Linking macroecology and community ecology: refining predictions of species distributions using biotic interaction networks

Abstract Macroecological models for predicting species distributions usually only include abiotic environmental conditions as explanatory variables, despite knowledge from community ecology that all species are linked to other species through biotic interactions. This disconnect is largely due to the different spatial scales considered by the two sub‐disciplines: macroecologists study patterns at large extents and coarse resolutions, while community ecologists focus on small extents and fine resolutions. A general framework for including biotic interactions in macroecological models would help bridge this divide, as it would allow for rigorous testing of the role that biotic interactions play in determining species ranges. Here, we present an approach that combines species distribution models with Bayesian networks, which enables the direct and indirect effects of biotic interactions to be modelled as propagating conditional dependencies among species’ presences. We show that including biotic interactions in distribution models for species from a California grassland community results in better range predictions across the western USA. This new approach will be important for improving estimates of species distributions and their dynamics under environmental change.

[1]  David R. Anderson,et al.  Model Selection and Multimodel Inference , 2003 .

[2]  N. Mouquet,et al.  On the integration of biotic interaction and environmental constraints at the biogeographical scale , 2016 .

[3]  P. Stephens,et al.  Predicting potential responses to future climate in an alpine ungulate: interspecific interactions exceed climate effects , 2014, Global change biology.

[4]  C. Mantyka‐Pringle,et al.  Prioritizing management actions for the conservation of freshwater biodiversity under changing climate and land-cover , 2016 .

[5]  J. Maron,et al.  Climate impacts on bird and plant communities from altered animal-plant interactions , 2012 .

[6]  J. Biesmeijer,et al.  Improving species distribution models using biotic interactions: a case study of parasites, pollinators and plants , 2013 .

[7]  R. Pearson,et al.  Predicting species distributions from small numbers of occurrence records: A test case using cryptic geckos in Madagascar , 2006 .

[8]  J. Lawton,et al.  Making mistakes when predicting shifts in species range in response to global warming , 1998, Nature.

[9]  Richard Fox,et al.  Temperature-Dependent Alterations in Host Use Drive Rapid Range Expansion in a Butterfly , 2012, Science.

[10]  M. Araújo,et al.  The importance of biotic interactions for modelling species distributions under climate change , 2007 .

[11]  Miguel G. Matias,et al.  Inferring biotic interactions from proxies. , 2015, Trends in ecology & evolution.

[12]  J. Grinnell The Niche-Relationships of the California Thrasher , 1917 .

[13]  Finn V. Jensen,et al.  Bayesian Networks and Decision Graphs , 2001, Statistics for Engineering and Information Science.

[14]  Carsten F. Dormann,et al.  Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents , 2012 .

[15]  A. Ives,et al.  Direct and indirect effects of warming on aphids, their predators, and ant mutualists. , 2014, Ecology.

[16]  M. N. S. Swamy,et al.  Graphs: Theory and Algorithms: Thulasiraman/Graphs , 1992 .

[17]  Antoine Guisan,et al.  Species distribution models reveal apparent competitive and facilitative effects of a dominant species on the distribution of tundra plants , 2010 .

[18]  G. Yohe,et al.  A globally coherent fingerprint of climate change impacts across natural systems , 2003, Nature.

[19]  Laura Uusitalo,et al.  Advantages and challenges of Bayesian networks in environmental modelling , 2007 .

[20]  A. Townsend Peterson,et al.  Novel methods improve prediction of species' distributions from occurrence data , 2006 .

[21]  M. Power,et al.  Effects of Fish in River Food Webs , 1990, Science.

[22]  Trevor Hastie,et al.  A statistical explanation of MaxEnt for ecologists , 2011 .

[23]  R. Almond,et al.  Mechanisms underpinning climatic impacts on natural populations: altered species interactions are more important than direct effects , 2014, Global change biology.

[24]  C. Parmesan Ecological and Evolutionary Responses to Recent Climate Change , 2006 .

[25]  John H. Holland,et al.  Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .

[26]  K. B. Suttle,et al.  Grassland responses to increased rainfall depend on the timescale of forcing , 2016, Global change biology.

[27]  Pieter T. J. Johnson,et al.  Experimental warming drives a seasonal shift in the timing of host-parasite dynamics with consequences for disease risk. , 2014, Ecology letters.

[28]  C. Johnson,et al.  Overfishing reduces resilience of kelp beds to climate-driven catastrophic phase shift , 2009, Proceedings of the National Academy of Sciences.

[29]  J. Diez,et al.  When Climate Reshuffles Competitors: A Call for Experimental Macroecology. , 2016, Trends in ecology & evolution.

[30]  Wilfried Thuiller,et al.  From species distributions to meta-communities. , 2015, Ecology letters.

[31]  Jorge Soberón,et al.  Niches and distributional areas: Concepts, methods, and assumptions , 2009, Proceedings of the National Academy of Sciences.

[32]  Michael J. Watts,et al.  Adapted conservation measures are required to save the Iberian lynx in a changing climate , 2013 .

[33]  Jorma Rissanen,et al.  Minimum Description Length Principle , 2010, Encyclopedia of Machine Learning.

[34]  J. Pearl Causality: Models, Reasoning and Inference , 2000 .

[35]  Xuemin Lin,et al.  A Fast and Effective Heuristic for the Feedback Arc Set Problem , 1993, Inf. Process. Lett..

[36]  Linda C. van der Gaag,et al.  Probabilistic Graphical Models , 2014, Lecture Notes in Computer Science.

[37]  Craig Packer,et al.  Climate Extremes Promote Fatal Co-Infections during Canine Distemper Epidemics in African Lions , 2008, PloS one.

[38]  Mark New,et al.  Ensemble forecasting of species distributions. , 2007, Trends in ecology & evolution.

[39]  Damien A. Fordham,et al.  Life history and spatial traits predict extinction risk due to climate change , 2014 .

[40]  Judea Pearl,et al.  Probabilistic reasoning in intelligent systems - networks of plausible inference , 1991, Morgan Kaufmann series in representation and reasoning.

[41]  A. Philip Dawid,et al.  Beware of the DAG! , 2008, NIPS Causality: Objectives and Assessment.

[42]  M. White,et al.  Selecting thresholds for the prediction of species occurrence with presence‐only data , 2013 .

[43]  R. Paine Food Web Complexity and Species Diversity , 1966, The American Naturalist.

[44]  O. Schmitz,et al.  Infusing considerations of trophic dependencies into species distribution modelling. , 2014, Ecology letters.

[45]  M. Luoto,et al.  Biotic interactions improve prediction of boreal bird distributions at macro‐scales , 2007 .

[46]  S. Finnegan,et al.  Climate Change and the Past, Present, and Future of Biotic Interactions , 2013, Science.

[47]  Omri Allouche,et al.  Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS) , 2006 .

[48]  J. Edmonds,et al.  Economic and environmental choices in the stabilization of atmospheric CO2 concentrations , 1996, Nature.

[49]  W. Thuiller,et al.  Predicting species distribution: offering more than simple habitat models. , 2005, Ecology letters.

[50]  Jorge Soberón Grinnellian and Eltonian niches and geographic distributions of species. , 2007, Ecology letters.

[51]  M. Edwards,et al.  Impact of climate change on marine pelagic phenology and trophic mismatch , 2004, Nature.

[52]  Robert P. Anderson,et al.  Maximum entropy modeling of species geographic distributions , 2006 .

[53]  Miguel B. Araújo,et al.  Using species co-occurrence networks to assess the impacts of climate change , 2011 .

[54]  O. Schmitz,et al.  Ecosystem Responses to Global Climate Change: Moving Beyond Color Mapping , 2003 .

[55]  Momme Butenschön,et al.  Modelling the effects of climate change on the distribution and production of marine fishes: accounting for trophic interactions in a dynamic bioclimate envelope model , 2013, Global change biology.

[56]  Charles C. Elton Animal Ecology , 1927, Nature.

[57]  M. Araújo,et al.  BIOMOD – a platform for ensemble forecasting of species distributions , 2009 .

[58]  M. Power,et al.  Species Interactions Reverse Grassland Responses to Changing Climate , 2007, Science.

[59]  Peter J. Morin,et al.  Environmental warming alters food-web structure and ecosystem function , 1999, Nature.

[60]  J. Hellmann,et al.  The influence of species interactions on geographic range change under climate change , 2012, Annals of the New York Academy of Sciences.

[61]  M. Kearney,et al.  Mechanistic niche modelling: combining physiological and spatial data to predict species' ranges. , 2009, Ecology letters.

[62]  Richard E. Neapolitan,et al.  Learning Bayesian networks , 2007, KDD '07.

[63]  Antoine Guisan,et al.  Combining food web and species distribution models for improved community projections , 2013, Ecology and evolution.

[64]  Jacob S. Ivan,et al.  Enhancing species distribution modeling by characterizing predator-prey interactions. , 2014, Ecological applications : a publication of the Ecological Society of America.

[65]  O. Phillips,et al.  Extinction risk from climate change , 2004, Nature.

[66]  M. Thomsen,et al.  CLIMATE CHANGE AND GRASSLAND RESTORATION IN CALIFORNIA: LESSONS FROM SIX YEARS OF RAINFALL MANIPULATION IN A NORTH COAST GRASSLAND , 2007 .

[67]  F. Stuart Chapin,et al.  Responses of Arctic Tundra to Experimental and Observed Changes in Climate , 1995 .

[68]  C. Dormann,et al.  Neighbour identity modifies effects of elevated temperature on plant performance in the High Arctic , 2004 .

[69]  W. Dietrich,et al.  SEASONAL REASSEMBLY OF A RIVER FOOD WEB: FLOODS, DROUGHTS, AND IMPACTS OF FISH , 2008 .

[70]  E. Post,et al.  Opposing plant community responses to warming with and without herbivores , 2008, Proceedings of the National Academy of Sciences.

[71]  P. Dayton Competition, Disturbance, and Community Organization: The Provision and Subsequent Utilization of Space in a Rocky Intertidal Community , 1971 .

[72]  J. Harte,et al.  Shifting Dominance Within a Montane Vegetation Community: Results of a Climate-Warming Experiment , 1995, Science.

[73]  Gary R. Graves,et al.  Macroecological signals of species interactions in the Danish avifauna , 2010, Proceedings of the National Academy of Sciences.

[74]  Alejandro F. Rozenfeld,et al.  The geographic scaling of biotic interactions , 2013 .

[75]  J. Bascompte,et al.  Global change and species interactions in terrestrial ecosystems. , 2008, Ecology letters.

[76]  Jean-Pascal van Ypersele de Strihou Climate Change 2014 - Synthesis Report , 2015 .

[77]  T. Dawson,et al.  Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful? , 2003 .

[78]  M. C. Urban Accelerating extinction risk from climate change , 2015, Science.

[79]  R. Paine Macroecology: Does It Ignore or Can It Encourage Further Ecological Syntheses Based on Spatially Local Experimental Manipulations? , 2010, The American Naturalist.

[80]  C. D’Antonio,et al.  Ecological resistance, seed density and their interactions determine patterns of invasion in a California coastal grassland. , 2006, Ecology letters.

[81]  Brian J. McGill,et al.  A network approach for inferring species associations from co-occurrence data , 2016 .

[82]  N. Gotelli,et al.  Climate change, genetic markers and species distribution modelling , 2015 .

[83]  J. Lubchenco,et al.  SPECIES INTERACTION STRENGTH: TESTING MODEL PREDICTIONS ALONG AN UPWELLING GRADIENT , 2004 .

[84]  M. N. Shanmukha Swamy,et al.  Graphs: Theory and Algorithms , 1992 .

[85]  Si Tang,et al.  Secondary extinctions in food webs: a Bayesian network approach , 2013 .

[86]  Daniel E. Schindler,et al.  CLIMATE CHANGE UNCOUPLES TROPHIC INTERACTIONS IN AN AQUATIC ECOSYSTEM , 2004 .

[87]  Robert P. Anderson,et al.  Ecological Niches and Geographic Distributions , 2011 .

[88]  Dominique Gravel,et al.  From projected species distribution to food‐web structure under climate change , 2014, Global change biology.