One of the major goals of the laboratory section of this course is to develop scientific writing skills. Students are required to write three (3) formal laboratory reports. These formal reports should follow the format of primary research papers found in scientific journals. This handout is a guideline describing the required structure for a formal report with the rubric for grading (Table 1). Table 1: This is the general rubric used for evaluating formal laboratory reports based on the guidelines explained below. A detailed rubric follows the guidelines (Table 2). Item Percentage Value Title 5 Abstract 15 Introduction 15 Methods 15 Results 15 Discussion 15 Literature Cited 10 Formatting 10 Total 100 Title · The title must be descriptive and informative. You can try to attract the reader’s attention, but this can often result in a misleading statement. In comparing the two titles below, the first certainly grabs the reader’s attention, but is the ocean really boiling? The second title is more descriptive, informative, and accurate. o “Boiling Sea Food: The Effects of Temperature and Salinity on the Mass Mortality of Pisaster ochraceus Along the California Coastline.” o “Increased Ocean Temperature May Result in Mass Mortality of Pisaster ochraceus Along the California Coastline.” · The title should also contain the major result, specifically whether or not there is a relationship between the independent and dependent variables (or two independent variables). The second title clearly states that an increase in ocean temperature may result in mass mortality. The first title vaguely describes some effect of temperature and salinity on mass mortality. · Finally, the title should identify the focus species, if applicable. In both titles, the species is clearly identified. · Below the title should be the author’s name, their institution, and their institution’s address. · “Grace, S., Suffolk University, Boston, Massachusetts 02108” Abstract An abstract is a concise summary of the paper. It should provide all the relevant information needed for the reader to understand the scope of the study. Abstracts do not include references and the best abstracts are written after all the other parts of the paper have been written. Abstracts should include the following: · an orientation to the theme of the experiment; the general purpose for conducting the study · the specific objective of the experiment with the hypotheses · a description of the most important methods · the specific results that addresses the hypotheses, with statistical values · a conclusion that addresses the general importance of the experiment, with respect to the theme Introduction The rationale of the introduction is to logically discuss the importance and the purpose and importance of the study. It is typically organized in an inverted triangle format, such that the first paragraph provides a broad background of the study. The introduction then gra.

1. One of the major goals of the laboratory section of this course
is to develop scientific writing skills. Students are required to
write three (3) formal laboratory reports. These formal reports
should follow the format of primary research papers found in
scientific journals. This handout is a guideline describing the
required structure for a formal report with the rubric for grading
(Table 1).
Table 1: This is the general rubric used for evaluating formal
laboratory reports based on the guidelines explained below. A
detailed rubric follows the guidelines (Table 2).
Item
Percentage Value
Title
5
Abstract
15
Introduction
15
Methods
15
Results
15
Discussion
15
Literature Cited
10
Formatting
10
Total
100
Title
· The title must be descriptive and informative. You can try to

2. attract the reader’s attention, but this can often result in a
misleading statement. In comparing the two titles below, the
first certainly grabs the reader’s attention, but is the ocean
really boiling? The second title is more descriptive,
informative, and accurate.
o “Boiling Sea Food: The Effects of Temperature and Salinity
on the Mass
Mortality of Pisaster ochraceus Along the California Coastline.”
o “Increased Ocean Temperature May Result in Mass Mortality
of Pisaster ochraceus Along the California Coastline.”
· The title should also contain the major result, specifically
whether or not there is a relationship between the independent
and dependent variables (or two independent variables). The
second title clearly states that an increase in ocean temperature
may result in mass mortality. The first title vaguely describes
some effect of temperature and salinity on mass mortality.
· Finally, the title should identify the focus species, if
applicable. In both titles, the species is clearly identified.
· Below the title should be the author’s name, their institution,
and their institution’s address.
· “Grace, S., Suffolk University, Boston, Massachusetts 02108”
Abstract
An abstract is a concise summary of the paper. It should
provide all the relevant information needed for the reader to
understand the scope of the study. Abstracts do not include
references and the best abstracts are written after all the other
parts of the paper have been written. Abstracts should include
the following:
· an orientation to the theme of the experiment; the general
purpose for conducting the study
· the specific objective of the experiment with the hypotheses
· a description of the most important methods
· the specific results that addresses the hypotheses, with
statistical values
· a conclusion that addresses the general importance of the
experiment, with respect to the theme

3. Introduction
The rationale of the introduction is to logically discuss the
importance and the purpose and importance of the study. It is
typically organized in an inverted triangle format, such that the
first paragraph provides a broad background of the study. The
introduction then gradually narrows to the last paragraph that
provides the specific hypotheses of the study. Below is a
general outline, but please follow the specific requirements
detailed in the lab handouts.
· The introduction should start with a broad background to
orient the reader to the general theme (natural selection, fitness,
demography, biodiversity, etc.), and why it is important to
study.
· The second part of the introduction should provide the premise
of the study. What is currently known about the theme? What
similar studies have been conducted to address the theme and
what are their results? This is where most of the previous
studies are used to make a case for the purpose of the study.
This part may consist of multiple paragraphs that each discuss a
single topic.
· The third part of the introduction should discuss what is still
unknown about the subject. What is the study trying to answer?
How will the study attempt to contribute to the body of
knowledge about the theme?
· Finally, the introduction should provide a testable hypothesis
with predictions. “Testable” means that there is a way to gather
data and the data can be analyzed to find an answer.
Methods
· The methods should contain enough detail so that the
experiment can be repeated. This should include the statistical
analyses.
· The methods should be written in paragraph format.
· The methods should be written in past tense because it
outlines what procedures were done.
· Do you best to use passive voice.
· The methods should identify the control (if any) and

4. treatments.
· Similarly, the methods should identify the independent
variables and dependent (if any) variables.
· The methods should explain why specific procedures were
taken.
· For example, “The salinity of each tide pool observed was
measured using a Vernier LabQuest 2 with a salinity probe. The
salinity was measured in parts per thousand (ppt) and it was
collected to determine whether there was a relationship with the
size of Lottia gigantea, such that smaller individuals were
associated with more saline conditions.”
· Statistical analyses should be explicitly stated, especially how
the test could support the hypothesis.
· For example, “A chi-squared test was performed to examine
whether the population of D. melanogaster deviated from
Hardy-Weinberg equilibrium during the course of the
experiment. A significant difference in allele frequency between
the beginning and the end of the experiment will show that at
least one criterion of Hardy-Weinberg equilibrium has been
violated.”
· If data were collected in the field, the study site should be
provided.
Results
There are two components that need to be in the results. The
first component is a written summary of the data trends and
statistics. The second component is figures and/or tables that
graphically display the trends and statistics. The written
summary has to come before the figures and tables; the former
provides the context for the latter. Additionally, the results
should contain as few figures and tables as possible. If a table is
showing the same information as a figure, get rid of the table.
· The written summary should objectively state the overall
outcomes and general trends of the experiment in paragraph
format. Describing each datum is not useful or informative.
· The results should not include any raw data; manipulated data
are okay.

5. · The results should not include interpretations of the results;
interpretations belong in the discussion section.
· The results should include the statistical
significance/insignificance (p-values) as often as they are
mentioned.
· The figures and tables should be referenced in the written
summary and are numbered independently.
· “Figure 1 shows…”
· “…population increased (Table 1).”
· The figures and tables should be arranged in order of reference
(sequentially). Do not talk about Figure 2 first if Figure 1
appears first. If you must, change the order of the figures and
tables.
· The results should include the fewest number of figures and
tables as possible.
· If figures are included, descriptive captions should be placed
below the figure. The importance of descriptive captions is that
the figure (or table) should be clear enough to stand on their
own.
· For example, “Figure 1: During the four weeks of sampling,
the number of A alleles (black lines) increased while the
number of a alleles (gray lines) decreased in D. melanogaster.
Weekly data are averaged and error bars are provided to show
the variation in the data. Population allelic frequencies for
Week 3 through Week 5 were statistically significant (p<0.05)
when compared to the initial population.”
· Figures should have axes clearly labeled with the appropriate
units. If you have dependent variables, it should be placed on
the y-axis.
· Do not include gridlines as they obscure the data.
· Titles are not necessary, as the caption should provide this
information.
· The data should fill the figure and the figure should be large
enough to show detail.
· If tables are included, they should convey a different set of
information from the figures.

6. If not, keep the figure and get rid of the table.
· Descriptive captions should be placed above the table.
· For example, “Table 1: Pairwise genetic distances of 16S
rRNA among specimens of Amusium pleuronectes, Ylistrum
balloti, and Ylistrum japonicum. Asterisks (*) indicate the
Ylistrum specimens. Values below the diagonal indicate percent
sequence similarity; pairwise comparisons above the diagonal
are presented as a heat map, with dark shades representing
higher similarities between sequences. Labels for Amusium and
Ylistrum specimens are as follows: source (SL, Serb Lab; GB,
Genbank), unique numerical identifier, and country (AU,
Australia; CN, China; JP, Japan; NC, New Caledonia; PH,
Philippines; QL, Queensland, Australia; TH, Thailand; WA,
Western Australia, Australia).”
· Tables should have clearly labeled column and row headings
with units (as necessary). If you have dependent variables, they
should be the column headings.
Discussion
The purposes of the discussion are to explain how the
experiment supports or do not support the hypotheses, and to
explain how the experiment relate to the general theme
discussed in the introduction. As opposed to the introduction,
the discussion follows a normal triangle (not inverted) format,
such that the first paragraph discusses the specific outcomes of
the study. The discussion then gradually broadens to the last
paragraph explaining the overall importance of the study.
· The first part of the discussion should restate the hypotheses,
the major outcomes, and the general trends. It should also state
whether the outcomes and trends do or do not support the
hypotheses.
· The second part of the discussion should explain how the
experiment helped in understanding of the general theme. This
should discuss similarities and/or differences in results
comparing similar studies. Be careful with making overly broad
generalizations. What do the results mean and what do they not
mean?

7. · The third part of the discussion should explain how the
experiment did not help in understanding of the general theme.
You may discuss the limitations and unexpected outcomes of
the study and how the experiment could be refined to further
help in understanding the general theme. However, do not state
any errors. Errors should have been avoided or corrected.
· The discussion should then conclude with a summary of the
overall importance, to science and to society, of examining the
general theme.
Literature Cited
The format of references vary. For this course, use the
following guidelines:
· The references must be listed alphabetically, by the first
author’s last name.
· The references must have the “hanging” paragraph format, as
shown in the examples below.
· There must be at least three (3) primary and peer-reviewed
references.
· Primary means that the authors who wrote the reference
conducted the study.
Books are considered secondary literature.
· Peer-reviewed means other scientists read the study and
agreed it was acceptable for publication.
· All three (3) references must be cited in the text.
· The in-text citations must be formatted according to the
following conventions:
· One author
· “Chan (2000) found that…”
· “According to Chan (2000), the…”
· “was not a major factor (Chan, 2000).” o Two authors
· “García and Smith (2000) found that…”
· “According to García and Smith (2000), the…”
· “was not a major factor (García and Smith, 2000).” o Three or
more authors (“et al.” is Latin for “and others.” Alternatively,
one can write “and colleagues” or “and coauthors.”)
· “Smith et al. (2000) found that…”

8. · “Smith and colleagues (2000) found that…” § “Smith and
coauthors (2000) found that…”
· “According to Smith et al. (2000), the…”
· “According to Smith and colleagues (2000), the…”
· “According to Smith and coauthors (2000), the…”
· “was not a major factor (Smith et al., 2000).”
· The references should either be in APA or Harvard format.
· For example, Journal article in APA format:
Spoelstra, K., Wikelski, M., Daan, S., Loudon, A. S., & Hau, M.
(2016). Natural selection against a circadian clock gene
mutation in mice. Proceedings of the National Academy of
Sciences, 113(3), 686-691.
· For example, Journal article in Harvard format:
Spoelstra, K., Wikelski, M., Daan, S., Loudon, A. S. and Hau,
M., 2016. Natural selection against a circadian clock gene
mutation in mice. Proceedings of the National Academy of
Sciences, 113(3), pp.686-691.
· For example, Book in Harvard format:
Fisher, R.A., 1930. The genetical theory of natural selection: a
complete variorum edition. Oxford University Press.
Formatting
There is a general format that most research papers follow, but
many vary. The most important format to follow is the one
provided by the publisher or instructor. For this course, use the
following guidelines:
· You must submit the report as a Word document so that the
following items can be assessed. If another document type is
submitted, points will be deducted because the correct
formatting cannot be evaluated.
· A cover page is not necessary.
· There is no page limit.
o The reason for this is that the focus needs to be on
communicating what the research is about, not on how many
pages it takes. Additionally, people’s communication skills
vary. However, there are some general patterns. For example, a
four-page report tends to lack sufficient information and detail.

9. In contrast, a 30-page report tends to be verbose and tangential.
As with any writing assignment, the best way to start is by
creating an outline. An outline ensures that only the necessary
and relevant information are in the report and it will help in
being organized and staying on task.
· Use 1.5 spacing paragraph format.
· Use either Arial or Times (New Roman) fonts.
· Use the standard 12-point font size.
· Use the standard one-inch margins on all sides of the paper.
· Use page numbers. It does not matter where on the page they
are, just be consistent.
· Use the appropriate measurement units where necessary.
Science uses the metric system, so make sure units are in
meters, liters, or grams.
· Use the correct species scientific names. Below is the
scientific name of the common fruit fly written in two
acceptable forms. The genus name is always capitalized but the
species name is never capitalized. The entire species name is
either italicized or underlined, but not both. o Drosophila
melanogaster o Drosophila melanogaster
o When the species is first introduced, the full species scientific
name should be used (as above). Subsequent mention of the
species can be shortened as D. melanogaster (or ).
· The report must be organized as this guideline is presented:
Title, Abstract, Introduction, Methods, Results, Discussion, and
Literature Cited.
· Each section of the report should have a natural flow from one
idea to another. It should not jump back and forth between
ideas.
· Similarly, each paragraph should have a natural flow with a
topic sentence about a single concept, a body that supports the
idea, and a conclusion or transition sentence.
· Be sure the report is easy to read (clear and effective
communication); keep spelling and grammar errors to a
minimum.

10. Table 2: Below is a detailed rubric used for evaluating formal
laboratory results. A P will indicate the specific criterion is met
and will receive a score of 10. An O will indicate the specific
criterion is not met and will receive a score of 5. “Most” and
“some” will indicate two different levels of meeting the
criterion, such that “most” will receive a score of 8 while
“some” will receive a score of 7.5. A “0” will indicate no
attempt was made to address the criterion and will receive a
score of 0. A “-” will indicate that the criterion is does not
apply and will not be scored.
Title: Criteria
Evaluation
Percentage (5)
Is it descriptive and informative?
Does it contain the major result with respect to the variables?
Is the focus species identified (if applicable)?

11. Is the author’s name included and formatted correctly?
Is the author’s institution included and formatted correctly?
Is the institution’s address included and formatted correctly?
Abstract: Criteria
Evaluation
Percentage (15)
Is the general purpose of the study stated?
Is the specific objective stated?
Are the hypotheses stated?
Is the most important method described?
Is the result that addresses the hypotheses stated?
Are statistical values provided?
Is a conclusion provided?
Does the conclusion address the general importance of the
experiment?

12. There should not be any references.
Introduction: Criteria
Evaluation
Percentage (15)
Does it follow an inverted triangle format?
Is the general theme explained?
Is the importance of the general theme explained?
Does the introduction explain what is known about the subject?
Does the introduction discuss similar studies and their results?
Does the introduction discuss what is unknown about the
subject?
Does the introduction provide the purpose of the experiment?
Does the introduction discuss how the experiment will
contribute to the body of knowledge about the theme?
Does the last paragraph contain a testable hypothesis?

13. Methods: Criteria
Evaluation
Percentage (15)
Can the experiment be repeated with the information provided?
Is the methods written in paragraph format?
Is the methods written in past tense?
Is passive voice used?
Are the controls (if any) and treatments identified?
Are the dependent (if any) and independent variables identified?
Do the methods explain why specific procedures were taken?
Were the statistical tests explicitly stated?
Were the statistical tests appropriate to answer the hypotheses?
Is the study site provided (if applicable)?
Results: Criteria

14. Evaluation
Percentage (15)
Does the section contain text that describes the trends?
Is the text written in paragraph format?
The text should not include each datum.
The text should not include raw data.
The text should not include interpretations.
Does the text include statistical significance/insignificance
(pvalues)?
Does the text appear before any figures and tables?
Are figures included?
Are figures referenced in the text?
Are the figures numbered independently?
Are the figures ordered sequentially?

15. Do the figures contain descriptive captions?
Are the captions placed below the figure?
Do the figure captions include p-values (if applicable)?
Are the figure axes clearly labeled?
Are the units included in the axes’ labels (if applicable)?
Are the dependent variables on the y-axis (if applicable)?
The figures should not have any gridlines.
The figures should not have any titles.
Does the data fill the figure?
Is the figure easy to read?
Are tables included?
Are tables referenced in the text?

16. Do the tables show different information from the figures?
Are the tables numbered independently?
Are the tables ordered sequentially?
Do the tables include descriptive captions?
Are the table captions placed above the table?
Do the table captions include p-values (if applicable)?
Are the rows and columns clearly labeled?
Are the units included in the row and column labels (if
applicable)?
Are the dependent variables on the column headings (if
applicable)?
Is the table easy to read?
Does the section contain the fewest number of figures and
tables?

17. Discussion: Criteria
Evaluation
Percentage (15)
Does the section follow a non-inverted triangle format?
Are the hypotheses restated?
Are the major outcomes and general trends restated?
Is the support (or lack thereof) of the hypotheses explained?
Is an explanation given on how the experiment helped in
understanding the general theme?
Is the experiment compared to similar studies?
There should not be any overly broad generalizations made.
Are the limitations discussed?
Are the unexpected outcomes discussed?
Are future directions discussed?
There should not be any errors discussed.

18. Is the overall importance to science discussed?
Is the overall importance to society discussed?
Literature Cited: Criteria
Evaluation
Percentage (10)
Are they listed alphabetically?
Are they in “hanging” paragraph format?
Are there at least three (3) primary and peer-reviewed
references?
Are they all cited in the text?
Are the in-text citations properly formatted?
Are they in APA format?
Formatting: Criteria
Evaluation
Percentage (10)
Is the report a Word document?
There should not be a cover page.

19. Does the report use the 1.5 spacing?
Is it written in either Arial or Times (New Roman) fonts?
Is it written using the 12-point font?
Does it have one-inch margins on all sides of the paper?
Does it have page numbers?
Are the appropriate measurement units used?
Are scientific names properly formatted?
Is the report organized (similar to the guideline)?
Does every section have a natural flow?
Does every paragraph consist of a single topic?
Is the report clear and easy to read?

20. Assessing and Treating Clients With
Dementia
Alzheimer’s Disease---------76-year-old
Iranian Male
At each decision point stop to complete the following:
Decision #1,#2,#3
Which decision did you select?
Why did you select this decision? Support your response with
evidence and references to the Learning Resources.
What were you hoping to achieve by making this decision?
Support your response with evidence and references to the
Learning Resources.
Explain any difference between what you expected to achieve
with Decision #1 and the results of the decision. Why were they
different?
BACKGROUND
Mr. Akkad is a 76 year old Iranian male who is brought to your
office by his eldest son for “strange behavior.” Mr. Akkad was
seen by his family physician who ruled out any organic basis for
Mr. Akkad’s behavior. All laboratory and diagnostic imaging
tests (including CT-scan of the head) were normal. According to
his son, he has been demonstrating some strange thoughts and
behaviors for the past two years, but things seem to be getting
worse. Per the client’s son, the family noticed that Mr. Akkad’s
personality began to change a few years ago. He began to lose
interest in religious activities with the family and became more
“critical” of everyone. They also noticed that things he used to
take seriously had become a source of “amusement” and
“ridicule.” Over the course of the past two years, the family has
noticed that Mr. Akkad has been forgetting things. His son also
reports that sometimes he has difficult “finding the right words”
in a conversation and then will shift to an entirely different line
of conversation.

21. SUBJECTIVE
During the clinical interview, Mr. Akkad is pleasant,
cooperative and seems to enjoy speaking with you. You notice
some confabulation during various aspects of memory testing,
so the PMHNP performs a Mini-Mental State Exam. Mr. Akkad
scores 18 out of 30 with primary deficits in orientation,
registration, attention & calculation, and recall. The score
suggests moderate dementia.
MENTAL STATUS
EXAM
Mr. Akkad is 76 year old Iranian male who is cooperative with
today’s clinical interview. His eye contact is poor. Speech is
clear, coherent, but tangential at times. He makes no unusual
motor movements and demonstrates no tic. Self-reported mood
is euthymic. Affect however is restricted. He denies visual or
auditory hallucinations. No delusional or paranoid thought
processes noted. He is alert and oriented to person, partially
oriented to place, but is disoriented to time and event [he
reports that he thought he was coming to lunch but “wound up
here”- referring to your office, at which point he begins to
laugh]. Insight and judgment are impaired. Impulse control is
also impaired as evidenced by Mr. Akkad’s standing up during
the clinical interview and walking towards the door. When the
PMHNP asked where he was going, he stated that he did not
know. Mr. Akkad denies suicidal or homicidal ideation.
Diagnosis: Major neurocognitive disorder due to Alzheimer’s
disease (presumptive)
RESOURCES
§ Folstein, M. F., Folstein, S. E., & McHugh, P. R. (2002).
Mini-Mental State Examination (MMSE). Lutz, FL:
Psychological Assessment Resources.
DECISION ONE
Begin Exelon (rivastigmine) 1.5 mg orally BID with an increase

22. to 3 mg orally BID in 2 weeks
Begin Aricept (donepezil) 5 mg orally at BEDTIME
Begin Razadyne (galantamine) 4 mg orally BID
DECISION TWO
Increase Aricept to 10 mg orally at BEDTIME
Discontinue Aricept and begin Razadyne (galantamine)
extended release 24 mg orally daily
Discontinue Aricept and begin Namenda (memantine) extended
release, 28 mg orally daily
DECISION THREE
Continue Aricept 10 mg orally at BEDTIME
Increase Aricept to 15 mg orally at BEDTIME x 6 weeks, then
increase to 20 mg orally at BEDTIME
Discontinue Aricept and begin Namenda 5 mg orally daily
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0.3579322767329.99.4119.750B31327.128.41.3114.20320.2857
142857-
0.3579322767215.050B31328.430.01.6218.870610.1428571429-
0.2779871642speciesabundancepipi*ln(pi)321.92.0336.41.4total
461.2718388817340.5-0.3465735903SpeciesAbundance
PiPi*Ln(Pi)transectnative covernonnative
coverspeciesabundancepipi*ln(pi)630.375-
0.367810969913100.9090909091-
0.0866456181190SpeciesAbundance pipi*ln(pi)450.5-
0.3465735903total370.7143845602610.0909090909-
0.2179904793214.201370.875-0.1168399685330.3-
0.3611918413total21110.3046360973322.30.0610.125-
0.25993019271320.2-
0.3218875825speciesabundancepipi*ln(pi)total280.3767701613t

24. otal3101.0296530141350.625-0.2937522683SpeciesAbundance
PiPi*Ln(Pi)Species AbundacePipi*ln(pi)630.375-
0.367810969913161316SpeciesAbundance
pipi*ln(pi)speciesabundancepipi*ln(pi)total10total10139720.5-
0.3465735903total380.6615632382total101210.25-
0.3465735903SpeciesAbundance pipi*ln(pi)310.25-
0.3465735903speciesabundancepipi*ln(pi)SpeciesAbundance
PiPi*Ln(Pi)1350.8333333333-
0.1519346307SpeciesAbundancepipi*ln(pi)total341.0397207708
310.25-0.3465735903610.1666666667-
0.29862657821350.7142857143-0.2403373119320.3333333333-
0.3662040962720.5-
0.3465735903total260.4505612089620.2857142857-
0.35793227672320.3333333333-0.3662040962710.1666666667-
0.2986265782total340.6931471806SpeciesAbundance
pipi*ln(pi)total270.59826958862410.1666666667-
0.2986265782610.0769230769-
0.1973037967total561.329661348913120.9230769231-
0.0738855763total2130.271189373restoredspabspabapabDiversi
ty for
restoredAverageVarience131031318goldenbush82a0.3046360.58
275446450.1950243359613247bush
sunflower18a0131133613laurel
sumac13a0.69314313176buckwheat7b07234121CA
sage6b0.4505621351382Lemonade
berry2b0.271189131632232Coyote
bush1c0.3767701613542241oak1c06145c0.59826161d1.2718388
813361d1.0296530113761d1.039720776161e0.71438456021396
2e0.661563238213561e1.3296613489626321632172Native
coveraverageNon-native
coveraverage7171a19.7522.618a01.38666666674272a15.05varie
ncea0varience3271a21.956.08236a26.819809523861121b19b04
51310b14.2b0331311b22.3b01321316c14.2c072135c18.87c0121
133c36.4c1.431137d30d521139d11.1d034135d27.6d063132e30e
235232e29e163241e29.9e9.421243223271241
goldenbush bush sunflower laurel sumac buckwheat

25. CA sage Lemonade berry Coyote bush oak 82 18
13 7 6 2 1 1
unrestoredgrouptransectspeciesbegin (m)end (m)cover
(m)grouptransectspeciesbegin (m)end (m)cover
(m)grouptransectspeciesbegin (m)end (m)cover
(m)grouptransectspeciesbegin (m)end (m)cover
(m)grouptransectspeciesbegin (m)end (m)cover
(m)F1200.90.9G1221.421.950.55H163.924.370.45I1228.729.140
.44J163.394.481.09F133.743.940.2G1222.1522.580.43H1616.25
18.211.96I152.42.770.37J11300.580.58F134.194.980.79G1227.
6928.290.6H1135.055.370.32I187.628.080.46J1136.587.340.76
F12011.3611.460.1G1323.5624.591.03H1136.546.790.25I1819.
2829.7410.46J1138.358.830.48F1131212.280.28G1328.3628.77
0.41H12002.492.49I1137.27.60.4J1139.410.380.98F11313.7414
.440.7G185.685.940.26H1202.492.650.16I1138.028.690.67J113
23.1423.40.26F12018.4818.60.12G186.6981.31H1204.14.960.86
I1138.588.740.16J1200.590.970.38F12019.619.760.16G11300.4
10.41H12029.17300.83I1138.68.970.37J1202.523.220.7F12020.
1420.240.1G1133.043.250.21H12028.5428.950.41I1138.879.280
.41J12024.1224.210.09F12020.920.930.03G1133.543.710.17H1
2027.4328.511.08I11399.460.46J12024.6624.750.09F12021.052
1.090.04G1133.733.90.17H12018.1118.790.68I1139.7910.380.5
9J12027.5327.880.35F12021.1221.140.02G1134.544.770.23H12
016.0616.440.38I11310.310.790.49J12028.68301.32F12021.212
1.310.1G1138.348.760.42H12015.9829.4113.43I11311.2811.830
.55J2100.70.7F12022.7823.670.89G11329.0429.150.11H229.79.
780.08I11312.15130.85J210.911.550.64F12027.4527.60.15G120
5.545.650.11H2225.826.91.1I11314.815.81J211.842.2F11328.0
928.60.51G1206.456.740.29H2822.923.30.4I11316.9317.560.63
J219.412.43F1628.6129.040.43G1207.047.40.36H213011I11317
.5818.340.76J2121.723.21.5F11329.0429.660.62G1208.769.260.
5H2131.732.20.47I11324.65250.35J2126.126.510.41F11329.733
00.27G1209.49.840.44H2136.887.240.36I1132626.40.4J220.720

26. .890.17F2200.51.480.98G12010.5510.770.22H21322.1522.650.5
I11323.9324.160.23J221.551.80.25F2201.72.080.38G12012.681
2.980.3H21327.66280.34I11318.43011.6J2246.32.3F2202.092.4
20.33G12013.514.090.59H2132828.10.1I11323.623.650.05J221
4.3150.7F2202.230.8G12014.2614.550.29H21329.129.790.69I1
2027.5228.30.78J2215161F2132.73.50.8G12019.8720.040.17H2
1329.8300.2I21911.32.3J221717.80.8F213451G12025.526.581.0
8H21814.3150.7I2111.917.35.4J2223.223.40.2F274.839.74.87G
2227.4728.40.93H21816.117.371.27I211919.90.9J2225.1260.9F
2154.39.284.98G271.2442.76H21818.24190.76I2121.722.20.5J2
226.5126.770.26F2710.2213.463.24G2728.829.91.1H21911.211.
80.6I2123.924.20.3J2512.413.91.5F2131416.472.47G2133.65.3
1.7H21913.213.540.34I22099J2524.8250.2F2716.4717.240.77G
2135.736.40.67H21919.5519.80.25I2211.311.90.6J2526.7727.22
0.45F21318.5819.40.82G2136.758.41.65H21920.320.820.52I22
17.318.31J266.47.851.45F2210.423.212.8G2139.9100.1H21926.
2427.271.03I2218.4190.6J261616.90.9F21324.2261.8G21313.65
13.750.1H21927.4527.720.27I222121.40.4J2789.41.4F2225.522
5.80.28G21318.1218.280.16H2202.130.9I222223.91.9J2717.721
.63.9F21126.0826.560.48G21325.826.160.36H2205.96.280.38I2
224.325.81.5J2728.1828.690.51F21126.827.30.5G21326.727.20.
5H2207.458.741.29I2226.927.40.5J2729.21300.79F21326.527.4
70.97G21329.89300.11H2209.7410.60.86I2229301J21428.729.3
10.61F2132828.70.7G22018.6718.90.23H22020.8221.570.75I23
27.427.90.5J310.024.654.63F2132929.70.7G22019.4719.740.27
H22121.3220.7I2520.120.60.5J314.85.70.9F2829.4329.90.47G2
2021.4722.20.73H3113.718.44.7I2719.920.60.7J315.76.20.5F31
00.20.2G22023.4824.140.66H312122.51.5I2725.727.41.7J31262
6.70.7F370.20.720.52G3101.741.74H3124.224.90.7I2727.828.7
0.9J3200.020.02F310.221.020.8G310.81.60.8H3129.6300.4I312
.510.58J324.654.750.1F371.022.61.58G312.22.60.4H32013.713.
7I3118.522.64.1J326.22215.8F372.630.4G317.47.850.45H321.4
2.51.1I3210.518.58J3226.8270.2F34341G311212.80.8H32229.6
27.6I3222.6307.4J3227303F3247.23.2G3113.914.80.9H323.951.
1I3602.52.5J31722.1263.9F3757.22.2G3115.1315.450.32H3215.
418.53.1F367.210.43.2G3116.118.42.3H3218.521.22.7transectn

27. ative covernonnative covertransectnative covernonnative
coverF3710.411.61.2G3119.3520.10.75H3223.825.11.3132.480.
4416.080F3111.616.14.5G320.750.80.05H3224.124.90.8230.216
.5226.746.58F3116.119.33.2G321.62.20.6H3225.828.83330.015
.4329.819.1F3219.319.70.4G327.858.851H3227.529.31.8F3619.
720.40.7G32110.170.62H3720.4210.6SpeciesAbundance
PiPi*Ln(Pi)F312128.27.2G3212.813.250.45H3722.623.10.5Spec
iesAbundance PiPi*Ln(Pi)610.0833333333-
0.2070755541F3228.2301.8G3214.815.130.331350.4166666667
-0.3647786406G3215.2516.060.81transectnative covernonnative
cover510.0454545455-0.14050192972060.5-
0.3465735903transectnative covernonnative
coverG3220.127.47.3123.30820.0909090909-
0.2179904793total3120.91842778516.410.9G3229301215.861.1
813180.8181818182-
0.1641851145240.1413.08G369.411.62.2364.656.22010.045454
5455-0.1405019297SpeciesAbundance
PiPi*Ln(Pi)332.15.4G3618.419.350.95total4220.6631794532G3
72.754.31.55SpeciesAbundance PiPi*Ln(Pi)530.3-
0.3611918413SpeciesAbundance
PiPi*Ln(Pi)G379.810.680.88620.1538461538-
0.2879695657620.2-
0.3218875825G3144.37.43.11320.1538461538-
0.2879695657SpeciesAbundance PiPi*Ln(Pi)740.4-
0.3665162927320.1176470588-
0.2517724898G3166.57.350.852090.6923076923-
0.25457869391410.1-0.23025850932090.5294117647-
0.3366999353G3169.39.90.6total3130.8305178253310.2-
0.3218875825total4101.27985422581350.2941176471-
0.3599339505G31611.611.90.3510.2-
0.3218875825610.0588235294-
0.1666596085G31613.313.90.6SpeciesAbundance
PiPi*Ln(Pi)730.6-
0.3064953743total4171.1150659841G31726.75292.25total350.9
502705392SpeciesAbundance PiPi*Ln(Pi)810.0416666667-
0.1324189096SpeciesAbundance PiPi*Ln(Pi)transectnative

28. covernonnative cover1380.3333333333-
0.3662040962SpeciesAbundance
PiPi*Ln(Pi)1712040.2105263158-
0.3280304459110.661.581830.125-
0.2599301927total101380.4210526316-
0.3642094474212.030.931960.25-
0.346573590361730.1578947368-
0.2914463196333.912.22050.2083333333-
0.3267949829total1101510.0526315789-
0.15497047262110.0416666667-
0.1324189096SpeciesAbundance
PiPi*Ln(Pi)total6241.56434068131120.1052631579-
0.23697808411370.3181818182-0.3643602786810.0526315789-
0.154970472620110.5-0.3465735903SpeciesAbundance
PiPi*Ln(Pi)total6191.5306052421820.0909090909-
0.2179904793721SpeciesAbundance
PiPi*Ln(Pi)320.0909090909-0.2179904793total220750.625-
0.2937522683total4221.1469148276410.125-
0.2599301927SpeciesAbundance PiPi*Ln(Pi)620.25-
0.3465735903total380.9002560513720.1428571429-
0.27798716421380.5714285714-0.3197804502 Unrestored
DiversityAverageVarience2040.2857142857-
0.3579322767F1.1150660.8883945170.2793705048total3140.95
56998911F1.5306052421F0.9002561SpeciesAbundance
PiPi*Ln(Pi)G1.1469G0.9556999620.2-
0.3218875825G1.4708720.2-0.3218875825H0.830517831410.1-
0.2302585093H1.564340681640.4-0.3665162927H01710.1-
0.2302585093I0.6631794532total5101.4708084763I0.95027053
92I0J0.918427785unrestoredspabspabspabspabJ1.279854225821
3235goldenbush36J0323241toyon282093155california
sage19Native covervariencenonnative
covervarience1354169mulefat19F6.41228.5761095238F0.9210.0
5753809526151719laurel sumac9F40.14F13.0820451819blue
fiesta flower6F32.1F5.413853112bush
sunflower5G10.66G1.5873611336black
sage5G12.03G0.9315162142monkey

29. flower4G33.9G12.162260151everlasting
flower3H23.3H011262164opunita2H15.86H1.188161172white
sage2H64.6H56.27561183elderberry2I32.48I0.444162196buckw
heat1I30.2I16.522732028marah1I30I15.46275211poison
oak1J6.08J013772J26.74J6.5820670J29.8J19.182722373327420
81728013881204822111260135701381411301641381711326213
81321302061352214181141138151183164196171205171211183
21019672209212045120082204131020020120529201312055121
1732261611352062953627414125171
goldenbush toyon california sage mulefat laurel sumac
blue fiesta flower bush sunflower black sage monkey
flower everlasting flower opunita white sage
elderberrybuckwheat marah poison oak 36 28
19 19 9 6 5 5 4 3 2 2 2 1
1 1
Diversity statsRestoredUnrestoreddof tcritical
value0.57261751760.9327165628-1.71872.048Since the
absolute value of the t value is less than the critical value, the
means are not significantly differentDiversity for
restoredAverageVariencestdevstd error
a0.3046360.58275446450.19502433590.44161559740.11402465
7a0a0.69314b0b0.45056b0.271189c0.37677016c0c0.5982d1.271
83888d1.02965301d1.03972077e0.7143845602e0.6615632382e1
.3296613489 Unrestored DiversityAverageVariencestdevstd
errorF1.1150660.8883945170.27937050480.52855511050.13647
23427F1.530605242F0.9002561G1.1469G0.9556999G1.4708H0
.83051783H1.56434068H0I0.663179453I0.950270539I0J0.9184
27785J1.279854226J0
Cover + Diversitynon-native coverspecies
diversity00.3046000000.450500.271100.37670001.029601.3972
00.830500.91840.440.52260.91.0870.930.927710.66151.181.56
431.40.59821.581.146920.636520.682951.32965.40.90026.581.
27989.41.329613.081.497616.50.50119.12020.621.470848.5056

30. .20
species diversity 0 0 0 0 0 0 0 0 0
0 0 0.44 0.9 0.93 1 1.18 1.4 1.58 2 2 5
5.4 6.58 9.4 13.08 16.5 19.12 20.62 48.5
56.2 0.30459999999999998 0 0
0.45050000000000001 0.27110000000000001
0.37669999999999998 0 1.0296000000000001
1.3972 0.83050000000000002 0.91839999999999999
0.52259999999999995 1.087 0.92769999999999997
0.66149999999999998 1.5643 0.59819999999999995
1.1469 0.63649999999999995 0.68289999999999995
1.329599999999999 9 0.9002 1.2798
1.3295999999999999 1.4976 0.501 0
1.4708000000000001 0 0
Non-native cover
Species Diversity
Cover StatsRESTOREDNative coveraverageNon-native
coveraveragedof tcrit
valuea19.7522.618a01.386666671710.362.11since our t value
exceeds the critical value, the means are significantly different
a15.05variencea0variencea21.956.08236a26.81980952b19b0b14
.2b0b22.3b0c14.2c0c18.87c0c36.4c1.4d30d5d11.1d0d27.6d0e30
e2e29e1e29.9e9.4UNRESTOREDNative covervariencenonnative
covervariencedoftcrit
valueF6.41228.5761095238F0.9210.0575380952283.01862.048s
ince the t value exceeds the critical value, the means are
significantly
differentF40.14averageF13.08averageF32.126.2866666667F5.49
.9633333333G10.66G1.58G12.03G0.93G33.9G12.16H23.3H0H1
5.86H1.18H64.6H56.2I32.48I0.44I30.2I16.5I30I15.4J6.08J0J26.
74J6.58J29.8J19.1Native Cover Stats Restored

31. NvarienceUnrestored N variencedoft valuecrit
value19.7556.082366.41228.576109523831-0.012232.04since
the t value is smaller than the critical value, the means are not
signifivantly different
15.05average40.14average21.922.61832.126.28666666671910.6
614.212.0322.333.914.223.318.8715.8636.464.63032.4811.130.
227.630306.082926.7429.929.8Non Native cover
statsrestoredaverageunrestoredaveragedoft valuecrit
value01.38666666670.99.963333333315-2.2552.131since the
absolute value of the calculated t exceeds the critical value, the
means are significantly different
0varience13.08varience26.81980952385.4210.057538095201.58
00.93012.160001.181.456.250.44016.5015.42016.589.419.1
Diversity Lab:
The Effect of Alien Species on Native Plant Diversity in
Coastal Sage Scrub
BIOL/ENVS251 Spring 2020
Updated 13/04/20 Alejandrino 1
Introduction (4/13 or 4/14)
Non-native, alien, species often have a devastating impact on
native species. This is
especially true when the non-natives become invasive and
overwhelm the native species through
increased competition or predation. In this lab, we investigate
the effect of non-native plant cover
on native species diversity in coastal sage scrub. Coastal sage
scrub (CSS) is a community
characterized by a diverse assemblage of plants many of which
are endemic to southern

32. California. Some species are shallow rooted, and survive the
summer by dropping their leaves
and going dormant. Other species are deeply rooted and survive
the summer drought by
accessing ground water deep in the soil, and by conserving
water by closing their stomata, pores
in the leaves that allow for the diffusion of CO2 in, but also
allow H2O to diffuse out. We have
lost most of our CSS habitat to development, and in the
remaining patches, invasive non-native
grasses and annuals often outcompete the native species after
disturbance, which results in the
conversion of shrublands to non-native grasslands.
Restoration attempts reverse the conversion of CSS by removing
non-native species and
introducing native species through planting or seeding. In one
sense, you can think of restoration
as instant succession. However, restoration is tricky, and
projects often fail, or require constant
maintenance to remove non-natives.
The purpose of this lab is to investigate the relationship
between invasive species cover, and
native species diversity in restored and un-restored CSS habitat.
We will compare the following:
• Invasive vs. native cover in restored and un-restored areas of
CSS.
• Invasive cover vs. species diversity in restored and un-
restored CSS.
• Native species diversity in restored and unrestored areas CSS.

33. Species ID
1. bare ground
2. all non-native species including all grasses
3. bush sunflower: yellow conspicuous flowers; inflorescent
head
4. buckwheat: characteristic amble inflorescence (three
branches); flowers not yellow as in
bush sunflower
5. black sage: poodles-like inflorescence; square stem; opposite
leaves
6. laurel sumac: leaves like taco shell with big red veins in
middle of leaf
7. California sage: 3 parted threadlike leaves; smells good
8. mulefat: conspicuous big shrub; easily recognizable; serrated
leaves
9. solanum: white flowers, anthers with a yellow crown
10. Verbinacea: with little purple flows
11. Opuntia: unmistakable cactus
12. coyote bush: large bush with really dark green fine leaves
13. goldenbush: no live flowers, yellow if present; toothed
leaves hairy seeds
14. white sage: whitish looking bush
15. Marah: a climber with medieval looking fruits; AKA
manroot or wild cucumber
16. monkey flower: opposite leaves, creamy flowers; looks like
sage but has no
inflorescence, has orange flowers
Diversity Lab:

34. The Effect of Alien Species on Native Plant Diversity in
Coastal Sage Scrub
BIOL/ENVS251 Spring 2020
Updated 13/04/20 Alejandrino 2
17. elderberry: a tree with opposite compound leaves,
blueberry-like fruits
18. everlasting flower: a herb with flowers in all individuals
19. blue fiestaflower: herb with purple flowers
20. toyon: large shrub with red berries (Hollywood); unlike taco
plant, leaves are serrated
21. POISON OAK-OAK LIKE LEAVES, DO NOT TOUCH
22. gooseberry: small shrub with dangling purple flowers
23. lemonadeberry: like oak but has berry like fruits rather than
acorns
24. oak: large tree with acorns
Materials
• 30-m line transect
• data sheet
• native plant guide
• clipboard
• writing utensil
Methods
1. Working in groups, you will establish a 30 meter line transect
with a measuring tape
(about 100 feet). You will record:
a. The cover of non-native species along the transect.

35. b. The identity of each native species and its cover along the
transect.
So your transect will look something like this:
2. Complete at least three (3) transects per site (restored and un-
restored CSS habitat). Your
data sheet should look like this (illustrative purposes only, see
provided data form):
Transect Species Start (m) Finish (m) Cover = finish - start
1 4 - buckwheat 0 3 3
1 20 - toyon 5 6 1
1 4 - buckwheat 10 15 5
1 23 - lemonade berry 20 25 5
1 16 - monkey flower 28 30 2
3. Enter your data into Excel, exactly as it is entered on the data
sheet and upload to
Moodle.
Data Calculations (4/18 or 4/19)
4. Download the Class Diversity Data from Moodle.

36. Diversity Lab:
The Effect of Alien Species on Native Plant Diversity in
Coastal Sage Scrub
BIOL/ENVS251 Spring 2020
Updated 13/04/20 Alejandrino 3
5. Process the data so that you can determine the following
attributes for each transect:
a. Count the number of individuals of each native species.
b. Add up the total native cover.
c. Add up the total non-native cover.
d. Calculate the species richness, S.
e. Calculate the Shannon diversity index, H’.
6. Construct rank abundance curves to compare species richness
between restored and
unrestored sites. The rank abundance curve is a very useful tool
because it makes
information on species richness, evenness, and diversity
accessible at a glance.
a. Calculate the abundance (number of individuals) of each
species in restored and
unrestored sites.
b. Rank the most abundant species as 1, the second most
abundant as 2 and so forth.
Plot the rank of each species on the x-axis and abundance on the
y-axis.
7. Use a scatter plot (linear regression) to test the effect of non-
native cover on species

37. diversity, i.e. graph the diversity index for each transect against
the non-native cover.
Statistical Analyses (4/25 or 4/26)
8. Conduct the following statistical tests:
a. Determine if there is greater diversity of natives in restored
or un-restored areas.
b. Determine if there is a difference in native cover and non-
native cover within
restored areas.
c. Determine if there is a difference in native cover and non-
native cover within un-
restored areas.
d. Determine if there is a difference in native cover between
unrestored and restored
areas.
e. Determine if there is a difference in non-native cover
between restored and un-
restored areas.
Specific requirements for the final paper
Introduction: Below is an outline of how the Introduction for
this paper should be organized and
what information should be included. Be sure to use scientific
literature to support your
explanations.
• Start with a paragraph that broadly explains what the

38. experiment is about. What is the
main idea of the experiment and why is it important to test?
Avoid talking about CSS.
• The next paragraph should be about native species, alien
species, and invasive species.
Explain what each are and how they relate to the main idea of
the experiment. What do
we know about native, alien, and invasive species with respect
to the main idea?
• The third paragraph should introduce the experimental system.
Why is the CSS an ideal
plant community for the experiment? What can it tell us about
native, alien, and invasive
species? What can it tell us about the main idea of the
experiment?
• The last paragraph should explain how experimenting on CSS
will help us understand
native, alien, and invasive species and the main idea (What is
the objective?) Don’t forget
to include your biological hypothesis and make sure your
references in the previous
paragraphs back it up.
Diversity Lab:
The Effect of Alien Species on Native Plant Diversity in
Coastal Sage Scrub
BIOL/ENVS251 Spring 2020
Updated 13/04/20 Alejandrino 4

39. Results: Below is a list of specific figures that need to be
included in the final paper.
• A rank abundance curve of the restored site.
• A rank abundance curve of the unrestored site.
• A scatter plot of the diversity indices with respect to non-
native cover.
Data Sheet
Transect Species Start (m) Finish (m) Cover = finish - start