Talk:Cladistics/to do

As it stands, this article confounds "cladistic" and Linnaean classification. What is being contrasted is not "cladistics versus Linnaean" but "Phylocode versus Linnaean." Fact is: any classification that contains monophyletic groups and is logically consistent with the underlying phylogeny is a "cladistic" classification. it may be Linnaean, an indented list, a classification that uses numerical prefixes, or a system that uses Phylocode. The article also confounds "Linnaean and evolutionary taxonomic classifications." A Linnaean classification that contains known paraphyletic groups is an evolutionary classification. A Linnaean classification that contains only monophyletic groups is a cladistic classification. In short, this article is in serious need of revision. Eowiley (talk) 19:57, 6 April 2009 (UTC).

--Aranae 02:27, 15 December 2006 (UTC)
 * Here are some suggestions to improve the article:
 * 1) I think the distinction between cladistics and phenetics should be addressed a second time once plesiomorphic and apomorphic terms are introduced. Cladistics is interested in synapomorphies.  Phenetics does not distinguish between the two.  An example of how the two could come up with a different tree would also help.
 * 2) I'm a bit unhappy with the discussion of what it means to be basal. I completely agree that usage of the term primarily refers to a taxon-poor clade that branches off early.  I also think that the term gets used in reference to the ingroup, the taxon sampling, and the question being asked.  For example, gibbons will commonly be said to be basal among the hominoids, yet there are 13 species of gibbons in four genera and only 7 species of great apes (also 4 genera).  In this case, the research question usually being posed is really about a focus organism (us) and relationships among the gibbons is less important in that particular discussion.  Bats and insectivorans are basal to the rest of the Laurasiatheria in spite of the fact that  over 50% of described laurasiatherian species are bats and 20% are insectivorans.  The research question is how are bats, insectivorans, carnivorans, pangolins, perissodactyls, and cetartiodactyls.  From that perspective, bats and insectivorans to qualify as basal to the cetferungulates.  Being "primitive" shouldn't qualify a group as basal (although it probably is used that way in some instances).  Bats fly, echolocate, and look nothing like the ancestor of the Laurasiatheria.
 * 3) The distinction between synapomorphy and autapomorphy should be clarified.
 * 4) The second paragraph of the section titled "Cladistic methods" is confusing. Plesiomorphies were present in the last common ancestor of group discussed.  Apomorphies arose subsequent to the last common ancestor of the group discussed.  To say that an apomorphy was present in the last common ancestor of the ingroup is false.  A synapomorphy was present in the last common ancestor of the clade it characterizes (and may have arisen anywhere along the branch leading to that clade).  Autapomorphies are also a type of apomorphy and they weren't present in the last common ancestor of any two taxa in the analysis.
 * 5) Eliminate the use of "we" in the 4th paragraph of the same section.
 * 6) I think at least 50% of the field would consider maximum likelihood and Bayesian methods to be both Hennigian and cladistic. They are still constructed on the basis of synapomorphies, they just incorporate information about how characters evolve and attempt to incorporate the potential for additional evolution hidden in a final parsimony analysis.  They are definitely not phenetic methods.  I'm also amazed that there still isn't an article on maximum likelihood in phylogenetics.
 * 7) The total evidence approach advocated in the 6th paragraph isn't universally accepted. I think it's safe to say that >50% of the field would agree, but there are those who argue that a little bit of quality data is better than a lot of noisy data or even a little bit of quality data + some noisy data.  Most (but not all) do agree that data where homology is questionable should be excluded.  That should be addressed in the paragraph as well and I'm not all that comfortable with the behavior example (without expansion and clarification) for that reason.  That statement that molecular, morphological, etc. not are all equal is definitely an opinion and is definitely disputed.  Homoplasy is more common in morphological data?  Are we sure about that?
 * 8) Paragraph 7. A small point, but cladistics does assume that evolution is bifurcating as opposed to hybridizing, reticulate, or having lateral transfer.
 * 9) In my opinion, the "Cladistic classification" section can reasonably stay, but seesm to ramble on as if it was written by several editors who had differing opinions and tried to jump back and forth in such a way as to make it sum up to NPOV. I'm not happy with the notion that about half of the text of a featured article on cladistics is spent discussing the PhyloCode and Linnean hierarchy.
 * 10) There is a subtle, but important philosophical difference between cladistics and parsimony. This article should address that clearly.
 * 11) The "see also" is an odd list. It should have links to phenetics, parsimony, maximum likelihood (phylogenetics), maybe Bayesian (phylogenetics), as well as some of what's already there.

Eyu100(t 15:36, 22 August 2007 (UTC)