Original Article
How to model species responses along ecological gradients – Huisman–Olff–Fresco models revisited
Abstract
Questions
In species response modelling, can a hierarchical logistic regression framework compete against GAM in terms of statistical inference? Are bimodal shapes useful to model species responses along ecological gradients?
Location
Germany.
Methods
In hierarchical logistic regression modelling [also known as Huisman, Olff, Fresco (HOF) models], the best model is chosen from a set of predetermined models using statistical information criteria, i.e. a balance between model fit to the data and simplicity of the model. We extended the classical five model types with two bimodal shapes. We improved the model optimization process to inhibit unrealistically steep slopes and abrupt changes. The stability of model choices is safeguarded through bootstrapping. The framework was tested on a data set of 547 vegetation plots of arable land with measured soil pHKCL. The ability to reproduce known shapes was tested with artificial data sets. Shape parameters, e.g. niche width and range, slope (turnover) and species optima, can be calculated from the models and used for further analyses. The model framework together with advanced plot functions is included in the package eHOF for the statistical software environment R.
Results
Based on the AIC, 66 out of 131 species are modelled with a better compromise between model fit and model complexity by one of the logistic regression models as compared to GAM with automatic smoother selection. Within the model framework, 17 species (13%) are best modelled with one of the new bimodal types. The test with artificial data of known shape reveals good reliability of eHOF models for unimodal responses in areas with homogeneous information, but increasing uncertainty if the sampling is uneven or if only a part of the response is covered within the observed gradient range.
Conclusions
Hierarchical logistic regression models offer a flexible way to efficiently fit species response data. They propose a sound theoretical background for ecological interpretation. Extended HOF models as presented here are judged as an effective tool for univariate species response modelling.
Citing Literature
Number of times cited according to CrossRef: 70
- Hyekyung Park, Jae Geun Kim, Temporal and spatial variations of vegetation in a riparian zone of South Korea, Journal of Ecology and Environment, 10.1186/s41610-020-00152-z, 44, 1, (2020).
- Kaarina Weckström, Benjamin Redmond Roche, Arto Miettinen, Diana Krawczyk, Audrey Limoges, Steve Juggins, Sofia Ribeiro, Maija Heikkilä, Improving the paleoceanographic proxy tool kit – On the biogeography and ecology of the sea ice-associated species Fragilariopsis oceanica, Fragilariopsis reginae-jahniae and Fossula arctica in the northern North Atlantic, Marine Micropaleontology, 10.1016/j.marmicro.2020.101860, (101860), (2020).
- Daphne López-Marcos, María-Belén Turrión, Felipe Bravo, Carolina Martínez-Ruiz, Can mixed pine forests conserve understory richness by improving the establishment of understory species typical of native oak forests?, Annals of Forest Science, 10.1007/s13595-020-0919-7, 77, 1, (2020).
- Jonathan F. Jupke, Ralf B. Schäfer, Should ecologists prefer model‐ over distance‐based multivariate methods?, Ecology and Evolution, 10.1002/ece3.6059, 10, 5, (2417-2435), (2020).
- F. Ayache, V. M. Santana, M. J. Baeza, Environmental and anthropogenic drivers of coniferous species distribution in Mediterranean drylands from North West Algeria, Folia Geobotanica, 10.1007/s12224-020-09362-8, (2020).
- Ryan C. Burner, Alison R. Styring, Mustafa A. Rahman, Frederick H. Sheldon, Occupancy patterns and upper range limits of lowland Bornean birds along an elevational gradient, Journal of Biogeography, 10.1111/jbi.13691, 46, 11, (2583-2596), (2019).
- Per‐Ola Hedwall, Jörg Brunet, Martin Diekmann, With Ellenberg indicator values towards the north: Does the indicative power decrease with distance from Central Europe?, Journal of Biogeography, 10.1111/jbi.13565, 46, 5, (1041-1053), (2019).
- Alberto Jiménez‐Valverde, Pablo Peña‐Aguilera, Vijay Barve, Lidia Burguillo‐Madrid, Photo‐sharing platforms key for characterising niche and distribution in poorly studied taxa, Insect Conservation and Diversity, 10.1111/icad.12351, 12, 5, (389-403), (2019).
- Michal Knapp, Miroslav Seidl, Jana Knappová, Martin Macek, Pavel Saska, Temporal changes in the spatial distribution of carabid beetles around arable field-woodlot boundaries, Scientific Reports, 10.1038/s41598-019-45378-7, 9, 1, (2019).
- Sonia J. Rowley, T. Edward Roberts, Richard R. Coleman, Heather L. Spalding, Eugene Joseph, Mae K. L. Dorricott, Pohnpei, Federated States of Micronesia, Mesophotic Coral Ecosystems, 10.1007/978-3-319-92735-0_17, (301-320), (2019).
- Yanjing Lou, Ying Liu, Zhanhui Tang, Ming Jiang, Xianguo Lu, Håkan Rydin, Testing unidimensional species distribution models to forecast and hindcast changes in marsh vegetation over 40 years, Ecological Indicators, 10.1016/j.ecolind.2019.05.024, 104, (341-346), (2019).
- Mimmi Oksman, Stephen Juggins, Arto Miettinen, Andrzej Witkowski, Kaarina Weckström, The biogeography and ecology of common diatom species in the northern North Atlantic, and their implications for paleoceanographic reconstructions, Marine Micropaleontology, 10.1016/j.marmicro.2019.02.002, (2019).
- T. Edward Roberts, Tom C. L. Bridge, M. Julian Caley, Joshua S. Madin, Andrew H. Baird, Resolving the depth zonation paradox in reef‐building corals, Ecology, 10.1002/ecy.2761, 100, 8, (2019).
- D. López Marcos, M.B. Turrión Nieves, C. Martínez-Ruiz, Restauración en laderas mineras: una oportunidad para estudiar la sucesión ecológica en procesos de pendiente, Cuadernos de la Sociedad Española de Ciencias Forestales, 10.31167/csecfv0i45.19480, 45, 2, (107-118), (2019).
- Ana Savić, Dejan Dmitrović, Peter Glöer, Vladimir Pešić, Assessing environmental response of gastropod species in karst springs: what species response curves say us about niche characteristic and extinction risk?, Biodiversity and Conservation, 10.1007/s10531-019-01905-6, (2019).
- Daphne López-Marcos, María-Belén Turrión, Felipe Bravo, Carolina Martínez-Ruiz, Understory response to overstory and soil gradients in mixed versus monospecific Mediterranean pine forests, European Journal of Forest Research, 10.1007/s10342-019-01215-0, (2019).
- Daphne López-Marcos, María Belén Turrión, Carolina Martínez-Ruiz, Linking soil variability with plant community composition along a mine-slope topographic gradient: Implications for restoration, Ambio, 10.1007/s13280-019-01193-y, (2019).
- Persy Gómez, Maureen Murúa, José San Martín, Estefany Goncalves, Ramiro O. Bustamante, Maintaining close canopy cover prevents the invasion of Pinus radiata: Basic ecology to manage native forest invasibility, PLOS ONE, 10.1371/journal.pone.0210849, 14, 5, (e0210849), (2019).
- Robert Hering, Morgan Hauptfleisch, Katja Geißler, Arnim Marquart, Maria Schoenen, Niels Blaum, Shrub encroachment is not always land degradation: Insights from ground‐dwelling beetle species niches along a shrub cover gradient in a semi‐arid Namibian savanna, Land Degradation & Development, 10.1002/ldr.3197, 30, 1, (14-24), (2018).
- Oskar Kärcher, Daniel Hering, Karin Frank, Danijela Markovic, Freshwater species distributions along thermal gradients, Ecology and Evolution, 10.1002/ece3.4659, 9, 1, (111-124), (2018).
- Karan Kakouei, Jens Kiesel, Sami Domisch, Katie S. Irving, Sonja C. Jähnig, Jochem Kail, Projected effects of Climate‐change‐induced flow alterations on stream macroinvertebrate abundances, Ecology and Evolution, 10.1002/ece3.3907, 8, 6, (3393-3409), (2018).
- Nico Heer, Fabian Klimmek, Christoph Zwahlen, Markus Fischer, Norbert Hölzel, Valentin H. Klaus, Till Kleinebecker, Daniel Prati, Steffen Boch, Hemiparasite-density effects on grassland plant diversity, composition and biomass, Perspectives in Plant Ecology, Evolution and Systematics, 10.1016/j.ppees.2018.01.004, 32, (22-29), (2018).
- V. K. Shitikov, A. E. Ivanova, K. A. Kydralieva, V. A. Terekhova, Use of the Field Data for Assessment of Hazardous Concentration of Pollutants in Soil and Modelling of Species Sensitivity Distribution, Megacities 2050: Environmental Consequences of Urbanization, 10.1007/978-3-319-70557-6_15, (137-149), (2018).
- Binu M. Tripathi, James C. Stegen, Mincheol Kim, Ke Dong, Jonathan M. Adams, Yoo Kyung Lee, Soil pH mediates the balance between stochastic and deterministic assembly of bacteria, The ISME Journal, 10.1038/s41396-018-0082-4, 12, 4, (1072-1083), (2018).
- Guoju Wu, Xiaohong Liu, Shichang Kang, Tuo Chen, Guobao Xu, Xiaomin Zeng, Wenzhi Wang, Bo Wang, Xuanwen Zhang, Huhu Kang, Age-dependent impacts of climate change and intrinsic water-use efficiency on the growth of Schrenk spruce ( Picea schrenkiana ) in the western Tianshan Mountains, China, Forest Ecology and Management, 10.1016/j.foreco.2018.02.008, 414, (1-14), (2018).
- Juri Nascimbene, Pier Luigi Nimis, Petra Mair, Daniel Spitale, Climate Warming Effects on Epiphytes in Spruce Forests of the Alps, Herzogia, 10.13158/heia.31.1.2018.374, 31, p1, (374-384), (2018).
- Paul J. Gordijn, Terry M. Everson, Timothy G. O’Connor, Resistance of Drakensberg grasslands to compositional change depends on the influence of fire-return interval and grassland structure on richness and spatial turnover, Perspectives in Plant Ecology, Evolution and Systematics, 10.1016/j.ppees.2018.07.005, 34, (26-36), (2018).
- Yanjing Lou, Chuanyu Gao, Yanwen Pan, Zhenshan Xue, Ying Liu, Zhanhui Tang, Ming Jiang, Xianguo Lu, Håkan Rydin, Niche modelling of marsh plants based on occurrence and abundance data, Science of The Total Environment, 10.1016/j.scitotenv.2017.10.300, 616-617, (198-207), (2018).
- Pedro A. Salgueiro, António Mira, João E. Rabaça, Sara M. Santos, Identifying critical thresholds to guide management practices in agro-ecosystems: Insights from bird community response to an open grassland-to-forest gradient, Ecological Indicators, 10.1016/j.ecolind.2018.01.008, 88, (205-213), (2018).
- Giulia Furlanetto, Cesare Ravazzi, Roberta Pini, Francesca Vallè, Michele Brunetti, Roberto Comolli, Massimo Domenico Novellino, Lorena Garozzo, Valter Maggi, Holocene vegetation history and quantitative climate reconstructions in a high-elevation oceanic district of the Italian Alps. Evidence for a middle to late Holocene precipitation increase, Quaternary Science Reviews, 10.1016/j.quascirev.2018.10.001, 200, (212-236), (2018).
- Giulia Furlanetto, Cesare Ravazzi, Federica Badino, Michele Brunetti, Elena Champvillair, Valter Maggi, Elevational transects of modern pollen samples: Site-specific temperatures as a tool for palaeoclimate reconstructions in the Alps, The Holocene, 10.1177/0959683618810395, (095968361881039), (2018).
- Pedro A. Salgueiro, António Mira, João E. Rabaça, Carmo Silva, Sofia Eufrázio, Denis Medinas, Giovanni Manghi, Bruno Silva, Sara M. Santos, Thinking outside the patch: a multi-species comparison of conceptual models from real-world landscapes, Landscape Ecology, 10.1007/s10980-017-0603-y, 33, 3, (353-370), (2017).
- Rachel M. Mitchell, Justin P. Wright, Greg M. Ames, Species’ traits do not converge on optimum values in preferred habitats, Oecologia, 10.1007/s00442-017-4041-y, 186, 3, (719-729), (2017).
- Miroslav Dvorský, Martin Macek, Martin Kopecký, Jan Wild, Jiří Doležal, Niche asymmetry of vascular plants increases with elevation, Journal of Biogeography, 10.1111/jbi.13001, 44, 6, (1418-1425), (2017).
- Monique Goguen, Paul A. Arp, Modeling and Mapping Forest Floor Distributions of Common Bryophytes Using a LiDAR-Derived Depth-to-Water Index, American Journal of Plant Sciences, 10.4236/ajps.2017.84059, 08, 04, (867-890), (2017).
- Jose R. Loaiza, Larissa C. Dutari, Jose R. Rovira, Oris I. Sanjur, Gabriel Z. Laporta, James Pecor, Desmond H. Foley, Gillian Eastwood, Laura D. Kramer, Meghan Radtke, Montira Pongsiri, Disturbance and mosquito diversity in the lowland tropical rainforest of central Panama, Scientific Reports, 10.1038/s41598-017-07476-2, 7, 1, (2017).
- Mohammad Naghi Adel, Hassan Pourbabaei, Seyed Jalil Alavi, Ali Salehi, Response curves of seventeen woody species to soil factors along a riparian forest in northern Iran, Russian Journal of Ecology, 10.1134/S1067413617030031, 48, 3, (219-225), (2017).
- I. Odriozola, G. García-Baquero, A. Etxeberria, A. Aldezabal, Patterns of species relatedness created by competitive exclusion depend on species niche differences: Evidence from Iberian Atlantic grasslands, Perspectives in Plant Ecology, Evolution and Systematics, 10.1016/j.ppees.2017.07.002, 28, (36-46), (2017).
- P. Saikia, J. Deka, S. Bharali, Amit Kumar, O. P. Tripathi, L. B. Singha, S. Dayanandan, M. L. Khan, Plant diversity patterns and conservation status of eastern Himalayan forests in Arunachal Pradesh, Northeast India, Forest Ecosystems, 10.1186/s40663-017-0117-8, 4, 1, (2017).
- Björn Wiström, Anders Busse Nielsen, Forest Edge Regrowth Typologies in Southern Sweden—Relationship to Environmental Characteristics and Implications for Management, Environmental Management, 10.1007/s00267-017-0851-2, 60, 1, (69-85), (2017).
- Karan Kakouei, Jens Kiesel, Jochem Kail, Martin Pusch, Sonja C. Jähnig, Quantitative hydrological preferences of benthic stream invertebrates in Germany, Ecological Indicators, 10.1016/j.ecolind.2017.04.029, 79, (163-172), (2017).
- Ruby Ghosh, Angela A. Bruch, Felix Portmann, Subir Bera, Dipak Kumar Paruya, P. Morthekai, Sheikh Nawaz Ali, A modern pollen–climate dataset from the Darjeeling area, eastern Himalaya: Assessing its potential for past climate reconstruction, Quaternary Science Reviews, 10.1016/j.quascirev.2017.09.002, 174, (63-79), (2017).
- Yu Shang, Johannes Sikorski, Michael Bonkowski, Anna-Maria Fiore-Donno, Ellen Kandeler, Sven Marhan, Runa S. Boeddinghaus, Emily F. Solly, Marion Schrumpf, Ingo Schöning, Tesfaye Wubet, Francois Buscot, Jörg Overmann, Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters, PLOS ONE, 10.1371/journal.pone.0173765, 12, 3, (e0173765), (2017).
- Arunava Datta, Ingolf Kühn, Mustaqeem Ahmad, Stefan Michalski, Harald Auge, Processes affecting altitudinal distribution of invasive Ageratina adenophora in western Himalaya: The role of local adaptation and the importance of different life-cycle stages, PLOS ONE, 10.1371/journal.pone.0187708, 12, 11, (e0187708), (2017).
- Mart Vlam, Peter van der Sleen, Peter Groenendijk, Pieter A. Zuidema, Tree Age Distributions Reveal Large-Scale Disturbance-Recovery Cycles in Three Tropical Forests, Frontiers in Plant Science, 10.3389/fpls.2016.01984, 7, (2017).
- Jana Michaelis, Martin R. Diekmann, Biased niches – Species response curves and niche attributes from Huisman-Olff-Fresco models change with differing species prevalence and frequency, PLOS ONE, 10.1371/journal.pone.0183152, 12, 8, (e0183152), (2017).
- A. V. Zhukov, A. Yu. Andryushchenko, Relief and ecological niche of mute swan (Cygnus olor (Gmelin, 1803)) wintering in Sivash, Acta Biologica Sibirica, 10.14258/abs.v3i2.2730, 3, 2, (20), (2017).
- Viktoria Wagner, Milan Chytrý, David Zelený, Henrik Wehrden, Annika Brinkert, Jiří Danihelka, Norbert Hölzel, Florian Jansen, Johannes Kamp, Pavel Lustyk, Kristina Merunková, Salza Palpurina, Zdenka Preislerová, Karsten Wesche, Regional differences in soil pH niche among dry grassland plants in Eurasia, Oikos, 10.1111/oik.03369, 126, 5, (660-670), (2016).
- Nobuo Imai, Hiromitsu Samejima, Malcom Demies, Atsushi Tanaka, John Baptist Sugau, Joan T. Pereira, Kanehiro Kitayama, Response of tree species diversity to disturbance in humid tropical forests of Borneo, Journal of Vegetation Science, 10.1111/jvs.12401, 27, 4, (739-748), (2016).
- Jana Michaelis, Angela Pannek, Martin Diekmann, Soil pH limits of forest vascular plants determine range size and threat level, Journal of Vegetation Science, 10.1111/jvs.12380, 27, 3, (535-544), (2016).
- Christian Piedallu, Jean‐Claude Gégout, François Lebourgeois, Ingrid Seynave, Soil aeration, water deficit, nitrogen availability, acidity and temperature all contribute to shaping tree species distribution in temperate forests, Journal of Vegetation Science, 10.1111/jvs.12370, 27, 2, (387-399), (2016).
- J. Reinecke, M. Wulf, L. Baeten, J. Brunet, G. Decocq, P. Frenne, M. Diekmann, B. J. Graae, T. Heinken, M. Hermy, A. Jamoneau, J. Lenoir, J. Plue, A. Orczewska, H. Calster, K. Verheyen, T. Naaf, Acido‐ and neutrophilic temperate forest plants display distinct shifts in ecological pH niche across north‐western Europe, Ecography, 10.1111/ecog.02051, 39, 12, (1164-1175), (2016).
- Dragana D. Jenačković, Ivana D. Zlatković, Dmitar V. Lakušić, Vladimir N. Ranđelović, Macrophytes as bioindicators of the physicochemical characteristics of wetlands in lowland and mountain regions of the central Balkan Peninsula, Aquatic Botany, 10.1016/j.aquabot.2016.06.003, 134, (1-9), (2016).
- Torbjörn Tyler, Pål Axel Olsson, Substrate pH ranges of south Swedish bryophytes—Identifying critical pH values and richness patterns, Flora, 10.1016/j.flora.2016.05.006, 223, (74-82), (2016).
- Falko Turner, Liping Zhu, Xinmiao Lü, Ping Peng, Qingfeng Ma, Junbo Wang, Juzhi Hou, Qiuqi Lin, Ruimin Yang, Peter Frenzel, Pediastrum sensu lato (Chlorophyceae) assemblages from surface sediments of lakes and ponds on the Tibetan Plateau, Hydrobiologia, 10.1007/s10750-015-2620-7, 771, 1, (101-118), (2016).
- Björn Wiström, Anders Busse Nielsen, Decisive environmental characteristics for woody regrowth in forest edges – Patterns along complex environmental gradients in Southern Sweden, Forest Ecology and Management, 10.1016/j.foreco.2015.12.025, 363, (47-62), (2016).
- J Sakari Salonen, Adrian J Verster, Stefan Engels, Janne Soininen, Mathias Trachsel, Miska Luoto, Calibrating aquatic microfossil proxies with regression-tree ensembles: Cross-validation with modern chironomid and diatom data, The Holocene, 10.1177/0959683616632881, 26, 7, (1040-1048), (2016).
- Mark J. Brewer, Robert B. O'Hara, Barbara J. Anderson, Ralf Ohlemüller, Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling, Methods in Ecology and Evolution, 10.1111/2041-210X.12609, 7, 12, (1489-1502), (2016).
- Jon D. Shuker, Clay A. Simpkins, Jean‐Marc Hero, Determining environmental limits of threatened species: the example of the wallum sedgefrog Litoria olongburensis, Ecosphere, 10.1002/ecs2.1384, 7, 6, (2016).
- Frieda Beauregard, Sylvie Blois, Rapid latitudinal range expansion at cold limits unlikely for temperate understory forest plants, Ecosphere, 10.1002/ecs2.1549, 7, 11, (2016).
- Andreas H. Schweiger, Carl Beierkuhnlein, Marie‐Josée Fortin, Scale dependence of temperature as an abiotic driver of species' distributions, Global Ecology and Biogeography, 10.1111/geb.12463, 25, 8, (1013-1021), (2016).
- Per‐Ola Hedwall, Jörg Brunet, Trait variations of ground flora species disentangle the effects of global change and altered land‐use in Swedish forests during 20 years, Global Change Biology, 10.1111/gcb.13329, 22, 12, (4038-4047), (2016).
- Wellinton de Sá Arruda, Jens Oldeland, Antonio Conceição Paranhos Filho, Arnildo Pott, Nicolay L. Cunha, Iria Hiromi Ishii, Geraldo Alves Damasceno-Junior, Inundation and Fire Shape the Structure of Riparian Forests in the Pantanal, Brazil, PLOS ONE, 10.1371/journal.pone.0156825, 11, 6, (e0156825), (2016).
- Stein J. Hegland, Knut Rydgren, Eaten but not always beaten: winners and losers along a red deer herbivory gradient in boreal forest, Journal of Vegetation Science, 10.1111/jvs.12339, 27, 1, (111-122), (2015).
- A. Olthoff, C. Martínez-Ruiz, J.G. Alday, Distribution patterns of forest species along an Atlantic-Mediterranean environmental gradient: an approach from forest inventory data, Forestry, 10.1093/forestry/cpv031, 89, 1, (46-54), (2015).
- Alexander J. Ferry, Tania Prvan, Brian Jersky, Xavier Crosta, Leanne K. Armand, Statistical modeling of Southern Ocean marine diatom proxy and winter sea ice data: Model comparison and developments, Progress in Oceanography, 10.1016/j.pocean.2014.12.001, 131, (100-112), (2015).
- Martin Diekmann, Jana Michaelis, Angela Pannek, Know your limits – The need for better data on species responses to soil variables, Basic and Applied Ecology, 10.1016/j.baae.2015.08.010, 16, 7, (563-572), (2015).
- Adam J. Heathcote, Joy M. Ramstack Hobbs, N. John Anderson, Patrick Frings, Daniel R. Engstrom, John A. Downing, Diatom floristic change and lake paleoproduction as evidence of recent eutrophication in shallow lakes of the midwestern USA, Journal of Paleolimnology, 10.1007/s10933-014-9804-4, 53, 1, (17-34), (2014).
- Gabriel Zorello Laporta, Maria Anice Mureb Sallum, Coexistence mechanisms at multiple scales in mosquito assemblages, BMC Ecology, 10.1186/s12898-014-0030-8, 14, 1, (2014).
- Andrea Buffagni, The lentic and lotic characteristics of habitats determine the distribution of benthic macroinvertebrates in Mediterranean rivers, Freshwater Biology, 10.1111/fwb.13596, 0, 0, (undefined).
