In the hopes of benefitting Jim, lets define some other terms which might help him to unde

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In the hopes of benefitting Jim, lets define some other terms which might help him to understand how biologists think about transitions. The first term is "intermediate". An intermediate organism is one that contains features that are used to classify two different groups of organisms (I'll discuss that more in a moment), or that contains a feature that is intermediate (along some scale) between the homologous features in two other groups of organisms. For example, feathers are a defining feature of birds, while a single row of undifferentiated teeth on each jaw is a defining feature of reptiles (turtles may disagree :-). Since _Archaeopteryx_ has both of these traits, it is an intermediate form. If an intermediate is located in the proper strata, then it can be postulated that the intermediate is also a transitional organism. This means that the features shared with one group are shared because the transitional organism descended from members of that group, while the features shared with the other group are shared because the transitional organism is an ancestor of the animals of that second group. In the above case, _Archaeopteryx_ is believed to contain undifferentiated teeth because it descended from other organisms (i.e. reptiles) that had that feature. Modern birds have feathers because they are descended from an organism (perhaps _Archaeopteryx_) that acquired that characteristic. The upshot of all of this is that we can *hypothesize* that _Archaeopteryx_ is a transitional organism between reptiles and birds. The hypothesis is subject to refutation. If it passes many possible tests, we'll gain enough confidence to call _Archaeopteryx_' status as a transition between reptiles and birds a fact. Currently the evidence in this case is equivocal. Why is that? Because the hypothesis of transitional status is a good scientific hypothesis, meaning that there are many tests it *can* (read must) pass in order to gain acceptance. So what are some of those tests? Let's start with one that's relatively easy to understand and that I've hinted at above. Does the organism's existance occur at the right time? One of the reasons that _Archaeopteryx_'s status is equivocal is that there are some fossils older than _A_ which appear to contain features which are not possessed by _A_, and yet which are possessed by modern birds. If it becomes well established that there are modern bird features possessed by earlier animals, then we can rule out _A_'s designation as transition between reptiles and birds. Going in the opposite direction, if there are reptilian features that _A_ does not possess, and that are retained in modern birds, the hypothesis will have been similarly refuted. As promised, I'm now going to ramble about features and classification. Chris is always telling us about the hierarchical pattern in which you can classify organisms. Let's dissect this a bit. Unfortunately I think that we have to begin with some vocabulary. A most important concept in evolutionary biology is polarity analysis. Polarity analysis is the comparison of features for the purpose of distinguishing the ancestral condition from the derived condition. Continuing with my previous example, for birds the ancestral condition is a beak full of teeth. The derived condition is a beak without teeth. The ancestral character is referred to as plesiomorphic or a plesiomorphy. The derived condition is referred to as apomorphic or an an apomorphy. Please note that polarity analysis implies *no* connotations of progress. Another set of definitions that you need here deal with phylogeny. A monophyletic grouping is a grouping of organisms that contains an ancestral form and all of its descendents. A paraphyletic grouping is one which contains an ancestor, and some of its descendents. A polyphyletic grouping is one which contains groups of organisms that are derived from different ancestors. These definitions are described with the help of a figure below: ^ | A B C * D t | \/ / \/ i | a \/ * / m | b\ / / * e | x \/ / | c\ / | d\ | \ | e | |__________________________ The *'s represent extinct lineages added for realism :-) Capitol letters are organisms alive now, small letters are organisms that were alive at some point in the past. A grouping which consists of A,a,B and b is paraphyletic, because it leaves out C, which is also one of b's descendents. A grouping which includes A,a,B, and D is polyphyletic because it lumps A,a, and B which are derived from b with D which is derived from c. A grouping which includes the whole chart is monophyletic because it consists of e and all of e's descendents. So how do you make a tree like the above? The answer is to use polarity analysis to determine characters which can be used to define groups. Apomorphies which define groups are called synapomorphies. Characteristics which exist in one group, but also in other groups outside of the group in question are called symplesiomorphies. To get an idea of how the nomenclature is used, feathers are a synapomorphy defining the clade aves, but are a symplesiomorphy shared between, for example, sparrows and starlings. This gets back to the hierarchy that Chris is always trying to hammer home; as you move back towards the root of the evolutionary tree, characteristics that are symplesiomorphies within the group become synapomorphies defining the (more inclusive) group. Once you get to the part of the tree where the characteristic is a synapomorphy, no organism outside of that group should have that trait (e.g. no animal outside of aves has feathers). When Chris says that characteristics fit into a hierarchical pattern, he means that comparative studies allow us to choose characteristics which meet the definition of synapomorphy above, and which can thus be used to generate a tree consistent with the idea that all traits arive from modifications of traits possessed by previous members of the same lineage. I suspect that with this background, Jim can now accept that a transitional organism can be defined as an organism in which a synapomorphy first appears (and all of its descendents will thus form a monophyletic group). Of necessity, said organism also contains characteristics used to define previously existing groups (e.g. undifferentiated teeth), and hence it will also be an intermediate. An intermediate need not be transitional, however. For example, in the diagram above, C might be intermediate between B and D (or more importantly, between b and D), but its intermediacy is predicated on the basis that it too is derived from c, rather because it is a part of the lineage connecting B and D. Mickey Rowe (rowe@pender.ee.upenn.edu)

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