Embed Size (px)
DESCRIPTION
Bio
Citation preview
Laboratory Manual for Biology 1020H
Fall 2014
Department of Biology
Trent University, Peterborough, Ontario
Name:______________________
2
TRENT UNIVERSITY
BIOLOGY 1020H – Current ISSUES IN BIOLOGY I
Table of Contents
Course Information
Course Outline…………………………3
Course Policies………………………...9
Policy on Labs and Lab Assignments…10
Laboratory Safety Rules………………12
Guidelines for Writing Reports……….14
Labs:
Ecology Project (Labs 1-3)
1. Site Tour; project design…………..24
2. Field work and data ………………27
3. Presentation……………..…………28
Lab 4: Genetics and Hardy Weinberg……29
Lab 5: Variation in Males and Females….39
3
BIOLOGY DEPARTMENT TRENT UNIVERSITY
COURSE CODE (BIOL1020H) ISSUES IN BIOLOGY
2014-15 (FA)
Peterborough
Instructors: Dr. Marcel Dorken
Dr. Erica Nol (Coordinator)
E-mail: [email protected]
Telephone:
705-748-1011ext 7585
705-748-1011ext 7640
Campus: Peterborough
Office Location: LHS C250
LHS D235
Office Hours: EN
course co-ordinator,
office hours: by
appointment and after
class
Secretary: Sandra Sisson
Email: [email protected]
Office Location: LHS D102 Telephone: 705 748 1011 ext 7424
Course Description: This half course concerns questions of biodiversity and evolution of life:
Part 1: Biodiversity
The increasing rate of extinction of species on earth caused by humans has led to serious concerns
regarding the future of biodiversity on our planet. In this section of the course we examine what
biodiversity means, how it is measured and why we should be concerned about its loss.
Part 2: Evolutionary Biology
Biodiversity is the product of evolution. In this part of the course, we will explore the major events
of evolution, and how the process of natural selection can explain the differences we see among and
within species. As well, understanding the past events in the history of the planet may help us to
predict more successfully what lies ahead.
LearningSystem/Blackboard: This course uses LearningSystem/Blackboard which includes
important information about the course and where you will find your grades. All students who are
registered in the course will have BIOL 1020h on their Blackboard site. Class announcements and
lab schedules will be posted here; be sure to check this regularly.
IF YOU HAVE NOT ALREADY DONE SO, YOU MUST GO TO COMPUTER SERVICES
AND GET YOUR PASSWORD FOR E-MAIL AND TRENT LEARNING
SYSTEM/BLACKBOARD LEARN. ALL COURSE INFORMATION WILL BE SENT VIA
THIS SERVICE.
Senior Demonstrator Dale McKay
Email: [email protected]
Office Location: LHS D115 Telephone: 705-748-1011 ext 7407
4
Required Textbook:
Reece, J.B. et al. 2012. Campbell Biology. Canadian Ed. Pearson Education Inc., New Jersey.
Note that other recent editions are acceptable.
Recommended:
Pechenik, J.A. 2012. A Short Guide To Writing About Biology. Longman/Pearson Education Inc.,
New York. (recommended).
LAB MANUAL: The lab manual contains descriptions, data tables, and instructions for all labs to
be completed in the course. You should read it before each lab and bring it to every lab. It will be
available for purchase at your first lab session. Please bring the correct change to the lab with you.
Cost: $4.00, CASH ONLY.
Important Dates: (see Trent Calendar at http://www.trentu.ca/calendar/ for a complete list of
deadlines and dates): Thursday September 4th Classes begin (Date of your first lecture, see schedule below).
Wednesday September 24th Final date to change or add Fall and Fall/Winter courses on myTrent
(See Academic Calendar for fees, http://www.trentu.ca/calendar/)
Tuesday, November 4th Final date for withdrawal from Fall-term courses without academic penalty.
iClickers: We will not be using the iClickers in this course.
Course Format: Peterborough Campus:
Type Day Time Location
Lecture 1 Tuesday 12:00-12:50 Wenjack Theatre ( OCA W101.2)*
Lecture 2 Thursday 12:00-12:50 Wenjack Theatre ( OCA W101.2)*
*Note that for the first week, the Thursday lecture is your first lecture. After that subjects will be
covered by the schedule above. Overflow room OCA 203(TUES.)and SC137(THURS.) will be
provided as necessary.
LECTURES: Two lectures each week. Note that the students who do well in university are those
who attend lectures regularly.
LABS: One 3-hour lab every other week. You will have been scheduled into a lab section by the
Registrar’s office. The rotation of lab sections through the fall semester is provided in Table 1, and
is also available on Blackboard Learn. For example, if you have been placed in Lab Section F03,
your lab will meet Wednesday from 9:00-11:50 a.m. (in timetable) in LHS D105. Table 1 will
tell you that Lab Section F03 meets in Week 1 rotation, so your first lab is Wednesday,
September 10th, 2014. Labs will NOT run on Thursday, September 4th, 2014, so those labs
meeting on Thursday will meet for the first time on Thursday September 11th.
5
Table 1: Weekly rotation of lab sections throughout the fall semester.
WEEK ONE WEEK TWO
Lab sections that meet
on Wed., and location in
LHS
Lab sections that meet
on Thurs., and location
in LHS
Lab sections that meet
on Wed., and location in
LHS
Lab sections that meet on
Thurs., and location in
LHS
F01, D106 F13, D106 F02, D106 F14, D106
F03, D108 F15, D108 F04 ,D108 F16, D108
F05, D106 F17, D106 F06, D106 F18, D106
F07 ,D108 F19, D108 F08, D108 No lab
F09, D106 F21, D106 F10, D106 No lab
No lab No lab No lab No lab
DATES your labs will
meet
DATES you labs will
meet
DATES your labs will
meet
DATES your labs will
meet
Sept. 10 Sept. 11 Sept. 17 Sept. 18
Sept.24 Sept. 25 Oct. 1 Oct. 2
Oct.8 Oct. 9 Oct. 15 Oct. 16
Reading Week Oct. 20-24/2014
Oct. 29 Oct. 30 Nov. 5 Nov. 6
Nov. 12 Nov. 13 Nov. 19 Nov. 20
*Certain lab sections may be collapsed, with student notification, once classes begin. See Blackboard for an
updated lab schedule.
A. Learning Outcomes/Objectives/Goals/Expectations from Lectures:
1. understand biological interactions that occur from the individual to the ecosystem level of
organization
2. understand the definition of biodiversity and factors that influence it.
3. understand the basic principles of evolution (historical aspects and key processes)
4. understand the current thinking on the origin and history of life
5. gain an appreciation for the importance of an understanding of biology as an informed citizen
B. The following list outlines specific objectives from the laboratory sessions:
1. use the scientific method as it applies to biology
2. carry out independent laboratory and field work
3. develop the habit of taking clear and useful notes while doing lab and field work
4. analyze data and use introductory statistics
5. critically evaluate your own work and the work of others
6. communicate scientific findings
7. write a clear, concise, well-organized and well-produced report
8. practice asking questions and seeking ways to answer them
9. appreciate the advantages and constraints of working in small groups
10. synthesize and apply knowledge gained from the course
Course Evaluation:
ASSESSMENT:
Lab Work---------------------------51%
Mid-term ---------------------------15 %
Final Exam------------- ------------30 %
Library orientation----------------- 2%
Discussion group contributions---2%
6
Details of Assessment:
Lab Assignment Value Due Returned
Lab 1 - Field Notes
2% -End of lab - End of lab
Lab 1 - Project Design 5%
-7 days after end of
lab 1
- prior to Lab 2
Lab 2
-Field Notes and data 2% -end of lab -end of lab
Lab 2
-Analysis 5% -7 days after end of
lab 2
-prior to Lab 3
Lab 3
- Presentation 5% - during lab - on-line
Lab 3 -Blackboard quiz on
writing lab reports
4% -marked on-line -end of quiz
Formal full lab
report
-reporting the work
and findings of the
Biodiversity project
10% Week 1 due Oct. 29
+ 30th.
Week 2 due Nov. 5
and 6.
tba
Lab 4 -genetics assignment 9% -7 days after lab 4
ends
tba
Lab 5 - sexual selection lab
assignment
9% -7 days after lab 5
ends
tba
Tba= to be announced.
Midterm and Exam Content Value
Midterm Lecture material from first half of course 15%
Final exam
Part 1 Lecture material from second half of course 20%
Part 2 Lecture material from first half of course 10%
Library Skills Program How to use the
library
2% Sept. 12/2014 Ends Oct.17/2014
Discussion Group
Participation
Ongoing 2% Sept. 4/2014 Ends Nov. 28/2014
Library Skills Program-Completion with 80% or better worth 2% of your final grade.
It is essential that you become familiar with the library and its electronic and hard copy resources.
You will learn about the Library Skills Program during ISW. The program for Biology will be
available by logging in to your My Trent Learning System from Friday Sept. 12th until Friday
October 17th. The program will be worth up to 2% of your final grade. A grade will be received
only if 80% or better is achieved, and that grade will be the exact grade achieved between 80 and
100. You will be given five (5) trials to complete the program, with only the best attempt counting.
Grades less than 80% receive a zero.
7
Contributions to course Discussion Group threads.
Students are expected to contribute posts related to the content of lectures and lab exercises using
the course’s Blackboard site Discussion Groups pages. Students can gain participation grades in the
course if they provide comments that are deemed to contribute positively to the discussion.
Students can gain a maximum of 2% towards the final mark based on contributions.
Week-by-week schedule of lectures and labs:
Part 1 -
Biodiversity
(Professor)
Lectures Lab
Group 1
Lab
Group 2
Refs
9th Ed
Week 1
Sept 4
Dr. E. Nol and
M. Dorken
Introduction to University
Biology
Ch. 1: pp. 1-
19.
Week 2
Sept 9, 11
Dr. E. Nol
- Scientific reasoning in
biology
- Hypothesis testing & field
experiments
Site tour + project
design
Ch. 1: pp. 19-
21.
Week 3
Sept 16, 18
Dr. E. Nol
- Niches, habitats, and
ecosystems
- Interactions
Site tour +
project design
Ch. 54
Week 4
Sept 23, 25
Guest Lecturers
- Ecologists at work
Field data
collection +
analysis
Readings on
Blackboard
Week 5
Sept 30, Oct 2
Dr. M. Dorken
- Dispersal and distribution
of organisms
- Organisms &
environmental change
Field data
collection +
analysis
Ch. 52
Week 6
Oct 7, 9
Dr. M. Dorken
- Populations: growth and
decline
Presentations Ch. 53
Week 7
Oct 14,16
Dr. M. Dorken
- Review of mid-term
material
- Mid-term test
Presentations
University Reading week Oct. 20-24
Week 8
Oct 28, 30
Dr. E. Nol
- Evidence for evolution:
- Micro- versus macro-
evolutionary processes
Genetics and
Hardy Weinberg
Ch.2
Week 9
Nov 4, 6
Dr. M. Dorken
- Contemporary evolution
- mechanisms of evolution,
Hardy-Weinberg
Genetics and
Hardy
Weinberg
Ch.23
Week 10
Nov 11, 13
Dr. E. Nol
- Genetic drift, gene flow,
isolation, speciation
Understanding
the causes of
phenotypic
variation
Ch. 24
8
Week 11
Nov 18, 20
Dr. E. Nol
- The Biosphere, early life
- Mass extinctions
- The tree of life
Understanding
the causes of
phenotypic
variation
Ch. 25, 26
Week 12
Nov 25, 27
Dr. M. Dorken
- Plant and animal diversity
- Reproductive systems
No lab Ch. 29,32
Ch. 38,46
Week 13
Dec 2
Review lecture- Summary No lab
Lecture topics above may be altered slightly from what is indicated.
Department and/or Course Policies:
POLICY ON TESTS, EXAMS, & ASSIGNMENTS
A) ELECTRONIC EQUIPMENT - cell phones and other electronic devices are not allowed
during tests/exams. Laptops can only be used during class for taking notes although research
demonstrates that hand-written notes are much more effective for learning.
B) TERM TESTS & FINAL EXAMINATIONS - Students should NOT make any commitments
(i.e., vacation, job related, or other travel plans) during either the term as a whole or the final
examination period. Students are required to be available for all examinations during the periods for
which they are scheduled (as published in course syllabi).
C) DEFERRAL OF MIDTERM / FINAL EXAMINATIONS/LAB ASSIGNMENTS -
Extensions of deadlines for completion of assignments or writing of midterms/final examinations
may be granted to students on the basis of illness, accident, or other extreme and legitimate
circumstances beyond his/her control. Requests for extension or deferral must be made prior to
the actual deadline or said midterm, exam, or lab assignment, and documentation must be
provided at that time or as reasonably close to the time of the request as possible. Requests coming
in days or weeks after the fact will not be considered. Consideration for deferrals will not normally
be granted on the basis of vacation/travel plans or job-related obligations.
D) SUPPORTING DOCUMENTATION - Students should expect that supporting documentation
will be required and must be submitted before a deferral is approved. For illness or accident,
supporting documentation will take the form of: (1) the Trent University Medical Certificate from
Health Services: http://www.trentu.ca/healthservices/medical.html , or (2) a certificate or letter
from the attending physician clearly indicating the start and end dates of the illness and the
student’s inability to write an examination, complete lab assignments, and/or attend classes, as
relevant to the particular request. For other circumstances, students should consult the instructor
about acceptable forms of documentation.
9
E) QUESTIONS - We welcome questions! All questions related to the content of lectures or labs
MUST be posted to the course Discussion Group pages. This is meant to enable informal discussion
of course topics and provide an alternate avenue for course participation. Please check that your
question has not already been posted to a Discussion Group thread before starting a new thread. If
you have questions that can only be answered by a specific TA, the course demonstrator or one of
the instructors, be sure to mention your lab section when you email us, so that we can help you
better.
Academic Integrity:
Academic dishonesty, which includes plagiarism and cheating, is an extremely serious academic
offence and carries penalties varying from a 0 grade on an assignment to expulsion from the
University. Definitions, penalties, and procedures for dealing with plagiarism and cheating are set
out in Trent University’s Academic Integrity Policy. You have a responsibility to educate yourself –
unfamiliarity with the policy is not an excuse. You are strongly encouraged to visit Trent’s
Academic Integrity website to learn more: www.trentu.ca/academicintegrity. Note that copying
from a web site or another students’ paper are two examples of plagiarism.
Access to Instruction: It is Trent University's intent to create an inclusive learning environment. If a student has
a disability and/or health consideration and feels that he/she may need accommodations
to succeed in this course, the student should contact the Student Accessibility Services
Office (SAS), (BH Suite 132, 705-748-1281 or email [email protected]).
For Trent University - Oshawa Student Accessibility Services Office contact 905-435-5102
ext. 5024 or email [email protected] . Complete text can be found under Access to
Instruction in the Academic Calendar.
All email correspondence with students in this course will be sent to the student’s Trent
University email address. If you use an alternate email account, please ensure that your Trent email
address forwards email to that address. Consult on-line information at the Trent University website
for help with forwarding email (www.trentu.ca/it).
Please see the Trent University academic calendar for University Diary dates, Academic
Information and Regulations, and University and departmental degree requirements.
POLICY ON LABS AND LAB ASSIGNMENTS 1) Each student will be assigned to a Lab Section upon registration. Once assigned you must attend
with your Section for the rest of the term. If for any reason you have to attend another Lab
Section for a temporary compelling reason, please obtain permission by email to
[email protected], and understand that YOU MUST STILL HAND IN ALL ASSIGNMENTS
ON THE DATE THEY ARE DUE FOR YOUR LAB SECTION, unless you obtain permission to
do otherwise. Failure to do so will result in late penalties.
2) Attendance at labs is mandatory. Assignments will NOT be accepted if records show you were not
in attendance at the lab for which assignments apply. If you are absent for any legitimate reason, you
must make arrangements with the Senior Demonstrator [email protected] prior to the time of the
lab or as reasonably close to the time of the lab as possible to make it up, and documentation may be
required to be presented at that time. Please see point 1) above if you attend another lab group.
10
3) Lab report or assignment requirements are indicated at the end of each lab in the Lab Manual. Refer
to the Guidelines for Writing Lab Reports in the introductory pages of this manual for help writing
your formal lab report.
4) All assignments are to be electronically submitted for this course either to the Assignment drop box
or to the SafeAssign drop box in Blackboard. SafeAssign utilizes plagiarism-checking software.
5) Assignments are due by 11:59 p.m. on due dates. Blackboard automatically marks your paper late as
soon as you submit past the due date time. Weekends are included in the count of days elapsed.
Please see point 1) above if you attended another lab group.
6) All assignments you submit for grading must be your own individual work. Although you may
work in small groups in lab, and even complete some aspects of a lab report in lab with a group, all
work must be your own. This includes all Figures (graphs), all written Methods, all Reference
searches, etc. Please note SafeAssign checks your work against work of other students as well as the
internet and primary literature.
7) Please submit your assignments in .doc or .docx format (Microsoft Word), so we can utilize track
changes for feedback. We will also accept .pdf (portable document) format, but will only be able to
provide feedback comments in the dialogue box, as opposed to the document itself. Assignments
not submitted in these formats will not be marked. It is your responsibility to ensure that your file is
valid and can be opened. Corrupt or invalid files will receive a grade of zero.
8) Take photos of, or scan diagrams; so they can be incorporated into your assignment. It is important
that you submit any assignment as ONE document.
9) Please allow a few minutes to load your assignment onto Blackboard. Allow a few minutes to
ensure that your file is received (i.e. do not shut your laptop without ensuring the file is transmitted).
Any technical difficulties should be reported immediately to IT at [email protected] , and prior to the due
date time. Having a short file name with no special characters seems to help. If you cannot submit
your document using your current browser (such as Safari), try a different browser (such as Google
Chrome).
10) Rubric information will either be posted directly to your assignments, or under Course Content.
11) Reports submitted later than 11:59 p.m. will receive a late penalty. Assignments will be accepted up
to three days late with a penalty of 5% per day (including weekends) unless you have arranged an
extension prior to the due date with the Senior Demonstrator or Course Coordinator (see points C
and D under Course Policies, page 4).
12) TA comments will be posted electronically to your assignments.
13) You will require a lab notebook for keeping records of lab work. Please be sure your lab notebook
has blank and graph paper, along with lined paper, as these types of paper are regularly used in lab.
14) Make it a practice to save a copy of your electronic work, either on a USB key device, or by any
method you choose.
Questions or problems with labs should be directed to the SENIOR DEMONSTRATOR
Dale McKay ([email protected] )(LHS D115, x7407) who will liaise with the
appropriate faculty member or the COURSE COORDINATOR, Dr. Erica Nol, as needed.
11
BIOLOGY DEPARTMENT
LABORATORY SAFETY RULES FOR BIOLOGY 1020H
In the home, the kitchen and bathroom are the sites of most accidents. The chemical or biological
laboratory poses similar hazards and yet it need be no more dangerous than any other classroom if
the following safety rules are always observed. Most of them are based on simple common sense.
1. Responsible behavior is essential. The dangers of spilled acids and chemicals and broken
glassware created by thoughtless actions are too great to be tolerated.
2. (a) If you should get a chemical in your eye, wash with flowing water from a sink or
fountain for at least 15 minutes. Get medical attention immediately. Note the
location of safety fountains in relation to your work bench.
(b) Do not wear contact lenses in the laboratory. Contact lenses prevent rinsing
chemical splashes from the eye. Vapors in the laboratory (HCl, for example)
dissolve in the liquids covering the eye and concentrate behind the lenses. "Soft"
lenses are especially bad as chemicals dissolve in the lenses themselves and are
released over several hours.
3. Carefully read the lab notes before coming to the laboratory. An unprepared student is a
hazard to everyone in the room.
4. Perform no unauthorized experiments. Consult your instructor if you have any doubts about
the instructions in the particular laboratory exercise being undertaken.
5. Be careful when heating liquids. Flammable liquids such as ethers, hydro-carbons, alcohols,
acetone, and carbon disulfide must never be heated over an open flame.
6. Test tubes being heated or containing reacting mixtures should never be pointed at anyone.
If you observe this practice in a neighbor speak to him or her or the instructor if needed.
7. Finally, and most importantly, think about what you're doing. Plan ahead. If you give no
thought to what you are doing, you predispose yourself to an accident.
8. There is no smoking allowed in laboratory at any time. Not only is smoking a fire hazard,
but chemicals in the laboratory air (both as vapors and as dust) are drawn into the lungs. It is
also against the law.
12
9. In case of fire or accident, call the instructor at once. Note the location of fire extinguishers
and safety showers now so that you can use them if needed.
a) Wet towels can be used to smother small fires.
b) In case of a chemical spill on your body or clothing, wash the affected area with
large quantities of running water. Remove clothing which has been wet by chemicals
to prevent further action with the skin.
10. Report all injuries to your instructor at once. Except for very superficial injuries, you will be
required to get medical treatment for cuts, burns, or fume inhalation. (Your instructor will
arrange for transportation if needed.)
11. Do not eat or drink anything in the laboratory.
a) This applies to both food and chemicals. The obvious danger is poisoning.
b) Not so obvious is that you never should touch chemicals. Many chemicals are
absorbed through the skin. Wash all chemicals off with large quantities of running
water.
c) Wash your hands thoroughly with soap and water when leaving the laboratory.
12. Avoid breathing fumes of any kind.
a) To test the smell of a vapor, collect some in a cupped hand.
b) Work in a fume hood if there is the possibility that noxious or poisonous vapors may
be produced.
13. Never use mouth suction in filling pipettes with chemical reagents. Always use a pipette bulb.
14. Never work alone in the laboratory.
15. Wear shoes. Bare or stocking feet are prohibited because of the danger from broken glass.
16. Confine long hair and loose clothing (such as ties) in the laboratory. It may either catch fire or
be chemically contaminated.
17. Keep your work area neat at all times. Clean up spills and broken glass immediately. Clutter
not only will slow your work but it leads to accidents. Clean up your work space, including
wiping the surface and putting away all chemicals and equipment, at the end of the laboratory
period.
13
GUIDELINES FOR WRITING LAB REPORTS, FIRST YEAR BIOLOGY
Part A:
Lab Report Format:
Lab reports are organized in the format of the scientific paper. This is a standard format that
begins with a Title; and is followed in sequence by a list of Authors, Introduction, Methods,
Results, Discussion, References, and Appendix. See Table 1 for a very brief summary of the
purpose of each of these sections.
Table 1: Brief summary of purpose of each part of the Scientific Paper.
Title Informative description of the essence of the paper
List of Authors Names of people who actively participated in the experiment
Introduction Describes your study’s objectives, and how it fits in with previous
work in this field. The Introduction explains why your study is
important, and how it seeks to extend knowledge. It also provides the
rationale for any hypotheses that you hope to test.
Methods Explains, in a way that is repeatable, how the study was conducted.
Results Shows the summarized data, usually some form of graphic
illustration, from your study; and tells the reader what was found
from the data collected.
Discussion Describes your results to the reader. Here you can say if you
supported your hypothesis, describe how your results relate to
existing knowledge, talk about inconsistencies in the data, discuss
sources of error, and future extensions of your work.
References Journal articles, textbooks, or peer-reviewed websites that you
referred to in the body of your paper (subject to strict formatting
rules).
Appendix Data used to compile graphic illustrations used in the Results, along
with samples of any calculations used to manipulate the data.
The lab report format relates to the steps in a scientific study; which include making observations,
asking a question, stating a hypothesis, designing an experiment or study, collecting the data,
analyzing the data, interpreting the data, drawing conclusions, and reporting the findings.
Part B:
Style: It is expected that reports will be well written and free from spelling and grammatical errors.
Marks will be deducted for poor writing skills. Those students who are not confident of their
writing technique should seek the advice of the Academic Skills Centre. We expect your report to
be prepared with word processing software. See Table 2 for help setting up your report.
14
Table 2: Information to help students prepare a lab report.
Paper 8½ x 11” white bond, one side only
Margins 1” left and right, 1” top and bottom
Font 12 pt.
Typeface Times Roman or another serif font.
Spacing Double
New Paragraph Indent 0.5”
Tense Past
Voice When you are not the subject, use active voice whenever possible.
Title (please do
not include Title
page)
Title should be centered on top of the first page. Author, lab section,
and date should appear aligned at the upper right hand corner of your
page.
Headings Align headings for the different sections of your paper on the left
margin.
Sub-headings Do not use these.
Figures for
Results section
Incorporate into text as close as possible after the point where first
mentioned. Use sequential numbering. Position Caption correctly;
i.e. Figure = foot, while Table = Top.
References List References in alphabetical order by first author’s last name. Use
a hanging indent (all lines but the first indented) to separate
individual references. Please use format indicated.
Appendix List Tables of data used to prepare graphics used in Results section.
Refer the reader to these Tables in the Results section. Also include
sample calculations used to prepare data.
Part C: Details about each section.
Title:
should usually be 12 words or less; concise and informative.
should be descriptive, i.e. capture all essential aspects of your study, so that the reader can
tell exactly what your study is about by reading the title alone.
Mention the organism (common and scientific names) you are working with, the experiment
or type of study, the aspects being investigated, and the habitat /location if it is a field study.
The correct format for writing the genus and species names should be used. Only the first
letter of the genus is capitalized, and both genus and species are italicized. Example: Homo
sapiens.
Your name and lab group must be printed on the top right hand corner of the page (for
sorting purposes).
Abstract:
We do not require an Abstract in first year Biology. I think we should have them write an abstract.
The abstract summarizes the primary objective of your study (1 sentence) plus your results (usually
2-3 sentences) and broader conclusion (e.g., “I conclude that the results were consistent with the
hypothesis that moisture affects plant growth patterns”).
15
Introduction:
The Introduction literally “sets the stage” for the study.
This section identifies the subject of the report. Where it applies, include both the common
and scientific name of your organism.
Provides the reader with necessary “background” information; such as:
o a review of the issue being investigated (an extensive review is not appropriate in this
section),
o existing scientific knowledge about your subject(s),
o definition of scientific terms
establishes why the study is important,
what is motivating your hypothesis?
The Introduction should end with a clear but brief summary of the scope and purpose of
your report. If your lab report tests a hypothesis (which will be the usual case), it is stated
here, along with your prediction and a brief rationale on which the prediction is based. You
should include a brief explanation of how your purpose will be addressed or hypothesis
tested. (Do not use sub-headings here).
Method:
The Method explains how a study was conducted, and explains it in such a way that the
reader could replicate your study.
Diagrams showing how measurements were made or maps to show location (if it is a field
study) are very helpful here.
Materials are not listed separately in the Method. Rather, materials are incorporated into the
text of the method as it is explained.
Use of past tense is appropriate here.
Methods are written in sentence/paragraph form, not itemized or in point form.
Write exactly what you did, in your own words. If you derived your own method, include:
- an explanation of your experimental design,
- measurement techniques,
- data acquisition methods, equipment used, units of measure,
- sample size, number of replicates, etc.
- include a statement of how the data were analyzed, i.e. what statistical methods were
used or if a specific type of calculation was used.
- For field studies, describe the study site and time of the study. You should also
include information on site location, which is important for replicating the study.
- If you used special equipment in the study, it is usual to report the make and model
of that equipment, but you do not have to explain how to operate it.
- If you need to reference the lab manual in this section, you should identify the
section of the manual you are referring to. The citation for the manual should be
stated as it would be for a book (see the Reference section).
16
Results:
This section tells the reader what your study found.
Has two parts: the Figure(s) (as a rule); and the text to explain what the Figure(s) show.
Usually, the raw data that are collected in Table format during the experiment are not
presented here. These raw data tables should appear in the Appendix, at the end of the
report.
The Results section contains a summarized version of the raw field data that were collected.
In the odd circumstance where these data cannot be visually displayed (i.e. graphed as a
Figure), you would present a summarized data table here in the Results section.
In most circumstances, the summarized data can be graphed. Each graph is called a Figure.
An example of a Figure might show the calculated means along with an estimate of
variation, such as the standard deviation.
While summarized data may be presented in either Table or Figure form in the Results,
Figure form is the preferred format for display because of its high visual effect. Do not
present both Table and Figure formats for the same data set in the Results section as the
same data set are never presented in more than one format. (The reason for this is that
scientific writing is concise, in part, because it is important to convey the information
concisely, but also, the practice of science is expensive and editors of scientific journals like
efficiencies in writing so that they do not pay as much for each word edited, printed, etc.).
Place your Figure into the text of the written Results as close as possible after the point
where you first refer to it.
The Results section also includes a written text, which helps to interpret the findings of
each Figure (or Table) to the reader. It is usual to integrate your actual data into the text of
the Results (i.e. state actual values) and to quantify trends. For example, if you see an
increasing trend, state the range of the values, or the percent by which they change, so the
reader can appreciate how much or how little they differ.
Each Figure (or Table) must be introduced (this is a good time to refer the reader to the
pertinent raw data in the Appendix) and the important trends and/or findings highlighted.
For example: “Figure 1 (Appendix 1) shows that as rainfall increases from 20 to 110 mm.
over the 3 month period, the growth of…”. Again, thinking about efficiencies in your
writing, it is not an efficient use of space to tell the reader that e.g., “The data for the
experiment are shown in Table 1)”. You might as well say “Plants grown in moist soils
have lower rates of mortality than those in dry soils (Table 1)” and of course Table 1 would
have the results of mortality studies on your plant species in the two soil types. You have
interpreted the results for the reader and also, at the same time, indicated where these results
are.
Figures and Tables:
Every Figure or Table in your Report must be assigned a label (e.g. Table 1,or Figure 1-
numbered consecutively) and a caption, which provides a concise indication on the contents
of said Figure or Table.
Example: Table 1: Brief summary of purpose of each part of scientific study.
(Label): (Caption)
17
Table labels and captions must appear ABOVE the Table itself,
Figure labels and captions must appear BELOW the actual Figure.
Be sure to label all axes (include units) on a Figure, and include a legend if necessary.
Label columns or rows, including units, on Tables.
indicate your sample size on these Figures or Tables.
Discussion:
This section interprets your results in terms of your hypothesis and attempts to provide a
plausible explanation of the observed results (i.e., why particular patterns were found).
Usually the first paragraph establishes whether you supported your hypothesis and
prediction or not.
The next few paragraphs explain your observed results and interprets your findings in light
of published work. It is important here to compare your findings to those of others, i.e.
support your ideas and suggestions in your Discussion with literature references.
Examples of a figure and table.Examples of a figure and table.
18
Try to avoid using direct quotes (i.e. copying an actual block of text). It is preferred that
you paraphrase (use your own words, and summarize what the author(s) is/are saying),
along with the proper citation (which will give rightful credit to ideas or information which
are/is not your own). To do this, talk about the work that you are referring to, and explain
how it relates to your study.
The Discussion also allows you the opportunity to critique your work. Some things to think
about here are inherent assumptions and alternate hypotheses. Are there aspects of your
study, which you assumed would not make a difference, but which may have played a role
in generating the data that were found? If so, does this point to another possible explanation
for your data (an alternate hypothesis)? Can you identify sources of anomalous data, which
could have affected your findings?
The Discussion is also the place to think about future work. Are there improvements you
would make if you were to do this study again? What direction should future work in this
area take? Are there current or future implications of your work?
Finally, conclude with a statement, which summarizes your work.
References:
There are two aspects of References to consider. One is the actual citation (referring to) of
References in the text of the report, while the other is the listing of the actual References
themselves in the Reference section.
Both aspects are subject to strict formatting rules. These rules may vary depending on the
Discipline or even the Publisher. We will talk here of how the References section should
appear for papers in first year Biology.
Citation:
First and foremost, all books/journal articles/web sites etc. that you list in the Reference
section must actually be referred to in the text of your report. This section is not a
Bibliography, where this rule does not apply. Similarly, if you refer to a document in the
text of your report, that reference must appear in your Reference section.
Citation is defined as stating the source of information, which is not your own in the text of
your lab report. This can be accomplished two ways.
The first is to state Author (s) and year of publication in parentheses at the end of the
sentence. If there is only one Author or two, one or both surnames are stated (in the order
they appear on the document), followed by the year.
Example: “(Burness 2012) or (MacKinnon and Kapron 2010).”
Where there are three or more Authors, only the first Authors surname is mentioned,
followed by the Latin “et al.” (short form of the Latin “et alias”, which literally translated
means “and others”), and then the year.
Example: “(Emery et al. 2001).”
19
The second method of text citation involves stating one or both Author(s) followed by the
year, (or the first Author et al. followed by the year in the case of three or more Authors, eg.
“Burness et al (2005) suggested that….”), at the beginning of the sentence. This method is
NOT PREFERRED because the point of a scientific paper is to emphasize the ideas (unless
it is a paper on the history of a particular field of study where the players are indeed
important) rather than the authors of the study. In good English, the subject that you would
like to emphasize and is most important in your study should go at the beginning of the
sentence. Try it! Read the following and see which of the two sentences give you the
message more directly: Students who attended class regularly, received higher marks than
those who did not (Pedagogo et al. 2014) OR Pedagogo et al. (2014) found that students
who attended class regularly received higher marks than those who did not.
Footnoting is not practiced in Biology lab reports.
Listing References: Books, Journal articles, and any peer-reviewed web references are
treated slightly differently in your Reference section (also called Literature Cited).
References to published works are given at the end of the Discussion in alphabetical order
under the first Author’s surname.
Use a hanging indent (all lines but the first indented) to separate individual references.
All Authors are listed here in the order in which they appear on the particular document.
The et al. abbreviation is not appropriate for use here.
Do not capitalize words in the titles of books and papers, except for words that are always
capitalized in normal sentences.
Books: a) Reference to a single book:
Surname, initials. followed by initials, surname(s). Year of
publication. Full title (edition or volume number if appropriate). Name of
publisher, place of publication. p. first page-last page.
Example: Freeland, J.R. 2005. Molecular ecology, 1st ed. John
Wiley & Sons Inc. Publishers, Hoboken, NJ. p. 176-196.
b) Reference to a chapter in a book:
Surname, initials. followed by initials, surname(s). Year of
publication. Title of chapter. In: surname(s), initials. of editors followed by
initials, surname(s)(eds), Title of book (edition or volume number if appropriate).
Name of publisher, place of publication. p. first page-last page.
Example: Scott, B.J. and J.A. Fisher. 2007. Selection of genotypes
tolerant of aluminum and manganese. In: Robinson, A.D.
(ed), Soil acidity and liming. Academic Press, NSW,
Australia. p.167-196.
20
Journal articles: Surname, initials. followed by initials. surname(s). Year of
publication. Full article title. Abbreviated journal title. Volume
number (issue number): first page-last page.
Example: Lewis, D.L., and C.R. Brunetti. 2006. Ectopic transgene expression in butterfly
imaginal wing discs using vaccinia virus. Biotechniques 40: 48-54.
Nol, E., S. P. Murphy & M. D. Cadman. 2012. A historical estimate of apparent survival
of American Oystercatcher (Haematopus palliatus) in Virginia. Waterbirds 35: 631-635.
Note that there are conventions around where the periods go, the pattern of capitalization and the
spacing between the volume of the journal and the page numbers. Try to be as consistent as you can
with all of your references. These minor details DO change from journal to journal (unfortunately
for the practicing scientist who much then use different styles with every new journal that they
submit a paper too!) but use this style for papers submitted in this course.
Web References: You are welcome to use peer-reviewed web references judiciously.
An appropriate reference should look like this:
Author(s) (if possible), date of last update, title, site address, date of
access.
If you are using the web to find journal articles, cite the journal article, not the
web site.
Appendix:
This is the last section of your report.
This section should contain your tables of raw data as well as sample calculations.
Remember that these are formal tables, so each should carry a proper label and caption.
The same is true for sample calculations, in that these should carry a label and caption.
You should refer the reader to the appropriate appendicized raw data table or sample
calculation in the text of your report. This is usually done in the Results.
PART D: CHECKLIST OF KEY FEATURES IN A FIRST-YEAR LAB
REPORT
TITLE
Concise, information title, e.g., mention organism, type of study, aspects being investigated,
also habitat/location if a field study
Student name and lab group printed in upper right hand corner
21
INTRODUCTION
Identify the subject
Provide background relevant to the subject
Reference to literature
End with a statement of hypothesis, prediction, and rationale if testing a hypothesis
Brief explanation of how hypothesis will be tested
METHODS
Sufficient detail to replicate study
Mention data analysis methods
Use sentence/paragraph form
Diagrams useful
RESULTS
Present summarized date in figure form
Assign each figure a label and a descriptive caption, which appear at the foot of the figure
Label axes, including units on figures
Include estimates of variation if applicable
Include a legend if necessary in figures
Written text which refers to and states the major findings of each figure
Integrate your data into the text, quantify trends
Refer to appropriate appendices for raw data tables and sample calculations
Must be free of interpretation
DISCUSSION
Refer to original hypothesis(es) and prediction(s)
Interpret your results
Cite published articles or text materials to support or compare your interpretation
Inherent assumptions? Alternate hypothesis(es)?
Comment on nature and cause of anomalous data
Improvements? Future work? Implications?
Concluding statement
22
REFERENCES (OR LITERATURE CITED)
Alphabetical order
All sources listed must be referred to in the text of the report
Use proper format
APPENDIX
Table of raw data as well as sample calculations(s)
Label and caption for each, which appear at the top
Tables-label rows and columns. Provide appropriate units
GENERAL POINTS
Quality of spelling/grammar
Special insight/original ideas
Overall quality/neatness of report
Part E: Order of writing a lab report: The order in which you write the various sections of your
report is not the order in which they appear in the report itself.
Remember you are writing your lab report for an audience that is your peers, that is you are
describing your work to your fellow students.
Be sure you have a clear idea of the purpose of your study, what question(s) you are trying
to answer.
Start by writing the Methods section. You begin by performing the experiment, so this is
the easiest section to write once the work is done.
Next write the Results section. Prepare your Appendix Tables and create your Figures.
Determine what your findings are. Prepare the text of the Results section to describe your
findings.
Next write the Discussion. This section provides you the opportunity to interpret your
findings and to see how your findings compare to those of others who have conducted
similar work.
Last, write the Introduction. This section of your lab requires that you put your study into
perspective from the point of view of what is known in the current literature, explain about
your study, and why you carried it out. This is the hardest, most important and often the
shortest section of a scientific paper so if you struggle, so do all scientists!
23
Biology 1020H
ECOLOGY PROJECT
Labs 1-3, Fall 2013
The purpose of this series of labs is to go through the process of doing science. Teams of
four students will ask an ecological question, develop a hypothesis, and design an experiment to
test the hypothesis. Equipment provided will be very simple; i.e. meter stick, quadrat, trowels, etc.
After the experimental design has been approved by the teaching assistants, data will be collected,
analyzed, and the results will be presented.
Those of you in Week 1 labs will begin the first week of classes, while those of you in Week 2
labs will begin the second week of classes. You have a lab every second week.
Week 1 Week 2
Week of
Sept. 8th
Lab #1 Site tour and plan project
- field notes graded at end of lab
(2%)
-Project Plan (5%) due in 7 days
time.
No lab
Week of
Sept.
15th
No lab, Project Plan due (5%)
Lab #1 Site tour and plan project
- field notes graded at end of lab (2%)
-Project Plan (5%) due in 7 days time.
Week of
Sept.
22nd
Lab #2 Field work and Data Analysis
(5%)
- field notes graded end of lab (2%)
-Data Analysis (5%) due in 7 days
time.
No lab, Project Plan due (5%)
Week of
Sept.
29th
No Lab, Data Analysis due (5%)
Lab #2 Field work and Data Analysis
(5%)
- field notes graded end of lab (2%)
-Data Analysis (5%) due in 7 days time.
Week of
Oct. 6th
Lab #3, Preparation and
Presentation (5%)
No lab, Data Analysis due (5%)
Week of
Oct. 13th
No Lab. Quiz on Blackboard about
writing lab reports (4%)
Lab #3, Preparation and Presentation
(5%) Quiz on Blackboard about
writing lab reports (4%)
Lab report (10%) due Oct. 29/30th. Lab report (10%) due Nov.5/6th.
**Reading Week Oct 20 to 24: no labs.
***Deadline for completion of Library Skills Program is October 17, 2014. It will not be
available after this date
24
Lab 1. Site Tour and importance of questions
Part 1: Introduction
In the first part of the lab you will be introduced to the scientific method. You will also be
introduced to the type of field equipment available for hands-on field use.
Site Tour (Observations)
You will be guided on a walking tour to observe the locations and conditions of at least three
different habitats on campus. Come prepared to walk a distance of about a kilometer in the
prevailing conditions. The walking tour is necessary in order to orient you, to demonstrate some of
the equipment, and to get you to start thinking about possible questions.
The key questions are: What do you see?
What questions can you think of about what you see?
How would try to answer those questions?
Notes about the habitats, sketches, thoughts, questions should all be recorded as you go, in
your lab note book. These will form the preliminary ideas for your hypotheses. These field notes
will be assessed at the end of the lab. They are worth 2%.
Part 2: Ecology Project Plan
PLAN PROJECT
You will work in teams of four people from each lab.
1. Class Brainstorming Session:
To begin, the teaching assistant will talk about hypothesis testing. All teams will be lead through a
practice “brainstorming” session using a habitat not available to the students. The group writes
down what they know about the habitat, and then what they would like to know about the habitat.
From the latter list, each team will formulate a specific question they would like to answer. From
this question; a hypothesis and a prediction is formulated. Teaching assistants will evaluate each
team’s hypothesis and prediction.
Hypotheses and Predictions: workshop.
What is the difference between a hypothesis and a prediction? You will have a short workshop on
this question, for it is critical to distinguish between the two concepts.
25
Science advances by formulating and testing hypotheses. In order to test a hypothesis, you must
first think of a clear question you can ask. Luckily for scientists, there are many questions about
living organisms that require answers. A hypothesis is a statement which tends to answer or explain
your question based on information we already know (inductive logic). Predictions are statements
made via deductive logic, which can be tested experimentally, and which should yield positive
results if the hypothesis is supported.
When doing experiments, we either find evidence that supports the hypothesis or does not support
it. Much of the work falls on the prediction. If the prediction is correct, then the hypothesis is
supported. If your prediction is not correct, then your hypothesis is not supported.
There is nothing wrong with “not supporting your hypothesis”. This does not mean that the science
is wrong. It simply means you need to develop a better hypothesis. This is the process of doing
science. More often hypotheses are not supported than supported. The great thing (YES GREAT!)
about having your data fail to support your prediction is that you then need to think about what else
might explain the patterns that you have found. This leads directly to Scientific Creativity (the most
exciting part of the scientific process)!
Remember when formulating statements such as questions, hypotheses, and predictions; to include
as many aspects of the study as necessary in the statement itself to make them clear and
understandable to the reader. For example; include the aspects being investigated, the subject (s),
the habitats, the variables, etc.
The following will guide the organization and relevance of your Biodiversity Project.
Question: what question are you asking? For example, if you are a community ecologist, you
may be wondering how species diversity of a cedar forest changes over time as the forest
matures?
Hypothesis: (possible explanation that can answer the question) With the above example and
based on preliminary observations, the hypothesis may state that “Mature cedar forests
provide more variability of habitat types and opportunities for increased species diversity.”
Prediction: this is a statement of projected outcome of the study. In the example given, the
ecologists predicted that “If this is true, then we will find more species in the mature than in
the immature cedar forest.”
The above prediction is right. For example, given the hypothesis, it would have been wrong
to state:
Prediction: If this is true, then we will find a difference in species diversity between mature
and immature cedar forests, or
Prediction: If this is true, then we will find fewer species in the mature than in the immature
cedar forest community.
A clear hypothesis and a clear prediction or set of predictions are essential for the success of
your project, as they are for any piece of science.
26
2. Project Design.
a) Each team of four will now choose a habitat, and follow the brainstorming procedure to
develop a question, hypothesis, and prediction.
b) The teaching assistant will then lead the lab group through a brief workshop on
experimental design. What is a dependent and an independent variable? How many
dependent variables should we include in our experimental plan? How many samples are
enough?
c) Each team will then complete their experimental designs by constructing a methods section
by which they can test their hypothesis, and constructing data tables ready to collect field
data. Time in the field should be gauged at no longer than 90 minutes.
d) Each team will also construct a brief sampling schedule, which will outline the time for
various components of field work.
LAB # 1 PROJECT PLAN: (due in 7 days time) (5%)
This outline must be submitted electronically to the Assignment Dropbox through
Blackboard, Assessments.
As this is an individual assignment, each person must submit their own outline.
1) Question
2) Hypothesis
3) Prediction
4) Rationale-reasonable explanation of why you expect the trend you predict
5) Method-point form is acceptable.
6) Itemized list of field equipment needed (so we can have it ready for you).
7) Schedule. How do you plan to do this work within the time constraints of the lab?
8) Outline of a Data Table (s) (ready to receive raw data)
9) First and Last Names of all Team Members
This assignment will be returned to you before the beginning of your next lab period.
27
Lab 2. Field Work and Data Analysis
In this lab, you are going into the field to collect the data (called the “raw” data) that you need to
answer the Question your team proposed. Please come dressed for the prevailing weather and
terrain conditions. At the end of the lab, your team should have time to share and assess your
data.
1) Make any necessary changes
Each team will have received back their Project Designs. Please look these over, and
incorporate any necessary changes to method BEFORE going into the field. Show
your changes to a TA before going into the field, to have them approved.
Please make a list of the items of field equipment taken out into the field. This must be left
with the T.A. for inspection on return to the lab (or leave your list out on your bench).
2) Data Collection
Field work should be completed in about 90 minutes.
Each member of the team should take detailed field notes about each site, about
methods, and about any problems that emerge, including any questions and comments.
Field notes will be assessed at the end of the lab. These are worth 2%.
3) Analysis
Each team should ensure that all team members leave with a copy of the data.
Teams can now take time to consider how best to analyze their data. Consider how the data
can be summarized, and presented in Figure form.
LAB # 2 Data Analysis (5%) due in 7 days time.
Each member of the team submits an individual copy.
Assignments are to be submitted electronically through the Assignment Dropbox on
Blackboard, Assessments.
These will be graded, and returned before the beginning of Lab 3.
The LAB # 2 Analysis Assignment should include:
a) Data Table (s), complete with Label(s) and descriptive Caption(s).
b) Figure(s) which graphically represent either this data, or perhaps a summarized form of
this data, with Label(s) and descriptive Caption(s).
c) Text which explains what your Figure(s) show.
d) Your preliminary conclusions as to whether or not your results supported (or did not
support) your original hypothesis and prediction. Please restate both for the reader prior
to your explanation.
28
Blackboard Quiz on writing lab reports (4%). Please read the Guidelines for
Writing Lab Reports, pages 13-22 in this manual. An online quiz will be available for 8
days for each half of the class to write it according to the following schedule:
Week One: Quiz available from October 3, 9:00 a.m. until October 10, 5:00 p.m.
Week Two: Quiz available from October 10, 9:00 a.m. until October 17, 5:00 p.m.
Lab 3. Presentations
Please do not make preparations for this lab ahead of time on your own. All students are expected
to have the same time and materials available to them for this presentation grade.
Lab 3 will be made up of two parts. Part A will be devoted to preparing your presentation.
Part B will be devoted to the presentations.
Everyone should have received their graded Data Analysis assignments back.
Part A: Preparation (first half)
In this lab you will continue to examine the data collected in lab 2, and discuss the results with your
team members. All teams will be provided with the same number of overhead transparencies and
pens to work with for the Presentation. You should think of the best way of presenting your results
(Tables, Figures), and summarize your findings on these overhead transparencies for presentation to
the class. Your team will then make a brief (5-10 minute) presentation on your findings. All team
members need to participate. A possible way to do this is to have one member introduce the
project, followed by another outlining the methods, and others presenting the other sections. Part of
the idea here is to get feedback from the other students about your project prior to your writing your
lab report.
Part B: Presentation (last half) (5%)
The last half of the lab, teams will present their projects, and participate both in grading and in
providing constructive comments on one another’s experiments.
Formal Lab Report; Labs 1, 2, and 3: (10%)
A formal written report from each member of the team is required. The report should follow
the format described in the Guidelines For Writing Lab Reports of this manual. Although
the wording of the methods and results may be similar (but not identical) to that of others in
your team, your introduction and discussion should be your own individual effort, and therefore
quite different from others.
29
Lab 4: Evolution and Genetic Variation
Introduction
Evolutionary change can occur only if there is genetic variation among individuals- and then only if
some of those individuals are more successful at reproducing than others, spreading their genes
more successfully to subsequent generations.
Reproductive success, which is something that we can measure, is what we consider to be the best
indication of the relative fitness of an individual. Reproductive success in fact means more than
just how many offspring an individual produces, but also how many of them actually live to
reproduce themselves in turn. Those who don’t reproduce, or whose offspring all fail to reproduce,
have a fitness of zero.
This lab is intended to explore some of the ways in which genetic variation within a population may
occur, and how that variation may change within that population, resulting in evolutionary change.
1. The language of genetics
In your high school courses you will have met the basic terms and concepts of genetics and cell
division, so this section should be a quick review for you.
The terms we use in discussing the genetics of populations include:
mitosis and meiosis gene and allele
chromosome and chromatid dominant and recessive
haploid and diploid homozygous and heterozygous
gamete and zygote genotype and phenotype
Filling in the following Tables will confirm you are comfortable with the language of genetics.
You will need to include the completed Tables as part of your lab report.
Table 1: Life cycle-In the life cycle of an organism, at what stage do the following occur?
Stage/Term haploid diploid mitosis meiosis
30
Table 2: Mitosis and Meiosis- Compare the two processes of cell division
Mitosis Meiosis
1 cell produces 2 or 4 new cells
Cell divides once or twice
Sister chromosomes “find each other”
Chromatids are formed
Tetrads are formed
Crossing-over (recombination) occurs
Resulting cells are haploid or diploid
Table 3: An example of an inherited trait involving one gene-for eye color
We’ll assume that eyes are either blue or brown (green and grey are variations of blue, hazel
of brown; resulting from the added action of other modifying genes).
We know that a single gene is responsible, and that it has 2 alleles: one that results in brown
pigment, the other in blue.
We know that the allele for brown dominates the allele for blue when they exist in the
heterozygous relationship. Let’s call the alleles “A” and “a” respectively.
Alleles “A” and “a”
Genotypes
Homozygous recessive
Heterozygote
Homozygous dominant
Genotypes: Brown
Blue
Your phenotype
Your father’s phenotype
Your mother’s phenotype
Your sib’s phenotype
Your probable genotype
We could assess any other single gene that has 2 alleles, one of them dominant, in exactly the
same way. You could therefore figure out a few of your genotypes for traits such as ear lobes,
index finger length, tongue rolling, hair texture, hair color, and many others if you wanted to.
What can we conclude about the frequencies of the alleles of the gene? What predictions can
we make? To get there, we need to understand more about a gene pool. We’ll continue to use
“eye color” as an example, since it is familiar, and it’s an innocuous trait to talk about.
31
1. Gene frequencies (continuing with eye color examples)
Most genes that we have are identical to those of every other human, but when a gene has 2 or more
alleles, then the gene may result in observable variation. Most of our genes that have more than
just one allele, have two (or more) alleles. For example, the gene for blood type has three alleles.
Other genes, like those that are involved in our immune responses, may have 20 or more. Of
course, each of us as individuals can have only two of the possible alleles, but we vary much more
from each other at those gene sites. But, let’s consider a gene that has 2 possible alleles, such as the
gene that we assumed controlled eye color in Table 3 above.
The frequency of a gene, e.g. the gene for eye color, in a population is 1.0. That just means that
every individual in the population has the gene. But as you noted in the table earlier, we each have
2 copies of the gene, and those copies may be identical alleles (homozygous genotypes) or they
may be different alleles (heterozygous genotype). As a result, three genotypes are possible.
As population geneticists, we can ask, what are the frequencies of the three possible genotypes in a
population? Their sum must of course still be 1.0, for no one can have more or less than one
genotype for eye color. And then, what are the frequencies of the 2 alleles in a population? Their
sum again must still be 1.
If we can answer those 2 questions, we can begin to measure and predict changes that may occur to
the frequencies of alleles and genotypes over a number of generations. If changes in frequencies
do occur, then evolutionary change has occurred.
We can say this with the simplest of formulas:
If p = frequency of one allele, q= frequency of the other allele
Then p + q = 1 (and so p =1 –q , and q =1 –p )
In terms of eye color, that’s a quick way of saying that the frequency of the “A” allele (for brown)
plus the frequency of the “a” allele (for blue) equals 1.0.
Thinking in terms of the three possible genotypes; AA, Aa, and aa, we can substitute p and q for
each “A” or “a” allele, to represent the frequencies of the genotypes:
Then pp + 2pq + qq = 1
(that is the same as (p +q)2=12 )
pp (or p2) = the frequency of AA in the population
2pq = the frequency of Aa in the population
qq (or q2) = the frequency of aa in the population
And then we’re in business. When we have an actual gene, with 2 alleles to think about, we can
make this more real. We’ll stay with eye color.
32
Since in the case of eye color, the allele for brown (A) dominates the allele for blue (a), the only
genotype that is clearly expressed is the homozygous recessive: if we look into the eyes of a brown
eyed person, we don’t know which genotype they have, but if we look into the eyes of a blue eyed
person, we know immediately their genotype must be “aa”.
This simple observation is in fact extremely powerful: if we know how many blue eyed people
there are in a population, then we can easily determine the frequency of each genotype in the
population, and we can determine the frequency of each of the 2 alleles in the population.
Example: in a group of 100 humans, we find that 81 have the blue eyed phenotype, and 19
have the brown eyed phenotype.
Therefore the frequency of “aa” in that population is 0.81, and we can easily figure out the
other frequencies. For example, it turns out that only 1 out of the 100 people in the group
should have the phenotype “AA”.
What happens to the frequencies of the alleles and the genotypes as the frequency of blue
eyed people decreases? Any surprises? What are your conclusions?
Table 4: Eye color allele and genotype frequencies
Frequency of
‘aa’ (=q2) in
population
Frequency of ‘a’
(=q) in the
population
√q2
Frequency of
‘A’ (=p) in
population
p=1-q
Frequency of
‘AA’ (=p2) in
population
Frequency of
‘Aa’ (=2pq) in
population
0.81 0.9 0.1 0.49 0.25 0.09 0.01
Lab group
33
Hardy-Weinberg work chart:
p=fr of A = 0.1
q=fr of a = 0.9
A a
A
AA(p2)
=0.1x0.1
=0.01
Aa (pq)
=0.1x0.9
=0.09
a
Aa (pq)
=0.1x0.9
=0.09
Aa(q2 )
=0.9x0.9
=0.81
p 2 +2pq +q2 = 1
p 2 = fr of AA = 0.01
pq + pq = 2pq = fr of Aa = 0.18
q2 = fr of aa = 0.81
Therefore, 18% of the people will have the genotype Aa, 1% will have the genotype AA.
Create similar worksheets in your lab notebook to calculate the remainder of the
frequencies.
2. genetic equilibrium
If, in generation after generation of the population that interests us, the 2 alleles and therefore the
three genotypes remain unchanged in frequency, then we consider the population to be in
equilibrium, at least as far as eye color is concerned.
Because two guys, Hardy and Weinberg, figured this out independently about 100 years ago, we
call the equation (p + q = 1) the Hardy-Weinberg equation, and we call the equilibrium that occurs
when allele and genotype frequencies remain unchanged over generations, the Hardy-Weinberg
Equilibrium.
A population that is in Hardy-Weinberg Equilibrium is therefore one that doesn’t change, where
no evolution occurs. Why then is it interesting? When that equilibrium is broken, we can measure
the rate and extent of evolutionary change, and that is an amazing thing to be able to do. We may
also be able to identify the causes of that change.
For a population to remain in equilibrium, generation after generation, some extraordinary
constraints, or assumptions, must be made. Does such a population exist except in the minds of
population geneticists?
If any of the assumptions is broken, allele frequencies may change, and evolution within that
population occurs. The actual definition of evolutionary change is remarkably simple.
34
Table 5: Breaking Hardy-Weinberg Equilibrium
HW Constraint Why? How does breaking this assumption disturb HW equilibrium?
No mutations from one
allele to another can
occur
Population must be
relatively large
Random mating of
individuals must occur
No immigration or
emigration of
individuals may occur
Natural selection
cannot occur
Understanding which HW assumptions are broken allows us to identify the factors that result in
changes in allele frequencies, and allows us to measure the rate and extent of evolutionary change.
3. Simulating Microevolution:
Objective: To test hypotheses concerning gene frequency changes in real examples when any of
the HW constraints are broken.
You will need to work in pairs in the lab using the lab computers-and it is good to have someone to
argue with. You should write up your reports independently.
This website Deme 2.0 software, free for educational purposes, is loaded onto our lab computers. It
allows almost unlimited opportunity to explore examples of micro-evolution, for it allows you to
break every assumption or constraint of Hardy-Weinberg equilibrium. It is full of graphical
information, is fast, powerful, and easy to use.
You will see a graph come up, which plots the changes of the frequencies of alleles and genotypes
over 50 generations. You will need to tell it which of the frequencies you wish it to plot on the
graph; e.g. just the frequency of the homozygous recessive, or the frequencies of p and q, or the
three genotypes all at once, or everything all at once.
35
It also has a few very short tables where you can change starting conditions. Again, assume you are
looking at a single gene with 2 alleles, one of which is dominant.
The starting conditions you can manipulate:
1) p and q
2) Selection pressure on each genotype. For example, a value of 1.0 means that 100%
survive to reproduce, while 0.1 means only 10% survive to reproduce.
3) Immigration (M) - number of each genotype that move into the population. This is a
good one to leave at zero until you are comfortable with manipulating the other
variables.
4) Size of population (N)- (note that it is log scale)-You should compare very small and
very large populations
5) Drift-On or Off- Leave it “Off” at first. Turn it “On” when you specifically wish to
assess the impact of genetic drift.
6) Mutation rate of each allele to its alternate form. Unless you specifically wish to look at
the impact of mutation, leave it at zero. If you do use it, remember that it is always a
very low number, usually in the order of one mutation tin every 10,000 to 10,000,000
meiotic events (or generations).
Each time you change a single condition, the graph immediately changes to accommodate it.
PART 1: NEWS ITEM (reported at the AIDS conference in Toronto, Aug. 2006)
One in 300 people infected with HIV virus do not develop AIDS. This appears to be true in
different populations in different parts of the world. It may be the result of a single gene with a
pair of alleles which, when homozygous recessive, prevents the virus from penetrating the host
cells.
Assume the homozygous recessive of a gene with 2 alleles provides the observed
immunity. It occurs in 1 in 300 people= 0.0033% of the population.
Therefore, q2 =0.003,
and so q=0.06 approx.
p=1-q, so 1-0.06=0.94, so p=0.94
What do you hypothesize will happen to the allele and genotype frequencies in the next
generations?
Simulating HW equilibrium:
Starting conditions: adjust p and q values to 0.94 and 0.06
Keep Selection for all three genotypes at 1.0
Keep Mutation and Immigration at 0, and Drift Off
Check all Plot Variable
Vary population size
36
1. Impact of Genetic Drift and Population Size (record data Table 6)
With population size at 10,000, 1,000, and then 100, click ‘Drift’ On and Off a few times.
What do you see?
With population size at 100, click ‘Drift’ On 20 different times. How many times does “q”
become zero? What happens to “p” when this happens?
When an allele is lost in this way, the remaining allele becomes ‘fixed’ in the population,
and no further evolution at that site is possible until mutation restores the lost allele.
2. Change in Selection pressure: (use blank tables)
Now assume ‘Selection’ is different for the three genotypes (Red box). Selection is
measured in terms of survival rate.
-if survival to reproduce rate of AA is 0.96 (this would mean for instance that 4% of the
population that is genotype AA has AIDS and will not survive, or if they survive will not
reproduce).
-and survival to reproduce rate of AB is 0.99 (this would mean that carrying one B allele
provides some limited protection from the virus)
-and that survival to reproduce rate of BB is 1.00 (meaning that all who carry the
homozygous recessive condition survive and reproduce successfully).
Then what happens over 50 generations, as you change population size, and then as you
permit genetic drift to occur?
If you run another 20 trials with a population size of 100, and ‘Drift’ On, how do the results
compare with the trials you ran when Selection was 1.0 for all three genotypes?
Table 6: Population size and the impact of genetic drift
Genera
tion
Gen 50
N=
10,000
Drift Off
Gen 50
N=1000
Drift Off
Gen 50
N=100
Drift Off
Gen 50
N=10,000
Drift On
Gen 50
N=1000
Drift On
Gen 50
N=100
Drift On
p 0.94
q 0.06
P2 fr of AA 0.88
q2 fr of BB 0.003
2pq (fr of AB) 0.112
Mean fitness ~96
37
Blank template table for different survival to reproduce rates
Genera
tion
Gen 50
N=10,000
Drift Off
Gen 50
N=1000
Drift Off
Gen 50
N=100
Drift Off
Gen 50
N=10,000
Drift On
Gen 50
N=1000
Drift On
Gen 50
N=100
Drift On
p
q
P2 fr of AA 0.96
q2 fr of BB
2pq (fr of AB)
Mean fitness
Blank template table for different survival to reproduce rates
Genera
tion
Gen 50
N=10,000
Drift Off
Gen 50
N=1000
Drift Off
Gen 50
N=100
Drift Off
Gen 50
N=10,000
Drift On
Gen 50
N=1000
Drift On
Gen 50
N=100
Drift On
p
q
P2 fr of AA
q2 fr of BB
2pq (fr of AB) 0.99
Mean fitness
Blank template table for different survival to reproduce rates
Genera
tion
Gen 50
N=10,000
Drift Off
Gen 50
N=1000
Drift Off
Gen 50
N=100
Drift Off
Gen 50
N=10,000
Drift On
Gen 50
N=1000
Drift On
Gen 50
N=100
Drift On
p
q
P2 fr of AA
q2 fr of BB 1.00
2pq (fr of AB)
Mean fitness
38
Lab # 4 Report: (9%) Due 7 days from scheduled completion of this full lab.
This is not a full, formal lab report, but you should use some of the formatting in
order to produce a tidy report that flows efficiently.
1. Include a brief Introduction that includes the purpose and overview of the lab exercises.
2. Completed review Tables 1-3.
3. Completed gene frequencies Table 4 along with worksheets. Please answer the following
questions:
a) From the HW eye color Table 4, and ignoring the data on the lab population: What
happens to the frequencies of the alleles and the genotypes as the frequency of blue
eyed people decreases?
b) What, in a biological sense, is a population? Why is the lab group not an example of
a population in HW Equilibrium? Why is it not even acceptable as a ‘population’?
4. Completed Table 5. Please answer the following question:
a) Can you think of any population of an organism that is in HW equilibrium?
5. Bioquest Simulation. Include completed Table 6. Answer the following questions:
a) What do you conclude about the impact of population size on the changes in
genotype frequencies?
b) What do you conclude about the impact of genetic drift?
c) What is genetic drift? Use your text book, but describe it briefly in your own words.
d) What happens when each genotype has a different survival to reproduce rate?
6. A Reference Section should be included with your assignment. You need to include at the
very minimum reference to at least one Journal article. Please provide the first page of the
PDF from the research paper as an appendix with your report. Find any recent paper (less
than 5 years since published) that has to do with Hardy-Weinberg Equilibria. It does not
have to tie in closely to your report.
39
Lab # 5: Sources of Variation
The objective of this lab is to give you the opportunity to think about variation, its possible sources,
and its adaptiveness. The example you consider will be one of your choosing, and will be somewhat
similar in design to the project you did in the Ecology Section of this course.
Natural selection can only occur if organisms vary, and if their variations are inherited. Variation is
a critical characteristic of every population of organisms. The extent of variation of course varies
immensely depending on the organism and on the trait we are looking at, but it is always present to
some degree. By now you have met some of the problems variation poses to those doing ecological
work, where we look for correlations, and try to make predictions about relationships. Variation can
then appear to mask the relationships you expect or hope to find, and you may need to collect a great
deal of data in order to show that a significant correlation exists. On the other hand, evolutionary
biologists view variation and its causes with some enthusiasm, hoping for further insight into how
natural selection may occur.
Why is there so much variation among individuals within populations? Why do individuals that live
close together often appear quite different in so many ways? What are the sources of that variation?
Are the traits that vary inherited and subjected to natural selection? Are they responses by genetically
similar individuals to different environmental conditions? Why do even cloned, genetically identical
individuals differ in small but measurable ways? In other words, is all this variation adaptive in some
way, or is some or much of it random and not inherited? These are questions that intrigue
evolutionary biologists.
Sexual Selection
Very often one sex invests much more time and energy in producing and caring for offspring than
does the other sex. Usually (but not always) that sex is female. When the female of a species invests
a considerable amount of her time and energy into each of her offspring, it should be to her advantage
to choose a particularly fit male to mate with, ensuring that her offspring will in turn be as fit as
possible. On the other hand, when the male of a species invests relatively little in each of his
offspring, it should be to his advantage to mate with as many females as possible, ensuring he will
have as many offspring as possible; there is no reason for him to be choosy about who he mates with.
Charles Darwin recognized that natural selection should act differently on males and females which
invest different amounts of time and energy in their offspring, and he called it sexual selection.
Species differ from each other immensely in how much the sexes differ in their investment in
offspring, and so the extent of sexual selection among species also varies immensely.
40
Objectives:
In order to think about large questions, we still need detail on specific examples. Any theory is only
as good as the examples that it rests on, and in this lab you will develop and analyze your own
example. To make it possible to draw some comparative conclusions, and to apply some basic
statistics to your data, you will need to measure:
1) One or more traits of 2 sexes of a species, OR
2) One or more traits of 2 related species.
The specific objectives of this lab are then:
1) To compare the extent, and reasons for, the variation in one or more traits in an example
of your choosing.
2) To collect some real data, and analyze them, using basic statistics and a t-test.
3) To design and write an independent report of your project (8%).
Some examples:
To get you started, there will be a selection of organisms in the lab to look at and think about. With
a lab partner, consider what traits of each organism might be interesting and possible to measure.
Project Design:
With a partner decide:
i) What organism or organisms you wish to use as your example of variation
ii) What trait or traits you are going to measure.
iii) What predictions you can make about the variation that may exist within and
between the sexes or species
iv) How you are going to gather the data
v) How large your sample size should be
vi) What statistics you plan to use
vii) How you wish to construct your data sheet
When you and your partner are comfortable with your project design, share it with the TA who will
keep a record of who is planning to do what.
Standardizing your data
A trait that differs between 2 sexes or species may also vary according to the size of the organisms
you look at. This variation could easily obscure the relationship you wish to focus on. It is
therefore usually best to standardize you data by comparing the trait what interests you with a
second trait of the same individual that represents its overall size (body length, for instance). For
each individual you then can determine the ratio of the trait of interest relative to a body length.
When you compare the 2 sexes or species, you will then compare the ratios of each of the
individuals.
41
Data gathering
Organize yourselves so that you can gather the data necessary to complete your data Tables.
Picturing your Data
Once you have your data (as ratios), how do you propose to display your data?? Even if you
haven’t yet had a chance to analyze them, you should be able to describe the patterns of variation
that exist.
Explore the graphics software. Graph your data in several ways. Which is the best way to display
your data??
Statistical analysis
What do the basic statistics concerning mean, range and standard deviations tell you about your
data? Once you have run a t-test, you should be able to decide whether or not any significant
difference exists between the two sexes or species in the trait or traits you have measured.
In-lab writing
While you and your partner are together in the lab, you should take time for the following:
1) Write a clear statement of your major hypothesis.
2) Think of some alternative explanations (or hypotheses) that could also account for your
results.
3) Draft the “Results” section of your report:
i) State in words what your statistical test tells you about means and variation
ii) Note (describe) any unusual patterns or outliers
iii) State as clearly as you can whether there is a significant difference between
your samples.
iv) State exactly what the ‘p’ value tells you.
You may wish to discuss these with other lab teams, and your TA’s will of course be eager to talk
with you about them.
End of lab
At the end of the lab period you should have a graph of your results, statistical analysis of your
results which you understand, a draft of the ‘Results” section of your lab report, a clear hypothesis
to build your “Introduction” around, and some ideas about alternative hypotheses that you can
consider in your “Discussion”.
42
Formal Lab # 5 Report (9%) Due 7 days from the end of lab.
You should follow the format outlined in the Guidelines for Writing Lab Reports provided on pages
13-22 in this lab manual. A rubric will be posted on Blackboard to help. You will require a Title
of your choosing.
1) Introduction (1 page)
You are looking at a specific example of some larger question. What is that question?
Why is it interesting? What hypothesis are you examining with your example?
2) Methods (1 page)
Include enough detail on what you measured and how you measured it that
someone else could duplicate what you did. You may wish to include a
diagram.
3) Results (2 pages)
Include a figure of your data and indicate ranges, standard deviations, and
means. Include a clear statement of your statistics and findings about
significant differences.
4) Discussion (3-4 pages)
This is the critical thinking part of your report. Have you supported or
rejected your major hypothesis? If there is no significant difference between
the two sexes or species, the result is still potentially interesting and should
provoke further questions.
The variation you have documented may be due to environmental or genetic
factors. Think of at least two other hypotheses that could account for your
Results. How would you further test all three hypotheses in order to reject or
support tech of them?
From what you have observed and read, to what extent do you think the
differences between the two sexes or species is due to genetic factors and
therefore subject to selection?
5) References (1 page)
You will find your textbook and other sources helpful, but most of your ideas
will probably come from talking about the questions with your partner.
Nonetheless, you should have other references besides your textbook. The
most useful may be sources that deal with your ideas rather than the
particular species you have work
