Evolutionary Ecology

, Volume 20, Issue 6, pp 591–602 | Cite as

Factors influencing changes in trait correlations across species after using phylogenetic independent contrasts

  • Priscilla Carvalho
  • José Alexandre Felizola Diniz-Filho
  • Luis Mauricio Bini
Original paper

Abstract

Comparative interspecific data sets have been analyzed routinely by phylogenetic methods, generally using Felsenstein’s phylogenetic independent contrasts (PIC) method. However, some authors have suggested that it may not be always necessary to incorporate phylogenetic information into statistical analyses of comparative data due to the low influence of shared history on the distribution of␣character states. The main goal of this paper was to undertake a comparison of results from non-phylogenetic Pearson correlation of tip values (TIPs) and phylogenetic independent contrasts analyses (PICs), using 566 correlation coefficients derived from 65 published papers. From each study we collected the following data: taxonomic group, number of species, type of phylogeny, number of polytomies in the phylogenetic tree, if branch length was transformed or not, trait types, the original correlation coefficient between the traits (TIPs) and the correlation coefficient between the traits using the independent contrasts method (PICs). The slope estimated from a regression of PIC correlations on TIP correlations was lower than one, and a paired t-test showed that correlations from PIC are significantly smaller than those obtained by TIP. Thus, PIC analyses tend to decrease the correlation between traits and usually increases the P-value and, thus, favoring the acceptance of the null hypothesis. Multiple factors, including taxonomic group, trait type and use of branch length transformations affected the change in decision regarding the acceptance of the null hypotheses and differences between PIC and TIP results. Due to the variety of factors affecting the differences between results provided by these methods, we suggest that comparative methods should be applied as a conservative approach to cross-species studies. Despite difficulties in quantifying precisely why these factors affect the differences between PIC and TIP, we also suggest that a better evaluation of evolutionary models underlying trait evolution is still necessary in this context and might explain some of the observed patterns.

Keywords

Phylogenetic independent contrasts method Felsenstein Phylogenetic signal Branch transformation Brownian motion Trait category 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ackerly DD (1999) Comparative plant ecology and the role of phylogenetic information. In: Press MC, Scholes JD, Barker, MG (eds) Physiological plant ecology. Blackwell Science, pp391–413Google Scholar
  2. Ackerly DD, Donoghue MJ (1998) Leaf size, sapling allometry, and Corner’s rules: Phylogeny and Correlated Evolution in Maples (Acer). Am Nat 152:767–791CrossRefGoogle Scholar
  3. Bennett PM, Owens IPF (2002) Evolutionary ecology of birds: life histories, mating systems an extinction. Oxford University Press, New YorkGoogle Scholar
  4. Björklund M (1997) Are “comparative methods” always necessary? Oikos 80:607–612Google Scholar
  5. Blomberg SP, Garland T Jr, Ives AR (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717–745PubMedCrossRefGoogle Scholar
  6. Carvalho P, Diniz-Filho JAF, Bini LM (2005) The impact of Felsenstein’s “Phylogenies and the comparative method” on evolutionary biology. Scientometrics 62:53–66CrossRefGoogle Scholar
  7. Cheverud JM, Dow MM, Leutenegger W (1985) The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution 39:1335–1351CrossRefGoogle Scholar
  8. Díaz-Uriarte R, Garland T Jr (1996) Testing hypotheses of correlated evolution using phylogenetic independent contrasts: sensitivity to deviations from Brownian Motion. Syst Biol 45:27–47CrossRefGoogle Scholar
  9. Díaz-Uriarte R, Garland T Jr (1998) Effects of branch length errors on the performance of phylogenetically independent contrasts. Syst Biol 47:654–672PubMedCrossRefGoogle Scholar
  10. Diniz-Filho JAF (2001) Phylogenetic autocorrelation under distinct evolutionary processes. Evolution 55:1104–1109PubMedCrossRefGoogle Scholar
  11. Diniz-Filho JAF, Tôrres NM (2002) Phylogenetic comparative methods and the geographic range size––body size relationship in new world terrestrial carnivora. Evol Ecol 16:351–367CrossRefGoogle Scholar
  12. Diniz-Filho JAF, de Sant’Ana CER, Bini LM (1998) An eigenvector method for estimating phylogenetic inertia. Evolution 52:1247–1262CrossRefGoogle Scholar
  13. Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1–15CrossRefGoogle Scholar
  14. Freckleton RP, Harvey PH, Pagel M (2002) Phylogenetic analysis and comparative data: a test and review of evidence. Am Nat 160:712–26CrossRefGoogle Scholar
  15. Garland T Jr, Adolph SC (1994) Why not to do two-species comparative studies: limitations on inferring adaptation. Physiol Zool 67:797–828Google Scholar
  16. Garland T Jr, Harvey PH, Ives AR (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst Biol 41:18–32CrossRefGoogle Scholar
  17. Gittleman JL, Anderson CG, Kot M, Luh H-K (1996) Phylogenetic lability and rates of evolution: a comparison of behavioral, morphological and life history traits. In: Martins EP (ed) Phylogenies and the comparative method in animal behavior. Oxford University Press, pp166–205Google Scholar
  18. Harvey PH, Pagel MD (1991) The comparative method in evolutionary biology. Oxford University PressGoogle Scholar
  19. Losos JB (1999) Uncertainty in the reconstruction of ancestral carácter states and limitations on the use of phylogenetic comparative methods. Anim Behav 58:1319–1324PubMedCrossRefGoogle Scholar
  20. Manly BFJ (1994). The design and analysis of research studies. Cambridge University Press,CambridgeGoogle Scholar
  21. Martins EP, Garland T Jr (1991) Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534–57CrossRefGoogle Scholar
  22. Martins EP, Hansen TF (1996) The statistical analysis of interspecific data: a review and evaluation of phylogenetic comparative methods. In: Martins EP (ed) Phylogenies and the comparative method in animal behavior, Oxford University Press, pp22–75Google Scholar
  23. Martins EP, Diniz-Filho JAF, Housworth EA (2002) Adaptative constraints and the phylogenetic comparative method: a computer simulation test. Evolution 56:1–13PubMedCrossRefGoogle Scholar
  24. Mazer SJ (1998) Alternative approaches to the analysis of comparative data: compare and contrast. Am J Bot 85:1194–1199CrossRefGoogle Scholar
  25. Morales E (2000) Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach. Evolution 54:475–484PubMedCrossRefGoogle Scholar
  26. Peters RH (1993) The ecological implications of body size. Cambridge University Press, CambridgeGoogle Scholar
  27. Pigliucci M (2003) Phenotypic integration: studying the ecology and evolution of complex phenotypes. Ecol Lett 6:265–272CrossRefGoogle Scholar
  28. Pigliucci M, Kolodynska A (2002) Phenotypic plasticity to light intensity in Arabidopsis thaliana: invariance of reaction norms and phenotypic Integration. Evol Ecol 16:27–47CrossRefGoogle Scholar
  29. Purvis A, Garland T Jr (1993) Polytomies in comparative analyses of continuous characters. Syst Biol 42:569–575CrossRefGoogle Scholar
  30. Rezende EL, Garland T Jr (2003) Comparaciones interespecíficas y métodos estadísticos filogenéticos. In: F Bozinovic (eds) Fisiología Ecológica & Evolutiva. Teoría y casos de estudios en animals. Ediciones Universidad Católica de Chile, Santiago, pp79–98Google Scholar
  31. Ricklefs RE, Starck JM (1996) Applications of phylogenetically independent contrasts: a mixed progress report. Oikos 77:167–172Google Scholar
  32. Sokal RR, Rohlf FJ (1995) Biometry. WH Freeman and Company, New YorkGoogle Scholar
  33. Stirling DG, Réale D, Roff DA (2002) Selection, structure and the heritability of behavior. J Evol Biol 15:277–289CrossRefGoogle Scholar
  34. Weathers WW, Siegel RB (1995) Body size establishes the scaling of avian postnatal metabolic rate: an interspecific analysis using phylogenetically independent contrasts. Ibis 137:532–542Google Scholar
  35. Westoby M, Leishman MR, Lord JM (1995) On misinterpreting the “phylogenetic correction”. J␣Ecol 83:531–534CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Priscilla Carvalho
    • 1
  • José Alexandre Felizola Diniz-Filho
    • 1
    • 2
  • Luis Mauricio Bini
    • 1
  1. 1.Departamento de Biologia Geral, ICBUniversidade Federal de GoiásGoiâniaBrazil
  2. 2.Departamento de Biologia / MCAS-PROPEUniversidade Católica de GoiásGoiâniaBrazil

Personalised recommendations