BIS2C. Biodiversity and the Tree of Life. At UC Davis Spring 2014. Lecture 1. Introduction and Overview. Slides for Lectures by Jonathan Eisen

1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1
1
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
!
Lecture 1:
Introduction and Overview
!
!
!
Prof. Jonathan Eisen

2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous lecture:
! Bis2B
• Current Lecture:
! 1: Introduction & Overview
• Next Lecture:
! 2: Phylogenetic trees
2

3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Reading
• Previous lecture:
!
• Current Lecture:
! 1: Chapter 22
• Next Lecture:
! 2: Chapter 22
3

4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
4

5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
5

6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
People
• Faculty
! Dr. Jonathan Eisen (jaeisen@ucdavis.edu)
! Dr. Peter Wainwright (pcwainwright@ucdavis.edu)
• Course Coordinator
! Dr. Joel Ledford (jmledford@ucdavis.edu)
• Course Assistant (enrollment issues)
! Hoorin Sandhu (hsandhu@ucdavis.edu)
! 530-752-7590
• TAs
! Contact information for Lab TAs sent separately
! The head TA is Geoff Benn
6

7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Schedule
• Section A:
! MWF: 11:00-11:50 AM Rock Hall
! M: 3:10-4:00 PM Freeborn Hall
• Section B:
! MWF: 1:10-2:00 PM Rock Hall
! M: 4:10-5:00 PM Freeborn Hall
• Midterm 1: Monday, April 21 (3:10-4; 4:10-5)
• Midterm 2: Monday May 12 (3:10-4; 4:10-5)
• Final:
! Section A: Wednesday, June 11, 6:00 - 8:00 PM
! Section B: Thursday, June 12, 3:30- 5:30 PM 7

8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Grading
Labs: 105 points
Lab practical: 45 points
Midterm 1: 100 points
Midterm 2: 100 points
Final: 150 points
!
Total: 500 points
!
Bonus points via clickers will be worth up to 25 points
8

9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Resources
• Smartsite
! Podcasts
! Lecture Slides
! Prelabs
• Book
! Life: The Science of Biology, 9th Edition
! Readings: see syllabus and lectures
• Lab
• CLC
• TA and Faculty Office Hours
9

10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
PreLab
10
Smartsite- http://smartsite.ucdavis.edu
• Check Smartsite regularly for updates
• Pre-lab link active on left
• Pre-lab link deactivated at 9:00 am Mondays
Hint: Once you have submitted your pre-lab, take a screenshot as a “receipt”.
Your first Pre-
lab is due
Monday,
January 13!

11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clickers
11
iClickers- http://www.iclicker.com
• Clickers will be used throughout the
class.
• iClicker v1 or iClicker v2 will both work.
• No other clicker systems are compatible.
Register your clicker online today. If you need help, drop by the CLC.
Registration
• In order for us to match your entries and
give you points, you must register online.
• Everyone needs to re-register, even if
you have done this last quarter.
• Enter your correct student ID number.
Please Don’t…
• Borrow another student’s clicker
• Forget to register
• Ask for a loaner clicker

12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Do Not Cheat
12
Cheaters Beware!
• Part of our job is to keep your education fair and honest.
!
What Happens?
• All suspected cases of academic dishonesty are immediately referred to SJA.
!
What is considered cheating?
• Wandering eyes during exams, including non-verbal cues, etc.
• Using more than one clicker at a time.
• Attending another lecture section on quiz days.
• Using or copying work from other students, including previously submitted work.
• Check with SJA online for any questions.
!
Plagiarism
• The answers that you submit on pre-labs and homework must be entirely your own.
• Avoid internet sites and use your lab manual and textbook (i.e. Yahoo Answers,
Quizlet, etc.)
• Try to answer the questions without using the internet.
!
Work Together
• We want you to work together in BIS 2C, but keep your answers entirely your own.
• If you are not sure, please ask first.
!

13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
13

14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Diversity of Life
14

15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogeny Is Critical to Understanding Diversity
15

16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
“There is grandeur in this view of life, with its
several powers, having been originally breathed
into a few forms or into one; and that, whilst this
planet has gone cycling on according to the fixed
law of gravity, from so simple a beginning endless
forms most beautiful and most wonderful have
been, and are being, evolved.”
16

17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
Phylogeny is a description of the evolutionary
history of relationships among organisms (or their
parts).
This is portrayed in a diagram called a
phylogenetic tree.
Ch. 25.1
17

18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
How to Read a Phylogenetic Tree
18

19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
How to Read a Phylogenetic Tree
18

20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
How to Read a Phylogenetic Tree
18

21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
The splits in branches
are called nodes, and
indicate a division of
one lineage into two.
How to Read a Phylogenetic Tree
18

22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
The splits in branches
are called nodes, and
indicate a division of
one lineage into two.
The positions of the nodes on
the time scale (if present)
indicate the times of the
corresponding speciation
events.
How to Read a Phylogenetic Tree
18

23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
The splits in branches
are called nodes, and
indicate a division of
one lineage into two.
The positions of the nodes on
the time scale (if present)
indicate the times of the
corresponding speciation
events.
How to Read a Phylogenetic Tree
18

24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
The splits in branches
are called nodes, and
indicate a division of
one lineage into two.
The positions of the nodes on
the time scale (if present)
indicate the times of the
corresponding speciation
events.
How to Read a Phylogenetic Tree
18

25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
Phylogenetic trees are oversimplifications of
evolutionary history.
19

26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogenetic trees are oversimplifications of
evolutionary history.
!
Example 1: Populations are not always shown.
20
Key Concept

27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
C
Oversimplification Example 1: Populations Not Shown
B
C
A
21

28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
22
Oversimplification Example 1: Populations Not Shown

29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
23
Oversimplification Example 1: Populations Not Shown

30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
24
Oversimplification Example 1: Populations Not Shown

31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
25
Oversimplification Example 1: Populations Not Shown

32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
26
Oversimplification Example 1: Populations Not Shown

33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
27
Oversimplification Example 1: Populations Not Shown

34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
28
Oversimplification Example 1: Populations Not Shown

35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 29
Oversimplification Example 1: Populations Not Shown

36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30
Oversimplification Example 1: Populations Not Shown

37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 31
Oversimplification Example 1: Populations Not Shown

38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogenetic trees are oversimplifications of
evolutionary history.
!
Example 2: Many branches are usually not shown.
32
Key Concept

39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Oversimplification Example 2: Many Branches Not Shown
33

40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 34
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages

41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 35
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages

42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 36
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages
Extinct lineages.

43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 37
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
37
Oversimplifications Combined

44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
Phylogenetic trees are critical for understanding
biodiversity.
38

45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 39
Where did HIV Come From?

46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where did HIV Come From?
40

47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 41
Where did HIV Come From?

48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 42
Who Transmitted Virus to Victim?

49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Who Transmitted Virus to Victim?
43

50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What if Dinosaurs Didn’t Go Extinct?
44

51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
45

52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
46

53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
47

54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Round-up to Attack Malaria?
48

55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Sudden Oak Death
Why won’t most anti fungals kill this?
49
A hillside in Big Sur, California, devastated by sudden
oak death - from Wikipedia!
From http://www.ars.usda.gov/Main/docs.htm?
docid=21999!

56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Are These Things Plants?
50

57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Microbes Are Living in My Gut?
51

58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
52

59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Major Topics of the Course
53
Concepts relating to phylogeny and biodiversity.
!
Facts about phylogeny and biodiversity.

60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
“The Tree of Life” is used to refer to phylogenetic
trees that include all of life.
“The Tree of Life” term is also sometimes used to
refer to the concept that all living organisms are
related to one another through shared ancestry.
54

61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
The Tree of Life (used in LIFE Version 10)
55

62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 56
BIS2C is ORGANIZED BY THE
TREE OF LIFE
and
PHYLOGENY
The Tree of Life (used in LIFE Version 10)

63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 57
Week 1
!
Phylogenetic
Trees
Week 1: Phylogenetic Trees

64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 58
Week 2
!
The Tree of Life
Week 2: The Tree of Life

65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
59
Week 2: Tree of Life
Week 2
!
The Tree of Life

66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
60
Week 3
!
Microbial
Diversity
Week 3: Microbial Diversity

67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Midterm 1
61
Midterm #1

68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
62
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 4-5
!
Plants

69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
63
Weeks 4-5
!
Plants

70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Week 6: Fungi
64
Week 6
!
Fungi

71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Week 6: Fungi
65
Week 6
!
Fungi

72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Midterm 2
66
Midterm #2

73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 7-9: Animals
67
Weeks 7-9
!
Animals

74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 7-9: Animals
68
Weeks 7-9
!
Animals

75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Final
69
Final Exam

76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concepts
Phylogeny is a description of the evolutionary
history of relationships among organisms (or their
parts).
Phylogenetic trees are oversimplifications of
evolutionary history.
Phylogenetic trees are critical for understanding
biodiversity.
“The Tree of Life” is used to refer to phylogenetic
trees that include all of life.
70

77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Viral Diversity
71

78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
When Did HIV Originate in Humans?
72

79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
When and Why Did “Swordtails” Originate?
7373

80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 7474
When and Why Did “Swordtails” Originate?

81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Which Came First Red or Green Fluorescence
75

82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Which Came First Red or Green Fluorescent Protein
76