B. Perez-Lamarque & H. Morlon (in press) Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions Systematic Biology

Morlon, 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

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

J.P. Drury, J.Clavel, J. A. Tobias, J. Rolland, C. Sheard & H. Morlon (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 syad044

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. (in press) Inferring the ecological and evolutionary determinants of community genetic diversity Molecular Ecology

Perez-Lamarque, B., Morlon, H. (in press) Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota Molecular Ecology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Manceau, M., Lambert, A., Morlon, H. (2017) A unifying comparative phylogenetic framework including traits coevolving across interacting lineages Systematic Biology 66: 551-568

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

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

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

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

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

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