LAB 2

Chapter 4: Principles of Classification and Systematics

Feel free to discuss this and other assignments with other students in the class. You can learn as much from them as you can from the TA and myself (sometimes). Reconstructing phylogenetic relationships and assigning species to higher taxa on the basis of those relationships is one of the primary goals of many paleobiologists. This exercise is designed to give you practice in the use of taxonomy and phylogenetic systematics ("cladistics").

4.1 Introduction to Systematics

If it were not for taxonomy and sytematics, our understanding of the relationships among living things would be formless and chaotic. Taxonomic classification provides the hangers on which we organize our knowledge of morphology and express hypotheses of relationships. The classification system that we use today was established by Carolus Linnaeus, a Swedish biologist, in the 18th century. It provides a hierarchy of categories used to classify each living organism. From the largest (most inclusive) to the smallest (least inclusive), these categories include:

Order of Hierarchy

Mnemonic (memorization device)

Kingdom

Kings

    Phylum

    Play

        Class

        Chess

            Order

            On

                Family

                Funny

                    Genus

                    Green

                        species

                        squares

 

 

In our studies of the actual organisms, we will focus mainly on the higher categories of phylum and class. We will deal with lower levels, such as specific genera and species principally when a specific one helps illustrate some important concepts (otherwise the names just get too numerous!). In order to keep information organized however, you will need to remember the order of this hierarchy. One way to memorize the order of these categories is to use a mnemonic such as the one above, or, if you prefer, make one up yourself.

4.1.1 Species Concepts and Binomial Nomenclature

Linneaus established in his taxonomy a system of binomial nomeclature, in which every living organism has a binomial ("two-part name") consisting of its genus name and species name, in that order. The best-known example of a binomial is Homo sapiens, the genus and species to which modern humans belong. The first letter of a genus name is always capitalized; the species name is never capitalized, and it never appears without the generic name or its initial (i.e. Homo sapiens or H. sapiens). Both names must have a certain Latin form and, for this reason, are underlined or italicized. All countries use both binomial nomenclature and the hierarchy of categories established by Linneaus (sub-categories are also often added); this makes it possible for systematists around the world to use a common system of names, regardless of their native language. If this seems odd, stop and imagine, for just a moment, what would happen if we all had to memorize a taxonomic name in all its possible translated forms. Can you imagine the confusion and extra names that might result? (It sometimes happens anyways)

For students, learning classification is one of the first steps toward sorting out the many new names and morphological characters that appear each lesson. At least at first, students usually prefer that classification remains as unchanging as possible. After all, who wants to see five alternate classifications, when one is coomplicated enough? Systematists, however, are part of a dynamic science for which an unchanging classification would represent a lack of progress in understanding the organisms they study. Both new evidence, such as new fossil discoveries, and new approaches constantly change our way of looking at relationships.

One of the most important changes in systematic thinking in recent years has been a shift to the use of phylogenetic systematics or "cladistics", as some people call it. According to phylogenetic systematics, whose philosophical father was a German entomologist named Willi Hennig, classification should always reflect evolutionary relationships of the organisms involved. Hennig's recommendation may sound obvious, but in fact most classifications were not-and many still are not-constructed strictly on the basis of evolutionary relationship.

4.1.2 Taxonomy vs. Systematics

Systematics is not taxonomy (and vice versa). Taxonomy is merely the classification and naming of organisms. It is not necessarily dependent on systematics, but most people agree that it should be. Grouping organisms according to the extent to which they are related is the most logical method, but other (subjective and somewhat less logical) methods have also been used.  Taxonomy is useful for identifying and discussing organisms. Systematics is a scientific discipline in its own right.

4.1.3 Phylogenetic Systematics

Phylogenetics is a method for determining the evolutionary relationships of organisms. The goal is to try to understand which organisms are most closely related to each other. This is accomplished by comparing ancestors and descendants.

4.1.3a How does it work? Trees . . .

Evolutionary relationships are represented by phylogenetic trees (a.k.a. phylogenies). In this section you will become familiar with the terminology used to describe phylogenetic trees and the relationships of the organisms in the phylogeny.

How this is different from taxonomy?  Taxonomy is merely the naming and classification of organisms (Remember: Kingdom, Phylum, Class, Order, Genus, Species).  Phylogenies, on the other hand, give paleobiologists valuable information about the relationship between an ancestor and its descendents.  It provides a hypothesis for the evolution of related organisms.

Figure 4.1  An example of a phylogenetic tree.  This phylogeny indicates that a horse and whale share a common ancestor  (implied by the node B’).  They are more closely related to each other than either is to the trout.  However, the horse, whale and trout are distantly related because they share an ancestor at node A’ (from Lucas,2000).

 

 

 

Tree terminology….

Indicate that there has been a change in character state
 

Nodes=

    Branch

     Points
 

Terminal

Taxa
 

TIME
 

PRESENT

 
 

PAST
 
                            

 

 

 

 

 

 

 

POLYPHYLETIC
 
Groups on a phylogenetic tree:

 

PARAPHYLETIC
 

MONOPHYLETIC
 
                           

A monophyletic group is often called a clade. It includes an ancestor and all of its descendants .

 

A polyphyletic group is one that is derived from many ancestors.

 

A paraphyletic group is one that includes the ancestor, but not all of its descendants.

 

Sister groups share a common ancestor and are each other's closest relatives.

(For example, D&E and B&C in the above figure)

 

 

 

 

 

 

 

 

 

 

 

 

 

4.2 Excercises

 

4.2.1 Questions

 

Use the tree below to answer the following questions.

 

 

 

 

 

G
 

F
 

E
 

D
 

C
 

B
 

A
 
                      

 

 

 

1. Circle those which are monophyletic groups:

ABC           CDE           EF           EFG           ABCD           BCEF           DEFG          

2. Which pairs are more closely related? (circle the right answer)

AB or BC           CD or EF           EF or DG           AB or EF          

3. AB is the sister group to? _________

4. D is the sister group to? _________

 

 

 

 

 

4.2.2 Characters

The study of phylogenetics groups organisms into groups (clades, as you learned earlier). A clade represents an ancestor and all of its descendants. Clades are united by shared derived characters (synapomorphies). But what is a character?

A character is any definite aspect of a particular organism. This means that any organism can have an almost infinite number of characters. So which ones do we use? Put another way, what makes a character appropriate for use in phylogenetic systematics?

At this time, the best characters are discrete characters. Discrete characters have a limited number of possible values. Discrete characters can either be binary or multistate. Binary characters are those that only have two states, like Present/Absent. For example, the ability to roll ones tongue is either Present or Absent. Or, a beetle may be colored either yellow or blue. Multistate characters on the other hand, have more than two states. For example, eye color can either be blue, brown or green, that's three character states.

Continuous characters such as size, are measurements on a continuous scale, and they are very hard to use. For example, the length of a femur can be 10.1cm, 12 cm, 10.4cm, 11.2cm, etc. The problem is, "Are these sizes "different enough" to group into separate groups? Or "similar enough" to group into the same group?" What is "different" and "similar" when it comes to size? These terms are very subjective and therefore, they will not help us to define any groups.

 

4.2.3 Coding Characters

The easiest way to do this is to create a code for the characters and their various character states and to use that information to make a character matrix.

Try this out with the example on the next page. If you get stuck, be sure to ask for help. Wait for the rest of the class. We'll go over these characters together.

 

 

 

 

 

 

4.2.4 Character Terminology

An apomorphy is a derived character that is shared by all of the members of a clade, but is not possessed by the immediate ancestors of the clade. If a character is shared by more than one of the descendants, it is called a synapomorphy, or a shared derived character. If a character is possessed by only one descendant, it is termed an autapomorphy.

A plesiomorphy is an ancestral character. It is a character that is possessed by an ancestor and, possibly, any of its descendants. Basically, shared ancestral characters (synplesiomorphies) are not useful in phylogenetic reconstruction. For example, it would be folly to use "lungs" as a character for grouping all primates because lungs arose much farther back in the tree of life as an adaptation to the colonization of land. Thus, “lungs” is not a derived character at the level of primates because they evolved in a common ancestor much, much earlier. The way “lungs” can be used as a phylogenetic character is as a shared derived character for lungfish (the first organism to possess lungs) plus all the other vertebrates related to lungfish that have them (this includes primates).  (Note: “derived” and “primitive” are relative terms).

In addition, shared derived characters that developed convergently are not useful in phylogenetic reconstruction. Many animals have wings: birds, bats, pterosaurs, insects to name a few. Wings however, are made in very different ways in birds, bats etc. They are analogous (similar) but not homologous (having the same genetic and developmental origins), and are therefore described as convergent. These different animals have "converged" in their evolution of similar features. The wings of bats are probably a shared derived feature for bats, but wings in the general sense are developed convergently. Bats are mammals and insects are arthropods, and there is abundant evidence that birds are derived from dinosaurs.

The only characters that help us in phylogenetics are synapomorphies. Synapomorphies define clades. The others provide information about the taxa in question, but do little to inform us as to their evolutionary relationships.

Cladistics is a relative science. We are always conducting phylogenetic analyses on different scales (like the difference between your family tree, the primate tree and the tree of all life). It is, therefore, important to note that a synapomorphy at one level on a phylogenetic tree, could be viewed as a plesiomorphy on another scale.

Using the tree that you created, and the characters that you mapped on, answer the following questions...

1. What one synapomorphy defines clade ED (Include the character and the change in character state)?

 

 

 

 

 

 

 

2. Of all the characters analyzed, which one is an autapomorphy? What taxon has that character?

 

 

 

 

 

3. When looking at clade ED, what is an example of a plesiomorphic, or ancestral character for this group? (Remember that means that the character arose earlier than that clade, so its a character that ED shares with other taxa.)

 

 

 

 

 

 

Your name:

 

Others in your group

 

 

 

 

 

 

The nuts and bolts of taxonomy

 

Each group has a bag that contains fifteen different species from the Kingdom Hardwarea, Phylum Fastneria.

 

Your groups’ job is to construct a hierarchical classification of the 15 species in the bag.  In doing so, you must identify the defining features (characters) of each class, order, family, genus and species.  You can give them names if you want, but that’s optional and not the purpose of this exercise.

 

In devising hierarchical schemes, some people work best “from the bottom up”, by grouping similar species in the same genus, similar genera (the plural of genus) in the same family, and so on...

 

Other people find it more natural to work “from the top down”, by finding the major divisions among the objects, and then further subdividing those.

 

Some ground rules:  each class must contain at least one order, each order at least one family, etc...  This means, for example, that several species could belong to the same genus, several genera to the same family, and so on...

 

In the space on the next page, sketch out your hierarchical scheme and list the defining morphological features (=characters) of each class, order, family, genus and species.  You will then compare your group’s classification scheme to the ones devised by the other lab groups.

 

Things to think about:

1.       Is function a useful way to classify objects?

2.       When the same characters appear in different groups, is this the result of ancestry (i.e., the character occurred in the common ancestor) or convergence (i.e., the character evolved independently in the two groups).

3.       Can classification be a good guide to evolutionary relationships?