1. Chapter 16 Opener

2. In-Text Art, Ch. 16, p. 316 (1)

3. In-Text Art, Ch. 16, p. 316 (1)

4. In-Text Art, Ch. 16, p. 316 (2)

5. In-Text Art, Ch. 16, p. 316 (2)

6. In-Text Art, Ch. 16, p. 316 (3)

7. In-Text Art, Ch. 16, p. 316 (4)

8. In-Text Art, Ch. 16, p. 316 (4)

9. In-Text Art, Ch. 16, p. 317

10. Figure 16.1 Clades Represent All the Descendants of a Common Ancestor

11. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Homologous features:
Shared by two or more species
Inherited from a common ancestor
They can be any heritable traits, including DNA sequences, protein structures, anatomical structures, and behavior patterns.

12. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait). Shared derived traits provide evidence of the common ancestry of a group and are called synapomorphies. The vertebral column is a synapomorphy of the vertebrates. The ancestral trait was an undivided supporting rod.

13. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Similar traits can develop in unrelated groups: Convergent evolution—when superficially similar traits may evolve independently in different lineages

14. Concept 16.1 All of Life Is Connected through Its Evolutionary History
In an evolutionary reversal, a character may revert from a derived state back to an ancestral state. These two types of traits are called homoplastic traits, or homoplasies.

15. Figure 16.2 The Bones Are Homologous, the Wings Are Not

16. Figure 16.2 The Bones Are Homologous, the Wings Are Not

17. Concept 16.1 All of Life Is Connected through Its Evolutionary History
In 2009 it was discovered by marine biologist Gary Dickinson and colleagues that some amino acid sequences in a species of barnacle (a marine invertebrate) exactly matched sequences in a human blood clotting protein.
Read the following description of their experiment and then discuss the question that follows.
REFERENCE:
Dickinson, G. H., Vega, I. E., Wahl, K. J., Orihuela, B., Beyley, V., Rodriguez, E. N., Everett, R. K., Bonaventura, J. and Rittschof, D. (2009). Barnacle cement: a polymerization model based on evolutionary concepts. J. Exp. Biol. 212: 3499–3510.

18. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Although they have hard shells like mussels and snails, barnacles are actually crustaceans—related to crabs and lobsters. A barnacle is “basically a shrimp that is glued down to the ground with its head, and kicks food into its mouth with its feet,” says marine biologist Gary Dickinson. Prior to his co-authored study, published in 2009 in the Journal of Experimental Biology, Dr. Dan Rittschof had been studying marine invertebrates for 30 years. He already knew that when you took certain chemical factors derived from human blood they sometimes triggered specific reactions in their ancient evolutionary cousins. For example, when he took factors C5A and C3A—blood clotting chemicals that attract white blood cells in the human body—and gave them to blue crabs that had eggs attached to their bodies, it caused the eggs to be released. So Rittschof proposed the seemingly far-fetched idea that perhaps barnacle glue was related to blood clotting and scab formation in humans, and his graduate student, Dickinson, set out to try to prove his professor wrong. Funny thing was, he couldn’t. It turned out that despite a number of independent analyses using atomic force microscopy, gel electrophoresis, and mass spectrophotometry, all of Dickinson’s experiments indicated that in fact barnacle glue was very similar, and in some respects identical, to the chemical components of human blood clotting.
INSTRUCTOR NOTE:
This summary could be given to students as a handout.
REFERENCE:
Dickinson, G. H., Vega, I. E., Wahl, K. J., Orihuela, B., Beyley, V., Rodriguez, E. N., Everett, R. K., Bonaventura, J. and Rittschof, D. (2009). Barnacle cement: a polymerization model based on evolutionary concepts. J. Exp. Biol. 212: 3499–3510.

19. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Dickinson started by figuring out how to use the barnacles as living glue sticks, prodding and gently squeezing them to release the glue. Using techniques called gel electrophoresis and mass spectrometry, Dickinson separated out the glue’s components. His first breakthrough was identifying a protease—an enzyme that cuts human blood proteins apart in preparation for scab formation. Next he found that the barnacle cement’s proteins had amino acid sequences that, despite a billion years of evolution, exactly matched factor XIII, a human blood clotting factor that cross-links scab fibers. Dickinson’s team suggests that barnacle cement is an evolutionary modification of wound healing, and suspects that this ancient chemical pathway is used by many other marine invertebrates that need to “get a grip.”
INSTRUCTOR NOTE:
This summary could be given to students as a handout.
REFERENCE:
Dickinson, G. H., Vega, I. E., Wahl, K. J., Orihuela, B., Beyley, V., Rodriguez, E. N., Everett, R. K., Bonaventura, J. and Rittschof, D. (2009). Barnacle cement: a polymerization model based on evolutionary concepts. J. Exp. Biol. 212: 3499–3510. 19

20. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Based on the description of this study provided on the previous slides, what do the researchers appear to be interpreting from their study about evolutionary history of barnacles and humans?
a. It’s just a coincidence, since barnacles and humans are not evolutionarily related.
b. Humans and barnacles share a common ancestor.
c. The presence of this protein is likely an ancestral, homologous trait.
d. Both b and c
e. None of the above
Answer: d
(They are inferring that the protein evolved in an ancestor common to both humans and barnacles. Approximately one billion years of evolution separate humans and barnacles.)
REFERENCE:
Dickinson, G. H., Vega, I. E., Wahl, K. J., Orihuela, B., Beyley, V., Rodriguez, E. N., Everett, R. K., Bonaventura, J. and Rittschof, D. (2009). Barnacle cement: a polymerization model based on evolutionary concepts. J. Exp. Biol. 212: 3499–3510. 20

21. Concept 16.1 All of Life Is Connected through Its Evolutionary History
Many very distantly related species of birds (e.g., penguins, ostriches, flightless ducks, and rails) share the trait of flightlessness even though their ancient common ancestors were able to fly. This independent evolution of flightlessness in many distantly related taxa exemplifies what type(s) of evolutionary/phylogenetic patterns?
a. Convergent evolution
b. Evolutionary reversal
c. A homoplastic trait
d. A synapomorphic trait
e. a, b, and c
Answer: e

22. Table 16.1 Eight Vertebrates and the Presence or Absence of Some Shared Derived Traits

23. Figure 16.3 Inferring a Phylogenetic Tree

24. Figure 16.3 Inferring a Phylogenetic Tree

25. Phylogeny can be reconstructed from traits of organisms
Apply the concept p.320
Phylogeny can be reconstructed from traits of organisms
This matrix supplies data for seven land plants and an outgroup (an aquatic plant known as a stonewort). Each trait is scored as either present (+) or absent (-) in each of the plants. Use this data matrix to reconstruct the phylogeny of land plants and answer the questions.
Which two of these taxa are most closely related?
Plants that produce seeds are known as seed plants. What is the sister group to the the seed plants among these taxa?
Which two traits evolved along the same branch of your reconstructed phylogeny?
Are there any homplasies in your phylogeny?

26. Apply the Concept, Ch. 16, p. 320

27. Figure 16.4 The Chordate Connection

28. Figure 16.4 The Chordate Connection

29. Figure 16.4 The Chordate Connection (Part 1)

30. Figure 16.4 The Chordate Connection (Part 2)

31. Figure 16.4 The Chordate Connection (Part 3)

32. Figure 16.4 The Chordate Connection (Part 4)

33. Figure 16.5 The Accuracy of Phylogenetic Analysis

34. Figure 16.5 The Accuracy of Phylogenetic Analysis

35. Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 1)

36. Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 2)

37. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
In a hypothetical study, physical fitness was measured in humans from seven European countries. Physical fitness levels were classified according to a scale from 1 (lowest) to 10 (highest).
Do you think it would be problematic to infer phylogenetic relationships (i.e., create a phylogeny) from such data?
Why or why not?

38. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
In a hypothetical study, physical fitness was measured in humans from seven European countries. Physical fitness levels were classified according to a scale from 1 (lowest) to 10 (highest). Inferring phylogenetic relationships from such data would be problematic because
a. it is difficult to find an outgroup for humans.
b. only molecular genetic data can be used to construct phylogenies.
c. physical fitness is a morphological trait that is predominantly environmental, and not heritable.
d. All of the above
e. None of the above
Answer: c

39. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
Using this hypothetical table of traits (left column) for these imaginary taxa (top row), construct a phylogeny, assuming that the Priltezon is the outgroup:

40. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
The constructed phylogeny would look like: a. b. c.
Answer: a

41. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
Parsimony principle—the preferred explanation of observed data is the simplest explanation In phylogenies, this entails minimizing the number of evolutionary changes that need to be assumed over all characters in all groups. The best hypothesis is one that requires the fewest homoplasies.
WEB ACTIVITY 16.1 Constructing a Phylogenetic Tree
INTERACTIVE TUTORIAL 16.1 Phylogeny and Molecular Evolution
APPLY THE CONCEPT Phylogeny can be reconstructed from traits of organisms

42. Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
Mathematical models are now used to describe DNA changes over time. Models can account for multiple changes at a given sequence position, and different rates of change at different positions. Maximum likelihood methods identify the tree that most likely produced the observed data. They incorporate more information about evolutionary change than do parsimony methods.

43. Figure 16.6 A Portion of the Leptosiphon Phylogeny

44. Figure 16.6 A Portion of the Leptosiphon Phylogeny

45. Figure 16.7 Phylogenetic Tree of Immunodeficiency Viruses

46. Figure 16.8 The Origin of a Sexually Selected Trait

47. Figure 16.8 The Origin of a Sexually Selected Trait

48. Figure 16.9 A Molecular Clock of the Protein Hemoglobin

49. Figure 16.9 A Molecular Clock of the Protein Hemoglobin

50. Figure 16.10 Dating the Origin of HIV-1 in Human Populations

51. Figure 16.10 Dating the Origin of HIV-1 in Human Populations

52. Figure 16.10 Dating the Origin of HIV-1 in Human Populations (Part 1)

53. Figure 16.10 Dating the Origin of HIV-1 in Human Populations (Part 2)

54. Concept Phylogeny Can Be Reconstructed from Traits of Organisms and Concept Phylogeny Makes Biology Comparative and Predictive
In flowering plants, self-compatibility (the ability to self-pollinate) independently evolved three times within the genus Leptosiphon. Discuss whether this pattern of evolution contradicts the principle of parsimony.

55. Does this pattern of evolution contradict the principle of parsimony?
Concept Phylogeny Can Be Reconstructed from Traits of Organisms and Concept Phylogeny Makes Biology Comparative and Predictive
In flowering plants, self-compatibility (the ability to self-pollinate) independently evolved three times within the genus Leptosiphon.
Does this pattern of evolution contradict the principle of parsimony?
a. Yes
b. No
c. Can’t be determined from the information given.
Answer: a
(The most parsimonious explanation would be that the trait evolved only once in a shared common ancestor. Instead it has evolved independently three times. There are some exceptions to parsimony in evolutionary relationships.)

56. Concept 16.3 Phylogeny Makes Biology Comparative and Predictive
The amino acid sequence of cytochrome c has been analyzed in over 100 eukaryotic species, and the molecular data support the idea that cytochrome c is an evolutionarily conservative protein.
Refer to the graph below showing the molecular clock for cytochrome c. You are given a sample of this protein that has roughly 60 amino acid changes per 100 sites, when compared to an ancestor. How many millions of years ago would you predict that the species the sample came from diverged from that ancestor?

57. Concept 16.3 Phylogeny Makes Biology Comparative and Predictive
How many millions of years ago would you predict that the species the sample came from diverged from that ancestor?
a. 400
b. 600
c. 800
d. 1,000
e. 1,200
Answer: e

58. Figure 16.11 Monophyletic, Polyphyletic, and Paraphyletic Groups

59. Figure 16.11 Monophyletic, Polyphyletic, and Paraphyletic Groups

60. Concept 16.4 Phylogeny Is the Basis of Biological Classification
In the following figure, which of the following groups are correctly described?
a. Chimpanzees, humans, and gorillas are polyphyletic.
b. Orangutans, gorillas, and humans are monophyletic.
c. Humans and gorillas are paraphyletic.
d. Chimpanzees, humans, and gorillas are paraphyletic.
e. None of the above
Answer: c

61. Figure 16.12 Same Common Name, Not the Same Species

62. Phylogeny is the basis of biological classification
Apply the concept p. 330
Phylogeny is the basis of biological classification
Consider this phylogeny and three possible classifications of the living taxa.
Which of these classifications contains a paraphyletic group?
Which of these classifications contains a polyphyletic group?
Which of these classifications is consistent with the goal of including only monophyletic groups in a biological classification?
Starting with the classification you named in question 3, how many additional group names would you need to include all the clades shown in this phylogenetic tree?

63. Apply the Concept, Ch. 16, p. 330

64. Figure 16.13 Evolution of Fluorescent Proteins of Corals

65. Figure 16.13 Evolution of Fluorescent Proteins of Corals