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    Reviewer A

    In this short and succinct paper, Wiley presents a clear and concise exposition of phylogenetic systematics, contrasting it with other systems of classification such as phenetics. Wiley's exposition is so clear and concise, that it is difficult to recall how much confusion resulted when phylogenetic systematics was first introduced. First and foremost, trees have to be distinguished from cladograms, and homologies must be distinguished from homoplasies. Even though some systematics reject the choices made by Wiley, they do not reject the distinctions that Wiley sets out. They may be disinclined to reject all paraphyletic taxa, but they acknowledge relevance of the distinction. Why does it matter which system of classification one adopts? It all depends on what you want to do with the resulting classifications. If you want to reconstruct a phylogeny, you have to limit yourself to homologies. Homoplasied are noise. If you want to uncover evolutionary processes, you have to limit yourself to homoplasies -- not all homoplasies but only homoplasies. Homologies are noise. The chief virtue of Wiley's paper is its clarity and coherence. All the elements of his exposition have become standard. What Wiley provides is a clear presentation of the various elements that make up phylogenetics.

    I recommend acceptance of this paper.

    I found one typo -- "no in the group" should be "not in the group."

    Reviewer B: Reviewer B

    This is a high quality and very useful article by one of the very top experts in the field and the man who literally wrote the book on “Phylogenetics” and I think it will make an excellent addition to Scholarpedia. I only have some very minor suggestions, all of which involve subtle changes in wording. I predict this should become a highly viewed and cited article, and I recommend that the article be accepted. Here are my comments:

    1st sentence, change to: whose books on the subject WERE published in 1950 in German and modified into English and Spanish in 1966

    2nd sentence, change to: The tree of life is one continuous stream of genealogical descent punctuated by divisionS of the stream

    Last sentence of the 1st paragraph in the section “Phylogenetic analysis” maybe change “argue” to “assess”

    1st sentence of 5th paragraph of that section, change to: We discriminate by looking outside the group and seeING what other or

    Next sentence, change to: but noT in the group.

    Further, perhaps you might explicitly say in this paragraph that this is referred to as the outgroup method, and maybe you might also explicitly use the terms “synapomorphy” and “symplesiomorphy”. Plesiomorphous is mentioned later in this section but it might be worthwhile to mention them up front: just a thought.

    Later in the chapter, homoplasous is used. I always have trouble with this one, but is it spelled homoplasious instead?

    5th sentence in last paragraph of that section, change to: Likelihood analysis is a statistical approach that EMPLOYS one or more specific models of how characters might change and USES these models to assess the likelihood of observing the data and model given a particular tree topology.

    Last section, first paragraph, 3rd sentence, change to: Such classifications would contain groups only comprised of REPRESENTATIVES that descended from a single common ancestral species and all descendants of that species.

    In the 6th sentence of that section change “no” to “not”

    Last sentence in that paragraph, change “Group” to “Groups” Further, I might insert a sentence before there just to explicitly state: “A monophyletic Reptilia must include birds.” Basically that’s moving the last sentence of the last paragraph up to this paragraph and you could remove it there. Again, just a thought.

    And then I’d add a last sentence to that paragraph: “For example, a group of flying vertebrates that solely contained pterosaurs, birds, and bats and no other species.” And then make the first sentence of the next paragraph what was the last sentence in this paragraph.

    Then in the 3rd sentence of the last paragraph, I know what you’re saying about these groups being considered monophyletic but perhaps it’s a bit confusing. Instead could you say something like “Such groups were considered perfectly appropriate.”

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