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Phylogenetic divergences have recently been included in analyses that aim to elucidate patterns of biodiversity in space and time. We introduce a generalized framework for two widely used phylogenetic diversity (PD) indices: Raos quadratic entropy (QE) and Faiths PD. We demonstrate how this framework can be used to partition diversity simultaneously across evolutionary periods and spatial (e.g. local communities in a region) and / or time units (e.g. a community investigated yearly). From a study of rockfish hotspot diversity from the Southern California Bight, the analysis of PD revealed a recent decrease in the amount of fish caught from six evolutionary deep lineages, with implications for the community structure of this speciose group. This approach, which can also be applied to trees assembled from functional traits, contributes to our understanding of the mechanisms that underpin community organization and to the description of the consequences of human-driven impacts in the environment.

Original publication




Journal article


Ecol Lett

Publication Date





898 - 908


Animals, Biodiversity, Biological Evolution, Fisheries, Fishes, Phylogeny, Time Factors