  30. Feixiang Wu & Philippe Janvier & Chi Zhang, 2023. "The rise of predation in Jurassic lampreys," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  31. Saúl F. Domínguez-Guerrero & Fausto R. Méndez-de la Cruz & Norma L. Manríquez-Morán & Mark E. Olson & Patricia Galina-Tessaro & Diego M. Arenas-Moreno & Adán Bautista- del Moral & Adriana Benítez-Vill, 2022. "Exceptional parallelisms characterize the evolutionary transition to live birth in phrynosomatid lizards," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  32. Yankuo Sun & Jiabao Xing & Samuel L. Hong & Nena Bollen & Sijia Xu & Yue Li & Jianhao Zhong & Xiaopeng Gao & Dihua Zhu & Jing Liu & Lang Gong & Lei Zhou & Tongqing An & Mang Shi & Heng Wang & Guy Bael, 2024. "Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  33. Iliana Bista & Jonathan M. D. Wood & Thomas Desvignes & Shane A. McCarthy & Michael Matschiner & Zemin Ning & Alan Tracey & James Torrance & Ying Sims & William Chow & Michelle Smith & Karen Oliver & , 2023. "Genomics of cold adaptations in the Antarctic notothenioid fish radiation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  34. Jordan Douglas & Rong Zhang & Remco Bouckaert, 2021. "Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model," PLOS Computational Biology, Public Library of Science, vol. 17(2), pages 1-30, February.
  35. Tamara Kaleta & Lisa Kern & Samuel Leandro Hong & Martin Hölzer & Georg Kochs & Julius Beer & Daniel Schnepf & Martin Schwemmle & Nena Bollen & Philipp Kolb & Magdalena Huber & Svenja Ulferts & Sebast, 2022. "Antibody escape and global spread of SARS-CoV-2 lineage A.27," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  36. Joachim Schmidt & Lars Opgenoorth & Steffen Höll & Ralf Bastrop, 2012. "Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-15, September.
  37. Hoan X. Dinh & Davinder Singh & Diana Gomez de la Cruz & Goetz Hensel & Jochen Kumlehn & Martin Mascher & Nils Stein & Dragan Perovic & Michael Ayliffe & Matthew J. Moscou & Robert F. Park & Mohammad , 2022. "The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  38. Haitao Shang & Daniel H. Rothman & Gregory P. Fournier, 2022. "Oxidative metabolisms catalyzed Earth’s oxygenation," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
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