See below for background information on how to do the assignment. Answers are given below the instructions.

The plastic bag contains 6 specimens representing 6 species of extinct organisms. You should work out the following:

• A data table listing characters of these species that you can use for classifying them (spread sheet format: names of species along one axis, characters along the other)
• A cladogram; all nodes should be labeled with the character that is present in all descendant species. Use same format as shown below in figure 1.
• A Venn diagram as shown below.

You can take the bag with specimens home, and hand in the assignment next class (Friday September 26) .

How to do it (see also below for more detailed instruction):

Start by listing characters that all individuals share, the shared inherited characters, which are typical for the whole group. Then find out which character(s) is/are shared by all except one species. That one species is the 'outgroup'. The others then should be subdivided by finding out which ones share the most characters, which ones the least.

BACKGROUND INFORMATION: HOW TO CLASSIFY SPECIES??

Until the 1960s, there was little discussion about the way in which to do taxonomy (naming of species): people described species, and except for sexually-reproducing, living taxa where it could be tested whether individuals actually interbreed, species were groups of organisms who were 'similar to each other', and were judged to be more similar to each other than to other groups. Such judgments are of course subjective, and dissatisfaction with conventional taxonomy grew. Taxonomy was seen increasingly as an 'art', difficult to transfer from one person to another, and heavily influenced by personal subjectivity. Since the 1960s much effort has concentrated on trying to make the business of taxonomy less subjective and more quantitative.

Since the 1960s a major upheaval has been occurring in the world of taxonomy and phylogenetic studies, and thus the way in which people classify organisms. Your textbook reflects this new mode of classification (e.g., pages 60-61), termed cladistics. After many extremely acrimonious discussions cladistics is now the standard way of dealing with relations between living organisms as well as with relations between living and fossil organisms. The first person to argue for this methods was a German called Willi Hennig, with a first publication in 1950 but a more extensive work published in 1966. Unfortunately he burdened the new field with many obscure terms and long jargon-words, making the field rather inaccessible to new comers. The basic principle of cladistics is that classification should reflect ONLY evolutionary history and ignore overall morphological similarity unless that similarity reflects close family relationships.

Cladists use computers a lot, and argue that, for a given problem, some characters observed in an organism (whether the character is some thing such as length, or genetic information does not matter) are much more useful than others. Specifically, we should look for characters that are shared within a group, but absent in other groups. For instance, the group mammals has hair and mammary glands and live-born young and a specific structure of the lower jaw and ear bones as shared characters. Such characters are called shared, derived characters (synapomorphies in cladistic language), because the ancestors of mammals did not have these characters, but all the mammals do. On the other hand, characters such as 'having four legs', 'presence of back bone', are characters that all mammals share, but they also share these with many other animals, and they inherited them from their ancestors (such characters are called symplesiomorphies in cladistic-speech: shared, primitive characters). In a study of classification of mammals, the characters shared by all mammals and inherited from their ancestors are useless because they will not show variations within the group of mammals; the characters we need to use are the evolutionary novelties that reflect evolution of various groups.

Note that the judgment whether a character is inherited or derived varies with each problem studied, and depends on what exactly is being studied. For instance, if we look at classification within the mammals, hair is a primitive character and not very useful for deciding how family relation lie within the group of mammals; it is a useful character if we are comparing mammals with other groups of vertebrates.

The working hypothesis of the cladists is the cladogram, a figure in which the characters are plotted for each group under study. The names of the groups are placed at the tips of branching lines, and the branching shows which taxa are most closely related to each other. Groups that are most closely related are called sister groups. The fork of each branch is called the node, and represents the character of the common ancestor of taxa. This node is given by the shared derived characters that all groups originating from that node share.

To make a cladogram, each character must be judged by the cladist: is it primitive or derived? This is most commonly done by trying to find out what more primitive relatives of group are like; such primitive relatives are called the outgroup. For instance, if we look at vertebrates that are not mammals, we see that vertebrae and four limbs are primitive characters: ancestors of mammals had these characters.

Note that in a cladogram all groups put together as sister groups MUST have the same shared, derived characters, and no other group must have these characters. Also note, that ancestors must plot in a group with all their descendant groups. Such a group containing an ancestor and all its descendants is called a monophyletic group. A group containing descendants from various ancestors is called polyphyletic; a groups excluding some descendants is called paraphyletic. The aim is to develop a cladogram with monophyletic groups. Groups placed more closely together in the cladogram are more closely related.

In the real, complex world commonly more than one cladogram can be constructed from existing data using the above rules. The more parsimonious (=simpler) cladogram should be preferred.

So to make your cladogram you do the following

• Select your group of organisms (you use all six specimens); give each some name or number so that you recognize it.
• Determine the characters (make the matrix of things you can see on these specimens; see figure 1 below)
• Determine whether each character is original for that specimen, or derived (present in ancestors). You do that by comparing it with an 'outgroup' (one of your specimens belongs to an outgroup), which preserves 'primitive' characters. You could also compare it to a fossil relative. You also assume that any charcater shared by all specimens in a group is inherited from an ancestor.
• Group your specimens so that specimens having shared, derived characters fall within one group
• Work out conflicts in grouping
• Build cladogram as follows:
  • All taxa names go to the ends of branches, NOT to nodes.
  • All nodes must have a list of the shared derived characters that all specimens listed at the ends of its branches share (unless modified later).
  • All shared derived characters must show up only once, unless you want to say that the character evolved several times independently (not probable).

Note that the first two columns list characters shared by all specimens, and thus must be primitive, shared and derived from an ancestor. The third column (ridge) shows that A differs from all others in its lack of pronounced ridges and flat head: two major characters. We thus assume that A is the outgroup, showing as close as possible what the ancestor of the whole group looked like. We then use the remaining characters to subdivide B through F. We have a choice whether to use color as our first, most important character, or use 'top head' as our first, most important character; we can not use both at the same time. Both choices lead to a consistent cladogram (see below). Note that in the first option, the color grey is ancertsal, and black has to evolve twice: one to lead to C, once to lead to D, E and F. In cladogram 2, however, the two species with a square indent on the head are not very closely related, with the species 'black, square indent' being more closely related to the several species that are 'black, cross head' than to the species 'grey, square head'. Several people hit upon another possiblity, a variant on the first cladogram: one can have the cross-head type branch off first. This can be done, but if you say that the head indent is the most important character, then the three cross-heads need to be on one side-branch , and not diverge from the main stem one by one (if they do, they would be a parapletic group, as 'fish' in figure 1, above).

We wanted to see all nodes labeled.

	SHAPE 1	HEAD	RIDGE	COLOR	TOP HEAD	RIDGES	LENGTH
A	LONG, THIN	ROUND	WEAK	GREY	FLAT		MEDIUM
B	LONG, THIN	ROUND	STRONG	GREY	SQUARE	WIDE	MEDIUM
C	LONG, THIN	ROUND	STRONG	BLACK	SQUARE	WIDE	SHORT
D	LONG, THIN	ROUND	STRONG	BLACK	CROSS	NARROW	LONG
E	LONG, THIN	ROUND	STRONG	BLACK	CROSS	WIDE	SHORT
F	LONG, THIN	ROUND	STRONG	BLACK	CROSS	WIDE	LONG

Note that the so-called 'convergent evolution' may result in superficially very similar looking organisms: living in a specific niche means, after all, that some shapes work better than other. A water-dwelling, fast-moving organism will work much better if it has the smooth torpedo shape of fish, dolphins and the extinct reptile Ichtyosaurus. Natural selection thus tends to influence the shape of an organisms so as to optimize how it works - and organisms that live in similar ways will obtain a similar (well-adapted) morphology, even if their basic structure is very different. We thus need to investigate very carefully whether a specific morphology reflects similar use, or similar basic structure.