BI107 CAS Fall 2015 Syllabus

Boston University – Department of Biology BI 107 Principles of Biology I Fall 2015 Professor Dr. Fred Wasserman [email protected] Dr. Sean Mullen [email protected] Dr. Kathryn Spilios [email protected] Dr. Michael Sorenson [email protected]

Topics Darwinian Evolution

Lecture Dates

Office Location

Office Hours*

Sept 2 – Sept 23

BRB 423

M, W, F (4-5) or by appt.

Macroevolution

Sept 24 – Oct 16

BRB 207

MWF 11-noon or by appt.

Ecology and Ecosystems

Oct 19 – Nov 10

SCI301 A

T (11-12), W (10-11 and 1-2) or by appt.

Animal Behavior

Nov 11 – Dec 10

BRB 529

T, Th, F (4-5) or by appt. * office hours during dates listed

Laboratory Director Dr. Kathryn Spilios

[email protected]

Lecture Sections (in SCI109) A1: Tuesday and Thursday, 12:30-1:50pm

Administrative Coordinator Ms. Chenille Hogan [email protected] A2: Monday, Wednesday and Friday, 3:00-3:50pm

Required Materials (see purchasing information posted on Blackboard) TEXTBOOK (also on reserve in the Science and Engineering Library) th Sadava D, Hillis DM, Heller HC, Berenbaum M. 2014. Life: The Science of Biology 10 ed. Sinauer Associates, Inc., Sunderland MA. COURSE WEBSITE (LaunchPad, which is integrated within Blackboard Learn) th LaunchPad for Life, 10 ed. has a wealth of study aids, including self-quizzing to help you practice for exams, animations, flashcards, activities, study ideas, help with math and statistics, and more. LABORATORY MANUAL Spilios KE and Godrick EC. 2015. Principles of Biology I. Hayden-McNeil Publishing, Plymouth, MI. CLICKER Clicker with required license We recommend the TurningPoint ResponseCard RF LCD, but you are welcome to use a TurningPoint ResponseCard that ID# ends in 03 or 04 you prefer (the same card can be used in multiple classes) Grading and Exam Policies • There are four lecture exams throughout the semester. Attendance at all exams is mandatory. Make up exams will only be allowed with official documentation of an absence provided within two business days of the exam. Please contact Chenille Hogan in SCI301 if you need to make up an exam. NOTE: If you miss an exam and cannot provide official documentation, there will be a 20% deduction on your make up exam. • If you are working with the Office of Disability Services you must provide their documentation to Chenille Hogan at least two weeks prior to the first exam. • Exam grades will be posted on the course website (Blackboard) approximately three business days after the exam has been taken. • Both a passing lecture grade and a passing laboratory grade are required to receive credit for this course. Please see the full grading outline provided in the lab manual. • Your course grade for BI 107 is calculated as follows: 4 Lecture Exams, each worth 15% 60% Lecture homework, 4 assignments 4% In-lecture clicker questions 4% Laboratory (see lab manual for breakdown) 32% Final Course Grade 100%

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Boston University – Department of Biology BI 107 Principles of Biology I Fall 2015

ACADEMIC INTEGRITY You are expected to exhibit ethical and honest work habits at all times. The College of Arts and Sciences holds a Zero Tolerance policy with respect to academic misconduct or misrepresentation. It is your responsibility to know, understand, and abide by the Academic Conduct Code. If you are at all uncertain about the definition of misconduct, plagiarism, “cheating” or “academic dishonesty” please refer to the student handbook or the university website for a full description. Please be aware that this issue is extremely serious and any confirmed incidents will be referred to the appropriate university administrator for additional disciplinary action.

LECTURE HOMEWORK You should arrive to lecture prepared for class be reading the associated lecture readings. Keep in mind that reading before lecture is intended to familiarize you with the material, you should thoroughly read again after lecture. Throughout the semester, we will have 4 lecture-based homework assignments. These homework assignments will be completed through LaunchPad using a program called LearningCurve. This program is an adaptive system and is set up like a game – your goal is to reach the target point score. Within each question, you will have access to hints and links to the ebook sections. After each answer, you will receive immediate feedback. You will earn fewer points for answering a question if you need help before you get it right, but you will never lose points. Once you reach the target point score, you will earn full credit for that assignment (there is no partial credit). You are welcome to return to the LearningCurve quiz to study – you will notice that your points will continue to increase, but your final grade on the assignment is based on your points earned at the due date.

Course Syllabus MONDAY

TUESDAY

Week 1 Professor

Topics

WEDNESDAY

Sept. 1

• • • • •

THURSDAY

FRIDAY

Sept. 3

Sept. 4

Sept. 2 Wasserman

Darwinism and the Evidence for Evolution Darwin’s Theory; Five Facts, Three Inferences Evidence for Macro Evolution Artificial Selection Evidence for Natural Selection.

Ch 1.2 Ch 1.3 Ch 21.1 Readings

Blackboard: Darwin Evidence for Evolution Natural Selection

Homework Laboratory

Lecture readings before each lecture No Labs This Week

2


Week 2 Professor

MONDAY

TUESDAY

Sept. 7

Sept. 8

Topics

No Class

• • • • • • • •

WEDNESDAY

THURSDAY

FRIDAY

Sept. 10

Sept. 11

Sept. 9 Wasserman

Evolutionary Processes Hardy-Weinberg Equilibrium Causes of Microevolution Genetic Drift, Gene Flow, Mutation, Non-Random Mating Origin of Species Prezygotic and Postzygotic Reproductive Isolating Mechanisms The Species Concept Dispersal, Colonization, and Vicariance

Ch 21 Ch 23 Blackboard: • Hardy-Weinberg • Species • Speciation • HHMI Biointeractive – The Making of the Fittest: Natural Selection and Adaptation

Readings

Homework

Lecture readings before each lecture AND LearningCurve quiz on LaunchPad (due 9pm Sept 11)

Laboratory

Module 1: Plant Evolution and Ecology (online prelab quiz due by beginning of lab); Monday labs must sign up for an alternate lab this week…come to SCI301

Week 3 Professor

Topics

MONDAY

TUESDAY

Sept. 14

Sept. 15

WEDNESDAY

THURSDAY

FRIDAY

Sept. 17

Sept. 18

Sept. 16 Wasserman

• Adaptive Radiation • Character Displacement • Allopatric, Sympatric and Parapatric Speciation • Directional Selection, Stabilizing Sel., Diversifying Sel. • Human Evolution Ch 23 Ch 33.5

Readings

Blackboard: Species Speciation Human Evolution

Homework

Lecture readings before each lecture

Laboratory

Module 2: Evolution and Population Genetics (online prelab quiz due by beginning of lab)

3


MONDAY

TUESDAY

WEDNESDAY

THURSDAY

FRIDAY

Week 4 Professor

Sept. 21

Sept. 22 Wasserman

Sept. 23

Sept. 24

Sept. 25

Topics

• Human Evolution

Exam 1 Section A1

Exam 1 Section A2

Class will be divided by last names – rooms TBA


Readings

Blackboard: • Human Evolution

Homework Laboratory

Week 5 Professor

Topics

Readings

Homework Laboratory

Mullen Macroevolutionary patterns and major events in the history of life on earth. How do we explain largescale patterns in the history of life? • Major events in the history of life • Adaptive radiation • Extinction • Geologic and extraterrestrial forcing factors • Contingency and determinism Ch 25: The History of Life on Earth Blackboard: • Macroevolution • Readings from “Wonderful Life” by Stephen Jay Gould. • HHMI Biointeractive - Changing Planet: Past, Present, Future. Deep time and the history of life. Lecture readings before each lecture

Module 3, lab 1: Scientific Writing and Avian Niche (online prelab quiz due by beginning of lab)

MONDAY

TUESDAY

Sept. 28

Sept. 29

WEDNESDAY

Sept. 30 Mullen Macroevolutionary patterns and major events in the history of life on earth. How do we explain large-scale patterns in the history of life? • Major events in the history of life • Adaptive radiation • Extinction • Geologic and extraterrestrial forcing factors • Contingency and determinism

THURSDAY

FRIDAY

Oct. 1

Oct. 2

• Phylogenetics and historical inference. Trees and tree-thinking. • Systematics and the Phylogenetic Revolution • Why does evolutionary history matter? • How do we use phylogenetic trees to make historical inference?

Ch 22: Reconstructing and Using Phylogenies; Ch. 31.1: What Characteristics Distinguish the Animals? Blackboard: • Sorting shells – constructing mollusk phylogeny • All in the family – exploring phylogenetic relationships • Journey into Phylogenetic Systematics: Introduction to cladistics Lecture readings before each lecture lecture; Working with the Data, Ch. 22, pg 457 – Does Phylogenetic Analysis Correctly Reconstruct Evolutionary History? Working with the Data, Ch. 31, pg. 631 – Reconstructing the Animal Phylogeny.

Ch 25: The History of Life on Earth; Ch. 27.1: How did the Eukaryotic Cell Arise? Blackboard: • Macroevolution • Readings from “Wonderful Life” by Stephen Jay Gould. The metaphor of replaying life’s tape and the contrast of determinism and contingency. • HHMI Biointeractive - Changing Planet: Past, Present, Future. Deep time and the history of life.

Module 3, lab 2: Avian Niche Field Lab (online prelab quiz due by beginning of lab)

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Week 6 Professor

Topics

Readings

Homework

MONDAY

TUESDAY

Oct. 5

Oct. 6

MONDAY

TUESDAY

Oct. 12

Oct. 13

WEDNESDAY Oct. 14 Schneider

How do we go from c. 20,000 genes to the entire complexity of life? How has evolutionary change in embryological development produced variety of form? HOLIDAY – NO CLASS (Tuesday is a Monday Schedule)

Homework

THURSDAY

FRIDAY

Oct. 8

Oct. 9

Module 4: Phylogenetic Trees (online prelab quiz due by beginning of lab)

Topics

Readings

Oct. 7 Mullen

• Phylogenetics and historical inference. Trees and tree-thinking. Evolution of Development • Systematics and the Phylogenetic • Origin of novelty and morphological change Revolution • How do we go from c. 20,000 genes to the entire complexity • Why does evolutionary history matter? of life? How has evolutionary change in the genetic control of • How do we use phylogenetic trees to embryological development produced variety of form? make historical inference? Ch 22: Reconstructing and Using Ch 19 (19.3 and 19.4) Phylogenies; Ch. 31.1: What Ch 20 Genes, Development & Evolution Characteristics Distinguish the Animals? Blackboard: Blackboard: • Sorting shells – constructing mollusk • HHMI Biointeractive – The Making of the Fittest: Evolving phylogeny Switches, Evolving Bodies • All in the family – exploring • HHMI Biointeractive – The Making of the Fittest: The Birth phylogenetic relationships and Death of Genes • Journey into Phylogenetic Systematics: Introduction to cladistics Lecture readings before each lecture; Working with the Data, Ch. 22, pg 457 – Does Phylogenetic Analysis Correctly Reconstruct Evolutionary History? Working with the Data, Ch. 31, pg. 631 – Reconstructing the Animal Phylogeny

Laboratory

Week 7 Professor

WEDNESDAY

Ch 19 (19.3 and 19.4) Ch 20 Blackboard: • HHMI Biointeractive – The Making of the Fittest: Evolving Switches, Evolving Bodies • HHMI Biointeractive – The Making of the Fittest: The Birth and Death of Genes Lecture readings before each lecture AND LearningCurve quiz on LaunchPad (due 9pm Wed Oct 14)

Laboratory

No labs this week

5

THURSDAY

FRIDAY

Oct. 15

Oct. 16

Exam 2 Section A1

Exam 2 Section A2




Week 8 Professor Topics

• • •

MONDAY

TUESDAY

Oct. 19

Oct. 20

WEDNESDAY

THURSDAY

FRIDAY

Oct. 22

Oct. 23

Oct. 21 Spilios

Introduction to Ecology The causes of our global climate A survey of the biomes

• •

Ecosystems, the big picture The Biosphere – how it all works

Ch 54: Ecology Readings

Ch 58: Ecosystems and Global Ecology (58.1, 58.2, and 58.3)

Blackboard: • Vergés et al., 2014

Homework


Laboratory

Module 5, lab 1: Diversity and Ecosystem Health (online prelab quiz due by beginning of lab)

MONDAY Oct. 26

Week 9 Professor

TUESDAY Oct. 27

WEDNESDAY Oct. 28

THURSDAY Oct. 29

FRIDAY Oct. 30

Spilios Community Ecology – how do populations interact? • The movement of energy through a community Ch 57: Community Ecology (57.1, 57.2, and 57.3) •

Topics

Readings

Blackboard: • Youngsteadt, 2008 • Estes et al., 2011

•

Life Histories and Population Ecology

Ch 55: Population Ecology

Homework


Laboratory

Module 5, Lab 2: Diversity and Ecosystem Health (online prelab quiz due by beginning of lab)

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•

MONDAY

TUESDAY

Nov. 2

Nov. 3

WEDNESDAY Nov. 4 Spilios

Ch 56: Species Interactions and Coevolution

Readings

Blackboard: • Preisser and Elkinton, 2008

FRIDAY

Nov. 5

Nov. 6

Biodiversity and Conservation Biology…is there a problem? What do we do?

•

Species interactions and coevolution

THURSDAY

Ch 59: Conservation Biology Blackboard: • Haddad et al., 2015

Homework

Lecture readings before each lecture AND LearningCurve quiz on LaunchPad (due 9pm on Fri Nov 6)

Laboratory

Module 6, lab 1: Chemical Communication (online prelab quiz due by beginning of lab)

Week 11 Professor

MONDAY

TUESDAY

WEDNESDAY

Nov. 9

Nov. 10

Nov. 11

Spilios

Readings

Exam 3 Section A1



Nov. 13

Ch 53.1 (1093-1096) What are the origins of behavioral biology?

Homework Laboratory

FRIDAY

Nov. 12 Sorenson

• historical background: Animal Behavior (Pavlov, Skinner) versus Ethology (von Frisch, Lorenz, Tinbergen) • species-specific behavior versus individual variation (nature AND nurture) • Tinbergen’s four questions

Topics

Exam 3 Section A2

THURSDAY

Lecture readings before each lecture Module 6, lab 2: Chemical Communication (online prelab quiz due by beginning of lab)

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Boston University – Department of Biology BI 107 Principles of Biology I Fall 2015 Week 13 Professor

MONDAY

TUESDAY

Nov. 16

Nov. 17

WEDNESDAY

THURSDAY

FRIDAY

Nov. 19

Nov. 20

Nov. 18 Sorenson

Topics

• evidence for the genetic basis of behavior • how changes in single genes influence behavior

Readings

• Ch 53.2 (1096-1098) How do genes influence behavior? Weber JN, Peterson BK, Hoekstra HE (2014) Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature, 493, 402–405.

• developmental effects on behavior • forms of imprinting and learning

Ch 53.3 (1098-1102) How does behavior develop?

Homework


Laboratory

Module 7: Keystone Predators (online prelab quiz due by beginning of lab)


MONDAY

TUESDAY

WEDNESDAY

THURSDAY

FRIDAY

Nov. 23

Nov. 24

Nov. 25

Nov. 26

Nov. 27

Sorenson • behavioral ecology • economic analyses of behavior, optimal foraging Thanksgiving Recess

Readings

Homework

Ch 53.4 (1102-1106) How does behavior evolve?


Laboratory

Week 14 Professor

Topics

Readings

No Labs This Week

MONDAY

TUESDAY

Nov. 30

Dec. 1

WEDNESDAY Dec. 2 Sorenson

• circadian rhythms • migration and homing • signals and communication

THURSDAY

FRIDAY

Dec. 3

Dec. 4

• social behavior • mating systems and sexual selection • kin selection

• Ch 53.5 (pp. 1106-1113) What physiological mechanisms underlie behavior? • Horton BM, Moore IT, Maney DL (2014) New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis. Animal Behaviour, 93, 207–219.

Ch 53.6 (pp. 1113-1117) How does social behavior evolve?

Homework

Lecture readings before each lecture AND LearningCurve quiz on LaunchPad (due 9pm on Fri Dec 4)

Laboratory

Final Lab Exam

8


MONDAY

TUESDAY

WEDNESDAY

THURSDAY

FRIDAY

Week 14 Professor

Dec. 7

Dec. 8 Sorenson

Dec. 9

Dec. 10

Dec. 11

Topics

Exam 4 Section A2

Exam 4 Section A1



NO CLASS

Readings

Homework Laboratory

No labs this week

These LEARNING OBJECTIVES are provided to help you prepare for the course, and to give you an indication of what specific knowledge and skills we expect you to possess after the course is over. We encourage you to be familiar with these learning objectives; they will give you an overall roadmap for the course as well as let you know our expectations for each unit. Unit 1: Darwinian Evolution (Prof. Wasserman) 1. Define “science”. Give examples of what is science and what is not science. 2. Define what we mean by evolution via the process of natural selection. 3. Compare macroevolution and microevolution. List evidence for each. 4. Determine if a population is in Hardy Weinberg equilibrium. 5. Debate the definition of a species. 6. Explain how new species form over evolutionary time. 7. Determine if humans are evolving. Unit 2: Macroevolution (Prof. Mullen) 1. Describe how earth history has affected life’s history. Describe the major geological and extraterrestrial events that affected life’s history. Relate geological and extraterrestrial events to both extinction and adaptive radiation. 2. Explain what is meant by “contingency” and “determinism” in explaining the evolution of biodiversity. 3. Explain the evidence that all life is related by a history of common ancestry and descent. Explain the logic underlying the inference of phylogenetic history. 4. Explain how changes in genes lead to changes in development and the origin of novel phenotypes (morphology, behavior, etc.). 5. Understand how gene expression is regulated and how the time and location of gene expression in developing embryos is controlled. 9

Boston University – Department of Biology BI 107 Principles of Biology I Fall 2015 6. Explain the role of changes in the time and place of gene expression in the evolution of novel morphological features and the evolution of the disparate animal body plans. 7. Explain in clear and concise terms how evolution works: beginning with mutations in the DNA, through changes in development, the production of variable phenotypes, and natural selection. Also explain the role that chance plays in evolution – what about evolution is random and what is deterministic. Unit 3: Ecology and Ecosystems (Prof. Spilios) 1. Describe the physical processes that give rise to the seasons and global climate patterns. 2. Discuss how climate change could impact the distribution of ecosystems. 3. Describe how ecologists study populations and what the mathematical calculations can tell us. 4. Compare and contrast the different categories of species interactions, and analyze the role of coevolution within each. 5. Define how energy flow, biomass distribution, and species interactions shape an ecological community. 6. Describe how chemical elements cycle through the biosphere. 7. Describe how biologists predict changes in biodiversity, possible impacts on biodiversity, and what is being done to protect it. Unit 4: Animal Behavior (Prof. Sorenson) 1. Outline Tinbergen’s four questions about behavior and explain how each question focuses on different but complementary explanations for why animals behave the way they do. 2. Understand the importance of evolutionary and ecological perspectives for understanding the behavior of any given species and the diversity of behavioral phenotypes observed in different organisms. 3. Distinguish between proximate and ultimate explanations of behavior. 4. Describe scientific evidence linking genetic variation to differences in behavior. 5. Explain the proximate effects of hormones and nerve cells in regulating behavior. 6. Explain how development, including imprinting and learning and interaction with environmental conditions, influences behavior. 7. Explain the evolutionary origins of complex social behaviors such as mate choice, cooperation and altruism.

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BI107 CAS Fall 2015 Syllabus

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