BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.

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

Where we are going and where we have been
• Previous lecture:
! Bis2B
• Current Lecture:
! 1: Introduction & Overview
• Next Lecture:
! 2: Phylogenetic trees
2

Reading
• Previous lecture:
!
• Current Lecture:
! 1: Chapter 22
• Next Lecture:
! 2: Chapter 22
3

Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
4

Lecture 1 Outline
!
!
5

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

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

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

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

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!

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

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.
!

Lecture 1 Outline
!
!
13

Diversity of Life
14

Phylogeny Is Critical to Understanding Diversity
15

“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

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

How to Read a Phylogenetic Tree
18

In the book, all phylogenetic trees
show the common ancestor for the
group on the left; this is called the
root of the tree.
18

root of the tree.
The splits in branches
are called nodes, and
indicate a division of
one lineage into two.
18

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.
18

Key Concept
Phylogenetic trees are oversimplifications of
evolutionary history.
19

!
Example 1: Populations are not always shown.
20
Key Concept

B
A
C
Oversimplification Example 1: Populations Not Shown
B
C
A
21

B
A
B
C
A
22

B
A
B
C
A
23

B
A
B
C
A
24

B
C
D
E
A
25

B
C
D
E
A
26

B
C
D
E
A
27

B
C
D
E
A
28

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 29

!
Example 2: Many branches are usually not shown.
32
Key Concept

Oversimplification Example 2: Many Branches Not Shown
33

Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
Additional modern lineages

Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan

Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
Extinct lineages.

Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!
Orangutan
Sumatran!
Orangutan
37
Oversimplifications Combined

Key Concept
Phylogenetic trees are critical for understanding
biodiversity.
38

Where did HIV Come From?

40

Who Transmitted Virus to Victim?

Who Transmitted Virus to Victim?
43

What if Dinosaurs Didn’t Go Extinct?
44

Birds ARE Dinosaurs
45

Birds ARE Dinosaurs
46

Birds ARE Dinosaurs
47

Round-up to Attack Malaria?
48

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!

Are These Things Plants?
50

What Microbes Are Living in My Gut?
51

Lecture 1 Outline
!
!
52

Major Topics of the Course
53
Concepts relating to phylogeny and biodiversity.
!
Facts about phylogeny and biodiversity.

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

The Tree of Life (used in LIFE Version 10)
55

BIS2C is ORGANIZED BY THE
TREE OF LIFE
and
PHYLOGENY
The Tree of Life (used in LIFE Version 10)

Week 1
!
Phylogenetic
Trees
Week 1: Phylogenetic Trees

Week 2
!
The Tree of Life
Week 2: The Tree of Life

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

Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
60
Week 3
!
Microbial 
Diversity
Week 3: Microbial Diversity

Midterm 1
61
Midterm #1

Weeks 4-5: Plants
62
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 4-5
!
Plants

Weeks 4-5: Plants
63
Weeks 4-5
!
Plants

Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Week 6: Fungi
64
Week 6
!
Fungi

Week 6: Fungi
65
Week 6
!
Fungi

Midterm 2
66
Midterm #2

Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
Life
Plants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 7-9: Animals
67
Weeks 7-9
!
Animals

Weeks 7-9: Animals
68
Weeks 7-9
!
Animals

Final
69
Final Exam

Key Concepts
Phylogeny is a description of the evolutionary
history of relationships among organisms (or their
parts).
Phylogenetic trees are critical for understanding
biodiversity.
“The Tree of Life” is used to refer to phylogenetic
trees that include all of life.
70

Viral Diversity
71

When Did HIV Originate in Humans?
72

When and Why Did “Swordtails” Originate?
7373

When and Why Did “Swordtails” Originate?

Which Came First Red or Green Fluorescence
75

Which Came First Red or Green Fluorescent Protein
76

BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.

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