How to make more out of community data? A conceptual framework and its implementation as models and software.
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species-to-species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R- and Matlab-packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time-series data. We illustrate the use of this framework through a series of diverse ecological examples.
Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.|Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
Otso
O
Ovaskainen
Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.
Gleb
G
Tikhonov
Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.
Anna
A
Norberg
Department of Mathematics and Statistics, McMaster University, 1280 Main Street West Hamilton, Ontario, L8S 4K1, Canada.|Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard Université Sherbrooke, Québec, J1K 2R1, Canada.
F
F
Guillaume Blanchet
Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA.
Leo
L
Duan
Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA.
David
D
Dunson
Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, 75651, Sweden.
Tomas
T
Roslin
Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.|Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, Helsinki, FI-00014, Finland.
Nerea
N
Abrego
D001499:Bayes Theorem; D044822:Biodiversity; D017753:Ecosystem; D008962:Models, Theoretical; D012984:Software
Assembly process; biotic filtering; community distribution; community modelling; community similarity; environmental filtering; functional trait; joint species distribution model; metacommunity; phylogenetic signal