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All life on Earth is united by evolutionary history; we are all evolutionary cousins — twigs on the tree of life. Phylogenetic systematics is the formal name for the field within biology that reconstructs evolutionary history and studies the patterns of relationships among organisms. Unfortunately, history is not something we can see. It has only happened once and only leaves behind clues as to what happened. Systematists use these clues to try to reconstruct evolutionary history.
Reading trees: A quick review
A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two descendents that split from the same node are called sister groups. In the tree below, species A & B are sister groups — they are each other's closest relatives. Many phylogenies also include an outgroup — a taxon outside the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees.
Evolutionary trees depict clades. A clade is a group of organisms that includes an ancestor and all descendants of that ancestor. You can think of a clade as a branch on the tree of life. Some examples of clades are shown on the tree below.
This site. or time. The words "phylogram" and "dendrogram" are also sometimes used to mean the same sort of thing with slight variations. whether the phylogeny represents a reconstructed hypothesis about the history or the organisms or an actual record of that history. nodes with more descendent lineages. To other biologists. a phylogenetic tree. one sees phylogenies that include polytomies. and E. "cladogram" suggests that the lengths of the branches in the diagram are arbitrary. These vocabulary differences are subtle and are not consistently used within the biological community. some biologists do use these words in more specific ways. For our purposes here. To some biologists. along with many biologists. the important things to remember are that organisms are related and that we can represent those relationships (and our hypotheses about them) with tree structures. There are many ways that the polytomy above could be resolved. D. creating a "pitchfork. an evolutionary tree." the branch lengths indicate the amount of character change. whether the tree's branch lengths represent nothing at all. Six are shown below." This can mean one of two things: • than two Lack of knowledge Usually. a polytomy means that we don't have enough data to figure out how those lineages are related. The context in which the term is used will tell you more details about the representation (e.g. use these terms interchangeably — all of them essentially mean a tree structure that represents the evolutionary relationships within a group of organisms.. use of the term "cladogram" emphasizes that the diagram represents a hypothesis about the actual evolutionary history of a group. . while "phylogenies" represent true evolutionary history.) However. Reading trees: Phylogenetic pitchforks Often. etc. genetic differences. C. not much. the scientists who produced the phylogeny are telling you not to draw any conclusions — and also to stay tuned: often gathering more data can resolve a polytomy.What's the difference between a phylogeny. while in a "phylogeny. B. and a cladogram? For general purposes. By not resolving that node. Only more data can help us decide which is the most accurate representation of the relationships between A.
phylogenetic classification names only clades. resulting in several phylogenetic polytomies. Advantages of phylogenetic classification Phylogenetic classification has two main advantages over the Linnaean system. For example. the phylogeny of these organisms reveals that the bird lineage actually branches off of the dinosaur lineage. Cichlid fish speciated quickly after their home lakes formed in Africa. a strictly Linnaean system of classification might place the birds and the nonAvian dinosaurs into two separate groups.Rapid speciation Sometimes a polytomy means that multiple speciation events happened at the same time. all the daughter lineages are equally closely related to one another. In contrast to the traditional Linnaean system of classification. phylogenetic classification does not attempt to "rank" . in phylogenetic classification. the birds should be considered a part of the group Dinosauria. which conveys the same sort of information that is conveyed by trees. phylogenetic classification tells you something important about the organism: its evolutionary history. and so. Biologists are taking advantage of this by using a system of phylogenetic classification. The phylogeny below shows the relationships among the members of a group of fish called cichlids. The researchers who have reconstructed the tree you are examining should tell you if they feel that the evidence indicates that this is the case. evolutionary trees convey a lot of information about a group's evolutionary history. First. Second. However. Using trees for classification Clearly. In this case.
For example. However. However.000 orchid species. Many orchids belonging to different genera are able to hybridize. Reconstructing trees: Cladistics . is also used as a phylogenetic name. There are about 35 cat species and 20. For example. phyla. Most of the specific names that you are accustomed to using (e. So it seems that there are many good reasons to switch to phylogenetic classification. Drosophila melanogaster) have not changed at all with the rise of phylogenetic classification.organisms. This means that your use of biological names doesn't have to change very much. the Linnaean system is misleading. How are biologists making the transition to phylogenetic classification? Switching to phylogenetic classification Biologists deal with phylogenetic classification by de-emphasizing ranks and by reassigning names so that they are only applied to clades. while the first orchids may have lived more than 100 million years ago. which is the class of birds in the Linnaean system.. since birds form a clade (right). Linnaean classification "ranks" groups of organisms artificially into kingdoms. But the same is not true of cats — house cats (belonging to the genus Felis) and lions (belonging to the genus Panthera) cannot form hybrids. This can be misleading as it seems to suggest that different groupings with the same rank are equivalent. Aves. Homo sapiens.g. The first representatives of the cat family Felidae probably lived about 30 million years ago. However. there are some names from Linnaean classification that do NOT work in a phylogenetic classification. In many cases. the reptiles do not form a clade (and cannot be a named group in the phylogenetic system) — unless you count birds as members of Reptilia too. the Linnaean names are perfectly good in the phylogenetic system. etc. For example. orders. They have different degrees of biological differentiation. the two groups are not comparable: • • • One has a longer history than the other. There is just no reason to think that any two identically ranked groups are comparable and by suggesting that they are. the cats (Felidae) and the orchids (Orchidaceae) are both family level groups in Linnaean classification. organisms have been named using the Linnaean system for many hundreds of years. The have different levels of diversity.
or traits. which represents a supported hypothesis about the relationships among the organisms. 3. 2. The result of a cladistic analysis is a tree. of the organisms in which we are interested. This assumption is supported by many lines of evidence and essentially means that all life on Earth today is related and shares a common ancestor. However. a method of reconstructing evolutionary trees. pattern of lineage-splitting. It is only when characteristics change that we are able to recognize different lineages or groups. This assumption suggests that when a lineage splits. These characters could be anatomical and physiological characteristics. Because of this. Assumptions There are three basic assumptions in cladistics: 1. The basis of a cladistic analysis is data on the characters. provided we have the right kind of information. or genetic sequences. it is important to keep in mind that the trees that come out of cladistic analyses are only as good as the data that go into them. it divides into exactly two groups. Change in characteristics occurs in lineages over time. we can take any collection of organisms and hypothesize a meaningful pattern of relationships. behaviors. There is a bifurcating. New and better data could change the outcome of a cladistic analysis. supporting a different hypothesis about the way that the organisms are related. We call the "original" state of the characteristic plesiomorphic and the "changed" state apomorphic.Cladistics is a method of hypothesizing relationships among organisms — in other words. or branching. Any group of organisms is related by descent from a common ancestor. . The assumption that characteristics of organisms change over time is the most important one in cladistics.
as they have evolved.There are some situations that violate this assumption. the plesiomorphic characteristic is "has legs" and the apomorphic characteristic is "doesn't have legs. What about primitive and derived characters? You might hear people use the term "primitive" instead of plesiomorphic and "derived" instead of apomorphic. We often think of primitive things as being simpler and inferior — but in many cases the original (or plesiomorphic) state of a character is more complex than the changed (or apomorphic state). For example. or near enough in time to be indistinguishable from such an event (as in the case of the cichlid fish described previously). many biologists accept the idea that multiple new lineages have arisen from a single originating population at the same time. The other objection raised against this assumption is the possibility of interbreeding between distinct groups. For example. However. which occurs at least occasionally in some groups (like plants)." . for many groups they are relatively rare and so this assumption often holds true. many biologists avoid using these words because they have inaccurate connotations. While such exceptions may exist. In the case of snakes. many animals have lost complex traits (like vision and limbs).