1. Biozones + Test Day 1: Thursday (191-221, 369-382)
Sponge: Set up Cornell Notes on pg. 59
Topic: 5.4 Cladistics
Essential Question: Why is it sometimes necessary to reclassify organisms?
5.4 Cladistics
Why is it sometimes necessary to reclassify organisms?
Key Vocabulary:
Cladistics
Clade
Phylogeny
Cladogram
Circumscription
BIOZONE:
Text:
Digital Text:
Biozones + Test Day 1: Thursday ( , )
Notebook  + Test Day 2: Friday
Dichotomous Keys due TUESDAY upon return

2. P. 58 DNA Sequences 1. 2. 3. 4. Cladogram: Worked Problems 1. 2. 3. 4.5.

3. Understandings:
A clade is a group of organisms that have evolved from a common ancestor

4. Clades
Cladistics: is a system of classification that groups taxa together according to the characteristics that have evolved most recently
Concept of common decent is crucial to deciding into which groups to classify organisms

5. Clades
To decide how close a common ancestor is, researchers look at how many primitive and derived traits the organisms share
Primitive traits: are characteristics that have the same structure and function and that evolved early in the history of the organisms being studied
Leaves, with vascular tissue to transport liquids around a plant
Derived traits: are also characteristics that have the same structure and function BUT have evolved more recently as modifications of a previous trait
Flowers, which evolved more recently than leaves with vascular tissue
They are an ADAPTATION of vascular leaves
Coniferophyta: Vascular plant
Angiospermophyta: Vascular plant but also have fruit/flowers

6. DO NOT HAVE VASCULAR TISSUE
Clades
DO NOT HAVE VASCULAR TISSUE
HAVE VASCULAR TISSUE
By systematically comparing such characteristics, results show which organisms have a more recent split in the evolutionary past and which have a more distant split
When a group can be split into two parts, on having certain derived traits that the other does not have, the groups form two separate clades

7. Clades A clade: is a monophyletic group (“single tribe”)
Derived from a SINGLE ancestral species
Gave rise to no species in any other taxa
Composed of the most recent common ancestor of the group and all of its descendants
*Can sometimes just have one species, but usually made up of multiple species

8. Understandings:
Cladograms are tree diagrams that show the most probable sequence of divergence in clades

9. Cladograms
Cladogram: a diagram used to represent the findings of cladistics in a visual way
A cladogram showing bats, sharks, and dolphins takes into account their skeletal structures and other characteristics, such as the fact that bats and dolphins are mammals
Thus, bats and dolphins are more similar to each other than sharks are to either.
mammals

10. Cladograms
Considered “sister taxa”

11. Cladogram: Worked Example
Study the cladogram below:
Paramecium are protozoa, which are a diverse group of unicellular eukaryotic organisms

12. Cladogram: Worked Example
What is the primitive(EARLIEST) characteristic in the cladogram shown?
Being Eukaryotic

13. Cladogram: Worked Example
2. Name the members of the MAMMAL clade in this cladogram?
Mammals: Hair, mammary glands
Koala
Camel
Human

14. Cladogram: Worked Example
3. What is the outgroup when considering the clade of multicellular organisms?
Outgroup: The group that doesn’t fit in
Paramecium

15. Cladogram: Worked Example
4. Do shark eggs have a protective membrane (the amnios) around them?
No. Sharks are not amniotes.

16. Cladogram: Worked Example
5. Explain why there are no bacteria shown in this diagram.
Eukaryotes have a nucleus and membrane-bound organelles. Bacteria does not share these traits because they are prokaryote.

17. Understandings:
Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species

18. Cladograms and classification
Every cladogram drawn is a working hypothesis
It is open for testing and falsification

19. Cladograms and classification
Mammals
Each time a derived characteristic is added to the list shared by organisms in a clade, the effect is similar to going up one level in the traditional hierarchy of the Linnaean classification scheme
Ex: the presence of hair is part of what defines a mammal
So any species found after the line marked “hair” should be in the class of mammals

20. Cladograms and classification
If an organism has feathers is it automatically a bird?
In traditional Linnaean classification, birds occupy a class of their own
But when making a cladogram, it becomes clear that birds share a significant # of derived characteristics with a group of dinosaurs called theropods
This suggests that birds are an offshoot of dinosaurs rather than a separate class of their own

21. Derived characteristics:
A fused clavicle (the “wishbone”)
Flexible wrists
Hollow bones
A characteristic egg shell
Hip and leg structure– have backward-pointing “knees”

23. This is evidence that birds more likely evolved from dinosaurs rather than from another common ancestor

24. Application:
Cladograms including humans and other primates
Skills:
Analysis of cladograms to deduce evolutionary relationships

25. Cladograms Homework
Answer the questions regarding the following cladograms.
Read article “There’s no such thing as reptiles” [highlight]
Read the article “How Dinosaurs Shrank and Became Birds” and write a ½ page summary on the article (tape on p. 58)

26. Biochemical evidence for common ancestry
The discovery of the genetic code nearly a century after Mendel’s work and Darwinian evolution only validated the idea of common ancestry
The fact that every known living organism on Earth uses DNA as its main source of genetic information is compelling evidence that all life on Earth had a common ancestor
Genetic engineering: any gene from any organism can be mixed and matched with DNA from other organisms
All proteins use the same 20 amino acids to form their polypeptide chains

27. Variations and phylogeny
Phylogeny is the study of evolutionary past of a species.
Species which are the most similar are most likely to be closely related
Usually done by examining morphology (physical features of an organism’s phenotype)
In more recent decades, attention has also been given to molecular differences and similarities

28. Understandings:
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

29. TOP
P. 58
By comparing the similarities in the DNA sequences of animals/plants, it is possible to trace their common ancestry
Here is an imaginary example of a DNA sequence from four different species:
Please circle the differences in the bases (from the first set) and write the total number of differences next to the DNA sequence
A A A A T T T T C C C C G G G G
2 A A A A T T T A C C C C G G G G #____
3 A A A A T T T A C C C G C G G G #____
4 A A C A T C T T C C A C G C T G #____

30. What can we infer from these results?
A A A A T T T T C C C C G G G G
2 A A A A T T T A C C C C G G G G difference
3 A A A A T T T A C C C G C G G G differences
A A C A T C T T C C A C G C T G differences
What can we infer from these results?
Who is more closely related to who?

31. A A A A T T T T C C C C G G G G 2 A A A A T T T A C C C C G G G G
3 A A A A T T T A C C C G C G G G
A A C A T C T T C C A C G C T G
1 and 2 have the most similarities
1 and 4 have the least similarities
The conclusion would be that species 1 and 2 are more closely related to each other than they are to species 3/4

32. Nearest common ancestor for species 1 and 2
(as well as for species 3 / 4)
“Node”
Nearest common ancestor for species 2 and 3
“Node”
Nearest common ancestor for species 3 and 4
“Node”

33. Understandings:
Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor

34. Biochemical differences (dotted red lines) can be used to see how far apart species are on a phylogenetic tree (in blue)

35. The evolutionary clock
Differences in polypeptide sequences accumulate steadily and gradually over time as mutations occur from generation to generation in a species
These changes can be used as kind of a “clock” to estimate how far back in time two related species split from a common ancestor

36. One technique which has been successful in measuring such differences in DNA hybridization:
Take one strand of DNA from species A and a homologous strand from species B and fuse them together
Where the bases pairs connect, there is a match; where they are repelled and do not connect, there is a difference in sequence
The more similarities in bases, the closer in time the two species split from a common ancestor

37. Understandings:
Traits can be analogous or homologous

38. Homologous Traits
Homologous structures: are ones derived from the same part of a common ancestor, Have same structure
The shape, # of bones, and function might vary, but the general format is the same
Five fingered limb (pentadactyl)

39. Analogous Traits
Analogous structures: are those that may have the same function, but they do not necessarily have the same structure and they are NOT derived from a common ancestor
Wings, used for flying
But not in the same clade simply because of their ability to fly
Fins in aquatic organisms
Sharks v. dolphins- both use pectoral fins in a similar way, but one is a fish and one is a mammal

40. Analogous Traits
Mammals

41. Application:
Reclassification of the figwort family using evidence from cladistics

42. Reclassification
From time to time, new evidence about a taxon requires a new classification.
The taxon can be moved up or down the hierarchy
Family to subfamily
Or from family to family

43. Reclassification: Figworts
Plants commonly known as figworts used to be classified in the family Scrophulariaceae (scrof-ū-lar-ē-ā-see)
Many of them have been used as herbal medicine
Its name “scrophs” comes from a time when plants were frequently named for the diseases they could be used to treat
Scrofula is an infection of the lymph nodes in the neck

44. Reclassification: Figworts
Before the mid-1900s:
Characterized by morphological features:
How flower petals were arranged in the bud before the flower opens
Do the flower petals overlap with each other?
Or are they arranged in a spiral?
What was the morphology of the nectaries? (parts of the flower that make nectar)

45. Reclassification: Figworts
Since the mid-1900s:
DNA analysis of the plant led botanists to rethink their classification
DNA analysis revealed that the old classification system did not share a most recent common ancestor
The old system was grouping together plants that belonged to separate branches
It was found that species in the figwort family were not a true clade
Five clades had incorrectly been combined into one family

46. Reclassification: Figworts
Plants that were in Scrophulariaceae family have been given new families to belong to.
Family Plataginaceae (plan-tăj-in-ā-c-ī): This is where we now find Foxgloves
This new classification shows that they are more closely related to plantains
No longer considered figworts

47. Reclassification: Circumscription
Circumscription: Moving the branches of the tree of life around and reclassifying taxon in a new branch.
Done in an efforts to place taxa where they clearly show monophyletic groups
Allowing us to show that they all share a recent common ancestor

48. This doesn’t sound like a big deal but….
It would be similar to someone meeting your extended family at a party and incorrectly assuming your second cousins were your siblings just because you looked alike.
DNA testing would clearly reveal that second cousins have a more distant common ancestor than siblings do
Share great-grand parents

49. Evolution Test Study Guide
Part I: MC 14 marks
Know what factors promote evolution in a species
How antibiotic resistance occurs
Know what natural selection is, and how it works
What causes the “struggle for survival”
Know what binomial nomenclature is and its purpose
Know the 7 taxa, and their order
Be able to read a cladogram
Part II: Short and Extended Answer 11 marks
Know what natural selection is, be able to describe it in detail and know examples of it
Know the different types of evidence of evolution and be able to explain how they are evidence
Know the formula for the Hardy-Weinberg Equation, and know how to calculate if populations are in equilibrium
Part III: Data Analysis x 2 8 marks
Part IV: Solve a Dichotomous Key 22 marks