Article

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

Johnston, A. S. A. ORCID: https://orcid.org/0000-0001-8781-4039, Meade, A., Ardö, J. ORCID: https://orcid.org/0000-0002-9318-0973, Arriga, N. ORCID: https://orcid.org/0000-0001-5321-3497, Black, A., Blanken, P. D. ORCID: https://orcid.org/0000-0002-7405-2220, Bonal, D. ORCID: https://orcid.org/0000-0001-9602-8603, Brümmer, C. ORCID: https://orcid.org/0000-0001-6621-5010, Cescatti, A., Dušek, J. ORCID: https://orcid.org/0000-0001-6119-0838, Graf, A. ORCID: https://orcid.org/0000-0003-4870-7622, Gioli, B. ORCID: https://orcid.org/0000-0001-7631-2623, Goded, I. ORCID: https://orcid.org/0000-0002-1912-325X, Gough, C. M. ORCID: https://orcid.org/0000-0002-1227-7731, Ikawa, H., Jassal, R. ORCID: https://orcid.org/0000-0002-6727-5215, Kobayashi, H. ORCID: https://orcid.org/0000-0001-9319-0621, Magliulo, V. ORCID: https://orcid.org/0000-0001-5505-6552, Manca, G. ORCID: https://orcid.org/0000-0002-9376-0310, Montagnani, L. ORCID: https://orcid.org/0000-0003-2957-9071, Moyano, F. E. ORCID: https://orcid.org/0000-0002-4090-5838, Olesen, J. E. ORCID: https://orcid.org/0000-0002-6639-1273, Sachs, T. ORCID: https://orcid.org/0000-0002-9959-4771, Shao, C., Tagesson, T. ORCID: https://orcid.org/0000-0003-3011-1775, Wohlfahrt, G. ORCID: https://orcid.org/0000-0003-3080-6702, Wolf, S. ORCID: https://orcid.org/0000-0001-7717-6993, Woodgate, W., Varlagin, A. ORCID: https://orcid.org/0000-0002-2549-5236 and Venditti, C. ORCID: 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: https://doi.org/10.1038/s41559-021-01398-z

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

Venditti, C. ORCID: https://orcid.org/0000-0002-6776-2355, Baker, J. ORCID: https://orcid.org/0000-0003-4904-6934, Benton, M. J. ORCID: https://orcid.org/0000-0002-4323-1824, Meade, A. and Humphries, S. ORCID: 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: https://doi.org/10.1038/s41586-020-2858-8

Wang, S. ORCID: https://orcid.org/0000-0002-7220-7305, Meade, A., Lam, H.-M. and Luo, H. ORCID: 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: https://doi.org/10.1128/mSystems.00438-20

Baker, J., Humphries, S., Ferguson-Gow, H., Meade, A. and Venditti, C. (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: https://doi.org/10.1111/ele.13431

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

Yu, H. Y., Meade, A. 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: https://doi.org/10.1134/S002626171904012X

Pagel, M., Beaumont, M. A., Meade, A., 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: https://doi.org/10.1073/pnas.1816994116

Kubo, T., Sakamoto, M., Meade, A. and Venditti, C. (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: https://doi.org/10.1073/pnas.1814329116

Gougoulias, C., Meade, A. 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: https://doi.org/10.1111/1758-2229.12631

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

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

Tobias, J. A., Sheard, C., Seddon, N., Meade, A., 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: https://doi.org/10.3389/fevo.2016.00074

Baker, J., Meade, A., Pagel, M. and Venditti, C. (2016) Positive phenotypic selection inferred from phylogenies. Biological Journal of the Linnean Society, 118 (1). pp. 95-115. ISSN 0024-4066 doi: https://doi.org/10.1111/bij.12649

Cooper, N., Thomas, G. H., Venditti, C., Meade, A. 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: https://doi.org/10.1111/bij.12701

Grollemund, R., Branford, S., Bostoen, K., Meade, A., Venditti, C. and Pagel, M. (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: https://doi.org/10.1073/pnas.1503793112

Baker, J. ORCID: https://orcid.org/0000-0003-4904-6934, Meade, A., Pagel, M. and Venditti, C. (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: https://doi.org/10.1073/pnas.1419823112

Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J., Meade, A., Pagel, M. 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: https://doi.org/10.1016/j.cub.2014.10.064

Currie, T. E., Meade, A., 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: https://doi.org/10.1098/rspb.2013.0695

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

Pagel, M., Atkinson, Q. D., Calude, A. and Meade, A. (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: https://doi.org/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. (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: https://doi.org/10.1111/2041-210X.12033

Venditti, C., Meade, A. and Pagel, M. (2011) Multiple routes to mammalian diversity. Nature, 479. pp. 393-396. ISSN 0028-0836 doi: https://doi.org/10.1038/nature10516

Greenhill, S. J., Atkinson, Q. D., Meade, A. 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: https://doi.org/10.1098/rspb.2010.0051

Venditti, C., Meade, A. and Pagel, M. (2010) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature, 463 (7379). pp. 349-352. ISSN 0028-0836 doi: https://doi.org/10.1038/nature08630

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

Atkinson, Q. D., Meade, A., Venditti, C., Greenhill, S. J. and Pagel, M. (2008) Languages evolve in punctuational bursts. Science, 319 (5863). p. 588. ISSN 0036-8075 doi: https://doi.org/10.1126/science.1149683

Pagel, M. and Meade, A. (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: https://doi.org/10.1098/rstb.2008.0178

Atkinson, Q. D., Meade, A., Venditti, C., Greenhill, S. J. and Pagel, M. (2008) Parsing the evolution of language - Response. Science, 320 (5875). p. 446. ISSN 0036-8075

Venditti, C., Meade, A. and Pagel, M. (2008) Phylogenetic mixture models can reduce node-density artifacts. Systematic Biology, 57 (2). pp. 286-293. ISSN 1063-5157 doi: https://doi.org/10.1080/10635150802044045

Pagel, M., Meade, A. 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: https://doi.org/10.1186/1471-2148-7-s1-s16

Barker, D., Meade, A. and Pagel, M. (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: https://doi.org/10.1093/bioinformatics/btl558

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

Organ, C. L., Shedlock, A. M., Meade, A., Pagel, M. 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: https://doi.org/10.1038/nature05621

Pagel, M. and Meade, A. (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: https://doi.org/10.1086/503444

Venditti, C., Meade, A. and Pagel, M. (2006) Detecting the node-density artifact in phylogeny reconstruction. Systematic Biology, 55 (4). pp. 637-643. ISSN 1063-5157 doi: https://doi.org/10.1080/10635150600865567

Pagel, M., Venditti, C. and Meade, A. (2006) Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science, 314 (5796). pp. 119-121. ISSN 0036-8075 doi: https://doi.org/10.1126/science.1129647

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

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

Pagel, M. and Meade, A. (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: https://doi.org/10.1080/10635150490468675

Sibly, R. M., Meade, A., 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: https://doi.org/10.1093/molbev/msg056

Book or Report Section

Meade, A. and Pagel, M. (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: https://doi.org/10.1007/978-1-0716-2691-7_12

Meade, A. and Pagel, M. (2008) A phylogenetic mixture model for heterotachy. In: Pontarotti, P. (ed.) Evolutionary Biology from Concept to Application. Springer Verlag, Heidelberg, 29-41 . ISBN 9783642009518

Pagel, M. and Meade, A. (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. and Meade, A. (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. and Meade, A. (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., 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. 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.