A major challenge in ecology is the need for a better theoretical framework for understanding how species assemblages (ecological communities) arise, why some are species-rich and others species-poor, and why some species are present or dominant whereas others are not.
Current community assembly theory is largely based on static models. However, ecological dynamics (e.g. ecological drift, competition, immigration), or evolutionary dynamics (e.g. genetic drift, natural selection, speciation) generate continual changes in the constituents of communities and the sources from which they are assembled. The dynamical models that do exist do not take the community perspective or do not readily allow inferences from data. Moreover, there is often a mismatch between models and data.
We attempt to solve these problems simultaneously by developing a fully stochastic, dynamical and data-friendly theory of community assembly, and testing and informing this theory with model-oriented experiments and field studies of both macro-organisms and micro-organisms. The theory should contain models of speciation, extinction, immigration and demographic change that vary in spatial, phylogenetic and biotic complexity, and which I design for confrontation with data by providing each model’s likelihood given the data.
We conduct evolutionary experiments on the mite Tetranychus urticae and the bacterium Escherichia coli, which are ideal model organisms due to their short generation times. The experiments will provide insight into how diversity affects diversification, a great unknown in current macro-evolutionary theory. Apart from these highly controlled experiments, we apply the theory to naturally occurring micro-landsnails in South-East Asia, and micro-organisms in geothermal pools in New Zealand. Their small size, endemism and spatially limited, discrete habitat create a miniature world that facilitates sampling and confrontation with models. We provide software tools for scientists and conservationists to assess the processes underlying natural communities and predict their future composition and diversity.
- Alex Pigot (September 2013 – present)
- Karen Bisschop (November 2014 – present), jointly supervised with D. Bonte, University of Ghent
- Kasper Hendriks (September 2014 – present), jointly supervised with M. Schilthuizen, Naturalis
- Richel Bilderbeek (September 2014 – present)
- Adriana Alzate Vallejo (March 2013 – present), jointly supervised with D. Bonte, University of Ghent
- Ellen van Velzen (January 2009 – October 2014, PhD degree expected on 2 March 2015)
- Thijs Janzen (September 2010 – November 2014, PhD degree expected on 27 March 2015)
- Xiaoguang Du (September 2008 – present)
- Saleta Perez-Vila (February 2007 – present), jointly supervised with B. Wertheim (RUG)
- Francisco Encinas-Viso (October 2008 – March 2013, PhD degree on 14 June 2013)
- Xubing Liu (May 2011 – March 2013, PhD degree on 14 June 2013)
PhD / postdoc positions available on eco-evolutionary assembly of ecological communities
Even though application through the links above is no longer possible, I am still seeking one or two candidates, so feel free to inquire.
DAMOCLES package for R. Simulation and likelihood methods for a dynamical community assembly that accounts for phylogenetic history.
DDD package for R. Calculates the likelihood of diversity-dependent diversification models for a given data set of branching times of a phylogenetic tree.
PBD package for R. Calculates the likelihood of the lineage-based protracted speciation model for a given data set of branching times of a phylogenetic tree.
Public Seelye lecture A simple view on biological complexity, New Zealand, November 2013
Predicting the past from the present. Hungary, August 2012
Al Hammal, O., D. Alonso, R.S. Etienne & S.J. Cornell (2015). When can species abundance data reveal non-neutrality? PLoS Computational Biology. In press.
Janzen, T., S. Hoehna & R.S. Etienne (2015). Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT. Methods in Ecology & Evolution. In press.
Van der Plas, F., T. Janzen, A. Ordonez, W. Fokkema, J. Reinders, R.S. Etienne & H. Olff (2015), A new modeling approach estimates the relative importance of different community assembly processes. Ecology. In press.
Liu, X., R.S. Etienne, M. Liang, Y. Wang & S. Yu (2015). Experimental evidence for an intraspecific Janzen-Connell effect mediated by soil biota. Ecology. In press.
Liang, M., X. Liu, R.S. Etienne, F. Huang, Y. Wang & S. Yu (2015). Arbuscular mycorrhizal fungi counteract the Janzen-Connell effect of soil pathogens. Ecology. In press.
Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163. Link to pdf.
Lambert, A., H. Morlon & R.S. Etienne (2015). The reconstructed tree in the lineage-based model of protracted speciation. Journal of Mathematical Biology 70: 367-397. Link to pdf.
Etienne, R.S., H. Morlon & A. Lambert (2014). Estimating the duration of speciation from phylogenies. Evolution 68: 2430-2440. Link to pdf.
Valente, L.M., R.S. Etienne & A.B. Phillimore (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B 281: 20133227. Link to pdf.
Encinas-Viso, F.A., T.A. Revilla, & R.S. Etienne (2014). Shifts in pollinator population structure may jeopardize pollination service. Journal of Theoretical Biology 352: 24–30. Link to pdf.
Encinas-Viso, F.A., T.A. Revilla, E. van Velzen & R.S. Etienne (2014). Frugivores and cheap fruits make fruiting fruitful. Journal of Evolutionary Biology 27: 313-324. Link to pdf.
Haegeman, B., Sari, T. & R.S. Etienne (2014). Predicting coexistence of plants subject to a tolerance-competition trade-off. Journal of Mathematical Biology 68: 1815–1847. Link to pdf.
Lee, J., H. Buckley, R.S. Etienne & G. Lear (2013). Both species sorting and neutral processes drive assembly of bacterial communities in aquatic microcosms. FEMS Microbiology Ecology 86: 288–302. Link to pdf.
Te Beest, M., K. Elschot, H. Olff & R.S. Etienne (2013). Invasion success in a marginal habitat: an experimental test of competitive ability and drought tolerance in Chromolaena odorata. PLoS One 8: e68274. Link to pdf.
McInerny, G.J. & R.S. Etienne (2013). 'Niche' or 'distribution' modelling? A response to Warrren. Trends in Ecology & Evolution 28: 191-192. Link to pdf.
Van Leeuwen, E. & R.S. Etienne (2013). Caught in the middle: asymmetric competition causes high variance in intermediate trait abundances Theoretical Population Biology. 85: 26-37. Link to pdf.
Van Velzen, E. & R.S. Etienne (2013). The evolution and coexistence of generalist and specialist herbivores under between-plant competition. Theoretical Ecology 6: 87–98. Link to pdf.
- Evaluated as New Finding and Tech Advance by James O' Dwyer on Faculty of 1000.
- Evaluated as New Finding and Interesting Hypothesis by Ben Bolker on Faculty of 1000.
Etienne, R.S. & B. Haegeman (2012). A conceptual and statistical framework for adaptive radiations with a key role for diversity-dependence. American Naturalist 180: E75-E89. Link to pdf.
Etienne, R.S. & J. Rosindell (2012). Comment on “Global correlations in tropical tree species richness and abundance reject neutrality”. Science 336: 1639. Link to pdf.
Price, C.A. J.S Weitz, V.M. Savage, J. Stegen, A. Clarke, D.A. Coomes, P.S. Dodds, R.S. Etienne, A.J. Kerkhoff, K. McCulloh, K.J. Niklas, H. Olff & N.G. Swenson (2012). Testing the metabolic theory of Ecology. Ecology Letters 15: 1465-1474. Link to pdf.
McInerny, G.J. & R.S. Etienne (2012). Ditch the niche - is the niche a useful concept in ecology or species distribution modelling? Journal of Biogeography 39: 2096-2102. Link to pdf.
McInerny, G.J. & R.S. Etienne (2012). Stitch the niche - a practical philosophy and visual schematic for the niche concept. Journal of Biogeography 39: 2103-2111. Link to pdf.
McInerny, G.J. & R.S. Etienne (2012). Pitch the niche - taking responsibility for the concepts we use in ecology and species distribution modelling. Journal of Biogeography 39: 2112-2118. Link to pdf.
Linder, H.P., O. Bykova, J. Dyke, R.S. Etienne, T. Hickler, I. Kuhn, G. Marion, R. Ohlemüller, S.J. Schymanski & A. Singer (2012). Environmental modulation and species distribution models. Journal of Biogeography 39: 2179-2190. Link to pdf.
Wennekes, P.L., J. Rosindell & R.S. Etienne (2012). The neutral - niche debate: a philosophical perspective. Acta Biotheoretica 60: 257-271. Link to pdf.
Rosindell, J., S.P. Hubbell, F. He, L.J. Harmon & R.S. Etienne (2012). The case for ecological neutral theory. Trends in Ecology & Evolution 27: 203-208. Link to pdf
Jønsson, K.A., P-H.Fabre, S.A. Fritz, R.S. Etienne, R.E. Ricklefs, T.B. Jørgensen, J. Fjeldså, C. Rahbek, P.G.P. Ericson, F. Woog, E. Pasqueth & M. Irestedt (2012). Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas. Proceedings of the National Academy of Sciences of the USA 109: 6620-6625. Link to pdf.
Etienne, R.S. & J. Rosindell (2012). Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Systematic Biology 61: 204–213. Link to pdf
Melián, C.J., D. Alonso, S. Allesina, R.S. Condit & R.S. Etienne (2012). Does sex speed up evolutionary rate and increase biodiversity? PLoS Computational Biology 8: e1002414. Link to pdf.
Etienne, R.S., S.N. de Visser, T. Janzen, H. Olff, J.L. Olsen & J. Rosindell (2012). Can clade alone explain the relationship between body size and diversity? Interface Focus 2: 170-179. Download pdf.
Etienne, R.S., B. Haegeman, T. Stadler, T. Aze, P.N. Pearson, A. Purvis & A.B. Phillimore (2012). Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proceedings of the Royal Society of London B 279: 1300 - 1309 Link to pdf.
- The DDD package for R, which computes the likelihood of a diversity-dependent model given branching times of a phylogenetic tree, can be downloaded here.
Encinas-Viso, F., T.A. Revilla & R.S. Etienne (2012). Phenology drives mutualistic network structure and diversity. Ecology Letters 15: 198-208. Link to pdf.
Liu, X., M. Liang, R.S. Etienne, Y. Wang, C. Staehelin & S. Yu (2012). Experimental evidence for a phylogenetic Janzen–Connell effect in a subtropical forest. Ecology Letters 15: 111–118.
Rosindell, J., P.A. Jansen & R.S. Etienne (2012). Age structure in neutral theory resolves inconsistencies due to reproductive size threshold. Journal of Plant Ecology 5: 64–71.
- Discussed on EEB & Flow
Hawley, D.M., R.S. Etienne , V.O. Ezenwa & A.E. Jolles (2011). Does animal behavior underlie covariation between hosts’ exposure to infectious agents and susceptibility to infection? Implications for disease dynamics. Integrative and Comparative Biology 51: 528-539. .
Rosindell, J., S.P. Hubbell & R.S. Etienne (2011). The unified neutral theory of biodiversity and biogeography at age ten. Trends in Ecology & Evolution 26: 340-348. .
Haegeman, B. & R.S. Etienne (2011). Independent species in independent niches behave neutrally. Oikos 120: 961-963. .
Du, X., S. Zhou & R.S. Etienne (2011). Negative density dependence can offset the effect of species competitive asymmetry: a niche-based mechanism for neutral-like patterns. Journal of Theoretical Biology 278: 127–134. .
Etienne, R.S. & J. Rosindell (2011). The spatial limitations of current neutral models of biodiversity. PLoS One 6(3): e14717. Download pdf.
Etienne, R.S. & B. Haegeman (2011). The neutral theory of biodiversity with random fission speciation. Theoretical Ecology 4: 87–109. Download pdf.
- Evaluated as "Tech Advance" by Ben Bolker on Faculty of 1000
- Evaluated as "Recommended" by Gabriele Sorci on Faculty of 1000.
Leigh Jr., E.G., J. Rosindell & R.S. Etienne (2010). Unified neutral theory of biodiversity and biogeography. Scholarpedia 5: 8822. Link to paper.
Ezenwa, V.O., R.S. Etienne, G. Luikart, A. Beja-Pereira, F. Gardipee & A.E. Jolles (2010). Hidden consequences of living in a wormy world: nematode-induced immune-suppression facilitates TB invasion in African buffalo. American Naturalist 176: 613–624. Link to paper.
Rosindell, J., S.J. Cornell, S.P. Hubbell & R.S. Etienne (2010). Protracted speciation revitalizes the neutral theory of biodiversity. Ecology Letters 13: 716–727.
Haegeman, B. & R.S. Etienne (2010). A self-consistent approach for neutral community models with speciation. Physical Review E 81: 031911.
Haegeman, B. & R.S. Etienne (2010). Entropy maximization and the spatial distribution of species. American Naturalist 175: E74-E90.
Haegeman, B. & R.S. Etienne (2009). Neutral models with generalised speciation. Bulletin of Mathematical Biology 71: 1507-1519.
Morlon, H., E.P. White, R.S. Etienne, J.L. Green et al. (2009). Taking species abundance distributions beyond individuals. Ecology Letters 12: 488-501. Link to online material.
Perry, G.L.W., N.J. Enright, B.P. Miller, B.B. Lamont, & R.S. Etienne (2009). Dispersal, edaphic fidelity, and speciation in species-rich Western Australian shrublands: evaluating a neutral model of biodiversity. Oikos 118:1349-1362.
Etienne, R.S. (2009). Maximum likelihood estimation of neutral model parameters for multiple samples with different degrees of dispersal limitation. Journal of Theoretical Biology 257: 510-514. . Link to online material.
Cromsigt, J.P.G.M., S.J. van Rensburg, R.S. Etienne & H. Olff (2009). Monitoring large herbivore diversity at different scales: comparing direct and indirect methods. Biodiversity and Conservation 18: 1219-1231.
Etienne, R.S. & M.E.F. Apol (2009). Estimating speciation and extinction rates from diversity data and the fossil record. Evolution 63: 244-255. Link to online material.
Etienne, R.S. (2009). Improved estimation of neutral model parameters for multiple samples with different degrees of dispersal limitation. Ecology 90: 847-852. Link to online material.
- Featured on ESI Special Topics.
Apol, M.E.F., R.S. Etienne & H. Olff (2008). Revisiting the evolutionary origin of allometric metabolic scaling in biology. Functional Ecology 22: 1070-1080. Link to online material.
Rosindell, J., Y. Wong & R.S. Etienne (2008). A coalescence approach to spatial neutral ecology. Ecological Informatics 3: 259-271.
Lof, M., R.S. Etienne, J. Powell, M. de Gee & L. Hemerik (2008). The effect of chemical information on the spatial distribution of fruit flies: I Model results. Bulletin of Mathematical Biology 70: 1827-1849. Link to online material.
Jabot, F., R.S. Etienne & J. Chave (2008). Reconciling neutral community models and environmental filtering: theory and an empirical test. Oikos 117: 1308-1320.
Haegeman, B. & R.S. Etienne (2008). Relaxing the zero-sum assumption in neutral biodiversity theory. Journal of Theoretical Biology 252: 288-294.
Jolles, A.E., V.O. Ezenwa, R.S. Etienne, W.C. Turner & H. Olff (2008). Interactions between macroparasites and microparasites drive infection patterns in free-ranging African buffalo. Ecology 89: 2239-2250. Link to online material.
Alonso, D., A. Ostling & R.S. Etienne (2008). The implicit assumption of symmetry and the species abundance distribution. Ecology Letters 11: 93-105. Link to online material.
McGill, B.J., R.S. Etienne, J.S. Gray, D. Alonso, M.J. Anderson, H.K. Benecha, M. Dornelas, B.J. Enquist, J.L. Green, F. He, A.H. Hurlbert, A.E. Magurran, P.A. Marquet, B.A. Maurer, A. Ostling, C.U. Soykan, K. Ugland & E. White (2007). Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecology Letters 10: 995-1015.
Etienne, R.S., D. Alonso & A.J. McKane (2007). The zero-sum assumption in neutral biodiversity theory. Journal of Theoretical Biology 248: 522-536.
Munoz, F., P. Couteron, B.R. Ramesh & R.S. Etienne (2007). Inferring parameters of neutral communities: from one single large to several small samples. Ecology 88: 2482-2488. Link to online material.
Etienne, R.S. & D. Alonso (2007). Neutral community theory: how stochasticity and dispersal-limitation can explain species coexistence Journal of Statistical Physics 128: 485-510.
Etienne, R.S. (2007). A neutral sampling formula for multiple samples and an "exact" test of neutrality. Ecology Letters 10: 608-618. Link to online material.
Etienne, R.S., M.E.F. Apol, H. Olff & F.J. Weissing (2007). Modes of speciation and the neutral theory of biodiversity. Oikos 116: 241-258.
- Featured in Gewin, V. (2006). Beyond neutrality - ecology finds its niche. PLoS Biology 4: 1306-1310.
- Featured in Schilthuizen, M. (2006). Ecologisch nihilism. Bionieuws 9: 8-9. In Dutch.
- Featured on Science Daily
Etienne, R.S., M.E.F. Apol & H. Olff (2006). Demystifying the West, Brown & Enquist model of the allometry of metabolism. Functional Ecology 20: 394-399.
Etienne, R.S., A.M. Latimer, J.A. Silander & R.M. Cowling (2006). Comment on "Neutral ecological theory reveals isolation and rapid speciation in a biodiversity hot spot". Science 311: 610b.
Jolles, A.E., R.S. Etienne & H. Olff (2006). Independent and competing disease risks: implications for host populations in variable environments. American Naturalist 167: 643-755. Link to online material.
Etienne, R.S. & Alonso, D. (2005). A dispersal-limited sampling theory for species and alleles. Ecology Letters 8: 1147-1156. Link to online material.
Van Gemerden, B.S., Etienne, R.S. Olff, H., Hommel, P.W.F.M. & Van Langevelde, F. (2005). Reconciling methodologically different biodiversity assessments. Ecological Applications 15: 1747-1760. Link to online material.
Etienne, R.S. & Olff, H. (2005). Confronting different models of community structure to species-abundance data: a Bayesian model comparison. Ecology Letters 8: 493-504. Link to online material.
Etienne, R.S. (2005). A new sampling formula for neutral biodiversity. Ecology Letters 8: 253-260. Link to online material.
Etienne, R.S. & Hemerik, L. (2005). The founder and Allee effects in the patch occupancy metapopulation model. Pages 203-232 in T.A.C. Reydon & L. Hemerik (eds.) Current themes in theoretical biology: a Dutch perspective. Dordrecht, The Netherlands : Springer.
- Featured on Blackwell : The Ecological Equivalent of Ellis Island: From Ancestry to Biodiversity.
Etienne, R.S. & Olff, H. (2004). A novel genealogical approach to neutral biodiversity theory. Ecology Letters 7: 170-175.
Etienne, R.S. & Olff, H. (2004). How dispersal limitation shapes species - body size distributions in local communities. American Naturalist 163: 69-83. Download appendices.
Etienne, R.S., Ter Braak, C.J.F. & Vos, C.C. (2004). Application of stochastic patch occupancy models to real metapopulations. Pages 105-132 in Ecology, Genetics, and Evolution of Metapopulations ( I. Hanski & O.E. Gaggiotti, eds.). London , U.K. : Elsevier Academic Press.
Etienne, R.S. & Verboom, J. (2004). Overleven in een versnipperd landschap. Pages 117-135 in: Heesterbeek, J.A.P., Diekmann, O. & Metz, J.A.J. (eds.). De wiskundige kat, de biologische muis en de jacht op inzicht. Utrecht , The Netherlands : Epsilon Uitgaven Utrecht.
Etienne, R.S., Vos, C.C. & Jansen, M.J.W. (2003). Ecological impact assessment in data-poor systems: a case study on metapopulation persistence. Environmental Management 32: 760-777.
Ter Braak, C.J.F. & Etienne, R.S. (2003). Improved Bayesian analysis of metapopulation data with an application to a tree frog metapopulation. Ecology 84: 231-241. Link to online material.
Etienne, R.S. & Nagelkerke, C.J. (2002). Non-equilibria in small metapopulations: comparing the deterministic Levins model with its stochastic counterpart. Journal of Theoretical Biology 219: 463-478.
Etienne, R.S. (2002). A scrutiny of the Levins metapopulation model. Comments on Theoretical Biology 7: 257–281.
Etienne, R.S., Wertheim, B., Hemerik, L., Schneider, P. & Powell, J. (2002). The interaction between dispersal, the Allee effect and scramble competition affects population dynamics. Ecological Modelling 148: 153-168.
Etienne, R.S.Striking the metapopulation balance. Mathematical models & methods meet metapopulation management Wageningen, The Netherlands : Wageningen University PhD. thesis. ISBN 90-5808-598-8. Download pdf or request a paper copy.
Etienne, R.S. & Heesterbeek, J.A.P. (2001). Rules of thumb for conservation of metapopulations based on a stochastic winking-patch model. American Naturalist 158: 389-407.
Etienne, R.S. (2000). Local populations of different sizes, mechanistic rescue effect and patch preference in the Levins metapopulation model. Bulletin of Mathematical Biology 62: 943-958. .
Etienne, R.S. & Heesterbeek, J.A.P. (2000). On optimal size and number of reserves for metapopulation persistence. Journal of Theoretical Biology 203: 33-50.
Etienne, R.S., Wertheim, B., Hemerik, L., Schneider, P. & Powell, J. (2000). Dispersal may enable persistence of fruit flies suffering from the Allee effect and scramble competition. Proceedings of the section Experimental and Applied Entomology of the Netherlands Entomological Society 11: 121-128.
Ragas, A.M.J., Etienne, R.S., Willemsen, F.H. & Van de Meent, D. (1999). Assessing model uncertainty for environmental decision making: a case of the coherence of independently derived environmental quality objectives for air and water. Environmental Toxicology and Chemistry 18: 1856-1867.
Etienne, R.S., Willemsen, F.H., Ragas, A.M.J. & Van de Meent, D. (1998). Uncertainties in evaluating the coherence of independently derived environmental quality objectives for air, water and soil. Pages 283-290 in Nienhuis, P.H., Leuven , R.S.E.W. & Ragas, A.M.J. (eds.). New concepts for sustainable management of river basins. Leiden: Backhuys Publishers.
Etienne, R.S., Ragas, A.M.J. & Van de Meent, D. (1997). Operational uncertainties in impleBox; operational uncertainty analysis of the air-water concentration ratio computed by SimpleBox for 11 volatile compounds. Bilthoven, The Netherlands : National Institute of Public Health and the Environment. Report No. 719101031.
Boersma, H.F. & Etienne. R.S. (1996). Characterization of the natural ambient sound environment. Proceedings of Internoise 1996 ( Liverpool , 1996), 2465-2468.
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