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THERE IS ASSIGNED HOMEWORK

CLADISTICS

HOW, IN DETAIL, DO WE WORK OUT RELATIONSHIPS?

There are several methods that have been used to work out the evolutionary relationships of organisms. The most successful of these is the so-called "cladistic" or "phylogenetic" method. This method is based on an older concept, that of "homologous characters".

 To begin, we supply some definitions:

Character:
A feature or thing we can examine or label. It is important that the feature be heritable.
Homologous Character:
Character which is shared by taxa by descent.
Analogous Character
Shared resemblance between characters by other means than descent, such as adaptation. This is often called a homoplastic character.
Homologous characters are the fundamental basis of cladistics. In cladistics we look for characters that we can hypothesis are shared because they were inherited from a common ancestor. The premise is that a species develops a new character and passes that character down to its daughter species. Each of the daughter species then can add new characters, but each adds a different one, since they are now separate species and on their own evolutionary trajectory. This continues to happen through time as more and more species split off.

 We see in retrospect characters shared between two species. How do we decide if a character is homologous or analogous?

 First we hypothesize them to be so. Then we look at the preponderance of other characters to test our hypothesis. Cladistics gives us a framework in which to do this. Cladistics was basically invented by Willi Hennig who was a specialist in flies. Here is a link to a site that describes in detail and in a different way how we do cladistics: http://www.ucmp.berkeley.edu/clad/clad1.html

 In cladistics we assume that we wish to focus on genealogical relationships and that our classifications of taxa should depend on our analysis of these genealogical relationships. Of prime importance is the historical sequence in which the taxa descended from a common ancestor. Hence, our cladistic hypotheses are based on our estimate of the historical sequence of the acquisition of novel characters.

 Next, some more definitions:

Primitive Character = Plesiomorphy
A character which is in the state shared by the common ancestor of the group.
Derived Character = Apomorphy
A character in a new state, not the primitive one.
Shared Character:
A character shared by all the members of the group.
Shared Derived Character = Synapomorphy
A character which is in a new state and shared by all the member of the group.
Unique Derived Character = Autapomorphy
A character found only in that taxon. Is a synapomorphy when discussed at the level of the members of a taxon.
The method in cladistics is to build and test relationships based on the distribution of the states of characters and to build groups by the recognition of synapomorphies.

 Let´s look at a specific example of a cladogram

VERTEBRATES
CICHLID -
has backbone, paired appendages (fins), dorsal nerve cord and aorta which are shared derived characters uniting the cichlid with frogs, turtles, kangaroos, mice, and humans.
FROG -
has all those plus legs.
TURTLE -
has all those plus a hard shelled egg called an amniotic egg.
KANGAROO -
all those plus hair, warm blood, and egg develops inside.
MOUSE -
all those plus placental development
HUMAN -
all those plus very large brain and loss of hair.
NOTE THAT FOR EACH SHARED DERIVED CHARACTER THERE IS A PRIMITIVE CHARACTER.
For example, kangaroos, mice and humans all share having hair. The corresponding primitive character is "not having hair". Fish, frogs and turtles lack hair, but these shared primitive characters are not evidence of relationship, because many other organisms lack hair that are outside the group we are considering - clams, for example.
NESTED SETS OF SHARED DERIVED CHARACTERS ARE DEPICTED ON THE CLADOGRAM OF THESE SYNAPOMORPHIES ALONG WITH THEIR CORRESPONDING SHARED PRIMITIVE CHARACTERS.
Cladogram:
A branching diagram depicting the hierarchical arrangement of taxa defined by the distribution of shared derived characters.
But there are also characters which are unique to each group (autapomorphies), not shared with the others
CICHLID -
symmetrical tail fin, spiny fins.
FROG -
long sticky tongue, tadpole.
TURTLE -
shell covering body, no teeth.
KANGAROO -
big grinding teeth, thick tail.
MOUSE -
ever-growing incisors.
HUMAN -
opposable thumb, reduced toes, huge brain.
WE CAN PUT THESE CHARACTERS ON A CLADOGRAM AS WELL.

 AND, THERE ARE CHARACTERS THAT MAKE NO SENSE AT ALL IN THE SET OF RELATIONSHIPS WE HAVE PRESCRIBED HERE. THESE ARE HOMOPLASTIC CHARACTERS, MANY OF WHICH ARE ANALOGOUS CHARACTERS AS WELL.

CICHLID -
thin scales (shared with turtle and mouse).
FROG -
no scales (shared with mammals but not turtle).
TURTLE -
reduced teeth (shared with man).
KANGAROO -
bipedal (shared with man) - big ears (shared with mouse).
MOUSE -
scales on tail (shared with turtle).
HUMAN -
no tail (shared with frogs).
IF WE PUT THESE CHARACTERS ON THE CLADOGRAM, YOU CAN SEE HOW THEY DO NOT MAKE A CLEAR PATTERN.

 A KEY FEATURE OF THE CLADISTIC METHOD IS THAT IT ALLOWS TESTING BY THE HYPOTHETICO-DEDUCTIVE METHOD

So we could have used some of these characters to group the taxa, but then the characters that we used as shared derived characters would have to be explained away by ad hoc explanations. Each ad hoc explanation makes the proposed hypothesis more and more untenable. If the number of characters that have to be explained away by ad hoc explanations gets larger than the number of shared derived characters that support the cladogram, the hypothesis (i.e. cladogram) should be rejected.
MUST BE BUTTRESSED BY MORE SHARED-DERIVED CHARACTERS - OR HYPOTHESIS MUST GO
LIKE ALL OF SCIENCE
A KEY FEATURE OF CLADISTICS IS THAT GROUPS OF ORGANISMS ARE DEFINED BY SYNAPOMORPHIES. THESE ARE MONOPHYLETIC GROUPS. THERE ARE OTHER KINDS OF GROUPS, THOUGHT TO BE MUCH LESS DESIRABLE BY CLADISTS, THAT ARE DEFINED BY HAVING MEMBERS SHARING OTHER KINDS OF CHARACTERS THAN SHARED DERIVED ONES.
Monophyletic Group:
A group containing an ancestor and all of its descendants - defined by one or more synapomorphies.
Paraphyletic Group:
A group consisting of an ancestor but not all of its descendants. It is defined by what it does not have.
Polyphyletic Group:
A group that does not include a common ancestor within the group. The common ancestor is placed in another group.
Out Group:
A group outside the groups in question which is used to define the polarity of character transformations (primitive to derived).
Sister Group:
A monophyletic group more closely related to the group under examination than any other group.
Ancestor Problem:
All possible ancestors are regarded as sister groups.
NOTE THAT THE CLADOGRAM OF THE MONOPHYLETIC GROUPS TRANSLATES DIRECTLY INTO TAXONOMIC CLASSIFICATION USING THE LINNEAN HIERARCHY.
Phylum Chordata
        Subphylum Osteichthyes
                Superclass Tetrapoda
                        Infraclass Amniota
                                Class Mammalia
                                        Species Homo sapiens
We will use the cladistic method in discussing the relationships of groups through the rest of the term.
Example: Homo sapiens, Crocodilus niloticus, Deinonychus antirrhopus, and Archaeopteryx lithographica
V. CLASSIFICATION
This Cladogram also directly translates into a classification
REFERENCES:

 http://www.ucmp.berkeley.edu/clad/clad1.html

 http://www.vims.edu/~mes/hennig/infohist/willi1.html which has as its home page

http://www.vims.edu/~mes/hennig/


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