Introduction to Interpreting Evolutionary Trees and Related Vocabulary

Introduction to interpreting evolutionary trees and related vocabulary One of Darwin's contributions was to depict the diversification of life using an evolutionary tree, or phylogeny. Let's start with the example shown in the phylogeny below. 1. Various lineages of organisms are descended from common ancestors. In the example, birds share a common ancestor with dinosaurs and then those two groups collectively share a more remote common ancestor with crocodiles, and those three collectively share an even more remote common ancestor with lizards plus snakes, which diverged from each other subsequently. These parts of this tree are well known. Others parts of the tree are still poorly known. Some data suggest that mammals diverged before the radiation of reptiles (turtles through dinosaurs on the phylogeny), while other data suggest that turtles or {lizards+snakes} diverged first. From here on, we'll assume mammals diverged first, then turtles, then the {lizard+snake} branch. turtles lizards snakes crocodiles dinosaurs birds mammals 2. It is often helpful to map character changes Character 1 2 on a phylogeny. As examples, consider two A C characters: 1. having continuous skull bone between the eye and the nostril (A) versus A C having an opening in that place (B); and 2. coldbloodedness (C) versus warmbloodedness (W). Character evolution A C is reconstructed on the phylogeny shown to the right. To do this, one looks for a branch B C in the tree where a change in character would 1 explain the distribution of character states in B ? all the taxa. For character 1, there is a single place in the tree, marked with a solid bar 2 ? labeled 1: a change from no opening to B W 2 having an opening along this lineage and inheritance of the opening in all descendants above this point would result in crocodiles, A W dinosaurs and birds having the opening. The opening is a shared derived character, or synapomorphy, of the group {crocodiles+dinosaurs+birds}. With some characters it is not possible to explain the character distribution with a single change. For character 2, two changes are required: warmbloodedness evolved in both the lineage leading to mammals and the lineage leading to birds. Since we do not know whether dinosaurs were warmblooded or not (just from these data), we can't say whether turtles lizards snakes crocodiles dinosaurs birds mammals warmbloodnessness arose before the dinosaur-bird split or afterwards. At any rate, it seems there was convergent evolution in warmbloodedness. The following words are essential vocabulary for speaking of character evolution. homology – a character that is similar due to common ancestry synapomorphy – shared derived character, e.g., being on land for tetrapods symplesiomorphy – shared ancestral character, e.g., being in the water for fishes + sharks homoplasy – a similarity between two kinds of organisms that is not due to common ancestry convergence – separate evolution in different lineages of a feature that ends up being similar reversal – changing back to a previous state One can use phylogenies to judge whether a similarity should be interpreted as a homology or a homoplasy, and (less easily) whether a homoplasy should be interpreted as a convergence or a reversal. The most frequently used criterion for making these judgments is parsimony, which in this context means choosing the explanation that requires the fewest changes in character state. 3. Parsimony is also the most frequently used criterion for judging among various possible trees: one choose the tree that requires the fewest steps, i.e., the smallest number of changes in state for all the characters used to infer the tree. There are many other methods for phylogenetic inference, most notably various maximum likelihood methods that model the processes of molecular evolution. If there were no homoplasy, inferring the tree would be easy (the similarities would tell you directly which trees were possible), but before you have the tree you cannot tell which similarities are homologies and which are homoplastic. The solution is to get a large number of presumably independent characters and go with the preponderance of evidence on the argument that common ancestry is the cause that most coordinates nested patterns of similarity. 4. Branching pattern (the sequence of common ancestors) does not necessarily represent overall similarity or relative difference. Overall similarity can be inflated due to convergent evolution, and when rates of evolution are unequal some lineages may diverge while others remain relatively similar. In the diagram below, the lineage that led to {C+D} diverged radically, while the lineages leading to A and to B remained static. AB C D AB C D Notice on the right that one might well group A and B together, although their most recent common ancestor is more remote than the common ancestor of B and {C+D}. In our previous example, the birds have evolved physiologically and anatomically very far (some would say) from the living reptiles (turtles though crocodiles). A group that contains a common ancestor and all of its descendants is monophyletic; it’s a whole branch of the tree of life. A group that excludes some of the descendants of its common ancestor is paraphyletic; {A+B} is paraphyletic by the exclusion of {C+D}. Traditional taxonomy was not developed based on a rigorous knowledge of phylogeny, so taxa (classes like Reptilia, orders, families, genera, etc.) cannot be presumed to be monophyletic. Cladistics refers to branching pattern. Someone who argues that taxonomy should be revised to only recognize monophyletic groups is a “cladist.” Phenetics refers to overall similarity. Phyletics refers to the length of branches on the phylogeny. 5. There is free rotation around any node. turtles turtles birds lizards dinosaurs snakes crocodiles crocodiles snakes dinosaurs lizards birds mammals mammals This means you have to be careful when viewing large complicated trees. They may look different but convey the same branching pattern. 6. Phylogenies can be based on morphology, or molecules, or combinations of data sets. Morphology might sometimes be very helpful if complex structures tend to evolve when groups-to-be are formed and then somehow become locked in place and made to be conservative. Phylogenetic conservatism is a prominent feature of biodiversity. Nevertheless, in principle one can get very large amounts of information by using molecular markers, so at present molecular approaches are adding greatly to our resolution of the tree of life. 7. Fossils can be included in a phylogenetic reconstruction. Since generally DNA cannot be gotten from fossils, fossils are probably best used in conjunction with a phylogeny whose superstructure is based on extant organisms. The value of adding fossils is much like the value of adding additional extant organisms. We could have inferred the relationships of birds, lizards, and mammals without knowing about crocodiles, but adding crocodiles tells us a bit more about the transition. Crocodiles are a link between lizards and birds. Dinosaurs are another link. When one finds a new link, one can add that “missing link”, and it improves one’s inferences about the branching pattern and about character evolution. The one way in which adding fossils is not just like adding an extant missing link, is that they allow one to date the appearance and disappearance of forms in the fossil record. 8. Methods such as parsimony can be used to infer branching pattern without rooting the tree. Rooting is done by outgroup comparison, by referring to organisms that are thought to be (just) outside one’s focal group, sharing a most recent common ancestor with the focal group that is more remote than the most recent common ancestors of all the species within the group. To know that one’s outgroups are not part of one’s focal group, someone must have already done at least a crude phylogenetic analysis of the larger group. By stepping inward, obvious relationships can be used in conjunction with more character data to resolve closer and closer relationships. 9. Although we can infer a great deal of the tree of life, we are very far from having complete resolution.