Sponge: Set up Cornell Notes on pg . 53 Topic: 5.4 Cladistics

1. 5.4 Cladistics Sponge: Set up Cornell Notes on pg. 53 Topic: 5.4 Cladistics Essential Question: Why is it sometimes necessary to reclassify organisms? Why is it sometimes necessary to reclassify organisms? Key Vocabulary: Cladistics Clade Phylogeny Cladogram Circumscription BIOZONE: 218-221 Text: 305-310 Digital Text: Biozones + Test Day 1: Thursday (191-221, 369-382) Notebook  + Test Day 2: Friday Dichotomous Keys due MONDAY upon return

2. DNA Sequences 1. 2. 3. 4. P. 52 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. 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. P. 52 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

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

26. 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. 52)

27. 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

28. 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

29. 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

30. TOP P. 52 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 AAA T TTT C CCC G GGG 2 A AAA T TTA C C CC G GGG#____ 3 A AAA T TTA C C CG C G GG#____ 4 A AC A T C T T C C A C G C T G #____

31. A AAA T TTT C CCC G GGG 2 A AAA T TTA C C CC G GGG 1 difference 3 A AAA T TTA C C CG C G GG 3 differences • A ACA T C T T C CA C G C T G 5 differences What can we infer from these results? Who is more closely related to who?

32. A AAA T TTT C CCC G GGG 2 A AAA T TTA C C CC G GGG 3 A AAA T TTA C C CG C G GG • A ACA T C T T C CA 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

33. 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”

34. 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

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

36. 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

37. 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

38. Understandings: • Traits can be analogous or homologous

39. Homologous Traits Homologous structures: areones 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)

40. 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 • Finsin aquatic organisms • Sharks v. dolphins- both use pectoral fins in a similar way, but one is a fish and one is a mammal

41. Analogous Traits Mammals

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

43. 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

44. 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

45. 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)

46. 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

47. 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

48. 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

49. 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

50. 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