UNDERGRADUATE THESIS

Bachelor of Science in Biology

(Policies and Guidelines 2019)

Section 1. GENERAL POLICIES

1. All graduating seniors who are in their last two semesters of academic work must enroll in
Biology 99R (3 units). They must have their oral defense before the faculty on banc at least one
semester before their graduation.
2. There is no limit for the number of times that a student can enroll in Biology 99R.
3. Final grades will only be released upon the submission of three bound copies and one PDF file to
the Department Secretary and
4. formally endorsed by the Department Chair.
5. Students and advisers must adhere to pre-set deadlines for presentations and submission. They
must also adhere to the format provided.

Section 2. SEQUENCE OF ACTIVITIES

THESIS PROPOSAL
(A) The thesis proposal is the final requirement of Biology 68 (Introduction to Research). The
proposal will then be orally presented to a thesis panel at scheduled dates. Those who cannot
present their thesis during these dates will have to wait until the next scheduled colloquium.
(B) Selection of Thesis Adviser –Refer to Section 4.
(C) At least a week before proposal presentation, the student must get a signed endorsement of
their manuscript from his/her adviser and provide copies of their manuscript to the Biology
68 teacher, Department Chair and members of their panel. The student has the option to
provide more copies for other faculty members.
(D) Oral Presentation/Colloquium - Refer to Section 6.
(E) The revised thesis proposal, which should incorporate all suggestions and revisions of the
thesis panel, must be submitted to the Department Chair and his/ her adviser to get a grade for
Bio 68.

DATA COLLECTION
(A) The student needs to apply for and secure an ethics clearance from the University Research
Ethics Committee (UREC) prior to data collection. The ethics clearance is a requirement for
scheduling the thesis presentation.
(B) After obtaining an ethics clearance, the student is encouraged to start data collection as soon
as possible. He/she must try to follow the submitted timetable of activities presented during
the colloquium.
(C) The student is encouraged to regularly consult with and submit monthly progress reports to
their adviser.

THESIS WRITING
(A) Thesis writing will be under the supervision of the adviser. The draft thesis manuscript must
be endorsed by the adviser prior to scheduling of the thesis presentation/oral defense.
(B) The thesis manuscript should follow the format prescribed in Section 8.

THESIS PRESENTATION
(A) The student must prepare at least four copies of the approved draft manuscript and distribute
it to his/her thesis panel members for perusal at least 5 days before (for thesis colloquium) or
10 days before (for thesis oral defense) the schedule of presentation.
(B) Schedule of presentations to the thesis panel will be posted at least 1 week before the date. A
student must present during their scheduled date. Failure to present without a valid,
documented excuse may cause the student to get a grade of ‘F’.
 (C) Failure to comply will mean a re-schedule of the thesis presentation within the semester;
however, if it is beyond the due date for presentations, the student will have to re-enroll the
subject in the succeeding semester.
(D) Body of the Oral Presentation – Refer to Section 6.

SUBMISSION OF BOUND COPIES

(A) Three bound copies and a PDF file of the approved thesis must be submitted to the
department secretary not later than 5 working days after the last day of final exams.
(B) It must incorporate all suggestions and revisions given by the thesis panel members. Before
the student sends his/her thesis for binding, the final manuscript must be passed among the
thesis panel members and they have to sign the Approval for Binding sheet (Appendix 1).
After binding, the faculty then signs the Approval Form (Appendix 2).
(C) A grade for Bio 99 and approval for graduation will only be given upon the submission by the
student of the bound and PDF copies of the approved thesis.
(D) The final thesis must have permanent, hard binding with a red cover and gold text. Format for
the cover of bound copies is shown in Appendix 3. Spine label must include name of student
and title of the thesis. If enough space is available, include year of admission.

Section 3. THESIS PANEL

1. The thesis panel is tasked to ensure that the basic minimum requirements for the undergraduate
thesis are satisfied by the proposal and the final thesis manuscript by suggesting necessary
revisions, modifications and others.
2. A panel is composed of the department chair, thesis adviser and two regular faculty members. If
the department chair is the thesis adviser of the student, a 3rd regular faculty member will be
added to the panel. All regular faculty members of the Biology department can be members of the
thesis panel. Professionals/researchers who are not part of the department may be included in the
panel upon the discretion of the Chair or recommendation of regular faculty members.
3. Considerations – Considerations will only be given to students who have valid reasons for not
finishing their thesis which may include seasonal sampling (as predicted from thesis proposal
stage), illness and other uncommon circumstances. The student has to write the Chair outlining
his/her reasons for not finishing his/her thesis and endorsed by the thesis adviser. Considerations
will be discussed only upon the final recommendation of the Chair.

Section 4. ADVISER

1. All faculty members with at least a Master’s degree are qualified to act as an undergraduate
adviser.
2. Each faculty adviser is limited to advise three undergraduate students only. This is to ensure that
majority of the faculty members will be involved in this activity and that the advisers will have
ample time for consultations with the students.
3. The faculty adviser is responsible for ensuring that their advisees graduate within the timetable
agreed upon with the student. Problems with student advisees must be reported as soon as
possible to the Chair of the Department who in turn will set up a committee so remedial measures
can be immediately instituted.
4. Selection of Adviser – Students are given the option to select their adviser but their choice is
subject to the approval of the involved faculty and the number of advisees. The student then
writes a formal letter to the Chair declaring his/her adviser (Appendix 4). The faculty in turn
endorses a formal letter thus indicating acceptance of the student.
5. Change of Adviser – If valid problems between student and adviser arise and remedial measures
proposed by the chair are not accepted, the student can change adviser only upon the approval of
the chair.

Section 5. TIMETABLE
 1. A timetable must be presented during the thesis proposal presentation. It should include the
inclusive dates, activity and other details. A sample of a timetable is shown in Appendix 5.
2. The timetable must be agreed upon by both students and adviser.
3. If a student does not comply with the agreed timetable, this may be used as a basis for the final
grade in Bio 99, and/or the adviser may elevate the matter to the chair who will then set up a
meeting for both parties involved. Remedial measures will then be discussed and agreed upon.

Section 6. PRESENTATION OF PROPOSAL AND THESIS

1. Proposal Presentation/colloquium – Student must present the title, scope of study, objectives,
theoretical framework, limitations of the study and methodology during the presentation. The
presentation must also include a timetable of activities.
2. Thesis Presentation/oral defense – During the presentation, the student briefly reiterates the title,
scope of study, objectives, theoretical framework and methodology. The presentation must focus
on the results and discussion of the study.
3. First semester presentations will be convened for the oral defense of senior students who are
graduating in the second semester. These will be scheduled during the last 4 weeks of the
semester but not later than final exam week.
4. Second semester presentations will be convened for thesis proposal presentations of Bio 68
(Introduction to Research) students and oral defense of senior graduating students (Bio 99).
These will be scheduled during the last 4 weeks of the semester but not later than final exam
week for graduating students.
5. A student is given 20 minutes for their presentation. Afterwards, thesis panel members may ask
questions, clarify points, provide comments and/or recommendations to the student regarding
his/her thesis. Advisers are discouraged from answering questions for their thesis advisees.
6. Only the faculty present during a specific presentation will be signatories of the approval sheets
(Appendix 1 and 2).
7. Equipment needed for presentation (LCDs and others) must be arranged and prepared by the
student before presentation. Department equipment can be used upon the approval of the Chair.

Section 7. SCOPE OF THE UNDERGRADUATE THESIS

1. The undergraduate thesis must be more complex than the usual course paper requirements.
2. Topics like one spot surveys and purely descriptive work are strongly discouraged. The
undergraduate thesis must incorporate quantitative measurements and statistical analysis
(parametric or non-parametric).
3. The thesis panel will decide if the scope of the proposed undergraduate thesis presented by the
student is sufficient.

Section 8. THESIS FORMAT

1. An original copy must be typed or reproduced on good quality unlined paper.

2. Page size must be letter size (8.5 inches X 11 inches).
3. Set the left margin at 40 mm and the top, right and bottom margins at 25 mm.
4. Typing must be double-spaced (except tables and figures) and paragraphs should aligned to the
left margin and not justified. Indent the first line of each paragraph of text 0.5 in. from the left
margin using the tab key. Sentences must be separated by single space after a period. Text may be
12 pt. Times New Roman, 11 pt. Calibri or 11 pt. Arial only.
5. Include a page number at the lower right corner of your manuscript. Pagination of thesis contents
must start at Chapter 1. All other sections preceding Chapter 1 must be numbered consecutively
using i, ii, iii, iv and so on.
6. All scientific names must be italicized. Authorities of the scientific names must be given during
first intention. Subsequent intention of the same species can be abbreviated. Scientific names
should be spelled out if used at the beginning of the sentence.
7. Contents – in the sequence they should appear in the bound thesis
▪ Title Page
 ▪ Approval sheets
▪ Acknowledgements
▪ Table of Contents
▪ List of Tables
▪ List of Figures
▪ Abstract
▪ Chapter 1. Introduction
▪ Chapter II. Review of Related Literature
▪ Chapter III. Methodology
▪ Chapter IV. Results and Discussion
▪ Chapter V. Conclusion and Recommendations
▪ Literature Cited
▪ Appendix (must include the UREC ethics clearance)
8. Title page – Contents is the same as that of the cover of the bound thesis (Appendix 3). All text
must be center justified. If scientific names are used, the title must include common name of the
species and its authority.
9. Table of Contents – Refer to Appendix 6.
10. Tables and Figures – can be embedded in the text or can be placed at the end of each chapter. If
more than one page, all tables and figures must be placed at the end of the chapter where they
were first mentioned. Tables and figures must appear in the sequence that they are mentioned in
the text. If they are in text, they must be inserted between paragraphs. Numbering of tables and
figures are separate. A sample of List of Tables is shown in Appendix 7 and for Figures
Appendix 8. All Tables and Figures must be listed with their corresponding pages in sheets
indicating “List of Tables” and “List of Figures “.
11. Tables – Tables include any part of the thesis that is presented in tabular form. They include
ANOVA tables or tables used in statistical tests, summary of data on means and standard
deviations and others. All tables must be presented in sequence as they are mentioned in the text.
They must not encroach into the margin. Minimum font size for Tables is 10 pt. Description of
the table must be in boldface 12 pt. and placed at the top (See Appendix 9). If abbreviations are
used, legends must be included in the table description.
12. Figures – Figures include map(s) of study site(s), photographs (species, study site, experimental
set up), drawings, pie charts and graphs. They must not encroach into the margin. Description of
the figure must be in boldface 12 pt. and placed below the figure (Appendix 10). If abbreviations
are used, legends must be included in the description. If photographs are used, students are
advised to scan them and paste them in the manuscript. Do not paste original photographs into
appropriate places. Description of the figure must include source of maps, drawing of species (if
obtained from other sources) and name of photographer. As much as possible, only original
photographs should be included in the thesis. For photograph credits, do not use “photographs by
author,” rather use your name (“photograph by M. Rodriguez”). For bar graphs that use means,
put error bars using the standard deviation or standard error (Appendix 10).
13. Abstract – limited to a maximum of 300 words or one page, whichever is shorter. This section
concisely presents the content and, more importantly, the significant results and contribution of
your research in words understandable to a non-specialist. Secondary literature should not be
cited in this section.
14. Numbers and Units
14.1 Numbers mentioned in the text – all numbers that are less than 10 must be spelled out and
more than 10 should be typed as numbers (ex. 10 species of Acropora, nine species of
bivalves, after six days, 10 h of exposure to 30 ppm).
14.2 Numbers that are part of a measurement should be in Arabic numbers. Units must be
abbreviated but without periods (ex. 5 g of giant clam mantle; 20 kg of salt). Put a space
between the number and unit.
14.3 Values below zero – Put a zero and a decimal point before the value (ex. 0.25 m2). Means
and standard deviations must be rounded off to two decimal numbers (ex. 0.27 cm,
 SD=0.02). Values obtained through computing statistical test must be expressed to four
decimal points (ex. P=0.2635, df=49).
14.4 Multiple units such as gram carbon per meter squared per day should be typed as g C m-2
day-1 not g C/m2/day.
15. Literature Cited – Full citation of all sources mentioned in the text must be placed in this section.
The APA style of in-text citation and referencing should be used. Students must make sure that
the citation includes the full name of journal, volume and issue numbers, pages, and number of
pages and publishing company (for books). Refer to the APA website for examples
[https://apastyle.apa.org/style-grammar-guidelines/references/examples].
15.1 All reference cited must be arranged alphabetically. All sources cited in the text must be
represented in the literature cited. Students are encouraged to cross-check their text with this
section. Students are reminded that a concept or even a sentence that does not cite a source is
considered their own.
15.2 All manuscripts will be checked for plagiarism. Ideas/concepts/results/discussions which are
not of the author’s must be cited appropriately. Other acts of academic dishonesty will not be
tolerated. These acts include, but are not limited to, cheating, plagiarism, making false
statements in relation to his/her studies, other forms of intellectual dishonesty, forgery,
falsification, misconduct etc. Students involved in academic dishonesty will be disciplined in
accordance with Silliman University regulations and procedures, which may include
automatic failure in the course, suspension or expulsion.
15.3 Since the thesis is a form of scientific research, majority of the literature cited must be from
scientific journals. Citations from books are not encouraged unless specific to the study
conducted or refer to general concepts that are often cited. General website references are
strongly discouraged since these are often not peer-reviewed and validated.
16. Appendix – The appendix should be placed after the Literature Cited section. Place a blank page
with APPENDIX printed at the center in 14 pt. bold Times New Roman to indicate the start of the
Appendix section. This section may include the ethics clearance approval sheet, permits, other
tables and statistical tests that were conducted but not included in the body of the thesis.

Section 9. CRITERIA FOR GRADING

The student must obtain a minimum grade of 2.0 for this subject. The final grade for the thesis will be
based on the following parameters:

1. Research performance (adviser evaluation) = 40%

2. Thesis manuscript & thesis defense = 60%

Research performance will be evaluated by the adviser based on the student’s compliance with ethical
requirements, conduct of field work and/or experiments, adherence to approved protocols/methods,
monthly progress reports, data presentation and analysis, and student-adviser consultations/discussions,
among others.

For the thesis manuscript and presentation/oral defense, the score will be given by the thesis panel based
on criteria for the written thesis manuscript and oral defense (see rubrics below). Theses that result in
publications and participation in conferences and competitions will be given due credit.

RUBRIC FOR ASSESSMENT – THESIS MANUSCRIPT

CRITERIA EXEMPLARY SATISFACTORY DEVELOPING BEGINNING
4 3 2 1
Introduction Presents a concise lead- Gives too much Gives very little Does not give any
in to the report with information; Statement information; Statement information about the
updated references; clear of the problem is of the problem is topic; No statement of
statement of the problem somewhat related to the unrelated to the research the problem
research
Review of Presents an in-depth Gives too much Information is lacking; Information is lacking
Related review of secondary information; theoretical review lacks coherence; and/or is irrelevant; No
Literature literature with updated framework is somewhat theoretical framework is theoretical framework
references; clear unclear unrelated to the research
 theoretical framework
Methodology Steps are logical and Most of the steps are Some of the steps are Not sequential, most
adequately detailed understandable; some understandable; most are steps are missing or are
lack detail or confusing confusing and lack detail confusing
Results & Accurate results and Minor inaccuracies in Minor inaccuracies; Major inaccuracies;
Analysis analysis; data table and results and analysis; data data table and graph data table and graph
graph are neat, properly table, graph are neat, but incomplete, not properly missing
formatted not properly formatted formatted
Interpretation of Logical explanations for Logical explanations for Illogical explanations for Illogical explanations for
Results/Discussi findings; addresses all findings; addresses most findings, addresses at findings, does not
on objectives of the study of the objectives of the least one or two out of address the objectives of
study five objectives of the the study
study
References Extensive and updated Extensive references; Limited and/or Limited and/or
references; uses correct wrong citation style unacceptable references; unacceptable references;
APA or MLA style uses correct citation stye wrong citation style
Organization & Well organized; correct Somewhat organized; Poorly organized; minor Poorly organized;
format format with minor errors in errors in format missing sections; wrong
format format
Grammar & All grammar and Only one or two errors More than two errors Very frequent grammar
spelling spelling are correct and/or spelling errors

RUBRIC FOR ASSESSMENT – ORAL DEFENSE/PRESENTATION

CRITERIA EXEMPLARY SATISFACTORY DEVELOPING BEGINNING
4 3 2 1
Content All concepts are clear Most concepts are clear Some concepts are clear Unclear concepts
Delivery Clear, audible, voice, Clear, audible, voice Demonstrates quick Monotone, reads the
projection, confident projection recovery from minor report
mistakes; occasional
reading
Visual Aids Well prepared visual Too much information; With visual aids with No visual aids
aids some are unnecessary hard-to-read fonts
Ability to answer Answers all questions Answers most of the Answers some question Does not answer any
questions questions question
Time management Within the given time NA NA Go beyond the allotted
time

Grading Scale:

Percent Range Grade Percent Range Grade

99.14 - 100.00 4 85.20 - 86.06 2.4
98.27 - 99.13 3.9 84.33 - 85.19 2.3
97.40 - 98.26 3.8 83.46 - 84.32 2.2
96.53 - 97.39 3.7 82.59 - 83.45 2.1
95.66 - 96.52 3.6 81.72 - 82.58 2
94.78 - 95.65 3.5 80.85 - 81.71 1.9
93.91 - 94.77 3.4 79.98 - 80.84 1.8
93.04 - 93.90 3.3 79.11 - 79.97 1.7
92.17 - 93.03 3.2 78.24 - 79.10 1.6
91.30 - 92.16 3.1 77.36 - 78.23 1.5
90.43 - 91.29 3 76.49 - 77.35 1.4
89.56 - 90.42 2.9 75.62 - 76.48 1.3
88.69 - 89.55 2.8 74.75 - 75.61 1.2
87.82 - 88.68 2.7 73.88 - 74.74 1.1
86.95 - 87.81 2.6 73.00 - 73.87 1
86.07 - 86.94 2.5 < 73 F
APPENDIX 1. Approval for Binding Sheet. The Chair only signs this sheet after all involved faculty
signed the form. Date at which Chair signs this form must be placed after his /her signature.
APPENDIX 2. Final Thesis Approval Sheet. The Chair only signs these sheets after all involved
faculty signed the form.
APPENDIX 3. Page layout for Cover and Title Page (all characters must be in boldface 16 pt.) single-
spaced and evenly distributed throughout the page. Cover should be red and text must be in gold.
APPENDIX 4. Adviser-Advisee Agreement. This agreement should be signed by the thesis adviser
prior to the schedule of the colloquium in Bio 68.
APPENDIX 5. Timetable. The timetable should be placed after the methodology section of the thesis proposal.

Task March April May June July August Sept October

2019 2019 2019 2019 2019 2019 2019 2019

Thesis proposal approval

UREC application

Apply for local permits

Preparation of materials for the morphology

analysis and water quality analysis
Collection of fish samples and water samples for
analysis
Analysis of fish samples and water quality

Thesis writing

Thesis presentation/oral defense

Submission of bound manuscript & PDF file

APPENDIX 6. Table of Contents. Be specific as much as you can when you make the Table of
Contents. Make sure that the pages correspond to the actual pages in the text.

TABLE OF CONTENTS
Approval Sheets i
Acknowledgements iii
List of Tables v
List of Figures vi
Abstract vii

CHAPTER 1. INTRODUCTION
Introduction 1
Statement of the problem 6
Objectives of the Study 6
Statements of Hypothesis 6
Significance of the Study 7
Scope and Delimitation 7
Species Description 8
Definition of Terms 11

CHAPTER II. REVIEW OF RELATED LITERATURE

Theoretical and Conceptual Framework 12
Review and Related Literature 13

CHAPTER III. METHODOLOGY

Description of the Study Site 14
Preliminary Studies 18
Field Sampling 19
Laboratory Proceeding 21
Statistical Analysis 23

CHAPTER 1V. RESULTS AND DISCUSSION

Density of Acanthaster planci 24
Morphometrics of Acanthaster planci 28
Feeding Preference of Acanthaster planci in the Field 31
Feeding Preference of Acanthaster planci under 35
Laboratory Conditions

CHAPTER V. CONCLUSIONS AND RECOMMENDATIONS

Summary 36
Conclusion 38
Recommendations 39

LITERATURE CITED 40

APPENDICES
Raw data – Density of Acanthaster planci 45
Raw data – Feeding preference of Acanthaster planci in the field 46
Raw data – Feeding preference of Acanthaster planci in the laboratory 47
Results of Homogeneity Tests 48
APPENDIX 7. List of Tables

Table 1. Criteria for total and fecal coliform for coastal and marine waters. 25
(DENR Administrative Order No. 34 1990)
Table 2. Mean E. coli, other coliform and total coliform, MPN in 28
October, 2003 and their tentative DENR Classification.
Table 3. Mean E. coli, other coliform and total coliform, MPN in 29
November, 2003 and their tentative DENR Classification.
Table 4. Tentative classification of BMT coastal water based on DENR standard 32
Table 5. Results of Mann-Whitney U Test (p values) for October High tide 36
against Low tide
Table 6. Results of Mann –Whitney u Test for October nearshore against offshore. 38
Table 7. Results of Mann –Whitney u Test for October high tide against low tide. 40
APPENDIX 8. List of Figures

Figure 1. Maps showing the study site within the Bohol Marine Triangle 12
Figure 2. Map of Bolod, Dauis showing sampling station 15
Figure 3. Map of Danao, Panglao showing sampling station 17
Figures 4. Map of Doljo, Panglao showing sampling station 20
Figure 5. Photograph of the crown –of-thorns seastar, Acanthaster planci 25
Figure 6. Mean length of arms of the crown –of – thorns seastar Acanthaster planci
in the different sampling sites 27
Figure 7. Mean disc diameter of the crown-of- thorns seastar, Acanthaster planci
in the different sampling sites 29
APPENDIX 9. Table

Table 7. Mean density (ind/Ha), mean estimated weight (g) and mean biomass (kg/Ha) for H.
arguinensis in each site and transect during the different seasons. Different letters indicate
significant differences among season within transect at each site (Nemenyi post hoc, P < 0.05).
APPENDIX 10. Figures

Figure 4. Specific growth rates (SGRs) of red type and green type of Apostichopus
japonicus at different light colors (mean±SE, n=16 per treatment). Values with different
letters in the same column represent significant differences from each other (P < 0.05).
Values with * represent significant differences between two types of sea cucumbers (P <
0.05).

Figure 1. The Asian lyrate hard clam Meretrix lyrata (Photo by C. Villamil)