Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Thursday, 25 October 2007

The Great Phenetic Revival 2: Phenetics

To all intents and purposes, by the late 1970s phenetics was dead. Why, then, some 30 years after its death, does Felsenstein (2004) in chapter 10 (Digression on history and philosophy) of his book Inferring Phylogenies begin by acknowledging Sokal and Sneath (1963), the first bible of phenetics, as the beginning, if not the foundation of phylogenetic methods (Felsenstein, 2004:124)?

Felsenstein notes (2004:145):
"Many systematists believe that it is important to label certain methods (primarily parsimony methods) as 'cladistic' and others (distance matrix methods, for example) as 'phenetic'."
Why does Felsenstein reduce the theory of cladistics and phenetics to different types of method? Part of the reason is that Felsenstein wishes to grant equal time to all quantitative (numerical) methodologies. Unwittingly (perhaps), he makes phylogenetics a 'realist' agenda for numerical systematics - rather than 'phenetic', a term carefully avoided.

Methods to one side, Felsenstein sees no purpose in discussions of classification, noting that,

"I would say that the effort put into this controversy is further evidence that systematists do not have their priorities straight. In their day-to-day work they really do not make much use of classifications, but they show a strange obsession with fighting about them for reasons that seem to me to be an historical curiosity" (Felsenstein 2005)
Felsenstein's dismissal of classification should not be surprising. Homology and monophyletic groups, crucial to the enterprise of classification, are not necessary under phenetics (in fact, Felsenstein mentions neither homology nor monophyly in his book) (see Williams & Ebach 2005).

So, what, exactly is phenetics? Or what has it become?

Phenetics is more than just a method of grouping by overall similarity; it's more than just a method. It's way to not do (to avoid) classification, namely to group taxa without any notion of homology beyond mere similarity, to form arbitrary groups without any notion of relationship (paraphyly) and work comfortably with branching diagrams depicting similarity without any specified hierarchy (unrooted trees). Phenetics is a synthesis that unites various numerical procedures to find non-groups that stem from ancestral 'vices' in a world in which the taxonomist and systematist has no prior knowledge or conviction of classification.

Perhaps there is a broader question: What are the fundamental differences between the Modern Synthesis, numerical phylogenetics, numerical taxonomy and phenetics? We know of none; all are based on simple similarity.

References
Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates Inc., Massachusetts.
Sokal, R.R., Sneath, P.H.A. 1963. Principles of Numerical Taxonomy. W.H. Freeman, San Francisco.
Williams, D.M., Ebach, M.C. 2005. Drowning by Numbers: Re-reading Nelson's Nullius in Verba. Botanical Review 72, 355-387.

1 comment:

Joe Felsenstein said...

I think I can make some comments to the post even if the book is not out yet:

1. "To all intents and purposes, by the late 1970s phenetics was dead. Why, then, some 30 years after its death, does Felsenstein (2004) in chapter 10 (Digression on history and philosophy) of his book Inferring Phylogenies begin by acknowledging Sokal and Sneath (1963), the first bible of phenetics, as the beginning, if not the foundation of phylogenetic methods (Felsenstein, 2004:124)?"

Maybe it's because I was *not* trying to give the history of "phylogenetic methods". I stated clearly that although phylogenies had been inferred since Darwin and Haeckel, I would concentrate only on algorithmic methods, those clearly enough defined to be carried out by a computer. Sokal and Sneath's work was the first such (in the clustering method used by Sokal and Michener to infer a phylogeny). It is nice to hear lots of history about folks like Naef, but did he have a numerical or algorithmic method that coped with conflict among characters? I think I was right to start with Sokal and Sneath, and this of course is separate from the lack of support which their position on classification got (and which I clearly mentioned in Chapter 10).

2. "Felsenstein notes (2004:145):
"Many systematists believe that it is important to label certain methods (primarily parsimony methods) as 'cladistic' and others (distance matrix methods, for example) as 'phenetic'." Why does Felsenstein reduce the theory of cladistics and phenetics to different types of method? Part of the reason is that Felsenstein wishes to grant equal time to all quantitative (numerical) methodologies."

I actually *complained* quite clearly in Chapter 10 about what I felt was the negative practice of using the terms "cladistic" or "phenetic" for methods of inferring phylogenies. The sentence quoted characterized this practice and then I condemned it. The passage in the blog is an outrageous misrepresentation of the content of my Chapter 10.


3. "Unwittingly (perhaps), he makes phylogenetics a 'realist' agenda for numerical systematics - rather than 'phenetic', a term carefully avoided."

This sounds horrible but I have no idea what it means.

[at this point I have deleted a paragraph of the original post which I was astounded to find correctly characterized my statements.]

4. "Felsenstein's dismissal of classification should not be surprising. Homology and monophyletic groups, crucial to the enterprise of classification, are not necessary under phenetics (in fact, Felsenstein mentions neither homology nor monophyly in his book) (see Williams & Ebach 2005)."

Good point, I should have had a brief definition of monophyletic, a term I did use in the book. There was probably no point in my spending time on a definition of homology.

5. "So, what, exactly is phenetics? Or what has it become?

"Phenetics is more than just a method of grouping by overall similarity; it's more than just a method. It's way to not do (to avoid) classification, namely to group taxa without any notion of homology beyond mere similarity, to form arbitrary groups without any notion of relationship (paraphyly) and work comfortably with branching diagrams depicting similarity without any specified hierarchy (unrooted trees). Phenetics is a synthesis that unites various numerical procedures to find non-groups that stem from ancestral 'vices' in a world in which the taxonomist and systematist has no prior knowledge or conviction of classification."

Of course phenetics is a philosophy of classification (maybe a bad one, maybe not, but a philosophy of classification nonetheless). Describing the inference of phylogenies as "phenetics" is, I think, misleading.


6. "Perhaps there is a broader question: What are the fundamental differences between the Modern Synthesis, numerical phylogenetics, numerical taxonomy and phenetics? We know of none; all are based on simple similarity."

First of all, numerical phylogenetics is not "based on simple similarity". It just isn't. There is no way you can compute either a parsimony tree, or a likelihood tree, from a table of similarities between species.

Second, the Modern Synthesis was an important development in understanding the mechanisms of evolution, how genetics illuminated evolutionary change. It was not simply a method of making trees or classifications.

I think people can see that I disagree totally with the post, and find it far from a crushing retort. I think it reflects either a massive misunderstanding or a massive redefinition of words that most everyone else uses in a sensible way.