Phylogenetic trees

systematics,

a.k.a.

evolutionary

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.

What's the difference between a phylogeny, an evolutionary tree, a phylogenetic tree, and a cladogram? For general purposes, not much. This site, along with many biologists, use these terms interchangeably all of them essentially mean a tree structure that represents the evolutionary relationships within a group of organisms. The context in which the term is used will tell you more details about the representation (e.g., whether the tree's branch lengths represent nothing at all, genetic differences, or time; whether the phylogeny represents a reconstructed hypothesis about the history or the organisms or an actual record of that history; etc.) However, some biologists do use these words in more specific ways. To some biologists, 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. To other biologists, "cladogram" suggests that the lengths of the branches in the diagram are arbitrary, while in a "phylogeny," the branch lengths indicate the amount of character change. The words "phylogram" and "dendrogram" are also sometimes used to mean the same sort of thing with slight variations. These vocabulary differences are subtle and are not consistently used within the biological community. For our purposes here, 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.

Reading trees: Phylogenetic pitchforks

Often, one sees phylogenies that include polytomies, nodes with more descendent lineages, creating a "pitchfork." 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. By not resolving that node, 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.

There are many ways that the polytomy above could be resolved. Six are shown below. Only more data can help us decide which is the most accurate representation of the relationships between A, B, C, D, and E.

Rapid speciation Sometimes a polytomy means that multiple speciation events happened at the same time. In this case, all the daughter lineages are equally closely related to one another. 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. The phylogeny below shows the relationships among the members of a group of fish called cichlids. Cichlid fish speciated quickly after their home lakes formed in Africa, resulting in several phylogenetic polytomies.

Using trees for classification

Clearly, evolutionary trees convey a lot of information about a group's evolutionary history. Biologists are taking advantage of this by using a system of phylogenetic classification, which conveys the same sort of information that is conveyed by trees. In contrast to the traditional Linnaean system of classification, phylogenetic classification names only clades. For example, a strictly Linnaean system of classification might place the birds and the nonAvian dinosaurs into two separate groups. However, the phylogeny of these organisms reveals that the bird lineage actually branches off of the dinosaur lineage, and so, in phylogenetic classification, the birds should be considered a part of the group Dinosauria.

Advantages

of

phylogenetic

classification

Phylogenetic classification has two main advantages over the Linnaean system. First, phylogenetic classification tells you something important about the organism: its evolutionary history. Second, phylogenetic classification does not attempt to "rank"

organisms. Linnaean classification "ranks" groups of organisms artificially into kingdoms, phyla, orders, etc. This can be misleading as it seems to suggest that different groupings with the same rank are equivalent. For example, the cats (Felidae) and the orchids (Orchidaceae) are both family level groups in Linnaean classification. However, the two groups are not comparable: One has a longer history than the other. The first representatives of the cat family Felidae probably lived about 30 million years ago, while the first orchids may have lived more than 100 million years ago. The have different levels of diversity. There are about 35 cat species and 20,000 orchid species. They have different degrees of biological differentiation. Many orchids belonging to different genera are able to hybridize. 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.

There is just no reason to think that any two identically ranked groups are comparable and by suggesting that they are, the Linnaean system is misleading. So it seems that there are many good reasons to switch to phylogenetic classification. However, organisms have been named using the Linnaean system for many hundreds of years. 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. This means that your use of biological names doesn't have to change very much. In many cases, the Linnaean names are perfectly good in the phylogenetic system. For example, Aves, which is the class of birds in the Linnaean system, is also used as a phylogenetic name, since birds form a clade (right). Most of the specific names that you are accustomed to using (e.g., Homo sapiens, Drosophila melanogaster) have not changed at all with the rise of phylogenetic classification. However, there are some names from Linnaean classification that do NOT work in a phylogenetic classification. For example, 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.

Reconstructing trees: Cladistics

Cladistics is a method of hypothesizing relationships among organisms in other words, a method of reconstructing evolutionary trees. The basis of a cladistic analysis is data on the characters, or traits, of the organisms in which we are interested. These characters could be anatomical and physiological characteristics, behaviors, or genetic sequences. The result of a cladistic analysis is a tree, which represents a supported hypothesis about the relationships among the organisms. However, 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. New and better data could change the outcome of a cladistic analysis, supporting a different hypothesis about the way that the organisms are related.

Assumptions
There are three basic assumptions in cladistics: 1. Change in characteristics occurs in lineages over time. The assumption that characteristics of organisms change over time is the most important one in cladistics. It is only when characteristics change that we are able to recognize different lineages or groups. We call the "original" state of the characteristic plesiomorphic and the "changed" state apomorphic.

2. Any group of organisms is related by descent from a common ancestor. 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. Because of this, we can take any collection of organisms and hypothesize a meaningful pattern of relationships, provided we have the right kind of information.

3. There is a bifurcating, or branching, pattern of lineage-splitting. This assumption suggests that when a lineage splits, it divides into exactly two groups.

There are some situations that violate this assumption. For example, many biologists accept the idea that multiple new lineages have arisen from a single originating population at the same time, or near enough in time to be indistinguishable from such an event (as in the case of the cichlid fish described previously). The other objection raised against this assumption is the possibility of interbreeding between distinct groups, which occurs at least occasionally in some groups (like plants). While such exceptions may exist, for many groups they are relatively rare and so this assumption often holds true. What about primitive and derived characters? You might hear people use the term "primitive" instead of plesiomorphic and "derived" instead of apomorphic. However, many biologists avoid using these words because they have inaccurate connotations. 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, as they have evolved, many animals have lost complex traits (like vision and limbs). In the case of snakes, the plesiomorphic characteristic is "has legs" and the apomorphic characteristic is "doesn't have legs."