I'm told by several people, including my adviser, that the use of molecular sequence data to infer phylogeny is a sort of phenetic interpretation. The argument is that, not only is the method of aligning sequences obscured and semi-mystic in the final publication, a sort of art, but that the phylogeny is inferred by overall sequence similarity and not by homologous characters.
I agree that molecular systematics is not cladistics, but neither is it phenetics.
Cladistics as a school places high emphasis on the use of special shared characters called synapomorphies or homologues to infer a phylogeny, so the thought of using something like a sequence, with no obvious characters or homologues other than the four base pairs as a way to generate a tree topology is a poor alternative. It is not surprising that a cladist would call molecular systematics like phenetics because algorithms such as maximum likelihood seem to mimic the overall similarity matrices of phenetics.
To understand why molecular systematics is not phenetics, one needs to return to the central premise of the phenetics school of thought. Phenetics was the reaction of strict empiricists to the earlier system of evolutionary taxonomy. The pheneticists wished to create a system with strict codes for determining hierarchy. They determined that the phylogeny of an organism is near impossible to be correctly inferred and therefore taxonomic hierarchy should not try to represent phylogeny.
Since molecular systematics at its heart is working to represent accurate phylogeny, it cannot be phenetics. So, if molecular systematics is neither cladist nor phenetic, what is it?
It seems to me that the combination of phylogenetic inference and some level of art mimics a /gradist/ school of thought, most similar to the early evolutionary taxonomy. I don't necessarily see it as a bad thing, to have two different schools of thought working together. Obviously phenetics is out, because I believe a topology should represent correct phylogeny as often as possible. Once we agree that taxonomy should include phylogeny, then there are two ways to go about inference. Either we work with the morphology, employing cladistic methods including parsimony and synapomorphy, or we work with molecular data, employing maximum likelyhood, baysian analysis, and other neogradist methods to derive phylogeny. Both are useful toolsets.
Just getting some things out of my head onto paper that have been rumbling for a while, concerning the fate of morphology based phylogenetics, and the argument by morphology based systematists against molecular methods.
Wow.
It's always good to realize how much you don't actually know, sometimes.
Quote from: LMNO on December 04, 2009, 08:45:31 PM
Wow.
It's always good to realize how much you don't actually know, sometimes.
If you'd like to learn more about this stuff, Biological Systematics: Principles and Applications (http://www.amazon.com/Biological-Systematics-Principles-Applications-2nd/dp/0801447992/ref=tmm_hrd_title_0) is an excellent introduction to the science of systematics and the applications it's used for. The first few chapters actually cover the history of the three schools (evolutionary taxonomy, phenetics and cladistics), and then the rest of the book goes into cladistic and neogradist methods (though I just sorta coined "neogradist" above, so they don't call it that in the book), and several chapters on applications.
Quote from: LMNO on December 04, 2009, 08:45:31 PM
Wow.
It's always good to realize how much you don't actually know, sometimes.
yeah, i was reading for a bit until i realized that the words were just hollowly running through my head and i felt like the 'I like turtles' kid....
Sorry. :/
Quote from: Kai on December 04, 2009, 09:42:11 PM
Sorry. :/
I understood some of it, though I've no right to, and it's kinda unusable knowledge for me.
What do you mean, no right to?
Quote from: Kai on December 04, 2009, 10:59:10 PM
What do you mean, no right to?
I don't know. Pulling a lot of info from context clues and very sparse knowledge.
Quote from: yhnmzw on December 05, 2009, 01:01:31 AM
Quote from: Kai on December 04, 2009, 10:59:10 PM
What do you mean, no right to?
I don't know. Pulling a lot of info from context clues and very sparse knowledge.
You should never feel like you don't deserve to understand something. If you can understand it, good on you!
I understood after looking up phenetics, but I'm a biology major (though just a freshman one).
Quote from: Kai on December 05, 2009, 01:23:22 AM
Quote from: yhnmzw on December 05, 2009, 01:01:31 AM
Quote from: Kai on December 04, 2009, 10:59:10 PM
What do you mean, no right to?
I don't know. Pulling a lot of info from context clues and very sparse knowledge.
You should never feel like you don't deserve to understand something. If you can understand it, good on you!
I know. It's a thrill.
Molecular Systematics is *not* Phenetics! Damn Right!
(just kidding, i have no idea what the fuck you're talking about)