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Sharks are a good candidate. Sharks have fins. Using sharks we can conclude that the ancestor of tunas, humans and lizards had fins; that fins are the primitive homology and that legs are the derived homology. As the derived homology, legs are valid confirming evidence that humans and lizards are more closely related to each other than either is to a tuna. We cannot conclude that basses are more closely related to tunas than either is to a lizard because both fishes have fins; nor can we conclude that tunas and basses are closely related to sharks.

The common ancestor or all these species basses, tunas, sharks, lizards and humans had fins. But, we can argue that all these species had a common ancestor because hagfishes, lampreys, amphioxus, and tunicates do not have fins.

Fins pectoral and pelvic fins are an evolutionary innovation that arose in the ancestor of all jawed vertebrates. All phylogenetic analysis is based on the reasoning presented above. All homologies are derived at some level of the tree of life. They confirm relationships at the level they are derived and once derived provide no further confirmation. Paired fins confirm the hypothesis that all jawed vertebrates share a common ancestral species but do not confirm that sharks are more closely related to tunas than tunas are to lizards.

In any one section of the tree homologies appear in two varieties. In some cases, every species of the group have the homology or something derived from that homologue all jawed vertebrates have paired appendages except some groups like snakes where the adults lost them. In some cases, they have different, but homologous characteristics some vertebrates have fins, others have legs.

Plesiomorphic characters do not show relationships within such a group because they already show relationships of a larger group. Fins confirm that jawed vertebrates are all related, legs show that tetrapod vertebrates form a group within jawed vertebrates.

Phylogenetics: The Theory and Practice of Phylogenetic Systematics

The hierarchy of genealogical evolution is reflected in the hierarchy of character modification Figure 2. Of course, not all similarities turn out to be homologous similarities. Sometimes very similar characters are evolved independently in different ancestors. There are two ways to sort out homologies and non-homologous homoplasous, convergent similarities. One way is to look at the characters in detail. For example, one might initially think that the fangs of marsupial lions and African lions are homologous.

But, the fangs are actually different teeth. The other way is to test the characters using other characters. Homeothermy in birds and mammals is considered a convergent similarity because all the other characters that have been analyzed indicate that the common ancestor of birds and mammals, a common ancestor that also gave rise to turtles, lizards, snakes, and others, was not warm-blooded.

Phylogenetic analysis of relatively simple data, such as that shown in Figure 2.

Phylogenetic System of Classification Hin

But, as data accumulate it becomes harder to insure that all possibilities are considered. Thus modern phylogenetic analysis uses computer algorithms that sort through and fit characters to trees using optimality criteria. There are two common criteria. Maximum parsimony adopts the criterion that the optimum tree is the one that explains all the data in the shortest number of evolutionary steps.

Likelihood analysis is a statistical approach that using 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. Two different tree topologies can be compared to see if one is statistically better than the other. No such statistical procedure is available for parsimony analysis, but both approaches yield similar results over a relatively wide range of evolutionary models.

Yet another approach is Bayesian analysis. It lacks an optimality criterion, but uses likelihood functions to assess the likelihood of the tree given the data and model. Phylogenetic classification is the third and final component of the Phylogenetic system. Hennig suggested that the most general and thus most useful classifications would be those originally advocated by Darwin: strict genealogical classifications.

Such classifications would contain groups only comprised of groups that descended from a single common ancestral species and all descendants of that species. Groups that contain an ancestral species and all its descendants are termed monophyletic groups. Hennig contrasted monophyletic groups with two other kinds of groups. Paraphyletic groups contain an ancestral species and some, but no all, of its descendants. For example, the pre-Hennigian concept of Reptilia included lizards, snakes, turtles, crocodiles and dinosaurs, but excluded birds.

Group that do not contain the common ancestor are termed polyphyletic groups. No one advocated polyphyletic groups. The controversy that ensued was over the nature of paraphyletic groups. Before Hennig, such groups were considered to be monophyletic groups. But to Hennig, such "incomplete" groups were as artificial as polyphyletic groups.

The problem was that there were and continue to be many well-loved and familiar paraphyletic groups. Reptilia without Aves is paraphyletic.

Pongidae without humans is paraphyletic. Try again later. Citations per year.

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Using the logical basis of phylogenetics as the framework for teaching biology

New citations to this author. New articles related to this author's research. Email address for updates. My profile My library Metrics Alerts. Sign in. Get my own profile Cited by View all All Since Citations h-index 41 23 iindex 85 Co-authors View all Jonathan R. Ed Wiley University of Kansas Verified email at suddenlink. Erin E.