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Phylogeny Part 2: Introducing Cladograms

The cladograms you learned to interpret in Part 1 of this exercise might have seemed difficult to conceptualize because they were merely branches and names. But cladograms are highly useful guides to a group of organisms. A particular cladogram hypothesis immediately suggests the genealogical branching pattern. For example, consider this cladogram from Part 1:


For review, the reason I said "cladogram" and not "cladograms" is that these are the same cladogram, just drawn a bit differently. In this cladogram, for example, a bird and crocodile are sister taxa, relative to a snake or lizard, or even more distantly related vertebrates. That information about branching pattern is useful in itself, but branching pattern alone does not really tell us much about the group or the sorts of evolutionary changes that occurred in it. Plus, one has to assume that there is some good reason why this cladogram is drawn, and not some other alternative cladogram, for example, one that puts birds and mammals together. After all, both birds and mammals are endothermic (i.e., "warm blooded"), and crocodiles, lizards, and snakes are not.

So Part 2 and later parts will be about how evidence is accumulated in support of one or more cladograms, to the exclusion of others. It is about the parsimony criterion, which is used to choose between alternative cladograms. Moreover, it is about how to interpret the evolution of characters (i.e., traits of organisms), which connects cladograms to notions like adaptation.

Consider again the cladogram above. It would be natural to be interested in the evolutionary history of land vertebrates, and the sorts of evolutionary innovations that might have occurred that might have been important in explaining patterns of diversity through time. We might especially be interested in the sorts of adaptations (or preadaptations = exaptations) that allowed some groups to become fantastically successful. In old-fashioned treatments of evolution, the movement of a group into a new "adaptive zone" (e.g., evolving powered flight as in birds) was often given great emphasis in tree diagrams (for example, in the writing of G.G. Simpson), but when these notions were added to tree figures the actual pattern of evolutionary branching often became obscured. Click here to open up a new window with an example of one of these sorts of "bubble diagram" trees.

CQ1: Look at this "bubble diagram" tree and use it to formulate a short conjecture (about 25 words or less) about what sort of ancestor a bird might have evolved from. Please do this before you proceed further. If you are really a glutton for punishment, attempt to draw a cladogram version of this figure.

Note, this "bubble" figure is from the current edition of the leading college zoology textbook, which should tell you something about the gap between the state of the art and what current textbooks are presenting.

In contrast, cladograms are based strictly on the hypothesized pattern of splitting events. This approach has the advantage of allowing an investigator to immediately see the hypothesized sister taxon relationships between taxa, but there is another important advantage. A cladogram also allows the investigator to present important events in the evolutionary history of the group.

One clarification is necessary before an example is presented. Some events might be important because they were "innovations" that led to explosive raditions. Other events might be important only because they allow someone to recognize living or fossil organisms as members of a group, and might actually have very little, if any, "adaptive" value.

Now we are ready to look at a cladogram that corresponds approximately to the bubble diagram above. Click here to open up a new window with an example cladogram, this one from Sandy Carlson's excellent dinosaur course website. Click here to open up another window with more detailed window of the dinosaur portion of the previous cladogram. [Note: As of 4/13/04 some students have experienced problems displaying these figures. Here are the same figures temporarily placed on our server: here and here.]

CQ2: Now, repeat what I asked you to do above in CQ1. Hypothesize what sort of ancestor gave rise to birds, only this time use the cladogram views. It might be helpful to start at the node where birds are on the second cladogram, then move down in the cladogram to the next node down, to include more general traits for more inclusive clades that also include birds, and keep moving down until you are at the bottom node of the first cladogram. If you forget what a clade is, remember the "snip rule."

CQ3: Briefly contrast the descriptions derived from the "bubble diagram" tree (CQ1) and the amniote/dinosaur cladograms (CQ2). What can you conclude about these alternative approaches with respect to making statements about the evolution of traits?

While you have the second, dinosaur cladogram, window open, note that below the cladogram is a good example of an "unranked indented classification," a portion of which is displayed below. This is a cladistic approach to classification that is becoming increasingly popular. The "unranked" means that none of the taxon names are preceeded by a rank (e.g., phylum, class, order, family, etc.). The classification does not need these because the "indented" form of the classification gives the hierarchical structure. Because cladistic classifications strictly conform to the "rule of monophyly" (i.e., only monophyletic taxa are allowed to have formal taxon names) we do not need to worry about ANY of these taxon names being paraphyletic. That is, each taxon includes all of the taxa indented directly underneath it. For example:

the taxon theropods includes everything indented underneath it, including the daughter taxa, ceratosaurs and coelurosaurs, and coelurosaurs likewise includes everything indented underneath it, including its daughter taxa, ornithomimosaurs, dromaeosaurids, and birds. Likewise, characters are hierarchically arranged, just like in nature. The taxon theropods is diagnosed as having sharp claws on grasping hands. This is not a "definition" of theropods, it is a diagnosis. The diagnosis is what is inferred to have been in the common ancestor of theropods, based on a technique in phylogenetic analysis known as "character optimization." The important point here is that if one of the descendants become secondarily modified to lose their sharp claws, it does not mean that this descendant is then somehow kicked out of the group. Think about a penguin. Does it have sharp claws? Do we have trouble thinking about it as a bird? Why should we have trouble thinking about it as a theropod?

Perhaps the biggest advantage of an indented classification like this is that it exactly corresponds to the cladogram hypothesis. You can construct a classification directly and unambiguously, given a cladogram. It works in reverse as well. Given an indented classification, you can turn it into a cladogram. If you would like to know how to turn an unranked indented classification into the corresponding cladogram, follow these instructions. From a student's perspective, having a classification that corresponds exactly to the best cladogram available simplifies studying considerably, because once a cladogram is learned, the classification naturally follows. That is not true of conventional classification systems, because many conventional taxa are paraphyletic. For example, Reptilia and Aves are at the same rank in a conventional classification, even if everyone agrees that Aves is nested within reptiles on the best supported cladogram. In other words, no one is disputing the cladogram, only how to best construct a classification system. The cladistic approach is simpler, albeit requiring you to give up familiar paraphyletic taxa.

Take a minute and look back at the dinosaur cladogram window, scrolling down to the unranked indented classification. Above we said that ceratosaurs and coelurosaurs were daugher taxa of theropods. They are also sister taxa of each other. We can tell this because they are at the same level of indentation, nested within theropods.

CQ4: Extend this reasoning to complete the following sentence. The taxon _____________ is the sister taxon of theropods, and these are daughter taxa nested within the higher taxon ____________. One trait that unites members of this higher taxon is ___________________.

Once you get the hang of thinking about cladograms, you can look at a new one, perhaps drawn somewhat differently, with nodes rotated, and with somewhat different terminal taxa. For example, click here and then click on the Play button (perhaps turn the sound down a bit first) to open up yet another window of a fun dinosaur cladogram from the American Museum of Natural History's OLogy website for kids.

CQ5: Find the node (blue dot) corresponding to the last shared common ancestor of birds in the OLogy cladogram, and complete the following sentence. The sister taxon of birds is _____________________ and within birds, the living but flightless bird, Eudromia elegans, is sister taxon of a clade of extinct birds, __________ and Presbyornis pervetus (according to this cladogram hypothesis). Extra challenge: If it is related to modern ducks, could Presbyornis pervetus quack, according its species card on this web page (click on its name, and then the yellow arrow)?

CQ6: Consult these Archaeopteryx web pages: 1 - 2 - 3. (See here for Wikipedia's more general description.) Name some derived (new) features that modern birds share that are lacking in the ancient bird, Archaeopteryx (and also lacking in other dinosaurs). Next, name some derived features that Archaeopteryx shares in common with those other dinosaurs known as birds.

Note that in the above question I am emphasizing the derived similarities only, not the "primitive" (technically termed "plesiomorphic") similarities that are merely inherited from a more ancient ancestor. For example, Archaeopteryx had teeth, but so do other reptiles and mammals and sharks, etc. The fact that both Archaeopteryx and T. rex had teeth does not help provide evidence that they are closely related. One has to find derived similarities that were present in their immediate common ancestor but not in their more ancient shared common ancestor with another taxon (e.g., the ornithiscian dinosaur, Triceratops). Note that a derived similarity can be the loss of a trait (e.g., teeth), provided it is a derived loss (i.e., was previously present in more ancient ancestors). Here are some examples of derived character states hypothesized for various taxa of terrestrial vertebrates. When this assignment is eventually expanded, the emphasis on shared derived (i.e., "special") similarities hypothesized to be homologous will be clarified. (Technically, these are termed "synapomorphies" for "syn" = shared, "apomorphies" = derived similarities.) Only shared derived similarities, not shared primitive similarities (= "plesiomorphies"), can provide evidence for the monophyly of taxa. For example, if one is comparing a turtle, a lizard, and a snake, the presence of four limbs does not help provide support for a turtle-lizard grouping because more distant relatives (e.g., mammals, salamanders) also have four limbs, so this similarity is a shared primitive trait. In contrast, the presence of two penises in a male lizard and a male snake is a shared derived trait, because other male reptiles and mammals only have one penis.

Until these distinctions can be explained in more detail, you might find the following links to other resources useful: 1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 9 - 10 (pdf) - 11 - 12 - 13 - 14


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This page created July 28, 2002, last modified February 17, 2011

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