Silva, A.C.A., Maliet, O., Aristide, L., Nogues-Bravo, D., Upham, N., Jetz, W, Morlon, H. (2025) Negative global-scale association between genetic diversity and speciation rates in mammals Nature Communications 16, 1796.
Veron, P., Andréoletti, J., Giraud, T., Morlon, H. (2025) Speciation completion rates have limited impact on macroevolutionary diversification Philosophical Transactions of the Royal Society B 380: 20230317
Quintero, I., Lartillot, N., Morlon, H. (2024) Imbalanced speciation pulses sustain the radiation of mammals Science 384: 1007-1012
Maestri, R., Perez-Lamarque, B., Zhukova, A., Morlon, H. (2024) Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses eLife 13:RP91745
Pichon, B., Le Goff, R., Morlon, H. & Perez-Lamarque, B. (2024) Telling mutualistic and antagonistic ecological networks apart by learning their multiscale structure Methods in Ecology & Evolution 15: 1113-1128
Perez-Lamarque, B. & Morlon, H. (2024) Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions Systematic Biology syae013
Morlon, H., Andréoletti, J., Barido-Sottani, J., Lambert, S., Perez-Lamarque, B., Quintero, I., Senderov, V., Veron, P. (2024) Phylogenetic insights into diversification Annual Review of Ecology, Evolution and Systematics 55: 1-21
Barreto, E., Boehm M.M.A., Ogutcen, E., Abrahamczyk, S., Kessler, M., Bascompte, J., Dellinger, A.S., Bello, C., Dehling, D.M., Duchenne, F., Kaehler, M., Lagomarsino, L.P., Lohmann, L.G., Maglianesi, M.A., Morlon, H. , Muchhala, N., Ornelas, J.F., Perret, M., Salinas, N.R., Smith, S.D., Vamosi, J.C., Varassin, I.G., Graham, C.H. (2024) Macroevolution of the plant–hummingbird pollination system Biological Reviews 99: 1831-1847
Luiselli, J., Overcast, I., Rominger, A., Ruffley, M., Morlon, H., Rosindell, J. (2024) Detecting the ecological footprint of selection PloS One 19: e0302794
Drury, J.P., Clavel, J., Tobias, J. A., Rolland, J., Sheard, C. & Morlon, H. (2024) Limited ecological opportunity influences the tempo of morphological evolution in birds Current Biology 34: 661-669
Andreoletti, J., Morlon, H. (2024) Exploring congruent diversification histories with flexibility and parsimony Methods in Ecology and Evolution 12: 2931-2941
Mazet, N., Morlon, H., Fabre, P.H., Condamine, F. (2023) Estimating clade-specific diversification rates and palaeodiversity dynamics from reconstructed phylogenies Methods in Ecology and Evolution 10: 2575-2591
Perez-Lamarque, B., Sommeria-Klein, G., Duret, L., Morlon, H. (2023) Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota Molecular Biology and Evolution 40: msad144
Lambert, S., Voznica, J., Morlon, H. (2023) Deep Learning from Phylogenies for Diversification Analyses Systematic Biology 72: 1262-1279
Quintero, I., Landis, M., Jetz, W., Morlon, H. (2023) The build-up of the present-day tropical diversity of tetrapods Proceedings of the National Academy of Sciences, 120: e2220672120
Barido-Sottani, J., Morlon, H. (2023) The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2 Systematic Biology syad027
Overcast, I., Noguerales, V., Meramveliotakis, E., Andújar, C., Arribas, P., Creedy, T.J., Emerson, B.C., Vogler, A.P., Papadopoulou, A., Morlon, H. (2023) Inferring the ecological and evolutionary determinants of community genetic diversity Molecular Ecology 32: 6093-6109
Perez-Lamarque, B., Morlon, H. (2023) Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota Molecular Ecology 23: 6671-6685
Andreoletti, J., Morlon, H. (in press) Comparing Extinction Rates: Past, Present and Future. Encyclopedia of Biodiversity 3rd Edition
Overcast, I., ,Morlon, H. (2023) Toward a Genetic Theory of Island Biogeography: Inferring Processes from Multi-Dimensional Community-Scale Data Global Ecology & Biogeography 32, 4-23
Emerson, B.C., Borges, P., Cardoso, P., Convey, P., deWaard, J., Economo, E., Gillespie, R., Kennedy, S., Krehenwinkel, H., Meier, R., Roderick, G., Strasberg, D., Thébaud, C., Traveset, A., Creedy, T., Meramveliotakis, E., Noguerales, V., Overcast, I., Morlon, H., Papadopoulou, A.,Vogler, A., Arribas, P., Andujar, C. (2022) Collective and harmonised high throughput barcoding of insular arthropod biodiversity: toward a Genomic Observatories Molecular Ecology 23: 6161-6176
Perez-Lamarque, B., Maliet, O., Pichon, B., Selosse, M. A., Martos, F., Morlon, H. (2022) Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks PCI Evolutionary Biology 2
Tara Ocean Foundation, Tara Oceans, European Molecular Biology Laboratory, European Marine Biological Resource Centre - European Research Infrastructure Consortium (2022) Priorities for ocean microbiome research Nature Microbiology 7, 937–947
Perez-Lamarque, B., Petrolli, R., Strullu-Derrien, C., Strasberg, D., Morlon, H., Selosse, M.A., Martos, F. (2022) Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities Environmental Microbiome 17, 38
Perez-Lamarque, B., Öpik, M., Maliet, O., Afonso Silva, A.C., , Selosse, M.A., Martos, F., Morlon, H. (2022) Analyzing diversification dynamics using barcoding data: the case of an obligate mycorrhizal symbiont Molecular Ecology 31: 3496-3512
Morlon, H., Robin, S., Hartig, F. (2022) Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues Trends in Ecology and Evolution 37: 497-506
Arribas, P., Andújar, C., Bohmann, K., deWaard, J.R., Economo, E.P., Elbrecht, V., Geisen, S., Goberna, M., Krehenwinkel, H., Novotny, V., Zinger, L., Creedy, T.J., Meramveliotakis, E., Noguerales, Overcast, I., Morlon, H.,Papadopoulou, A., Vogler, A.P., Emerson, B.C. (2022) Toward global integration of biodiversity big data: a harmonised metabarcode data generation module for terrestrial arthropods GigaScience 11: giac065
Perez-Lamarque, B., Krehenwinkel, H., Gillespie, R., Morlon, H. (2022) Limited evidence for microbial transmission in the phylosymbiosis between Hawaiian spiders and their microbiota mSystems 7(1) e01104-21
Sommeria-Klein, G., Watteaux, R., Ibarbalz, F.M., Pierella Karlusich, J.J.; Iudicone, D.; Bowler, C., Morlon, H. (2021) Global drivers of eukaryotic plankton biogeography in the sunlit ocean Science 374: 594-599
communiqué de presse
press release
Noguerales, V., Meramveliotakis, E., Castro-Insua, A., Andujar, C., Arribas, P., Creedy, T., Overcast, I., Morlon, H., Emerson, B., Vogler, A., Papadopoulou, A. (2021) Community metabarcoding reveals the relative role of environmental filtering and dispersal in metacommunity dynamics of soil microarthropods across a mosaic of montane forests Molecular Ecology
Creedy, T., Andujar, C., Meramveliotakis, E., Noguerales, V., Overcast, I., Papadopoulou, A., Morlon, H., Vogler, A., Emerson, B., Arribas, P. (2021) Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonization Molecular Ecology Resources 22: 847-861
Maliet, O., Morlon, H. (2021) Fast and accurate estimation of species-specific diversification rates using data augmentation Systematic Biology syab055
Julia codes available here
Drury, J., Clavel, J., Tobias, J. A., Rolland, J., Sheard, C., Morlon, H. (2021) Tempo and mode of morphological evolution are decoupled from latitude in birds PloS Biology 19(8): e3001270
R codes available here
primer by Dan Rabosky
Arribas, P., Andújar, C., ..., Overcast, I., Morlon, H., Vogler, A.P., Papadopoulou, A., Emerson, B.C. (2021) Connecting high-throughput biodiversity inventories – opportunities for a site-based genomic framework for global integration and synthesis Molecular Ecology 30 (5), 1120-1135
Dorrell, R.G., Villain, A., Perez-Lamarque, B., Audren de Kerdrel,G., McCallum, G., Watson, A., ait-Mohamed, O., Alberti, A., Corre, E., Frischkorn, K.R., Juan José Pierella Karlusich, J.J., Pelletier, E., Bapteste, E.P., Morlon, H., Bowler, C., Blanc, G. (2021) Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes Proceedings of the National Academy of Sciences 118: e2009974118
Manceau, M., Marin, J.,Morlon, H., Lambert, A. (2020) Model-based inference of punctuated molecular evolution Molecular Biology and Evolution 37: 3308–3323
Maliet, O., Loeuille, N., Morlon, H. (2020) An individual based model for the eco-evolutionary emergence of bipartite interaction networks Ecology Letters 11: 1623-1634
R codes available here
Clavel, J., Morlon, H. (2020) Reliable phylogenetic regressions for multivariate comparative data: illustration with the MANOVA and application to the effect of diet on mandible morphology in phyllostomid bats Systematic Biology 69: 927-943
R codes available here
Morlon, H., Rolland, J., Condamine, F. (2020) Response to Technical Comment ‘A cautionary note for users of linear diversification dependencies’ Ecology Letters 7:1172-1174
R codes available here
Perez‐Lamarque, B., Selosse, M. A., Öpik, M., Morlon, H., & Martos, F. (2020) Cheating in arbuscular mycorrhizal mutualism: a network and phylogenetic analysis of mycoheterotrophy New Phytologist 226: 1822-1835
Lewitus, E., Aristide, L., Morlon, H. (2019) Characterizing and Comparing Phylogenetic Trait Data from Their Normalized
Laplacian Spectrum Systematic Biology 69: 234–248
R codes available here
Billaud, O., Moen, D. S., Parsons, T. L., Morlon, H. (2019) Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past Systematic Biology 69: 363–383
R codes available here
Aristide, L., Morlon, H. (2019) Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification Ecology Letters 22: 2006-2017
R codes available here
Condamine, F.L., Rolland, J., Morlon, H. (2019) Assessing the causes of diversification slowdowns: temperature-dependent and diversity-dependent models receive equivalent support Ecology Letters 22: 1900-1912
Perez-Lamarque, B., Morlon, H. (2019) Characterizing symbiont inheritance during host‐microbiota evolution: application to the great apes gut microbiota Molecular Ecology Resources 19: 1659-1671
R codes available here
Maliet, O., Hartig, F., Morlon, H. (2019) A model with many small shifts for estimating species-specific diversification rates Nature Ecology and Evolution 3: 1086-1092
News & Views by Tanja Stadler
R codes available here
Onstein, R. E., Kissling W.D., Chatrou, L.W., Couvreur, T.L.P., Morlon, H., Sauquet, H. (2019) Which frugivory-related traits facilitated historical long-distance dispersal in the custard-apple family (Annonaceae)? Journal of Biogeography 46: 874-1888
Clavel, J., Aristide, L., Morlon, H. (2019) A Penalized Likelihood Framework for High-Dimensional Phylogenetic Comparative Methods and an Application to New-World Monkeys Brain Evolution Systematic Biology 68: 93-116
R codes available here and here
Lewitus, E., Bittner, L., Malviya, S., Bowler, C., Morlon, H. (2018) Clade-specific diversification dynamics in marine diatoms since the Jurassic Nature Ecology and Evolution 2:1715-1723
communiqué de presse
Nogues-Bravo, D., Rodriguez-Sanchez, F., Orisini, L., de Boer, E., Jansson, R., Morlon, H., Fordham, D., Jackson, S.T. (2018) Cracking the code of past biodiversity response to climate change Trends in Ecology and Evolution 30: 765-776
Drury, J., Tobias, J.A., Burns, K.J., Mason, N.A., Shultz, A.J., Morlon, H. (2018) Contrasting impacts of competition on ecological and social trait evolution in songbirds PloS Biology 16(1): e2003563
primer by Lauren Richardson
Bravo, G.A., Antonelli, A., Bacon, C.D., Bartoszek, K., Blom, M.P.K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., Morlon, H., Nakhleh, L.K., Oxelman, B., Pfeil, B., Schliep, A., Wahlberg, N., Werneck, F.P., Wiedenhoeft, J., Willows-Munro, S., Edwards, S.V. (2018) Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics PeerJ 6 e26449v2
Lewitus, E., Morlon, H. (2018) Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations Systematic Biology 67:576-593
R codes available here
Drury, J., Grether, G.F., Garland, T., Morlon, H. (2017) An assessment of phylogenetic tools for analyzing the interplay between interspecific interactions and phenotypic evolution Systematic Biology 67:413-427
R codes available here
Clavel, J., Morlon, H. (2017) Accelerated body-size evolution during cold climatic periods in the Cenozoic Proceedings of the National Academy of Sciences 114: 4183-4188
R codes available here
press release in Physics Today
press release in Arstechnica
communiqué de presse
Manceau, M., Lambert, A., Morlon, H. (2017) A unifying comparative phylogenetic framework including traits coevolving across interacting lineages Systematic Biology 66: 551-568
R codes available here
Sanchez-Reyes, L., Morlon, H., Magallon, S. (2017) Uncovering higher-taxon diversification dynamics from clade age and species-richness data Systematic Biology 66: 367-378
Lewitus, E., Morlon, H. (2016) Natural constraints to species diversification PloS Biology 14(8): e1002532
commentary by Mike Benton
summary for Cell Systems
résumé pour médecine/sciences
Chazot, N., Willmott, K.R., Condamine, F.L., de-Silva, D.L., Freitas, V.L., Lamas, G., Morlon, H., Giraldo, C.E., Jiggins, C.D., Joron, M., Mallet, J., Uribe, S., Elias, M. (2016) Into the Andes: multiple independent colonizations drive montane diversity in the Neotropical clearwing butterflies Godyridina Molecular Ecology 25: 5765–5784
Drury, J., Clavel, J., Manceau, M., Morlon, H. (2016) Estimating the effect of competition on trait evolution using maximum likelihood inference Systematic Biology 65: 700-710
R codes available here
Lewitus, E., Morlon, H. (2016) Characterizing and comparing phylogenies from their Laplacian spectrum Systematic Biology 65: 495-507
R codes available here
Missa, O., Dytham, C., Morlon, H. (2016) Understanding how biodiversity unfolds through time under neutral theory Philosophical Transaction Royal Society B 371: 20150226
Morlon, H., Lewitus, E., Condamine, F.L., Manceau, M., Clavel, J., Drury, J. (2016) RPANDA: an R package for macroevolutionary analyses on phylogenetic trees Methods in Ecology and Evolution 7: 589-597
R codes available here
Moen, D.S., Morlon, H., Wiens, J.J. (2016) Testing convergence versus history: convergence dominates phenotypic evolution for over 150 million years in frogs Systematic Biology 65: 146-160
Rolland, J., Condamine, F.L., Champak, R.B., Jiguet, F., Morlon, H. (2015) Dispersal is a major driver of the latitudinal diversity gradient of Carnivora Global Ecology and Biogeography 24: 1059-1071
Mouquet, N., Lagadeuc, Y., Devictor, V., Doyen, L., Duputié, A., Eveillard, D., Faure, D., Garnier, E., Gimenez, O., Huneman, H., Jabot, F., Jarne, P., Joly, D., Julliard, J., Kéfi, S., Kergoat, G.J., Lavorel S., Le Gall, L., Morlon, H., Pinay, G., Pradel, R., Schurr, F.M., Thuiller, W., Loreau, M. (2015) Predictive ecology in a changing world Journal of Applied Ecology
Morlon, H., O'Connor, T., Bryant, J.A., Charkoudian, L.K., Docherty, K.M., Jones, E., Kembel, S., Green, J.L., Bohannan, B.J.M. (2015) The biogeography of putative microbial antibiotic production PloS One 10(6): e0130659
Manceau, M., Lambert, A., Morlon, H. (2015) Phylogenies support out-of-equilibrium models of biodiversity Ecology Letters 18:347-356
R codes available here
Condamine, F., Nagalingum, N.S., Marshall, C.R., Morlon, H. (2015) Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating BMC Evolutionary Biology 15:65
Lambert, A., Morlon, H., Etienne, R.S. (2015) The reconstructed tree in the lineage-based model of protracted speciation Journal of Mathematical Biology 70: 367-397
Alvarado, S., Baraloto, C., Bremond, L., Bretagnolle, F., Buisson, E., Caillon, S., Claudet, J., Dounias, E., Elias, M., Favier, C., Fontaine, C., Forget, P.M., Garine-Wichatitsky, E., Hossaert-McKey, M., Mavingui, P., McKey, D., Morlon, H., Murienne, J., Poncy, O., Prugnolle, F.
(2015) Écologie tropicale: de l'ombre à la lumière. Edition cherche midi
Warren, B.H., Simberloff, D., Ricklefs, R.E., Aguilée , R., Condamine, F.L., Gravel, D., Morlon, H., Mouquet, N., Rosindell, J., Casquet, J., Conti, E., Cornuault, J., Fernández-Palacios, J.M., Hengl, T., Norder, S.J., Rijsdijk, K.F., Sanmartín, I., Strasberg, D., Triantis, K., Valente, L.M., Whittaker, R.J., Gillespie, R.G., Emerson, B.C., Thébaud, C. (2014) Islands as model systems in ecology and evolution:
prospects fifty years after MacArthur-Wilson Ecology Letters 8: 200–216
Reyes, E., Morlon, H., Sauquet, H. (2014) Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae New Phytologist 207:401-410
Morlon, H., Kefi, S., Martinez, N. (2014) Effects of trophic similarity on community composition Ecology Letters 17: 1495-1506
Etienne, R.S., Morlon, H., Lambert, A. (2014) Estimating the duration of speciation from phylogenies Evolution 68(8): 2430-2440
Moen, D., Morlon, H.
(2014) From dinosaurs to modern bird diversity - Extending the time-scale of adaptive
radiation PLoS Biology 12(5): e1001854
comment by the press
Rolland, J., Jiguet, F., Jonsson, K.A., Condamine, F.L., Morlon, H.
(2014) Settling down of seasonal migrants promotes bird diversification Proceedings of the Royal Society B 281: 20140473
communiqué de presse
Moen, D., Morlon, H.
(2014) Why does diversification slow down? Trends in Ecology and Evolution 29: 190-197
Morlon, H.
(2014) Understanding how biodiversity is distributed in space and time Formal Methods in Macro-Biology Lecture Notes in Computer Science Volume 8738, pp 36-39
Morlon, H.
(2014) Phylogenetic approaches for studying diversification Ecology Letters 17: 508-525
R codes available here
Rolland, J., Condamine, F.L., Jiguet, F., Morlon, H.
(2014) Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient PloS Biology 12(1): e1001775
Condamine, F.L., Rolland, J., Morlon, H.
(2013) Macroevolutionary perspectives to environmental change Ecology Letters 16: 72-85
R codes available here
Jaunatre, R., Buisson, E., Muller, I., Morlon, H., Mesléard, F.,
Dutoit, T.
(2013) New synthetic indicators to assess community resilience and restoration success Ecological Indicators 29:468-477
Dornelas, M., Magurran, A., Buckland, S.T., Chao, A., Chazdon, R.L., Colwell, R.K., Curtis, T., Gaston, K.J., Gotelli, N.J., Kosnik, M., McGill, B., McCune, J.L., Morlon, H., Mumby, P.J., Øvreas, L., Studeny, A., Vellend, M.
(2012) Quantifying temporal change in biodiversity: challenges and opportunities Proceedings of the Royal Society B 280: 20121931
Morlon, H., Kemps, B., Plotkin, J.B., Brisson, D.
(2012) Explosive radiation of a bacterial species group Evolution 66: 2577–2586
Rolland, J., Cadotte, M.W., Davies, J., Devictor, V., Lavergne, S., Mouquet, N., Pavoine, S., Rodrigues, A., Thuiller, W., Turcati, L., Winter, M., Zupan, L., Jabot, F., Morlon, H.
(2011) Using phylogenies in conservation: new perspectives Biology Letters 8: 692-694
Morlon, H., Parsons, T.L., Plotkin, J.
(2011) Reconciling molecular phylogenies with the fossil record Proceedings of the National Academy of Sciences 108: 16327-16332
press release communiqué de presse
R codes available here
McInnes, L., Baker, W.J., Barraclough, T.G., Dasmahapata, K.K., Goswami, A., Harmon, L.J., Morlon, H., Purvis, A., Rosindell, J., Thomas, G.H., Turvey, S.T., Phillimore, A.B.
(2011) Integrating ecology into macroevolutionary research Biology Letters 7: 644-646
Morlon, H., Schwilk, D., Bryant, J., Marquet, P., Rebelo, T., Tauss, C., Bohannan, B. and Green, J. (2011) Spatial patterns of phylogenetic diversity Ecology Letters 14: 141-149
press release
Morlon, H., Potts, M. and Plotkin, J. (2010) Inferring the dynamics of diversification: a coalescent approach
PloS Biology 8(9): e1000493
press release
R codes available here
Kembel, S.W., Cowan, P., Helmus, M. R., Cornwell, W., Morlon, H., Ackerly, D., Blomberg, S. P.,
Webb, C. O. (2010) Picante: R tools for integrating phylogenies and ecology Bioinformatics 26 : 1463-1464
Morlon, H., White, E. P., Etienne, R. S., Green, J. L., Ostling, A., Alonso, D., Enquist, B. J., He, F.,
Hurlbert, A., Magurran, A. E., Maurer, B. A., McGill, B. J., Olff, H., Storch, D., Zillio, T. (2009) Taking
species abundance distributions beyond individuals Ecology Letters 12 : 488-501
Bryant, J., Lamanna, C., Morlon, H., Enquist, B., Green, J. (2008) Microbes on mountainsides:
Contrasting elevational patterns of bacterial and plant diversity Proceedings of the National Academy of
Sciences 105 : S1505-S1511
Morlon, H., Chuyong, G., Condit, R., Hubbell, S., Kenfack, D., Thomas, D., Valencia, R., Green, J.
(2008) A general framework for the distance-decay of similarity in ecological communities Ecology Letters 11 : 904-917
Morlon, H., Fortin, C., Adam, C., Garnier-Laplace, J. (2006) Selenite transport and its inhibition in the
unicellular green alga Chlamydomonas reinhardtii Environmental Toxicology and Chemistry 5 : 1408-17
Morlon, H., Fortin, C., Floriani, M., Boudou, A., Garnier-Laplace, J. (2005). Toxicity of selenite in the
unicellular green alga Chlamydomonas reinhardtii: comparison between effects at the population and subcellular
level Aquatic toxicology, 73 : 65-78
Morlon, H., Fortin, C., Adam, C., Garnier-Laplace, J. (2005). Establishing links between toxicity and
bioaccumulation of selenite in the unicellular green alga Chlamydomonas reinhardtii Radioprotection, 40.
S101-S106