Bis2C: Lecture 10 extras on "New View of the Tree of Life" paper
BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.
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Transcript of BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.
![Page 1: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/1.jpg)
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
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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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Reading
• Previous lecture: !
• Current Lecture: ! 1: Chapter 22
• Next Lecture: ! 2: Chapter 22
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![Page 4: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/4.jpg)
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
![Page 5: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/5.jpg)
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
![Page 6: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/6.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
People
• Faculty ! Dr. Jonathan Eisen ([email protected]) ! Dr. Peter Wainwright ([email protected])
• Course Coordinator ! Dr. Joel Ledford ([email protected])
• Course Assistant (enrollment issues) ! Hoorin Sandhu ([email protected]) ! 530-752-7590
• TAs ! Contact information for Lab TAs sent separately ! The head TA is Geoff Benn
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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
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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
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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
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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!
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clickers
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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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Do Not Cheat
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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. !!
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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
![Page 14: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/14.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Diversity of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogeny Is Critical to Understanding Diversity
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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.”
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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. 25.117
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
How to Read a Phylogenetic Tree
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
How to Read a Phylogenetic Tree
18
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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
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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
![Page 22: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/22.jpg)
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
![Page 23: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/23.jpg)
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
![Page 24: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/24.jpg)
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
![Page 25: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/25.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
Phylogenetic trees are oversimplifications of evolutionary history.
19
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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
![Page 27: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/27.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
C
Oversimplification Example 1: Populations Not Shown
B
C
A
21
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
22
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
23
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
A
B
C
A
24
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
25
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
26
Oversimplification Example 1: Populations Not Shown
![Page 33: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/33.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
27
Oversimplification Example 1: Populations Not Shown
![Page 34: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/34.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
B
C
D
E
A
28
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 29
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30
Oversimplification Example 1: Populations Not Shown
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 31
Oversimplification Example 1: Populations Not Shown
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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
![Page 39: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/39.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Oversimplification Example 2: Many Branches Not Shown
33
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 34
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!OrangutanSumatran!Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages
![Page 41: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/41.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 35
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!OrangutanSumatran!Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages
![Page 42: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/42.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 36
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!OrangutanSumatran!Orangutan
Oversimplification Example 2: Many Branches Not Shown
Additional modern lineages
Extinct lineages.
![Page 43: BIS2C. Biodiversity and the Tree of Life. 2014. L1. Introduction and Overview.](https://reader031.fdocuments.us/reader031/viewer/2022022412/58f30dc31a28ab276a8b45f9/html5/thumbnails/43.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 37
Chimp
Bonobo
E. Gorilla
W. Gorilla
Bornean!OrangutanSumatran!Orangutan
37
Oversimplifications Combined
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept
Phylogenetic trees are critical for understanding biodiversity.
38
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 39
Where did HIV Come From?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where did HIV Come From?
40
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 41
Where did HIV Come From?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 42
Who Transmitted Virus to Victim?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Who Transmitted Virus to Victim?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What if Dinosaurs Didn’t Go Extinct?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
45
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Birds ARE Dinosaurs
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Round-up to Attack Malaria?
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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!
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Are These Things Plants?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What Microbes Are Living in My Gut?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 1 Outline
• Administrative details
!
• Phylogeny and phylogenetic trees
!
• Outline of the course
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Major Topics of the Course
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Concepts relating to phylogeny and biodiversity. !
Facts about phylogeny and biodiversity.
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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.
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
The Tree of Life (used in LIFE Version 10)
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BIS2C is ORGANIZED BY THE
TREE OF LIFE
and
PHYLOGENY
The Tree of Life (used in LIFE Version 10)
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 57
Week 1 !Phylogenetic Trees
Week 1: Phylogenetic Trees
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Week 2 !The Tree of Life
Week 2: The Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
LifePlants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
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Week 2: Tree of Life
Week 2 !The Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
LifePlants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
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Week 3 !MicrobialDiversity
Week 3: Microbial Diversity
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Midterm 1
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Midterm #1
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
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Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
LifePlants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 4-5 !Plants
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 4-5: Plants
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Weeks 4-5 !Plants
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
LifePlants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Week 6: Fungi
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Week 6 !Fungi
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Week 6: Fungi
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Week 6 !Fungi
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Midterm 2
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Midterm #2
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Protists
BACTERIA
ARCHAEA
EUKARYA
Mitochondria
Chloroplasts
LifePlants
Protists
Protists
Protists
Protists
Protists
Fungi
Animals
Weeks 7-9: Animals
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Weeks 7-9 !Animals
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Weeks 7-9: Animals
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Weeks 7-9 !Animals
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Final
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Final Exam
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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.
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Viral Diversity
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
When Did HIV Originate in Humans?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
When and Why Did “Swordtails” Originate?
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When and Why Did “Swordtails” Originate?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Which Came First Red or Green Fluorescence
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Which Came First Red or Green Fluorescent Protein
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