The comparative method
"The comparative approach is not new. Indeed, it was Darwin's favoured technique. ... In short, comparative studies have taught us most of what we know about adaptation." (Harvey and Pagel, 1991, p. v)
How is this graph using correlation and the comparative method?
But consider this quote.
"Yet, one of the most embarrassing things that could be done to a group of respected biologists would be to ask them to spend a few minutes to write down what is meant by the comparative method, and what are the basic goals and principles of biological comparison." (Bock, 1989, p. 18 [cited in Starck, 1998, p. 110])
Why? Because so much of what "should" be compared depends on the questions asked?
Examples:Herbivores and tadpoles
So the comparative method in some sense depends on us knowing what to compare which depends on organisms relationships or phylogeny.
This is a film probably about "the" classic example of using phylogeny to examine such relationships.
For your information only, an additional reference on whales https://www.smithsonianmag.com/science-nature/how-did-whales-evolve-73276956/
Usually if you are using the comparative method you are trying to test relationships as seen in the film, or you are asking a question about some adaptation.
Usually however researchers are trying to establish the role of "environmental signals or pressures" versus the role of "phylogenetic signals", or what we have termed historic constraints, shaping the adaptation.
Classic examples:
Example one: Strong environmental signal. Usually this signifies the adaptation came about 100 % as natural selection working on the trait in a particular environment.
Illustration of the assembly of oak communities in northern Florida.
Here it is obvious that distantly related species change morphology with habitat. The implication then is that this is an adaptation to the environment and not due simply to the trait being inherited form an closely related ancestor they all shared.
Caution: Not so in all investigations. In large-scale studies of plant communities, such as tropical forests, several studies have detected significant clustering of related species, likely due to shared habitat preferences across broad clades (Webb, 2000).
Another example: The evolution of feathers. Old idea was that feathers evolved with and for flight in birds. The new idea is that they evolved for another purpose, perhaps insulation, and have been refined for flight in modern birds and their more immediate ancestors. Here we have what I term a strong historic or phylogenetic signal.
If you do not use a phylogeny or account for the groups' evolutionary history then you are assuming that any species used in your comparison are independent points (mathematically) or evolutionary history doesn't matter.
But we all share a history, so when can you treat species as independents? This is the practical problem facing all comparative studies. Adequate sample size is another.
Strict independence versus strong phylogeny among species
In some studies that involve more closely related species in which the phylogeny is known, methods have been developed to accommodate historic or phylogenetic effects.
Example:
How can relatedness of species affect this correlation?
Consider if we only had six species, but they really clustered into two groups because of relatedness.
In reality, we have two points, not 6.
One way to minimize the problem.
Felsenstein's method applied to the bat data.
There are many uses for trees that have nothing to do with the study of a particular adaptation or reconstruction of phylogeny.
Example:
http://evolution.berkeley.edu/evolibrary/article/0_0_0/conservation_08
http://evolution.berkeley.edu/evolibrary/article/0_0_0/conservation_10
http://evolution.berkeley.edu/evolibrary/news/081201_phylogeneticconservation
http://evolution.berkeley.edu/evolibrary/news/081101_hivorigins
https://evolution.berkeley.edu/evolibrary/news/060101_batsars
https://evolution.berkeley.edu/evolibrary/news/111101_hla
http://evolution.berkeley.edu/evolibrary/article/0_0_0/phylogenetics_12----------https://evolution.berkeley.edu/evolibrary/article/0_0_0/evotrees_treesmatter_05 (First paragraph--do not do venoms unless instructed to do so.)
The information you conclude from a phylogenetic comparative study is only as good as the trees used.
