The Life System and Environmental & Evolutionary Biology II EESC V2300y / ENVB W2002y Laboratory 1 (01/28/03) Systematics and Taxonomy 1
SYNOPSIS In this lab we will give an overview of the methodology of biological systematics and taxonomy by using real techniques on a series of non-biological taxa nails and screws. We do this so we don t get bogged down in getting the right answer for real taxa or complex morphological nomenclature. We will: 1) look at the evolutionary relationships with cladistic techniques. 2) develop a taxonomic classification based on this method. 3) examine a key in a field guide. INTRODUCTION Systematics and taxonomy are venerable names for the human penchant to classify things into groups. Biological systematics is the study of order in biological diversity and its evolution. Taxonomy, a subdivision of systematics, is the science of biological classification and identification. In fact, it is the profound order that is apparent when different organisms are compared that give special meaning to systematic so that the exercise has more meaning than arranging postage stamps. The study of systematics long predates Darwin or any evolutionary theory, but ever since Darwin there has been an emphasis on systematics that focuses on the evolutionary relationships of organisms. In other words systematics has become the mechanism for unraveling evolutionary history and this history is called a phylogeny. It may come as a surprise to learn that fossils really do not in general provide a series of forms that indicate ancestor-descendent relationships. Instead evolutionary transmutation is inferred from the information inherent within organisms themselves so that it is possible to infer evolutionary history using only living forms (if fossils are lacking). Darwin was an apologist for the fossil record, because at the time, systematic theory predicted a series of intermeadate forms between major groups of organsism, say birds and reptiles, or humans and apes, that simply were not known. Darwin felt that this was a result of a very incomplete fossil record. However the combination of pre-evolutionary systematics and Darwinian evolution predicted quite clearly specifically what intermeadtate forms should look like and which groups they would unite. In other words the groups which would have intermeadiates is highly non-random. On of the most strikingly beautiful things about systematic is in fact that by now so many spectacular and 2
utterly convincing intermeadiate forms have been found, after they were predicted to have existed (despite the wishful thinking of creationsists). Systematic techniques have now matured to a point that the evolutionary history groups ranging in scale from the species level to kingdoms and domains can understood in considerable detail. Taxonomic classifications are produced for specific purposes. A classifications that separates out edible from inedible organisms will tend to be very different from one which proports to reflect evolutionary relationships. Since Darwin, increasing importance has been placed on natural classifications, and this has come to mean classifications that reflect the evolutionary history of the organsisms that are classified. There are however exceptions, most notably in bacterial relationships, where this concept is by no means taken for granted. A key is a device for identifying unknown organisms to some taxonomic level (e.g., species, genus, family, etc.). Keys assume all the taxa in an area of interest (biologically or geographically) are known. The most common type of key is the dichotomous key, which is constructed of a series of couplets, each consisting of two statements describing characteristics of a particular organism or group of organisms. A choice between the two statements is made that best fits the organism in question that leads to yet another pair of choices. The statements typically begin with broad characteristics and become narrower as one proceeds down the sequence of choices. Keys have no necessary logical connection with either a classification (until names are identified) nor do they have a necessary basis in evolutionary relationships. They are very useful, however, in identifying taxa you have never seen before. I. DEVELOP HYPOTHESES OF EVOLUTIONARY RELATIONSHIPS Introduction As you might imagine, all inferences of evolutionary relationships, and hence phylogenies are based on similarity, of which there are two kinds: general similarity and special similarity. Cladistic uses a specific kind of special similarity. Before discussing classtics, however, we need to have a few bits of jargon defined. character: a feature, thing, or measurement we wish to quantatize (as opposed to quantify) for our analysis. Characters can be represented by a description, a name, a picture, or a number. 3
Cladistics homologous character: a character shared by two taxa by their descent from a common ancestor. The main bones of the fore limbs (e.g. humerus) of birds, bats, and pterosaurs (extinct flying relative of dinosaurs) are homologous characters. In other words, the ancestor of birds, bats, and pterosaurs had these bones. analogous characters: a character shared by two taxa because of independent convergent evolution in separate lineages. The wing of birds, bats, and pterosaurs are and analogous character because the common ancestor of birds, bats, and pterosaurs did not have a wing, instead each group developed wings independently. In cladistics, only homologous characters are considered to have information indicative of evolutionary relationships (i.e., special similarity). Characters inherited without change from ancestors are considered to have no information of value to relationships. In cladistics i the meaning of characters and the hypothesis of relationship are iteratively interdependent. In other words, whether or not a character is homologous is defined by the specific hypothesis of relationship between taxa. Each analogous that is a consequence of the specific hypothesis of relationship is cause for an ad hoc explanation. The principle of parsimony dictates that the hyothesis with the least number of ad hoc explanations is the best it is another version of Occam s razor. A cladogram is kind of branching diagram that depicts the sequence that various characters were acquired though time among a group of related organisms. Cladistics can be done using morphological, behavioral, or molecular data on living or fossil taxa. Cladistics is also termed Phylogenetic Systematics or Phylogenetic Taxonomy. How we do Cladistics We will use the cladistic method in this lab since it allows us to build and test relationships based on the distribution of the states of the characters and to build groups by the recognition of shared derived characters, i.e. homologous characters. Cladistics is a process that consists basically of a search for shared derived characters with which to recognize monophyletic groups (groups descended from acommon ancestor included within the group). 4
In this lab we will use nails and screws as proxy organisms firs with diagrams of hypothetical examples, then with real ones. This avoids the potential snags of a complex anatomical nomenclature, or search for the right set of phylogenetic relationships when real organisms are used. The mechanics of the process consists of a set of hypotheses and tests. 1. Construct a hypothesis of relationship for the organisms in question. This hypothesis can come from anywhere, but a good way to begin is to look for a logical set of transformations by lining then up in a row. 2. Choose one of the taxa as an outgroup, it should look like it might be the most primitive form. 3. Define characters that allow you to define groups. 4. Look for the distribution of primitive characters that stand in contrast to the derived characters. 5. Look for unique derived characters that define each of the organisms. 6. Construct a cladogram and hang the distribution of the characters on it. OK - now we have groups defined by shared derived characters and we have our cladogram with our characters. 7. It is now time to test the hypothesis by looking at the characters that could define groups other than the hypothesis in question. These characters are in conflict and must be explained by some ad hoc argument other than simple descent from a common ancestor. If you need more ad hoc arguments to justify your cladogram than you have shared derived characters supporting your cladogram, your cladogram must be discarded. 8. If your cladogram survives this test, the next step is to look for more characters and hang them on your cladogram and see how they fit. 9. If they do not and there are a lot of them, again your hypothesis fails 10. If your hypothesis fails, you must look for a new and better one. 11. Try moving one or more taxa around on your cladogram. See if you get a better result. 12. Your hypothesis may suggest modifications in the characters or additional better characters use them! 13. Once you get a highly corroborated cladogram, identify the monophyletic groups and the shared derived characters that define them. Remember, the cladogram is not an evolutionary tree of ancester-descendent relationships. The branching points reflect the sequence in which characters were aquired. 5
Hypothetical Example (we have selected the outgroup for you). OTHER METHODOLOGIES FOR ASSESSING EVOLUTIONARY RELATIONSHIPs Phenetics In phenetics all characters are more or less equal. Relationships are inferred by the degree of general similarity, which is generally determined numerically and with an algorithm. Today, it is common for molecular data to be analyzed phenetically. A branching diagram called a phenogram is often used to depict the phenetic relationships, in which the lengths of the branches denote the distance between taxa. Hypotheses of relationship are a consequence of the preponderance of similarity between taxa as estimated from the characters via the specific algorithm. Different algorithms can give different results for the same data. Phenetics can be done using morphological, behavioral, or molecular data on living or fossil taxa. Phenetics is also called Numerical Taxonomy. While this method may seem more objective, in fact the results are strongly biased by primitive characters and while the clusters so produced may quite stables, they generally tell little about evolutionary relationships, unless the data are a significant part of the organisms genome. 6
Evolutionary Systematics In Evolutionary Systematics a hypothesis of relationship is primarily based on ancestor-descendant relationships. These relationships are generally (but not necessarily) determined by general similarity, of temporally closely spaced fossils assumed to comprise a lineage. Relationships are expressed by an evolutionary tree in which all branches are considered to be lineages of ancestors and descendants. Neither cladograms or phenograms are evolutionary trees. Evolutionary Systematics can only be done with fossil or real-time data or with the assumption that some living taxa are representative of ancient ones (i.e., that a living taxon could be ancestral to another living taxon. II. CONSTRUCT A TAXONOMIC CLASSIFICATION Using the two cladograms from the above exercise, produce a classification (inclusive hierarchy) for one of the taxa in each. Give the taxa names. III. Examination of a field guide key, Look over and analyze the attached key. Imagine keying out a species of mushroom using it. The following and the key are extracted from: Lange, M. and Hora, F. B., 1963, A guide to Mushrooms and Toadstools, E. P. Dalton & Co., 257 p. While this guide is intended for lap persons, the methodology employed is exactly the same in technical identification keys. Questions: 1. What are some of the problems with using this kind of key. 2. What are the principle advantages of using this key. 7
USE OF THE KEY The Key should present no difficulties to those familiar with the usual dichotomous (paired, contrasted characters) type. First the fungi are divided into six main divisions on the basis of fruit-body shape, and then, within each division, subsequent dichotomies lead for most divisions to a genus. The species is then determined with the help of the illustrations and descriptions. After a little experience, the main divisions can be spotted on sight. In the Agaric division (Key A), it is also necessary to know the colour of spores in the mass, i.e. from a thick spore print on white paper. For those unfamiliar with the dichotomous type of key, it may be pointed out that at each stage, two sets of contrasted characters are given and the appropriate one followed on; or, sometimes, one set of characters only is given. The alternative being "not so" or "otherwise. For example: 13. Red, densely scaly, 14 13. Otherwise, 15 If the fungus under consideration s both red and densely scaly, one would proceed to the next set of characters under 14; if the fungus was red and smooth or brown and densely scaly, one would then go to 15. Where two sets of contrasted characters are given, only that set is chosen which is wholly applicable. Thus: 15. Brown, flesh thick, on wood, 16 15. Brown or reddish violet, on soil, 17 If the fungus is brown and thick-fleshed but grows on soil, one would take the second set of characters because "Brown or reddish violet, on soil" is wholly applicable. If neither of the alternatives apply, it is possible that one may have slipped up at an earlier point in the Key, or the specimen under consideration may be abnormal or it may be an excluded species of unusual characters not covered by the Key. 8