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Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

  • Community ecology - Original research
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Abstract

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.

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Acknowledgments

We thank the anonymous referees for their very constructive comments on a previous version of our paper. Data collection in Brussels (dataset A) was financed by the Brussels Institute for Environment Management (IBGE-BIM) in the framework of the research project ‘Information and survey network on the biodiversity in Brussels’. G.B. is grateful to Alessandro Chiarucci for providing useful ideas and support during the MOBISIC data collection phase (dataset C). G.B. also warmly acknowledges the valuable support of Elisa Baragatti, Giulia Bennati, Domenico Bernardini, Marta Chincarini, Alessia Delli Bove, Francesco Geri, Sara Ghisleni, Sara Landi, Lia Pignotti, Duccio Rocchini, Elisa Santi, Mauro Taormina, Emanuele Vallone and Arianna Vannini during data collection and plant identification.

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Authors and Affiliations

  1. Department of Environmental Biology, University of Rome ‘La Sapienza’, Rome, Italy

    Carlo Ricotta & Michela Marignani

  2. BIOCONNET, Biodiversity and Conservation Network, Department of Environmental Sciences ‘G Sarfatti’, University of Siena, Siena, Italy

    Giovanni Bacaro

  3. National Botanic Garden of Belgium, Meise, Belgium

    Sandrine Godefroid

  4. Laboratory of Plant Biology and Nature Management (APNA), Vrije Universiteit Brussel, Brussels, Belgium

    Sandrine Godefroid

  5. Laboratory of Systems Ecology and Resource Management, Université libre de Bruxelles, Brussels, Belgium

    Sandrine Godefroid

  6. Department of Horticulture, Botany and Plant Pathology, University of Naples ‘Federico II’, Portici, Italy

    Stefano Mazzoleni

  7. Department of Life and Environmental Sciences, University of Cagliari, Viale S.Ignazio da Laconi 13, 09123, Cagliari, Italy

    Michela Marignani

Authors
  1. Carlo Ricotta
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  2. Giovanni Bacaro
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  3. Michela Marignani
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  4. Sandrine Godefroid
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  5. Stefano Mazzoleni
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Corresponding author

Correspondence to Michela Marignani.

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Communicated by Melinda Smith.

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Ricotta, C., Bacaro, G., Marignani, M. et al. Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?. Oecologia 170, 501–506 (2012). https://doi.org/10.1007/s00442-012-2318-8

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  • DOI: https://doi.org/10.1007/s00442-012-2318-8

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