From Organisms to Ecosystems

University of California - Irvine

Patterns of diversity, ecology, and evolutionary biology. Emphasis is on the Tree of Life and how its members are distributed and interact.

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Brad Hughes

BIO SCI 94 Syllabus for Brad Hughes — Winter 2019

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Organisms to Ecosystems (BIO SCI 94 Lec C 05222)
Mon, Wed, Fri | 3:00-3:50 PM | BS3 1200
Instructor Information:
Professor: Brad Hughes, Ph.D.
Office: NS1 1144 (& SH 301 by appointment)
TA Information:
Administrative TA: Kasia Bitner
Professor Hughes' Office Hours: Monday 2:00 - 2:30 PM, Wednesday 4:00 - 4:30 PM at NS1 1144 (or
SH 301 by appointment or announcement)
Office hours are held jointly with the Administrative TA and Professor, occurring during the time between
Lecture F and Lecture C at NS1 1144 or if announced or by appointment they may occasionally occur in SH
301. Students are also encouraged to e-mail the Administrative TA (
( ) ( with questions and to ask questions in Discussion.
Office hour Schedule:
January 7th
2 - 230 pm
January 9th
4 - 430 pm
February 4th
OH Cancelled
February 6th
4 - 430 pm
March 4th
2 - 230 pm
March 6th
January 14th
2 - 230 pm
January 16th
4 - 430 pm
February 11th
2 - 230 pm
February 13th
4 - 430 pm
March 11th
OH Cancelled
March 13th
4 - 430 pm
January 21st
January 23rd
4 - 430 pm
February 18th
February 20th
4 - 430 pm
January 28th January 30th February 25th February 27th
2 - 230 pm
4 - 430 pm
2 - 230 pm
4 - 430 pm
TA Office Hours:
Name Email OH Day OH Time Location
Andrew Friday 9-10 AM SH 329
Janio, Emily Tuesday 8am-9am DBH 1429
Khalaj, Farzy
Li, Cindy Thursday 1:00 PM SH 329
Stipp, Shaun Friday 2:00 PM SH 267
Yin, Yue Thursday 5:00 PM SSL 393
Textbook (Required):
There is a custom 5 edition made for UCI which includes unique access codes for Mastering Biology. This
content will be optional but may improve your learning. You can purchase the custom 5 edition at the UCI
bookstore or (Course access code hughes44895). You can also purchase
just the custom access codes online, which give you access to the eBook. Finally, you can buy the regular
5 edition from various retailers. The regular 5 edition does not have access codes to Mastering Biology; it
contains additional chapters that we skip in this course, but the chapters are numbered in the same order.
Do NOT buy the 6 edition: it does not contain some required content from the 5 edition.
Freeman, Biological Sciences BIO 94 (Custom Package for University of California, Irvine)
ISBN-10: 1323000984
ISBN-13: 9781323000984
Lecture Chapter Subject(s) covered Week Session Date
Chapter 1 Biology and the Tree of Life 1 1 1-7
Chapter 25 Evolution by Natural Selection 1 2 1-9
Chapter 26, part 1 Evolutionary Processes 1 3 1-11
Chapter 26, part 2 Evolutionary Processes 2 4 1-14
Chapter 27 Speciation 2 5 1-16
Chapter 28 Phylogenies and the History of Life 2 6 1-18
th th
th th
- Holiday 3 - 1-21
Chapter 29 Bacteria and Archaea 3 7 1-23
Chapter 30, part 1 Protists 3 8 1-25
Chapter 30, part 2 Protists 4 9 1-28
Midterm 1 Chapters 1, 25, 26, 27, 28, 29, 30 4 - 1-30
Chapter 31, part 1 Green Algae and Land Plants 4 10 2-1
Chapter 31, part 2 Green Algae and Land Plants 5 11 2-4
Chapter 32 Fungi 5 12 2-6
Chapter 33 An Introduction to Animals 5 13 2-8
Chapter 34, part 1 Protostome Animals 6 14 2-11
Chapter 34, part 2 Protostome Animals 6 15 2-13
Chapter 35, part 1 Deuterostome Animals 6 16 2-15
- Holiday 7 - 2-18
Chapter 35, part 2 Deuterostome Animals 7 17 2-20
Midterm 2 Chapters 31, 32, 33, 34, 35 7 - 2-22
Chapter 36 Viruses 8 18 2-25
Chapter 52 An Introduction to Ecology 8 19 2-27
Chapter 53 Behavioral Ecology 8 20 3-1
Chapter 54 Population Ecology 9 21 3-4
Chapter 55, part 1 Community Ecology 9 22 3-6
Chapter 55, part 2 Community Ecology 9 23 3-8
Chapter 56 Ecosystems and Global Ecology 10 24 3-11
Chapter 57 Biodiversity and Conservation Biology 10 25 3-13
Midterm 3 Chapters 36, 52, 53, 54, 55, 56, 57 10 - 3-15
Final Exam Cumulative - - 3-18
Assessment Component % Points
iClicker Lecture Questions 10 100pts
Discussion (participation & activity achievement) 10 100pts
Midterm 1 15 150pts
Midterm 2 15 150pts
Midterm 3 15 150pts
Final Exam 35 350pts
Total Combined 100 1000pts
Our grading is based upon the administrative requirement that only 25% of students receive A's in bio 94. So
our grading process in this course utilizes a curve applied to an initial target of letter grades corresponding to
the following percentages:
>96.0% = A+; >93.0% = A; >90.0% = A-; >86.0% = B+; >83.0% = B; >80.0% = B-; >76.0% = C+;
>73.0% = C; >70.0% = C-; >66.0% =D+; >63.0% = D; >60.0% =D-; < 60.0% = F
Once all scores (including 3 Midterms, Final, Lecture Questions, Discussions) are calculated, if the
total percentages of A+, A and A- grades are less than 25% of the total number of students enrolled then the
grades will be curved up. If the total percentages of A+, A and A- grades are more than 30% of the total
number of students enrolled then the grades will be curved down, although in this case only the A grades
will be shifted down to B+ grades with no downward shift for other students with non-A grades. To reduce
unfairness due to discrepant grading systems amongst TA's Discussion sections, all Discussion section
grades will be normalized, so they all have the same average score.
iClicker version 1 or 2: Please be registered by the first day of class (Jan 7th). You must register your
iClicker through Canvas or your scores won’t synchronize with our gradebook (Don’t register through Simply login to Canvas and select our course. To the right of your blue EEE canvas toolbar,
click on the “iClicker registration” tab. Follow the link and input your iClicker Remote ID (Devices available
for purchase at the UCI bookstore).
Lecture Questions: 10% of Grade. You will need to register your iClicker on Canvas. There will be at
least 3 iClicker lecture questions per lecture session. These questions will test your comprehension of
information in the present lecture. The questions will be shown on screen and you will use your iClicker
device to answer them. Accommodations for students with visual disabilities will be made at request.
There are a total of 100 points possible to be earned through lecture questions, for 10% of your course
grade. All Lecture Questions are Discussion-Centered and Participation-Based, so you will be able to
help one another with thinking through your answer choices. It is the intention of the course design to
lower stress during class and use the class time as an introduction and overview of the material
BEFORE you read through the textbook on your own. Having an incorrect response still awards you
100%, a correct response awards you 100% and this is to reward attendance and participation. However,
if you do not click in to respond to all of the Lecture Questions during a session you will not be given any
of the points for that day. The first two sessions are considered practice, so they are not scored. In
addition, the lecture question grades from your two lowest scoring sessions will be automatically
Discussion: 10% of Grade. You will have been assigned a specific Discussion section prior to reading
this. Your attendance, participation, and achievement in Discussion will be assessed by the TA
administering your section. Discussion will include Q&A and guidance, as well as potential activities
implemented by your TA to meet the specific needs of your section at any given time. Activities might
include discussions, presentations, quizzes, and other pedagogies. Activities may not always be worth
points, but your TA will let you know when they are. If you miss your discussion section you cannot
attend another section. Your lowest two discussion scores will be dropped, including discussions you
missed. Each discussion is worth 10 points, for a total of 100 points.
Assessments: MT 1 (15%), MT 2 (15%), MT 3 (15%), Final Exam (35%). There will be three in-class
midterms and one final exam. All concepts and content material that will be tested on may be found in
the textbook, which will be the official reference source for every Assessment question and its answer
(Lecture Questions are based on Lectures and are NOT strictly based on the textbook). The lectures will
support and complement the textbook very closely, so study review may be conducted most efficiently
and comprehensively by reviewing the textbook. Each midterm will have 25 multiple-choice questions on
the material from the previous 8 or 9 lecture sessions. The chapters covered in each assessment are
listed in the table above. The final exam is cumulative and will include 50 multiple choice questions. Each
question on the midterms is worth 6 points, and each question on the final is worth 7 points. Exams
cannot be rescheduled and make-ups will not be available. If you miss one or two midterms due to a
documented illness or emergency, your score on the other midterm(s) will be weighted proportionally to
count for the missed midterm(s). If you miss all three midterms due to a documented illness or
emergency, the midterms will be dropped from your grade, and the final score will count for 80% of your
grade. If you miss the final exam due to a documented emergency or illness, it will be dropped from your
grade and each of your midterms will be weighted to compensate.
Electronic Devices: iClickers are required during class to gain class participation points associated with the
iClicker Lecture Questions. Students may also use their other electronic devices to take notes, although
research has shown that students who take handwritten notes perform statistically significantly better, on
average, than when using laptops to take notes. Electronic devices should not be used during Lecture
Questions (simply lower screen or move aside, during the questions, depending on your specific device) and
may not be used during any of the Midterms or the Final Exam.
Accommodations: I provide accommodations for any students with disabilities. Please contact me via
email to initiate an individualized solution. Alternate exam policies can be coordinated together with the UCI
Disability Services center at (
PPT NOTES: As additional support for note-taking you can access PPT Files from the Files section of the
Canvas site. This optional tool can be printed out for writing notes on, or alternatively used electronically on
your laptop or phone.
Makeup Policy: Lecture Questions may not be made up, but the two lowest lecture questions are
automatically dropped from your grade. Regarding discussions and assessments, extensions for
extenuating circumstances can be requested via email. Documentation is typically required.
Academic Honesty: There is zero tolerance for cheating, including “clicking-in” for someone, in this class,
or unfair use of electronic devices. In the event of cheating, the appropriate campus-wide policies will be
followed, including contacting the appropriate deans.
Refer to
( for details.
Academic dishonesty or cheating is defined as an intentional act of fraud in which a student seeks to claim
credit for the work or efforts of another. This includes assisting other students in acts of dishonesty or
coercing students into acts of dishonesty, whether it is on writing, lab work, or exams. If you are not sure if
something is cheating or not, please ask! If you observe cheating, please bring it to the immediate attention
of any instructor. You will remain anonymous.
Discussion Sections:
Section Course
#Day Time Location TA E-mail Office Hour
C1 05223 Mon 9-9:50 am BS3
2130 Andrew Dang
C2 05224 Mon 12-12:50
2130 Andrew Dang
C3 05225 Mon 11-11:50
2130 Andrew Dang
C4 05226 Tue 9-9:50 am DBH
1429 Emily Janio
C5 05227 Tue 10-10:50
1429 Emily Janio
C6 05228 Tue 11-11:50
1429 Emily Janio
Read a phylogenetic tree and understand the role of similarities and differences in
constructing phylogenetic trees.
Describe what biologists do¾that is, how they approach problems and why they do
Chapter 25
Define evolution,fitness,and adaptationusing the biological definitions.
Describe the nature of the evidence regarding (1) whether species change through time and (2) whether
they are related by common ancestry.
Assess whether Darwin’s four postulates are true in any given example, explain to a friend why evolution
mustoccur if all four are true, and explain whether evolution will occur if any of the four are nottrue.
Identify common misconceptions about evolution and give examples to illustrate why they are not true.
(For example: Is evolution progressive? Do animals do things “for the good of the species”? Does
evolution result in perfection?)
Chapter 26
Test whether evolution or nonrandom mating is occurring at a particular gene, using the Hardy-Weinberg
Describe the four evolutionary mechanisms, and list whether each one causes adaptation, introduces
new alleles, acts randomly, or causes genetic variation to increase or decrease.
Explain how nonrandom mating can affect genotype frequencies without causing
Define sexual selection. Explain which sex is more strongly affected by sexual selection, and why.
Chapter 27
Explain the roles that gene flow, selection, genetic drift, and mutation play in the process of speciation.
Define, compare, and contrast the three “species concepts.” Explain why we need three
different sets of criteria to recognize species.
Describe the processes of allopatric speciation, sympatric speciation, and polyploidy, and give examples
of each.
Predict what will happen when two partially divergent populations come into contact again under various
Chapter 28
Draw and interpret phylogenetic trees, and understand how they depict specific hypotheses of
evolutionary relatedness.
Describe how fossils form. List the major strengths and limitations of the fossil record.
Name the three major eras of the Phanerozoic, and list the major evolutionary events and dominant taxa
characteristic of each era.
Describe why adaptive radiations occur, and give several examples.
Explain the difference between mass extinction and background extinction. Describe
what is (and isn’t) known about the causes of the end-Cretaceous and end-Permian mass extinctions.
Chapter 29
Defend the statement that bacteria and archaea are the most important, diverse, and
abundant organisms on the planet.
Explain the six "feeding strategies" that bacteria and archaea use to produce ATP and
obtain carbon building blocks.
Give several examples of the importance of bacteria in human health, in bioremediation, and in
Chapter 30
Define protistand explain why the protists are considered a paraphyletic group.
Give several examples illustrating the medical and ecological importance of protists.
Describe these key innovations of the protists, explain why they were important, and
outline the major hypotheses for how they evolved: nuclear envelope, multicellularity, structures for
support and protection, mitochondria, chloroplasts.
Describe the diversity of feeding, locomotion, and reproduction seen in protists.
Chapter 31
Explain the ecological importance of green algae and land plants.
Describe the evolutionary adaptations that allowed plants to survive and reproduce on land.
Compare the traits of green algae, bryophytes, seedless vascular plants, gymnosperms, and
angiosperms, and give a few examples from each group.
Chapter 32
Describe the ecological importance of fungi.
Describe at least four types of symbiotic relationships that fungi can have with other
organisms and give an example of each.
List some fungal adaptations associated with the absorption of nutrients.
Describe how fungal life cycles differ from animal or plant life cycles.
Identify the distinct reproductive structures of the four traditional groups of fungi.
Chapter 33
Define what makes an animal an animal.
Describe the fundamental changes in morphology and development that occurred as
animals diversified (symmetry, cephalization, germ layers, limbs, etc.).
Place the major lineages of animals correctly on a phylogenetic tree.
List several examples of the diversity that animals have evolved in adaptations for senses, feeding,
movement, and reproduction.
Chapter 34
Describe the major characteristics that differentiate the Ecdysozoa and the
List and describe the basic traits of four major phyla of lophotrochozoans (including
subgroups of mollusks) and two major phyla of ecdysozoans (including subgroups of
Describe the major evolutionary innovations that triggered the diversification of the protostomes,
especially relating to the water-to-land transition, appendages and mouthparts, and metamorphosis.
Chapter 35
List the basic traits of echinoderms and describe their ecological role.
List the basic traits of vertebrates and describe their ecological role.
Describe these innovations that occurred during the evolution of the vertebrates: jaws, limbs, flight, the
amniotic egg, the placenta, and parental care.
Briefly describe the known history of the hominid lineages, starting from the common
ancestor shared with chimpanzees and continuing to modern humans.
Chapter 36
Define virusand explain why viruses are not considered to be alive.
Explain the difference between enveloped and nonenveloped viruses.
List the six steps of a viral replicative (lytic) cycle and contrast it with the lysogenic cycle.
Describe some of the problems caused by emerging viral diseases and give at least one example.
Explain how the diversity of viruses is related to their genetic material.
Chapter 52
Explain the goals of the branch of biology called ecology.
List the primary factors that limit the distribution and abundance of both aquatic species and terrestrial
Understand how climate varies and how it is changing.
Explain how a species distribution is affected by historical, biotic, and abiotic factors.
Chapter 53
Explain proximate and ultimate causes of behavior and how genetic and physiological mechanisms
affect fitness.
Describe how foraging decisions maximize energy gain and minimize costs.
Explain how sexual hormones affect behavior and explain female mate choice.
Describe the various cues that animals use to navigate.
Describe the various ways in which animals communicate.
Explain why animals might behave altruistically.
Chapter 54
Use life tables to describe how likely it is that individuals in each age class in a population will survive
and reproduce.
Calculate the growth rate of a population from life-table data or from direct observation of changes in
population size over time.
Describe the variety of patterns in population size changes over time.
Explain the link between understanding population dynamics and applying the data to
endangered species.
Chapter 55
Discuss the various interactions among species, such as competition, consumption, and mutualism.
Explain why an assemblage of species in a biological community changes over time.
Explain why a biological community is primarily a function of climate and chance historical events.
Explain why species richness is higher in the tropics and lower toward the poles.
Explain why species richness is higher on large islands near a mainland than on small,
isolated islands.
Chapter 56
Course Summary:
Date Details
Lecture 1 (
Lecture 2 (
List and describe the four components of an ecosystem.
Explain how energy flows from producers to consumers and decomposers in a food web.
Describe how productivity in aquatic and terrestrial ecosystems is limited.
Explain how reservoirs are important in understanding nutrient cycles.
Explain how nutrient addition by humans is causing pollution.
Explain how burning of fossil fuels has led to global warming.
Chapter 57
Describe the three levels at which biodiversity is quantified.
Explain the evidence supporting the notion that a mass extinction is currently occurring.
Explain how humans are dependent on biodiversity.
Discuss the various solutions to the biodiversity crisis.

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