Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities.

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.

[1]  Robert M. May,et al.  Taxonomy as destiny , 1990, Nature.

[2]  R. Díaz-Uriarte,et al.  Covariation of Life-History Traits in Lacertid Lizards: A Comparative Study , 1997, The American Naturalist.

[3]  P. Jouventin,et al.  Mate fidelity in monogamous birds: a re-examination of the Procellariiformes , 2003, Animal Behaviour.

[4]  T. Garland,et al.  TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE , 2003, Evolution; international journal of organic evolution.

[5]  T. F. Hansen,et al.  Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data , 1997, The American Naturalist.

[6]  R. Geary,et al.  The Contiguity Ratio and Statistical Mapping , 1954 .

[7]  Marc Mangel,et al.  Life–history trade–offs and ecological dynamics in the evolution of longevity , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[8]  J. Ahlquist,et al.  The Birds Reclassified. (Book Reviews: Phylogeny and Classification of Birds. A Study in Molecular Evolution.) , 1991 .

[9]  G. J. G. Upton,et al.  Spatial data Analysis by Example , 1985 .

[10]  Anne-Béatrice Dufour,et al.  Is the originality of a species measurable , 2005 .

[11]  M. Donoghue,et al.  Leaf Size, Sapling Allometry, and Corner's Rules: Phylogeny and Correlated Evolution in Maples (Acer) , 1998, The American Naturalist.

[12]  F. James Rohlf,et al.  COMPARATIVE METHODS FOR THE ANALYSIS OF CONTINUOUS VARIABLES: GEOMETRIC INTERPRETATIONS , 2001, Evolution; international journal of organic evolution.

[13]  T. Coburn.  Spatial Data Analysis by Example , 1991 .

[14]  P. Couteron,et al.  Orthonormal Transform to Decompose the Variance of a Life‐History Trait across a Phylogenetic Tree , 2006, Biometrics.

[15]  Malcolm M. Dow,et al.  An autocorrelation analysis of genetic variation due to lineal fission in social groups of rhesus macaques , 1985 .

[16]  Jean Thioulouse,et al.  Multivariate analysis of spatial patterns: a unified approach to local and global structures , 1995, Environmental and Ecological Statistics.

[17]  E. Abouheif.  A method for testing the assumption of phylogenetic independence in comparative data , 1999 .

[18]  D. Faith.  Conservation evaluation and phylogenetic diversity , 1992 .

[19]  J. Crook.  The adaptive significance of avian social organisations , 1964 .

[20]  José Alexandre Felizola Diniz‐Filho.  PHYLOGENETIC AUTOCORRELATION UNDER DISTINCT EVOLUTIONARY PROCESSES , 2001 .

[21]  J. Felsenstein.  Phylogenies and the Comparative Method , 1985, The American Naturalist.

[22]  T. Tregenza,et al.  Phylogenies and the Comparative Method in Animal Behaviour , 1997 .

[23]  R. H. Kent,et al.  The Mean Square Successive Difference , 1941 .

[24]  M. Jones,et al.  Detecting two-dimensional spatial structure in biological data , 1977, Oecologia.

[25]  N. Mantel.  The detection of disease clustering and a generalized regression approach. , 1967, Cancer research.

[26]  D. Schluter,et al.  Using Phylogenies to Test Macroevolutionary Hypotheses of Trait Evolution in Cranes (Gruinae) , 1999, The American Naturalist.

[27]  P. Moran.  The Interpretation of Statistical Maps , 1948 .

[28]  J. Cheverud,et al.  THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES , 1985, Evolution; international journal of organic evolution.

[29]  N. Giannini.  Canonical phylogenetic ordination. , 2003, Systematic biology.

[30]  T. Clutton‐Brock,et al.  Primate ecology and social organization , 2009 .

[31]  Mark Kot,et al.  Adaptation: Statistics and a Null Model for Estimating Phylogenetic Effects , 1990 .

[32]  Issei Fujishiro,et al.  The elements of graphing data , 2005, The Visual Computer.

[33]  M. Bonsall.  The evolution of anisogamy: the adaptive significance of damage, repair and mortality. , 2006, Journal of theoretical biology.

[34]  T. Clutton‐Brock,et al.  Comparison and adaptation , 1979, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[35]  T. F. Hansen,et al.  TRANSLATING BETWEEN MICROEVOLUTIONARY PROCESS AND MACROEVOLUTIONARY PATTERNS: THE CORRELATION STRUCTURE OF INTERSPECIFIC DATA , 1996, Evolution; international journal of organic evolution.

[36]  Charles Semple,et al.  Cyclic permutations and evolutionary trees , 2004, Adv. Appl. Math..

[37]  Jean Thioulouse,et al.  The ade4 package - I : One-table methods , 2004 .