Activity: Cladistics

How Do We Reconstruct Evolutionary Events in the Past using Evidence in the Present?

Phylogenetic analysisPhylogenetic Analysis:
Analytical method used to find a hypothesis of relationships among species, by coding the various states of homologous characters; also called cladistics., or cladistics, is a technique that was developed specifically to learn about the evolution and relationships of biological species. Scientists use large datasets and computer programs to conduct their analyses, but a simple demonstration, using five taxaTaxon:
An organism or group of organisms of the same rank, e.g., members of an order, family, genus, or species. (pl. taxa) (species) and five charactersCharacter:
A single attribute of an organism. (features) can demonstrate the basic principles.

Step 1. Choose your taxa.

For this example, let's use:

Mercenaria (Clam)
Mytilus (Blue Mussel)
Crassostrea (Oyster)
Pecten (King Scallop)
Mimachlamys (Noble Scallop)

Note: We are intentionally using two scallops in this example — let's see if they turn out to be most closely related in our analysis!

Without any character data at all, if we are constructing this tree manually, we can already draw the tree. Note that there are two common ways of representing the tree. Although they look different, they mean the same thing.

Step 2. Define your first character — modify the tree.

Each character must be the same feature in every species — we call these homologousHomologous:
Having the same structure and origin, although current function might differ. — so that we are not trying to “compare apples and oranges.” Each character must exist in your set of taxa in two or more conditions — called “states” — and at least one state should exist in more than one taxon. The simplest character states are “present” and “absent.” Homologous characters are presumably those that evolved from one state to another over time within the lineage.

Let's use the “ears” (called “auricles”) that are clearly present on the two scallops. So our first character is:

(1) Auricles: absent (0) or present (1)

We assign a numerical “code” to each state. Traditionally, the most primitive state is coded 0, and the more advanced (called “derived”) states are coded 1, 2, etc. [This is determined through comparison with a taxon outside the immediate study group, called an “outgroup,” but is not discussed in detail here.] We enter these codes in a data matrix or data table.

	(1) Auricles
Mercenaria	0 Absent
Mytilus	0 Absent
Crassostrea	0 Absent
Pecten	1 Present
Mimachlamys	1 Present

So we add this information to the tree by grouping the taxa according to their character states.

We indicate the character state change by a notch on the branch that means “character 1 (auricles) changes from absent (0) to present (1).”

Step 3. Define and code additional characters — refine the tree.

For each of these characters, we code all of the taxa, add the codes to the data matrix, and add the pattern to the tree. See if you can follow along.

(2) Radial sculpture: absent (0) or present (1)

Radial sculpture is the pattern of ridges radiating from the “beak” of the shell, called the “umbo,” to the edge.

	(1) Auricles	(2) Radial
Mercenaria	0 Absent	0 Absent
Mytilus	0 Absent	0 Absent
Crassostrea	0 Absent	0 Absent
Pecten	1 Present	1 Present
Mimachlamys	1 Present	1 Present

Notice that the branching pattern has not changed, but we now have two characters supporting the branch (called a cladeClade:
A group of organisms (usually species) that are more closely related to each other than any other group, implying a shared common ancestor.) containing Pecten and Mimachlamys.

(3) Muscle scars: two (0) or one (1)

For this character, we need to look at the interior surface of the valves. Bivalve shells are held together by two muscles that attach to each valve, called anterior and posterior “adductor muscles.” Click here to review the Anatomy section. Some bivalves have lost one of the two muscles and moved the remaining one to the center of the shell. Where each of these muscles attach to the shell is represented by a scar — clearly impressed in some species, or more subtle in others. We have colored these muscle scars black here for clarity.

Mercenaria
Mytilus
Crassostrea
Pecten
Mimachlamys

	(1) Auricles	(2) Radial	(3) Scars
Mercenaria	0 Absent	0 Absent	0 Two
Mytilus	0 Absent	0 Absent	0 Two
Crassostrea	0 Absent	0 Absent	1 One
Pecten	1 Present	1 Present	1 One
Mimachlamys	1 Present	1 Present	1 One

(4) 18S Positions #1-2: CG (0) or TA (1)

Molecular sequences can be used as characters too. Here are five real sequences (part of the 18S ribosomal gene):

Mercenaria:	C G C C T T T A C A C G G C A A A A C T
Mytilus:	T A C T T T T A C A T A G T G A A A C C
Crassostrea:	T A C T C T T G C A C A G T G A A A C C
Pecten:	T A C T T T T T G A T G G T G A A A C C
Mimachlamys:	T A C T T T T T G A T G G T G A A A C C

Remember from the structure of DNA that: A = adenine, C = cytosine, G = guanine, T = thymine. (These letters are traditionally color coded for easier reading.)

	(1) Auricles	(2) Radial	(3) Scars	(4) Pos 1-2
Mercenaria	0 Absent	0 Absent	0 Two	0 CG
Mytilus	0 Absent	0 Absent	0 Two	1 TA
Crassostrea	0 Absent	0 Absent	1 One	1 TA
Pecten	1 Present	1 Present	1 One	1 TA
Mimachlamys	1 Present	1 Present	1 One	1 TA

Can you code more differences (molecular characters) from these sequences?

About multistate characters

This example used very simple “binary” characters, that is, those with only two states. However, there are many characters in bivalves that can exist in more than two states — these are called “multistate” characters.

One example is muscle scars (see character 3 above).

The muscle scars could have been coded as: two of equal size (0), two of unequal size (1), one muscle scar (2).

This sequence reflects the reduction (in size) of one of the muscles, presumably in the evolutionary pathway toward losing it entirely. If we substitute this coding for character 3:

	(1) Auricles	(2) Radial	(3) Scars	(4) Pos 1-2
Mercenaria	0 Absent	0 Absent	0 Two equal	0 CG
Mytilus	0 Absent	0 Absent	1 Two unequal	1 TA
Crassostrea	0 Absent	0 Absent	2 One	1 TA
Pecten	1 Present	1 Present	2 One	1 TA
Mimachlamys	1 Present	1 Present	2 One	1 TA

We see that this change did not change the branching pattern on the tree. Character three now exists as two changes on the tree, from 0 to 1 between Mercenaria and Mytilus, and from 1 to 2 between Mytilus and the other three taxa.

This is the final tree incorporating all the branches and character changes.

We conclude that the two scallops (Pecten and Mimachlamys) are most closely related, supported by the presence of auricles and radial sculpture. They are most closely related to the oyster (Crassostrea), supported by the single muscle scar. These three taxa are most closely related to the mussel (Mytilus), supported by the molecular sequence in our dataset. We also see that muscle scars evolved (reading from the base to top of the tree) from two equal scars (in Mercenaria), to two unequal scars (in Mytilus), then to a single scar (in Crassostrea, Mimachlamys, and Mimachlamys).

Can you see that changing just one number in this matrix might change the relationships portrayed on the tree? Try it!