Function-valued traits in evolution

Journal of the Royal Society Interface

Volumn 10, Issue 82, 2013, Pages

  Hadjipantelis, Pantelis Z ^a   Jones, Nick S ^b   Moriarty, John ^c   Springate, David A ^c   Knight, Christopher G ^c  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Ancestral reconstruction; Comparative analysis; Functional Gaussian process regression; Functional phylogenetics; Non parametric Bayesian inference; Ornstein Uhlenbeck process

Indexed keywords

BAYESIAN NETWORKS; COMPUTER SIMULATION; GAUSSIAN DISTRIBUTION; GAUSSIAN NOISE (ELECTRONIC); INFERENCE ENGINES; STOCHASTIC MODELS;

COMPARATIVE ANALYSIS; GAUSSIAN PROCESS REGRESSION; NON-PARAMETRIC BAYESIAN INFERENCES; ORNSTEIN-UHLENBECK PROCESS; PHYLOGENETICS;

BIOLOGY;

ARTICLE; BIOLOGICAL TRAIT; CONTROLLED STUDY; EVOLUTION; HUMAN; PHYLOGENY; SIMULATION; STOCHASTIC MODEL; ANIMAL; BIOLOGICAL MODEL; MOLECULAR EVOLUTION; NORMAL DISTRIBUTION; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; STATISTICS;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; NORMAL DISTRIBUTION; PHYLOGENY; QUANTITATIVE TRAIT LOCI; STOCHASTIC PROCESSES;

MLCS; MLOWN;

EID: 84881286155     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2012.1032     Document Type: Article

References (38)

1. Maddison DR, Schulz KS. 2007 The tree of life web project. See http://tolweb.org.
2. Li H et al. 2006 TREEFAM: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580. (doi:10.1093/nar/gkj118)
3. Yang Z, Rannala B. 2012 Molecular phylogenetics: principles and practice. Nat. Rev. Genet. 13, 303-314. (doi:10.1038/nrg3186)
4. 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)
5. 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)
6. The Functional Phylogenies Group. 2012 Phylogenetic inference for function-valued traits: speech sound evolution. Trends Ecol. Evol. 27, 160-166. (doi:10.1016/j.tree.2011.10.001)
7. Stinchcombe JR, Kirkpatrick M, Function-valued traits working group 2012 Phylogenetic inference for function-valued traits: speech sound evolution. Trends Ecol. Evol. 27, 637-647. (doi:10.1016/j.tree.2012.07.002)
8. Pletcher SD, Geyer CJ. 1999 The genetic analysis of age-dependent traits: modeling the character process. Genetics 153, 825-835.
9. Kingsolver JG, Gomulkiewicz R, Carter PA. 2001 Variation, selection and evolution of functionvalued traits. Genetica 112-113, 87-104. (doi:10.1023/A:1013323318612)
10. Zhang Z, Müller HG. 2011 Functional density synchronization. Comput. Stat. Data Anal. 55, 2234-2249. (doi:10.1016/j.csda.2011.01.007)
11. Moss SP, Joyce DA, Humphries S, Tindall KJ, Lunt DH. 2011 Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biol. Evol. 3, 1187-1196. (doi:10.1093/gbe/ evr090)
12. Knight CG, Kassen R, Hebestreit H, Rainey PB. 2004 Global analysis of predicted proteomes: functional adaptation of physical properties. Proc. Natl Acad. Sci. USA 101, 8390-8395. (doi:10.1073/pnas.0307270101)
13. Jones NS, Moriarty J. 2013 Evolutionary inference or function-valued traits: Gaussian process regression on phylogenies. J. R. Soc. Interface 10, 20120616. (doi:10.1098/rsif.2012.0616)
14. Yao F, Coquery J, Le Cao KA. 2012 Independent principal component analysis for biologically meaningful dimension reduction of large biological data sets. BMC Bioinformatics 13, 13-24. (doi:10.1186/1471-2105-13-13)
15. Butler MA, King AA. 2004 Phylogenetic comparative analysis: a modelling approach for adaptive evolution. Am. Nat. 164, 683-695. (doi:10.1086/426002)
16. Beaulieu JM, Jhwueng DC, Boettiger C, O'eara BC. 2012 Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution 8, 2369-2383. (doi:10.1111/j.1558-5646.2012.01619.x)
17. Breiman L. 1996 Bagging predictors. Mach. Learn. 24, 123-140.
18. Venditti C, Meade A, Pagel M. 2010 Phylogenies reveal new interpretation of speciation and the red queen. Nature 463, 349-352. (doi:10.1038/nature08630)
19. Hansen T. 1997 Stabilizing selection and the comparative analysis of adaptation. Evolution 51, 1341-1351. (doi:10.2307/2411186)
20. Rasmussen CE, Williams CKI. 2006 Gaussian processes for machine learning. Cambridge, MA: MIT Press.
21. Hyvärinen A, Oja E. 2000 Independent component analysis: algorithms and applications. Neural Netw. 13, 411-430. (doi:10.1016/S0893-6080(00)00026-5)
22. Bishop C. 2006 Pattern recognition and machine learning. Berlin, Germany: Springer.
23. Revell LJ. 2009 Size-correction and principal components for interspecific comparative studies. Evolution 63, 3258-3268. (doi:10.1111/j.1558- 5646.2009.00804.x)
24. Scholz M, Gatzek S, Sterling A, Fiehn O, Selbig J. 2004 Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20, 2447-2454. (doi:10.1093/bioinformatics/bth270)
25. Minka TP. 2000 Automatic choice of dimensionality for PCA. Adv. Neural Inf. Process. Syst. 13, 514.
26. Blaschke T, Wiskott L. 2004 CuBICA: independent component analysis by simultaneous third- and fourth-order cumulant diagonalization. IEEE Trans. Signal Process. 52, 1250-1256. (doi:10.1109/TSP.2004.826173)
27. Hansen T, Martins E. 1996 Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50, 1404-1417. (doi:10.2307/2410878)
28. Pagel M. 1997 Inferring evolutionary processes from phylogenies. Zool. Scr. 26, 331-348. (doi:10.1111/j.1463-6409.1997.tb00423.x)
29. Jaynes ET. 1984 Prior information and ambiguity in inverse problems. Inverse Probl. 14, 151-166.
30. Salamin N, Wuest RO, Lavergne S, Thuiller W, Pearman PB. 2010 Assessing rapid evolution in a changing environment. Trends Ecol. Evol. 25, 692-698. (doi:10.1016/j.tree.2010.09.009)
31. Hadfield JD, Nakagawa S. 2010 General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J. Evol. Biol. 23, 494-508. (doi:10.1111/j.1420-9101.2009. 01915.x)
32. Kerr M. 2012 Evolutionary inference for functional data: using Gaussian processes on phylogenies of functional data objects. MSc Thesis, University of Glasgow, Glasgow, UK.
33. Yao F, Müller HG, Wang JL. 2005 Functional data analysis for sparse longitudinal data. J. Am. Stat. Assoc. 100, 577-590. (doi:10.1198/ 016214504000001745)
34. Cardoso JF. 1999 High-order contrasts for independent component analysis. Neural Comput. 11, 157-192. (doi:10.1162/089976699300016863)
35. Collar DC, O'Meara BC, Wainwright PC, Near TJ. 2009 Piscivory limits diversification of feeding morphology in centrarchid fishes. Evolution 63, 1557-1573. (doi:10.1111/j.1558-5646.2009.00626.x)
36. Revell LJ, Collar DC. 2009 Phylogenetic analysis of the evolutionary coreally using likelihood. Evolution 63-64, 1090-1100. (doi:10.1111/j.1558-5646. 2009.00616.x)
37. Hansen T, Pienaar J, Orzack SH. 2008 A comparative method for studying adaptation to a randomly evolving environment. Evolution 8, 1965-1977. (doi:10.1111/j.1558-5646.2008.00412.x)
38. Pagel M. 1999 Inferring the historical patterns of biological evolution. Nature 401, 877-884. (doi:10.1038/44766)