Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies

Journal of the Royal Society Interface

Volumn 10, Issue 78, 2013, Pages

  Jones, Nick S ^a   Moriarty, John ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Gaussian processes; Morphometrics; Phylogenetic inference

Indexed keywords

BAYESIAN NETWORKS; BIOLOGY; BROWNIAN MOVEMENT; GAUSSIAN NOISE (ELECTRONIC); INFERENCE ENGINES;

BAYESIAN INFERENCE; BIOLOGICAL DATA; FUNCTIONAL DATAS; GAUSSIAN PROCESS REGRESSION; GAUSSIAN PROCESSES; MODEL SELECTION; MORPHOMETRICS; NON-PARAMETRIC BAYESIAN; OBSERVED DATA; ORNSTEIN-UHLENBECK; PHYLOGENETIC INFERENCE; PHYLOGENETIC RELATIONSHIPS; PHYLOGENETICS; POSTERIOR DISTRIBUTIONS; PRIOR DISTRIBUTION; STATISTICAL MODELS;

GAUSSIAN DISTRIBUTION;

ARTICLE; BAYESIAN LEARNING; BIOINFORMATICS; BIOLOGICAL TRAIT; KERNEL METHOD; PHYLOGENY; PROCESS MODEL; REGRESSION ANALYSIS; BIOLOGICAL MODEL;

MODELS, BIOLOGICAL; PHYLOGENY;

EID: 84871303564     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2012.0616     Document Type: Article

References (19)

1. Hadjipantelis PZ, Jones NS, Moriarty J, Springate D, Knight CG. 2012 Ancestral inference from functional data: statistical methods and numerical examples. (http://arxiv.org/abs/1208.0628)
2. Ramsay JO. 1982 When the data are functions. Psychometrika 47, 379-396. (doi:10.1007/BF02293704)
3. Ramsay JO, Silverman BW. 2005 Functional data analysis. Berlin, Germany: Springer.
4. Lande R. 1976 Natural selection and random genetic drift in phenotypic evolution. Evolution 30, 314-334. (doi:10.2307/2407703)
5. Rasmussen CE, Williams CKI. 2006 Gaussian processes for machine learning. Cambridge, MA: MIT Press.
6. Stein ML. 1999 Interpolation of spatial data: some theory for Kriging. Berlin, Germany: Springer.
7. Patil GP, Rao CR. 1993 Multivariate environmental statistics. Amsterdam, The Netherlands: North-Holland.
8. Kingsolver JG, Gomulkiewicz R, Carter PA. 2001 Variation, selection and evolution of function-valued traits. Genetica 112-113, 87-104. (doi:10.1023/A:1013323318612)
9. Kirkpatrick M, Heckman N. 1989 A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters. J. Math. Biol. 27, 429-450. (doi:10.1007/BF00290638)
10. Wiens JJ. 2001 Character analysis in morphological phylogenetics: problems and solutions. Syst. Biol. 50, 689-699. (doi:10.1080/ 106351501753328811)
11. Catalano SA, Goloboff PA, Giannini NP. 2010 Phylogenetic morphometrics (I). The use of landmark data in a phylogenetic framework. Cladistics 26, 539-549. (doi:10.1111/j.1096-0031.2010.00302.x)
12. Felsenstein J. 1985 Phylogenies and the comparative method. Am. Nat. 125, 1-15. (doi:10.1086/284325)
13. Cheverud JM, Dow MM, Leutenegger W. 1985 The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution 39, 1335-1351. (doi:10.2307/2408790)
14. Hansen TF, Martins EP. 1996 Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50, 1404-1417. (doi:10.2307/2410878)
15. Butler MA, King AA. 2004 Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164, 683-695. (doi:10.1086/426002)
16. Martins EP, Hansen TF. 1997 Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149, 646-667. (doi:10.1086/286013)
17. Diniz-Filho JAF. 2001 Phylogenetic autocorrelation under distinct evolutionary processes. Evolution 55, 1104-1109. (doi:10.1111/j.0014-3820.2001. tb00630.x)
18. Gittleman JL, Kot M. 1990 Adaptation: statistics and a null model for estimating phylogenetic effects. Syst. Zool. 39, 227-241. (doi:10.2307/2992183)
19. Aston JAD, Buck D, Coleman J, Cotter CJ, Jones NS, Macaulay V, MacLeod N, Moriarty J, Nevins A. 2011 Phylogenetic inference for function-valued traits: speech sound evolution. Trends Ecol. Evol. 27, 160-166. (doi:10.1016/j.tree. 2011.10.001)