Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods

@article{Losos1999UncertaintyIT,
  title={Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods},
  author={Jonathan B. Losos},
  journal={Animal Behaviour},
  year={1999},
  volume={58},
  pages={1319-1324}
}
  • J. Losos
  • Published 1999
  • Medicine, Geography
  • Animal Behaviour
Phylogenetic approaches to the study of comparative data have a long history in the field of animal behaviour (e.g. Lorenz 1941; Greene & Burghardt 1978; Gittleman 1981). However, since the publication in 1991 of Brooks & McLennan’s Phylogeny, Ecology and Behavior and Harvey & Pagel’s The Comparative Method in Evolutionary Biology, there has been a huge increase in the use of phylogenetic methods in comparative studies. Indeed, a comparative study would be unpublishable in most journals today… Expand

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References

SHOWING 1-10 OF 37 REFERENCES
Applications of phylogenetically independent contrasts : a mixed progress report
TLDR
It is argued that it is premature at this point to insist upon particular phylogenetically based approaches to comparative analysis, even though pressure is mounting to reject conventional practices of calculating regressions and correlations from trait values of taxa in favor of PICs. Expand
Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data
TLDR
A generalized linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character. Expand
An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values
TLDR
Three phylogenetically based statistical methods are presented, including phylogenetically independent contrasts, Monte Carlo computer simulations to obtain null distributions of test statistics, and phylogenetic autocorrelation, which allow traditional topics in comparative and ecological physiology to be addressed with greater rigor. Expand
Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts
TLDR
Any (continuous) trait that is inherited from ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic or cultural), according to Felsenstein's method. Expand
Are 'comparative methods' always necessary ?
TLDR
It is argued here that the approaches commonly used in systematics can be of great value in analysing the phylogenetic component of character state distribution over a set of taxa, and can help to decide whether the data can be used as they stand, or whether the authors will have to use comparative methods. Expand
Phylogenies and the Comparative Method
TLDR
A method of correcting for the phylogeny has been proposed, which specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. Expand
A method for testing the assumption of phylogenetic independence in comparative data
TLDR
This work presents the application of a statistical diagnostic called the ‘test for serial independence’, which can be applied to almost all currently employed PCMs, including Felsenstein’s (1985) independent contrasts. Expand
LIKELIHOOD OF ANCESTOR STATES IN ADAPTIVE RADIATION
TLDR
It is concluded that measures of uncertainty are useful and should always be provided, despite simplistic assumptions about the probabilistic models that underlie them, and if uncertainty is too high, reconstruction should be abandoned. Expand
EXAMINING TWO STANDARD ASSUMPTIONS OF ANCESTRAL RECONSTRUCTIONS: REPEATED LOSS OF DICHROMATISM IN DABBLING DUCKS (ANATINI)
  • K. E. Omland
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 1997
TLDR
Character state mapping reconstructs monochromatic ancestors for the genus Anas as well as most of its main clades and cautions against the uncritical use of unordered parsimony as the sole criterion for inferring ancestral states. Expand
THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES
TLDR
The separation of phylogenetic from specific effects proposed here also allows phylogenetic factors to be explicitly included in cross‐species comparative analyses of adaptation, which solves a long‐standing problem in evolutionary comparative studies. Expand
...
1
2
3
4
...