Ecology LettersQuintero, I., Lartillot, N., Morlon, H. (in press) Imbalanced speciation pulses sustain the radiation of mammals Science



Ecology LettersPichon, B., Le Goff, R., Morlon, H. & Perez-Lamarque, B. (in press) Telling mutualistic and antagonistic ecological networks apart by learning their multiscale structure Methods in Ecology & Evolution



Ecology LettersMorlon, H., Andréoletti, J., Barido-Sottani, J., Lambert, S., Perez-Lamarque, B., Quintero, I., Senderov, V., Veron, P. (in press) Phylogenetic insights into diversification American Review of Ecology, Evolution and Systematics



Ecology LettersMaestri, R., Perez-Lamarque, B., Zhukova, A., Morlon, H. (2024) Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses eLife



Ecology LettersDrury, 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



Ecology LettersAndreoletti, J., Morlon, H. (2024) Exploring congruent diversification histories with flexibility and parsimony Methods in Ecology and Evolution 12: 2931-2941



Ecology LettersMazet, 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



Ecology LettersPerez-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



Ecology LettersLambert, S., Voznica, J., Morlon, H. (2023) Deep Learning from Phylogenies for Diversification Analyses Systematic Biology syad044



Ecology LettersQuintero, 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



Ecology LettersBarido-Sottani, J., Morlon, H. (2023) The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2 Systematic Biology syad027



Ecology LettersOvercast, I., Noguerales, V., Meramveliotakis, E., Andújar, C., Arribas, P., Creedy, T.J., Emerson, B.C., Vogler, A.P., Papadopoulou, A., Morlon, H. (in press) Inferring the ecological and evolutionary determinants of community genetic diversity Molecular Ecology



Ecology LettersAndreoletti, J., Morlon, H. (in press) Comparing Extinction Rates: Past, Present and Future. Encyclopedia of Biodiversity 3rd Edition



Ecology LettersOvercast, 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



Ecology LettersEmerson, 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



Ecology LettersPerez-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



Ecology LettersTara 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



Ecology LettersPerez-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



Ecology LettersPerez-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



Ecology LettersMorlon, H., Robin, S., Hartig, F. (2022) Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues Trends in Ecology and Evolution 37: 497-506



Ecology Letters 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



Ecology LettersPerez-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



Ecology LettersSommeria-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

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Ecology LettersNoguerales, 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



Ecology LettersCreedy, 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



Ecology Letters Maliet, O., Morlon, H. (2021) Fast and accurate estimation of species-specific diversification rates using data augmentation Systematic Biology syab055

Julia codes available here



Ecology Letters 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



Ecology Letters 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



Ecology LettersDorrell, 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



Ecology Letters Morlon, H. (2020) Diversity hotspots: Coldspots of speciation? Science (Perspective) 370: 1268-1269



Ecology LettersManceau, M., Marin, J.,Morlon, H., Lambert, A. (2020) Model-based inference of punctuated molecular evolution Molecular Biology and Evolution 37: 3308–3323



Ecology LettersMaliet, 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



Ecology LettersMorlon, 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



Ecology LettersPerez‐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



Ecology LettersLewitus, 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



Ecology LettersBillaud, 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



Ecology LettersPerez-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



Ecology LettersMaliet, 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



Ecology LettersOnstein, 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



Ecology LettersClavel, 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



Ecology LettersLewitus, 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

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Ecology LettersNogues-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



Ecology LettersDrury, 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

R codes available here
primer by Lauren Richardson



Ecology LettersBravo, 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



Ecology LettersLewitus, 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



Ecology LettersDrury, 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



Ecology LettersClavel, 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
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Ecology LettersManceau, 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



Ecology LettersSanchez-Reyes, L., Morlon, H., Magallon, S. (2017) Uncovering higher-taxon diversification dynamics from clade age and species-richness data Systematic Biology 66: 367-378



Ecology LettersChazot, 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


Ecology LettersDrury, 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



Ecology LettersLewitus, E., Morlon, H. (2016) Characterizing and comparing phylogenies from their Laplacian spectrum Systematic Biology 65: 495-507

R codes available here



Ecology LettersMissa, O., Dytham, C., Morlon, H. (2016) Understanding how biodiversity unfolds through time under neutral theory Philosophical Transaction Royal Society B 371: 20150226



Ecology LettersMorlon, 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



Ecology LettersMoen, 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



Ecology LettersRolland, 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



Ecology LettersMouquet, 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

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Ecology LettersMorlon, 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



Ecology LettersManceau, M., Lambert, A., Morlon, H. (2015) Phylogenies support out-of-equilibrium models of biodiversity Ecology Letters 18:347-356

R codes available here



Ecology LettersCondamine, 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



Ecology Letters 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



Ecology Letters 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


Ecology Letters 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

Ecology Letters 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



Ecology Letters Morlon, H., Kefi, S., Martinez, N. (2014) Effects of trophic similarity on community composition Ecology Letters 17: 1495-1506



Ecology Letters Etienne, R.S., Morlon, H., Lambert, A. (2014) Estimating the duration of speciation from phylogenies Evolution 68(8): 2430-2440



Ecology Letters 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

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Ecology Letters Moen, D., Morlon, H. (2014) Why does diversification slow down? Trends in Ecology and Evolution 29: 190-197



Ecology Letters 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


Ecology Letters Morlon, H. (2014) Phylogenetic approaches for studying diversification Ecology Letters 17: 508-525

R codes available here



Ecology Letters Condamine, F.L., Rolland, J., Morlon, H. (2013) Macroevolutionary perspectives to environmental change Ecology Letters 16: 72-85

R codes available here



Ecology Letters 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

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Ecology Letters Morlon, H. (2012) Microbial cooperative warfare Science (Perspective) 337: 1184-1185



Ecology LettersDornelas, 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

Ecology Letters Morlon, H., Kemps, B., Plotkin, J.B., Brisson, D. (2012) Explosive radiation of a bacterial species group Evolution 66: 2577–2586


Ecology Letters 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


Ecology Letters 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

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R codes available here


Ecology LettersMcInnes, 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


Ecology Letters 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

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Ecology Letters Morlon, H., Potts, M. and Plotkin, J. (2010) Inferring the dynamics of diversification: a coalescent approach PloS Biology 8(9): e1000493

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R codes available here

Ecology LettersKembel, 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


Ecology Letters 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


Ecology LettersBryant, 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

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Ecology Letters 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


Ecology Letters 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


Ecology Letters 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


Ecology Letters 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