Uncertainties due to within-species variation in comparative studies: Measurement errors and statistical weights

Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology

Volumn , Issue , 2014, Pages 157-199

  Garamszegi, László Zsolt ^a  

^a DEPARTMENT OF CONSERVATION BIOLOGY   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84939139320     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-662-43550-2_7     Document Type: Chapter

References (65)

1. Adolph SC, Hardin JS (2007) Estimating phenotypic correlations: correcting for bias due to intraindividual variability. Funct Ecol 21(1):178-184
2. Arnold C, Nunn CL (2010) Phylogenetic targeting of research effort in evolutionary biology. Am Nat 176:601-612
3. Ashton KG (2004) Comparing phylogenetic signal in intraspecific and interspecific body size datasets. J Evol Biol 17:1157-1161
4. Blomberg S, Garland TJ, Ives AR (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more laible. Evolution 57:717-745
5. Bolker BM, Brooks ME, Clark CJ, Geange SW, Poulsen JR, Stevens MHH, White JSS (2009) Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol Evol 24:127-135
6. Bollen KA (1989) Structural equations with latent variables. Wiley, New York
7. Buonaccorsi JP (2010) Measurement error: models, methods, and applications. Chapman and Hall, New York
8. Caro TM, Roper R, Young M, Dank GR (1979) Inter-observer reliability. Behaviour 69:303-315. doi:10.1163/156853979x00520
9. Chesher A (1991) The effect of measurement error. Biometrika 78(3):451-462. doi:10.1093/biomet/78.3.451
10. Cheverud JM, Dow MM, Leutenegger W (1985) The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism of body weight among primates. Evolution 39:1335-1351
11. Christman MC, Jernigan RW, Culver D (1997) A comparison of two models for estimating phylogenetic effect on trait variation. Evolution 51(1):262-266. doi:10.2307/2410979
12. Cornillon PA, Pontier D, Rochet MJ (2000) Autoregressive models for estimating phylogenetic and environmental effects: accounting for within-species variations. J Theor Biol 202(4):247-256. doi: 10.1006/jtbi.1999.1040
13. de Villemereuil P, Wells JA, Edwards RD, Blomberg SP (2012) Bayesian models for comparative analysis integrating phylogenetic uncertainty. BMC Evol Biol 12: doi:10.1186/1471-2148-12-102
14. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J Roy Stat Soc Ser B Methodol 39(1):1—38
15. Doughty P (1996) Statistical analysis of natural experiments in evolutionary biology: comments on recent criticisms on the use of comparative methods to study adaptation. Am Nat 148:943-956
16. Draper NR, Smith H (1981) Applied regression analysis. Wiley, New York (2nd edn)
17. Edwards SV, Kot M (1995) Comparative methods at the species level: geographic variation in morphology and group size in Grey-crowned Babblers (Pomatostomus temporalis). Evolution 49:1134-1146
18. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1-15
19. Felsenstein J (2002) Contrasts for a within-species comparative method. In: Slatkin M, Veuille M (eds) Modern developments in theoretical population genetics. Oxford University Press, Oxford, pp 118-129
20. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland
21. Felsenstein J (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat 171(6):713-725
22. Fisher DO, Blomberg SP, Owens IPF (2003) Extrinsic versus intrinsic factors in the decline and extinction of Australian marsupials. Proc R Soc Lond Ser B-Biol Sci 270(1526):1801-1808
23. Freckleton RP (2009) The seven deadly sins of comparative analysis. J Evol Biol 22(7):1367-1375
24. Fuller WA (1987) Measurement error models. Wiley, New York
25. Garamszegi LZ, M0ller AP (2010) Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta-analytic review. Biol Rev 85:797-805
26. Garamszegi LZ, M0ller AP (2011) Nonrandom variation in within-species sample size and missing data in phylogenetic comparative studies. Syst Biol 60:876-880
27. Garamszegi LZ, M0ller AP (2012) Untested assumptions about within-species sample size and missing data in interspecific studies. Behav Ecol Sociobiol 66:1363-1373
28. Gelman A, Hill J (2007) Data analysis using regression and multilevel/hierarchical models. Cambridge University Press, Cambridge
29. Geman S, Geman D (1984) Stochastic relaxation, gibbs distributions, and the bayesian restoration of images. Ieee Transactions on Pattern Analysis and Machine Intelligence 6(6):721-741
30. Gittleman JL, Kot M (1990) Adaptation: statistics and a null model for estimating phylogenetic effects. Syst Zool 39(3):227-241. doi:10.2307/2992183
31. Grafen A (1989) The phylogenetic regression. Philos Trans R Soc B 326:119-157
32. 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
33. Hansen TF, Bartoszek K (2012) Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. Syst Biol 61:413-425
34. Harmon LJ, Losos JB (2005) The effect of intraspecific sample size on type I and type II error rates in comparative studies. Evolution 59:2705-2710
35. Hastings WK (1970) Monte carlo sampling methods using markov chains and their applications. Biometrika 57(1):97-109. doi:10.2307/2334940
36. Housworth EA, Martins EP, Lynch M (2004) The phylogenetic mixed model. Am Nat 163:84-96
37. Ives AR, Midford PE, Garland T (2007) Within-species variation and measurement error in phylogenetic comparative methods. Syst Biol 56(2):252-270
38. Judge GG, Griffiths WE, Hill RC, Lutkepohl H, Lee T-C (1985) The theory and practice of econometrics. Wiley, New York
39. Kreft IGG, de Leeuw J, Aiken LS (1995) The effect of different forms of centering in hierarchical linear models. Multivar Behav Res 30:1-21
40. Kutsukake N, Innan H (2012) Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny. Evolution (in press)
41. Lessells CM, Boag PT (1987) Unrepeatable repeatabilities: a common mistake. Auk 104:116-121
42. Lynch M (1991) Methods for the analysis of comparative data in evolutionary biology. Evolution 45(5):1065-1080
43. Madansky A (1959) The fitting of straight lines when both variables are subject to error. J Am Stat Assoc 54:173-205
44. Manisha S (2001) An estimation of population mean in the presence of measurement errors. J Indian Soc Agric Stat 54:13-18
45. Martins EP (1994) Estimating the rate of phenotypic evolution from comparative data. Am Nat 144:193-209
46. Martins EP (2004) COMPARE, version 4.6b. Computer programs for the statistical analysis of comparative data. Distributed by the author at http://compare.bio.indiana.edu/, Department of Biology, Indiana University, Bloomington IN
47. 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
48. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087-1092
49. M0ller AP, Garamszegi LZ (2012) Between individual variation in risk taking behavior and its life history consequences. Behav Ecol 23:843-853
50. Monkkonen M, Martin TE (2000) Sensitivity of comparative analyses to population variation in trait values: clutch size and cavity excavation tendencies. J Avian Biol 31(4):576-579. doi:10.1034/j.1600-048X.2000.310417.x
51. Nakagawa S, Freckleton R (2008) Missing inaction: the dangers of ignoring missing data. Trends Ecol Evol 23:592-596. doi:10.1016/j.tree.2008.06.014
52. Nakagawa S, Schielzeth H (2010) Repeatability for Gaussian and non-Gaussian data: a practical guide for biologists. Biol Rev 85:935-956
53. Neter J, Kutner MH, Nachtsheim CJ, Wasserman W (1996) Applied linear statistical models. Irwin, Chicago
54. Paradis E (2011) Analysis of phylogenetics and evolution with R, 2nd edn. Springer, Berlin
55. Purvis A, Rambaut A (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Comput Appl Biosci 11:247-251
56. Purvis A, Webster AJ (1999) Phylogenetically independent comparisons and primate phylogeny. In: Lee PC (ed) Comparative primate socioecology. Cambridge University Press, Cambridge, pp 44-70
57. Reed GF, Lynn F, Meade BD (2002) Use of coefficient of variation in assessing variability of quantitative assays. Clin Diagn Lab Immunol 9(6):1235-1239. doi:10.1128/cdli.9.6.1235-1239.2002
58. Revell LJ (2010) Phylogenetic signal and linear regression on species data. Methods Ecol Evol 1(4):319-329. doi:10.1111/j.2041-210X.2010.00044.x
59. Revell LJ, Reynolds RG (2012) A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution 66(9):2697-2707. doi: 10.1111/j.1558-5646.2012.01645.x
60. Ricklefs RE, Starck JM (1996) Applications of phylogenetically independent contrasts: a mixed progress report. Oikos 77(1):167-172
61. Snijders TAB, Bosker RJ (1999) Multilevel analysis—an introduction to basic and advanced multilevel modelling. Sage, London
62. Sokal RR, Rohlf FJ (1995) Biometry, 3rd edn. W. H. Freeman and Co, New York
63. Stone GN, Nee S, Felsenstein J (2011) Controlling for non-independence in comparative analysis of patterns across populations within species. Philos Trans R Soc Lond B Biol Sci 366:1410-1424
64. Taper ML, Marquet PA (1996) How do species really divide resources? Am Nat 147:1072-1086
65. van de Pol MV, Wright J (2009) A simple method for distinguishing within- versus between-subject elfects using mixed models. Anim Behav 77(3):753-758