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Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities

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  • Pavoine, Sandrine
  • Ollier, Sébastien
  • Pontier, Dominique
  • Chessel, Daniel

Abstract

Abouheif adapted a test for serial independence to detect a phylogenetic signal in phenotypic traits. We provide the exact analytic value of this test, revealing that it uses Moran's I statistic with a new matrix of phylogenetic proximities. We introduce then two new matrices of phylogenetic proximities highlighting their mathematical properties: matrix A which is used in Abouheif test and matrix M which is related to A and biodiversity studies. Matrix A unifies the tests developed by Abouheif, Moran and Geary. We discuss the advantages of matrices A and M over three widely used phylogenetic proximity matrices through simulations evaluating power and type-I error of tests for phylogenetic autocorrelation. We conclude that A enhances the power of Moran's test and is useful for unresolved trees. Data sets and routines are freely available in an online package and explained in an online supplementary file.

Suggested Citation

  • Pavoine, Sandrine & Ollier, Sébastien & Pontier, Dominique & Chessel, Daniel, 2008. "Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities," Theoretical Population Biology, Elsevier, vol. 73(1), pages 79-91.
    • Handle: RePEc:eee:thpobi:v:73:y:2008:i:1:p:79-91
    DOI: 10.1016/j.tpb.2007.10.001
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    References listed on IDEAS

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    1. S. Ollier & P. Couteron & D. Chessel, 2006. "Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree," Biometrics, The International Biometric Society, vol. 62(2), pages 471-477, June.
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    1. Regina Gabriela Medina & Andrés Lira-Noriega & Ezequiel Aráoz & María Laura Ponssa, 2020. "Potential effects of climate change on a Neotropical frog genus: changes in the spatial diversity patterns of Leptodactylus (Anura, Leptodactylidae) and implications for their conservation," Climatic Change, Springer, vol. 161(4), pages 535-553, August.
    2. Hernán López-Fernández & Kirk O Winemiller & Carmen Montaña & Rodney L Honeycutt, 2012. "Diet-Morphology Correlations in the Radiation of South American Geophagine Cichlids (Perciformes: Cichlidae: Cichlinae)," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-14, April.
    3. Clotilde Hardy & Emmanuel Fara & Rémi Laffont & Jean-Louis Dommergues & Christian Meister & Pascal Neige, 2012. "Deep-Time Phylogenetic Clustering of Extinctions in an Evolutionarily Dynamic Clade (Early Jurassic Ammonites)," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-7, May.

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