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 ([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

6

mailto:[email protected]





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!

http://smartsite.ucdavis.edu


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

http://www.iclicker.com/register-student-remote


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. 25.117


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



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


18



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!OrangutanSumatran!Orangutan


Additional modern lineages


Chimp

Bonobo

E. Gorilla

W. Gorilla





Chimp

Bonobo

E. Gorilla

W. Gorilla




Extinct lineages.


Chimp

Bonobo

E. Gorilla

W. Gorilla


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!

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

LifePlants

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

LifePlants

Protists

Protists

Protists

Protists

Protists

Fungi

Animals

60

Week 3 !MicrobialDiversity

Week 3: Microbial Diversity


Midterm 1

61

Midterm #1


Weeks 4-5: Plants

62

Protists

BACTERIA

ARCHAEA

EUKARYA

Mitochondria

Chloroplasts

LifePlants

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

LifePlants

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

LifePlants

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