title: Scale decisions can reverse conclusions on community assembly processes.
abstract: OBJECTIVE
  Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales.
  
  
  METHODS
  European Alps.
  
  
  METHODS
  We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub-dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α-diversities of local communities, and statistics commonly used together with null models in order to infer non-random diversity patterns (i.e. phylogenetic clustering versus over-dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses.
  
  
  RESULTS
  Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over-dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over-dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients.
  
  
  CONCLUSIONS
  Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Tamara
authors.initials: T
authors.lastname: Münkemüller
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Gallien
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lavergne
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Renaud
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Cristina
authors.initials: C
authors.lastname: Roquet
authors.affiliation: Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Abdulhak
authors.affiliation: Department of Conservation Biology, Vegetation- and Landscape Ecology, Faculty Centre of Biodiversity, Rennweg 14, 1030 Vienna.
authors.forename: Stefan
authors.initials: S
authors.lastname: Dullinger
authors.affiliation: Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France.
authors.forename: Luc
authors.initials: L
authors.lastname: Garraud
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland ; Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Antoine
authors.initials: A
authors.lastname: Guisan
authors.affiliation: Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS), Plant Biodiversity Lab, Jules Verne University of Picardie, 1 Rue des Louvels, FR-80037 Amiens Cedex 1, France.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Lenoir
authors.affiliation: Ecoinformatics and Biodiversity Group, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
authors.forename: Jens-Christian
authors.initials: JC
authors.lastname: Svenning
authors.affiliation: Domaine de Charance, Conservatoire Botanique National Alpin, Gap, 05000, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Van Es
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland ; Institute of Earth Sciences, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Pascal
authors.initials: P
authors.lastname: Vittoz
authors.affiliation: Vienna Institute for Nature Conservation and Analyses, Giessergasse 6/7, 1090 Vienna, Austria.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Willner
authors.affiliation: Landscape Dynamics, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wohlgemuth
authors.affiliation: Landscape Dynamics, Swiss Federal Research Institute WSL, CH-8903 Birmensdorf, Switzerland.
authors.forename: Niklaus E
authors.initials: NE
authors.lastname: Zimmermann
authors.affiliation: Laboratoire d'Ecologie Alpine, UMR CNRS 5553, University Joseph Fourier, Grenoble 1, BP 53, 38041 Grenoble Cedex 9, France.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Thuiller
keywords: Alpha diversity; assembly rules; community ecology; ecophylogenetics; null models; sampling design