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Article

Campoy, A. N. orcid id iconORCID: https://orcid.org/0000-0002-6434-4326, Rivadeneira, M. M., Hernández, C. E. orcid id iconORCID: https://orcid.org/0000-0002-9811-2881, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2023) Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals. Nature Communications, 14. 7458. ISSN 2041-1723 doi: 10.1038/s41467-023-43287-y

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, O’Donovan, C. orcid id iconORCID: https://orcid.org/0000-0003-4770-4227 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2022) General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism. Nature Communications, 13 (1). 1113. ISSN 2041-1723 doi: 10.1038/s41467-022-28595-z

Johnston, A. S. A. orcid id iconORCID: https://orcid.org/0000-0001-8781-4039, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Ardö, J. orcid id iconORCID: https://orcid.org/0000-0002-9318-0973, Arriga, N. orcid id iconORCID: https://orcid.org/0000-0001-5321-3497, Black, A., Blanken, P. D. orcid id iconORCID: https://orcid.org/0000-0002-7405-2220, Bonal, D. orcid id iconORCID: https://orcid.org/0000-0001-9602-8603, Brümmer, C. orcid id iconORCID: https://orcid.org/0000-0001-6621-5010, Cescatti, A., Dušek, J. orcid id iconORCID: https://orcid.org/0000-0001-6119-0838, Graf, A. orcid id iconORCID: https://orcid.org/0000-0003-4870-7622, Gioli, B. orcid id iconORCID: https://orcid.org/0000-0001-7631-2623, Goded, I. orcid id iconORCID: https://orcid.org/0000-0002-1912-325X, Gough, C. M. orcid id iconORCID: https://orcid.org/0000-0002-1227-7731, Ikawa, H., Jassal, R. orcid id iconORCID: https://orcid.org/0000-0002-6727-5215, Kobayashi, H. orcid id iconORCID: https://orcid.org/0000-0001-9319-0621, Magliulo, V. orcid id iconORCID: https://orcid.org/0000-0001-5505-6552, Manca, G. orcid id iconORCID: https://orcid.org/0000-0002-9376-0310, Montagnani, L. orcid id iconORCID: https://orcid.org/0000-0003-2957-9071, Moyano, F. E. orcid id iconORCID: https://orcid.org/0000-0002-4090-5838, Olesen, J. E. orcid id iconORCID: https://orcid.org/0000-0002-6639-1273, Sachs, T. orcid id iconORCID: https://orcid.org/0000-0002-9959-4771, Shao, C., Tagesson, T. orcid id iconORCID: https://orcid.org/0000-0003-3011-1775, Wohlfahrt, G. orcid id iconORCID: https://orcid.org/0000-0003-3080-6702, Wolf, S. orcid id iconORCID: https://orcid.org/0000-0001-7717-6993, Woodgate, W., Varlagin, A. orcid id iconORCID: https://orcid.org/0000-0002-2549-5236 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2021) Temperature thresholds of ecosystem respiration at a global scale. Nature Ecology & Evolution, 5. pp. 487-494. ISSN 2397-334X doi: 10.1038/s41559-021-01398-z

Baker, J. orcid id iconORCID: https://orcid.org/0000-0003-4904-6934, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2021) Nothing wrong with the analysis of clades in comparative evolutionary studies. Systematic Biology, 70 (1). pp. 197-201. ISSN 1063-5157 doi: 10.1093/sysbio/syaa067

Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Baker, J. orcid id iconORCID: https://orcid.org/0000-0003-4904-6934, Benton, M. J. orcid id iconORCID: https://orcid.org/0000-0002-4323-1824, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Humphries, S. orcid id iconORCID: https://orcid.org/0000-0001-9766-6404 (2020) 150 million years of sustained increase in pterosaur flight efficiency. Nature, 587. pp. 83-86. ISSN 0028-0836 doi: 10.1038/s41586-020-2858-8

Wang, S. orcid id iconORCID: https://orcid.org/0000-0002-7220-7305, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Lam, H.-M. and Luo, H. orcid id iconORCID: https://orcid.org/0000-0001-8452-6066 (2020) Evolutionary timeline and genomic plasticity underlying the lifestyle diversity in rhizobiales. mSystems, 5 (4). 00438-20. ISSN 2379-5077 doi: 10.1128/mSystems.00438-20

Baker, J. orcid id iconORCID: https://orcid.org/0000-0003-4904-6934, Humphries, S., Ferguson-Gow, H., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2020) Rapid decreases in relative testes mass among monogamous birds but not in other vertebrates. Ecology Letters, 23 (2). pp. 283-292. ISSN 1461-0248 doi: 10.1111/ele.13431

Campoy, A. N., Addamo, A. M., Machordom, A., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Rivadeneira, M. M., Hernández, C. E. and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2020) The origin and correlated evolution of symbiosis and coloniality in Scleractinian corals. Frontiers in Marine Science, 7. p. 461. ISSN 2296-7745 doi: 10.3389/fmars.2020.00461

Yu, H. Y., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Liu, S. J. (2019) Phylogeny of Clostridium spp. based on conservative genes and comparisons with other trees. Microbiology, 88 (4). pp. 469-478. ISSN 1608-3237 doi: 10.1134/S002626171904012X

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Beaumont, M. A., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Verkerk, A. and Calude, A. (2019) Dominant words rise to the top by positive frequency-dependent selection. Proceedings of the National Academy of Sciences of the United States of America, 116 (15). pp. 7397-7402. ISSN 1091-6490 doi: 10.1073/pnas.1816994116

Kubo, T., Sakamoto, M., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2019) Transitions between foot postures are associated with elevated rates of body size evolution in mammals. Proceedings of the National Academy of Sciences of the United States of America, 116 (7). pp. 2618-2623. ISSN 0027-8424 doi: 10.1073/pnas.1814329116

Gougoulias, C., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Shaw, L. (2018) Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS. Environmental Microbiology Reports, 10 (3). pp. 245-254. ISSN 1758-2229 doi: 10.1111/1758-2229.12631

O’Donovan, C., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2018) Dinosaurs reveal the geographical signature of an evolutionary radiation. Nature Ecology & Evolution, 2 (3). pp. 452-458. ISSN 2397-334X doi: 10.1038/s41559-017-0454-6

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2018) The deep history of the number words. Philosophical Transactions of the Royal Society B-Biological Sciences, 373 (1740). 0517. ISSN 0962-8436 doi: 10.1098/rstb.2016.0517

Tobias, J. A., Sheard, C., Seddon, N., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Cotton, A. J. and Nakagawa, S. (2016) Territoriality, social bonds, and the evolution of communal signaling in birds. Frontiers in ecology and evolution, 4. 74. ISSN 2296-701X doi: 10.3389/fevo.2016.00074

Baker, J. orcid id iconORCID: https://orcid.org/0000-0003-4904-6934, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2016) Positive phenotypic selection inferred from phylogenies. Biological Journal of the Linnean Society, 118 (1). pp. 95-115. ISSN 0024-4066 doi: 10.1111/bij.12649

Cooper, N., Thomas, G. H., Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Freckleton, R. P. (2016) A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies. Biological Journal of the Linnean Society, 118 (1). pp. 64-77. ISSN 0024-4066 doi: 10.1111/bij.12701

Grollemund, R., Branford, S., Bostoen, K., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2015) Bantu expansion shows that habitat alters the route and pace of human dispersals. Proceedings of the National Academy of Sciences of the United States of America, 112 (43). pp. 13296-13301. ISSN 0027-8424 doi: 10.1073/pnas.1503793112

Baker, J. orcid id iconORCID: https://orcid.org/0000-0003-4904-6934, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 (2015) Adaptive evolution toward larger size in mammals. Proceedings of the National Academy of Sciences of the United States of America, 112 (16). pp. 5093-5098. ISSN 0027-8424 doi: 10.1073/pnas.1419823112

Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Bhattacharya, T. (2015) Detecting regular sound changes in linguistics as events of concerted evolution. Current Biology, 25 (1). pp. 1-9. ISSN 0960-9822 doi: 10.1016/j.cub.2014.10.064

Currie, T. E., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Guillon, M. and Mace, R. (2013) Cultural phylogeography of the Bantu Languages of sub-Saharan Africa. Proceedings of the Royal Society B-Biological Sciences, 280 (1762). 20130695. ISSN 1471-2954 doi: 10.1098/rspb.2013.0695

Altschuler, E. L., Calude, A., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2013) Linguistic evidence supports date for Homeric epics. Bioessays, 35 (5). pp. 417-420. ISSN 0265-9247 doi: 10.1002/bies.201200165

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Atkinson, Q. D., Calude, A. and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2013) Ultraconserved words point to deep language ancestry across Eurasia. Proceedings of the National Academy of Sciences of the United States of America, 110 (21). pp. 8471-8476. ISSN 0027-8424 doi: 10.1073/pnas.1218726110

Hernández, C. E., Rodríguez-Serrano, E., Avaria-Llautureo, J., Inostroza-Michael, O., Morales-Pallero, B., Boric-Bargetto, D., Canales-Aguirre, C. B., Marquet, P. A. and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2013) Using phylogenetic information and the comparative method to evaluate hypotheses in macroecology. Methods in Ecology and Evolution, 4 (5). pp. 401-415. ISSN 2041-210X doi: 10.1111/2041-210X.12033

Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2011) Multiple routes to mammalian diversity. Nature, 479. pp. 393-396. ISSN 0028-0836 doi: 10.1038/nature10516

Greenhill, S. J., Atkinson, Q. D., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Gray, R. D. (2010) The shape and tempo of language evolution. Proceedings of the Royal Society B-Biological Sciences, 277 (1693). pp. 2443-2450. ISSN 1471-2954 doi: 10.1098/rspb.2010.0051

Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2010) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature, 463 (7379). pp. 349-352. ISSN 0028-0836 doi: 10.1038/nature08630

Organ, C. L., Janes, D. E., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2009) Genotypic sex determination enabled adaptive radiations of extinct marine reptiles. Nature, 461 (7262). pp. 389-392. ISSN 0028-0836 doi: 10.1038/nature08350

Atkinson, Q. D., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Greenhill, S. J. and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2008) Languages evolve in punctuational bursts. Science, 319 (5863). p. 588. ISSN 0036-8075 doi: 10.1126/science.1149683

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2008) Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Philosophical Transactions of the Royal Society B-Biological Sciences, 363 (1512). pp. 3955-3964. ISSN 0962-8436 doi: 10.1098/rstb.2008.0178

Atkinson, Q. D., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Greenhill, S. J. and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2008) Parsing the evolution of language - Response. Science, 320 (5875). p. 446. ISSN 0036-8075

Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2008) Phylogenetic mixture models can reduce node-density artifacts. Systematic Biology, 57 (2). pp. 286-293. ISSN 1063-5157 doi: 10.1080/10635150802044045

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Scott, D. (2007) Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes. Bmc Evolutionary Biology, 7. p. 11. ISSN 1471-2148 doi: 10.1186/1471-2148-7-s1-s16

Barker, D., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics, 23 (1). pp. 14-20. ISSN 1367-4803 doi: 10.1093/bioinformatics/btl558

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Atkinson, Q. D. and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2007) Frequency of word-use predicts rates of lexical evolution throughout Indo-European history. Nature, 449 (7163). 717-U7. ISSN 0028-0836 doi: 10.1038/nature06176

Organ, C. L., Shedlock, A. M., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Edwards, S. V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature, 446 (7132). pp. 180-184. ISSN 0028-0836 doi: 10.1038/nature05621

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2006) Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist, 167 (6). pp. 808-825. ISSN 0003-0147 doi: 10.1086/503444

Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2006) Detecting the node-density artifact in phylogeny reconstruction. Systematic Biology, 55 (4). pp. 637-643. ISSN 1063-5157 doi: 10.1080/10635150600865567

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Venditti, C. orcid id iconORCID: https://orcid.org/0000-0002-6776-2355 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2006) Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science, 314 (5796). pp. 119-121. ISSN 0036-8075 doi: 10.1126/science.1129647

Lester, L., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2006) The slow road to the eukaryotic genome. Bioessays, 28 (1). pp. 57-64. ISSN 0265-9247 doi: 10.1002/bies.20344

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Barker, D. (2004) Bayesian estimation of ancestral character states on phylogenies. Systematic Biology, 53 (5). pp. 673-684. ISSN 1063-5157 doi: 10.1080/10635150490522232

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2004) A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53 (4). pp. 571-581. ISSN 1063-5157 doi: 10.1080/10635150490468675

Sibly, R. M. orcid id iconORCID: https://orcid.org/0000-0001-6828-3543, Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Boxall, N., Wilkinson, M. J., Corne, D. W. and Whittaker, J. C. (2003) The structure of interrupted human AC microsatellites. Molecular Biology and Evolution, 20 (3). pp. 453-459. ISSN 0737-4038 doi: 10.1093/molbev/msg056

Book or Report Section

Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2022) Ancestral state reconstruction using Bayes traits. In: Luo, H. (ed.) Environmental Microbial Evolution: Methods and Protocols. Methods in Molecular Biology. Humana, New York, pp. 255-266, XI, 362. ISBN 9781071626900 doi: 10.1007/978-1-0716-2691-7_12

Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 (2008) A phylogenetic mixture model for heterotachy. In: Pontarotti, P. (ed.) Evolutionary Biology from Concept to Application. Springer Verlag, Heidelberg, pp. 29-41. ISBN 9783642009518

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2006) Estimating rates of lexical replacement on phylogenetic trees of languages. In: Forster, P. and Renfrew, C. (eds.) Phylogenetic methods and the prehistory of languages. McDonald institute Monographs, pp. 173-182. ISBN 9781902937335

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2005) Bayesian estimation of correlated evolution across cultures: a case study of marriage systems and wealth transfer at marriage. In: Mace, R., Holden, C.J. and Shennan, S. (eds.) The Evolution of Cultural Diversity: a phylogenetic approach. University College London Press, London, pp. 235-256. ISBN 9781844720651

Pagel, M. orcid id iconORCID: https://orcid.org/0000-0001-7287-8865 and Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 (2005) Mixture models in phylogenetic inference. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny. Oxford University Press, pp. 121-142. ISBN 9780198566106

Conference or Workshop Item

Manjunathaiah, M., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711, Thavarajan, R., Protopapas, P. and Dave, R. (2019) Big data scalability of bayesPhylogenies on Harvard’s ozone 12k cores. In: The 12th International Joint Conference on Biomedical Engineering Systems and Technologies, 22-24 Feb 2019, Prague, Czech Republic, pp. 143-148.

Johnson, D., Meade, A. orcid id iconORCID: https://orcid.org/0000-0001-7095-7711 and Alexandrov, V. N. (2009) A lightweight supercomputing web portal for inferring phylogenetic trees. In: 5th IEEE International Conference on e-Science Workshops, 2009, Oxford, UK.

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