UNIT ____: Cladistics Name: ________________________

IB Assessment Statements and Class Objectives

Natural classification helps in identification of species, the prediction of shared characteristics within a group, and depicts evolutionary relationships between organisms (5.3.U6 and 5.3.U8) .

Define classification and homology.
Outline the process of natural classification.
Outline how natural classification allows for prediction of characteristics and evolutionary relationships between species.
Compare natural classification to traditional classification schemes.

A clade is a group of organisms that have evolved from a common ancestor (5.4.U1).

Define clade.
Identify a clade as a branch in a phylogeny.

Cladograms are tree diagrams that show the most probable sequence of divergence in clade (5.4.U5, 5.4.A1, 5.4.S1).

Analyze a cladogram to deduce evolutionary relationships, common ancestry and clades.
Interpret a cladogram depicting primate species.

Cladograms can be interpreted to determine if traits, such as development of scurvy, are homologous or analogous (D.1.A1 and D.1.NOS).

Interpret cladograms to determine if traits are homologous or analogous.
State the function of ascorbic acid, Vitamin C.
Analyze a cladogram based on the mutations in the GLO gene, used in Vitamin C synthesis.
Outline the cause, symptoms and treatment of scurvy.
Based on cladistics, explain why some animals are poor models for the study of scurvy.

Evidence for which species are part of a clade can be obtained from the base sequences of a gene or the corresponding amino acid sequence of a protein (5.4.U2).

State that DNA and amino acids sequences can be molecular homologies.
Outline the relationship between time, evolutionary relationships and biological sequences (nitrogenous base or amino acid).

The development of bioinformatics applications allows for rapid and accurate identification of conserved sequences between species (3.1.S1 and 7.3.NOS).

Define bioinformatics.
Use a database to access the base sequence of a gene.
Use an online tool to construct a cladogram using DNA sequences.

There is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor (5.4.U3).

State the source of differences between biological sequences (nitrogenous base or amino acid).
Outline the use of a “molecular clock” to determine time since divergence between two species.

Cladograms based on the base sequences of a gene or the corresponding amino acid sequence of a protein have shown the classifications of some groups based on visible characteristics did not correspond with the evolutionary origins of a group or species (5.3.U7, 5.4.U6, 5.4.A2, 5.4.NOS).

Outline why historical cladograms were based on visible characteristics.
Outline the role of technological advancements in the development of cladistics.
Explain why the development of cladistics lead to the reclassification of some species.
Outline the reason and evidence for the reclassification of the figwort family.

NATURAL CLASSIFICATION

Natural Classification

Members of the same taxonomic group have:

Focuses on:

Evidence of molecular homology can be seen when:

species classified together will have…

One should be able to predict the…

One should be able to determine the…

TRADITIONAL CLASSIFICATION

NATURAL CLASSIFICATION

Cladistics

What is cladistics?

What is a cladogram?

What does a “node” in a cladogram depict?

What does the “root” of the tree depict?

Define clade.

How are cladograms used in biology?

Based on what characteristics are cladograms created?

Why is it important to consider only homologous characteristics in constructing cladograms?

How has the advent of computer software revolutionized phylogenic tree construction?

Bioinformatics and DNA Sequence Alignment

Bioinformatics

Sequence Alignment

How can DNA and Protein Sequences be distinguished?

One reason we would do this is to determine what parts of the sequences are conserved from one species to the next. Another reason would be to see how much an organism has diverged from other organisms simply by comparing their DNA sequences. The more similar two gene sequences are to one another, the more closely the organisms are related. And the more dissimilar the two sequences, the farther the two genes are in evolutionary relationship.

DNA SEQUENCE ANALYSIS #1

Imagine that I gave a class of 10 students an assignment to write 10,000 word essays on a certain topic. On the due date, I get back 10 papers that are almost identical. I get one superb paper from John; James’ paper is identical with one exception: word number 300 is different, and the sentence containing the difference now makes no sense at all. Jan’s paper is identical to James’, except it has two nonsensical mistakes . . . the very same mistake at word #300, plus another at word #1,100. And Susan’s paper shares the very same mistakes at words #300 and #1,100, plus a new one at word #124.

How would you interpret this? Well first of all, the papers were not written independently. Even with the few differences, they are far too similar. Could they all have been copied from the same source, or all copied directly from John? Unlikely. The chance of Susan independently making exactly the same mistakes, at words #300 and 1100, that Jan made is extremely small. And extending the analysis, the chance of the tenth student independently making exactly the same eight errors as the previous student is basically zero. The only reasonable explanation is that James copied from John, and then Jan copied from James, etc.

Determine the order that the sentences below were incorrectly copied. Identify the differences between the sentences and then order the sentences from 1 to 10, with 1 being the original sentence and 10 being the most divergent.

ID	Sentence	ORDER
A	We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). structure has novel feature which is of considerable biological interests.
B	We wish to suggest a structure for the salt of deoxyribose nucleic arid (D.N.A.). structure has novel feature of biological interests.
C	We wish to suggest a structure for the salt of deoxyribose nucleic arid (DNA). structure has novel feature of interests.
D	We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.
E	We wish to suggest a structure for the salt of deoxyribose nucleic arid (D.N.A.). structure has novel feature of interests.
F	We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). structure has novel feature which are of considerable biological interest.
G	We wish to suggest a structure for the salt of deoxyribose nucleic arid (D.N.A.). structure has novel feature which is of considerable biological interests.
H	We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). structure has novel features which are of considerable biological interest.
I	We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). structure has novel feature which is of considerable biological interest.
J	We wish to suggest a structure for the salt of deoxyribose nucleic arid (D.N.A.). structure has novel feature of considerable biological interests.

DNA SEQUENCE ANALYSIS #2

Complete the table to compare the number of DIFFERENCES in a section of the Hemoglobin gene sequences between species:

	Cow	Chimpanzee	Chicken	Goat	Frog	Human
Cow
Chimpanzee
Chicken
Goat
Frog
Human

Based on the similarities between sequences, draw the cladogram depicting the relationships between the species based on homology in the hemoglobin gene.

Molecular Clocks

What is a “molecular clock?”