Phylogenetic Targeting of Research Effort in Evolutionary Biology

@article{Arnold2010PhylogeneticTO,
  title={Phylogenetic Targeting of Research Effort in Evolutionary Biology},
  author={Christian Arnold and Charles L. Nunn},
  journal={The American Naturalist},
  year={2010},
  volume={176},
  pages={601 - 612}
}
Many questions in comparative biology require that new data be collected, either to build a comparative database for the first time or to augment existing data. Given resource limitations in collecting data, the question arises as to which species should be studied to increase the size of comparative data sets. By taking hypotheses, existing data relevant to the hypotheses, and a phylogeny, we show that a method of “phylogenetic targeting” can systematically guide data collection while taking… Expand
Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms.
TLDR
An overview of phylogenetic approaches and their importance for studying the evolution of physiological processes and mechanisms is provided, and the conceptual framework underlying these methods are discussed, and when and how phylogenetic information should be employed are explained. Expand
Using the BirdTree.org website to obtain robust phylogenies for avian comparative studies: A primer.
TLDR
It is argued that BirdTree, due to the ease of use and the major advantages over previous 'traditional' methods to obtain phylogenetic hypotheses of bird species (e.g. supertrees or manual coding of published phylogenies), will become the standard reference in avian comparative studies for years to come. Expand
The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses
TLDR
It is argued that even recent molecular phylogenies should be treated cautiously because they rely on many assumptions and have many shortcomings, and primatologists are urged to be aware of the current limitations of phylogenetic reconstructions when applying phylogenetic comparative methods. Expand
Patterns of Research Effort in Birds
TLDR
This work identifies avian taxa that are under- and overstudied and addresses the importance of research effort biases in evaluating vulnerability to extinction, with non-threatened species studied twice as much as threatened ones. Expand
Untested assumptions about within-species sample size and missing data in interspecific studies
TLDR
Testing information on within-species sample sizes and missing data from five independent comparative datasets of European birds indicates that the accuracy of sampling is repeatable and distributed non-randomly among species, as several species-specific attributes determined the probability of observation. Expand
Comparative analysis of experimental data
1.We consider the problem of how to analyse data from experiments conducted on multiple species. This seems to have been largely overlooked in the literature, and we highlight that the use of speciesExpand
Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.
  • W. Barr, R. Scott
  • Biology, Medicine
  • American journal of physical anthropology
  • 2014
TLDR
In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was, and in short, DFA offered no indication that differences between categories might be explained by phylogenetics signal, while PGLS did. Expand
Statistical Issues and Assumptions of Phylogenetic Generalized Least Squares
Using phylogenetic generalized least squares (PGLS) means to fit a linear regression aiming to investigate the impact of one or several predictor variables on a single response variable whileExpand
Uncertainties Due to Within-Species Variation in Comparative Studies: Measurement Errors and Statistical Weights
TLDR
This chapter reviews different analytical solutions that have been recently developed to account for the unwanted effect of within-species variation and emphasizes that within- Species variation should not necessarily be regarded as a confounder, but in some cases, it can be subject to evolutionary forces and delineate interesting biological questions. Expand
How does cognition evolve? Phylogenetic comparative psychology
TLDR
Here, it is explained how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. Expand
...
1
2
3
...

References

SHOWING 1-10 OF 104 REFERENCES
Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence
TLDR
Simulations show λ to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. Expand
Phylogenetic comparison and artificial selection. Two approaches in evolutionary physiology.
  • T. Garland
  • Biology, Medicine
  • Advances in experimental medicine and biology
  • 2001
TLDR
Interspecific comparison has a long and productive history in physiology, and several new statistical methods correct for problems caused by phylogenetic relatedness and descent with modification, the most common being phylogenetically independent contrasts. Expand
Phylogenetic approaches in comparative physiology
TLDR
It is the personal opinion that the incorporation of phylogeny information into comparative studies has been highly beneficial, not only because it can improve the reliability of statistical inferences, but also because it continually emphasizes the potential importance of past evolutionary history in determining current form and function. Expand
TAXON SAMPLING, CORRELATED EVOLUTION, AND INDEPENDENT CONTRASTS
  • D. Ackerly
  • Biology, Medicine
  • Evolution; international journal of organic evolution
  • 2000
TLDR
The simulations showed that random samples, with respect to the traits under consideration, provide statistically robust estimates of trait correlations, but exact significance tests are highly dependent on appropriate branch length information; equal branch lengths maintain lower Type I error than alternative topological approaches, and adjusted critical values of the independent contrast correlation coefficient are provided. 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
The comparative method in conservation biology.
TLDR
It is concluded that comparative methods are stimulating research into the ecological mechanisms underlying conservation, and are providing information for preemptive screening of problem species. Expand
Testing character correlation using pairwise comparisons on a phylogeny.
  • W. Maddison
  • Biology, Medicine
  • Journal of theoretical biology
  • 2000
TLDR
In comparative biology, pairwise comparisons of species or genes (terminal taxa) are used to detect character associations, and algorithms are developed that find all taxon pairings that maximize the number of pairs without constraint. 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
Inference from binary comparative data
TLDR
This work resurrects in this context a different model of randomness, the random assignment of treatments, which it is argued provides a rationally acceptable basis for inference in relation to controversial associations between warning coloration and larval gregariousness in butterflies. Expand
Phylogenies and Community Ecology
TLDR
A common pattern of phylogenetic conservatism in ecological character is recognized and the challenges of using phylogenies of partial lineages are highlighted and phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes are reviewed. Expand
...
1
2
3
4
5
...