PERANCANGAN AKADEMIK

ACADEMIC PLANNER

1. PENERANGAN KURSUS / COURSE INFORMATION

Kod Kursus / Course Code JIB 531
Nama Kursus / Course Name Biosystematics and Taxonomy
Unit / Hours 4
Semester Academic Session 2022/2023
Penilaian / Assessment Coursework 50%, Final Assessment 50%
Tahun / Year 2022/2023
Masa Syarahan @ Tutorial/ Webex 1: 5 November 2022 12-1pm
Lecture @ Tutorial Time Webex 2: 7 Jan 2023 11am-12pm
Webex 3: 14 Jan 2023 9-10am
Webex 4: 18 Feb 2023 9-10am
Lokasi / Venue Via Cisco WEBEX meeting link
Email leesim.lim@usm.my

2. PENSYARAH / LECTURER
Beban Pengajaran / Teaching
Bil. Pensyarahan / Lecturer Tanggungjawab / Roles
Load
1 Dr Lim Lee Sim Course Manager 4 units
(1 academic session)

3. SINOPSIS KURSUS / COURSE SYNOPSIS

Bahasa Malaysia:
Kursus ini memberi gambaran keseluruhan konsep-konsep, kaedah-kaedah dan
penggunaan sistematik biologi dan taksonomi. Topik-topik dalam kursus ini termasuk
pengenalan dan falsafah sistematik, kepentingan dan penggunaan hasil kajian
kladistik, kaedah-kaedah taksonomi, cara-cara analisis filogenetik, serta kaedah-
kaedah dan peralatan/program yang digunakan dalam sistematik molekul.

English:
This course is an overview of essential concepts, methods and application of biological
systematics and taxonomy. The topics include the introduction and philosophy of
systematics, the importance and application of cladistic results, methods of taxonomy,
the ways of phylogenetic analyses, and the methods and tools/programs commonly
used in molecular systematics.

1
4. HASIL PEMBELAJARAN / COURSE OUTCOMES (CO)
HASIL PEMBELAJARAN / PENILAIAN /
No Course Outcomes (CO) PO Assessment
1 Menerangkan prinsip utama konsep klasifikasi dan PO1 • Peperiksaan berterusan
spesies. Continuous assessment
Explain the main principles of classification and • Peperiksaan akhir
species concepts. Final exam
2 Mengaplikasi pengetahuan dalam kehidupan seharian PO3 • Tugasan
dan sektor perindustrian seperti pertanian, perubatan Assignment
dan pemuliharaan biologi.
Apply the knowledge in the daily life and industrial
sectors such as agriculture, medicine, and conservation
biology.

3 Memahami kaedah persampelan dan pemprosesan PO2 • Peperiksaan berterusan

sampel untuk analisis filogenetik, cara-cara analisis Continuous assessment
dan penilaian filogenetik. • Peperiksaan akhir
Understand sampling and sample processing Final exam
methods for phylogenetic analyses, types of
phylogenetic analyses and evaluations.

4 Mengaplikasi kaedah persampelan, menganalisis dan PO3 • Laporan Amali

membina hubungan filogenetik untuk Lab report
mendemonstrasi klasifikasi dan proses evolusi
terhadap sesuatu organisma.
Apply sampling methods, analyse and construct
phylogenetic relationships to demonstrate classification
and evolutionary process of organisms.

2
5. RANGKA KURSUS / COURSE FRAME
PENILAIAN /
No Topik / Topics CO
Assessment
1 Pengenalan kepada sistematik
Introduction to systematics
• Peperiksaan berterusan
1 Continuous assessment
2 Sistematik dan falsafah sains • Peperiksaan akhir
Systematics and the philosophy of science Final exam

3 Penggunaan hasil/keputusan kladistik • Peperiksaan berterusan

Application of cladistic results Continuous assessment
• Peperiksaan akhir
2
Final exam
• Tugasan
Assignment
4 Teknik dan kaedah taksonomi I • Peperiksaan berterusan
Taxonomy techniques and methods I Continuous assessment
3,4 • Peperiksaan akhir
5 Teknik dan kaedah taksonomi II Final exam
Taxonomy techniques and methods II • Laporan Amali
Lab report
6 Pengenalan kepada analisis filogenetik/kladistik
• Peperiksaan akhir
Introduction to phylogenetic/cladistic analyses 1
Final exam
7 Analisis filogenetik/kladistik
Phylogenetic/cladistic analyses

8 Penilaian keputusan filogenetik dan kladistik

Evaluation of phylogenetic and cladistic results
• Peperiksaan akhir
Final exam
9 Kaedah-kaedah sistematik molekul I
• Tugasan
Molecular systematic methods I 3,4
Assignment
10 Kaedah-kaedah sistematik molekul II • Laporan Amali
Molecular systematic methods II Lab report

11 Kaedah-kaedah sistematik molekul III

Molecular systematic methods III

3
6. PENILAIAN KURSUS / COURSE ASSESSMENT
No Kaedah Penilaian / Assessment Methods Markah /
Marks
1 PEPERIKSAAN BERTERUSAN / CONTINUOUS ASSESSMENT

This assessment will be conducted during the Intensive Course from 1-21 Mac
2023. The actual date for the test will be announced in the e-portal after the 4th 20
Webex Session. Students will be tested on Topic 1 – 5 and relevant materials from
the Webex conferencing lectures.

2 TUGASAN / ASSIGNMENT

Tugasan 1/ Assignment 1(10%)

Biosystematics is all about the classification of living things.
Search one latest finding on phylogenetic relationships of some species on Earth
from the journal Molecular Phylogenetics and Evolution. Summarise the key
findings in this study, then suggest how this molecular systematic outcome help in
our daily life or in relevant industries such as agriculture, medicine, nature protection
etc. 10
Complete this task within SIX-page in MS Word document and save as Pdf format.
Figures and tables can be added. Referred resources should be cited and listed in the
References section, which will be the last section of this assignment.

Submission deadline: 31 Mac 2023

Mode of submission: soft copy via the assignment submission link at e-portal

3 AMALI / LAB PRACTICALS

Four practical classes will be conducted at Universiti Sains Malaysia main campus
during Intensive Course 2023 or via online virtual lab sessions, depend on the Covid
19 pandemic’s situation. Lab Manual can be downloaded from the e-portal.

Report writing guidelines: Appendix I 20

NOTE: Attendance is compulsory except for students who are repeating the
course within three years but have passed this component previously. All practical
reports are to be completed individually and submitted via a submission link set
up at e-portal.

4 PEPERIKSAAN AKHIR / FINAL EXAM

The final exam will be held at the end of the 2022/2023’s academic session. The
duration of the final exam is 2 hours. Students will be examined on all chapters by 50
answering 4 essay questions.

TOTAL 100

4
 7. GRED / GRADE
Grade A A- B+ B B- C+ C C- D+ D D- F
Point 4.00 3.67 3.33 3.00 2.67 2.33 2.00 1.67 1.33 1.00 0.67 0.00
Range
of the 80-100 70-79 64-69 58-63 52-57 46-51 40-45 36-39 32-35 23-31 25-27 0 -24
mark

Final grade of each coursework (one continuous assessment, two assignments and four lab practical
sessions), final exam and total coursework and exam mark will be evaluated based on Table 7.
No plagiarism or copying is allowed for all assigned coursework, or you will be penalised by getting
zero mark if detected.

5
8. RUBRIK / RUBRIC
Course
Marks
outcome Assessment Rubric Description
(%)
(CO)
CO1, CO3 Continuous ANSWER SCHEME 20
Assessment
CO1, ANSWER SCHEME 50
CO2,
Final Exam
CO3,
CO4
Assignment 1
CO2 Appendix II 10
(5-page Essay)
CO4 Lab report Appendix III 20
TOTAL 100

9. RUJUKAN / REFERENCES
Schuh, R.T. & Brower, A.V.Z. 2009. Biological Systematics: Principles and
1
Applications, Cornell University Press, 2nd Edition [textbook 1]
2 Simpson, M. G. 2010. Plant Systematics. Elsevier Science, 2nd Edition [textbook 2]
Goto, H.E. 1982. Animal Taxonomy, Edward Arnold (Publishers) Limited [textbook
3
3]
Ryan, J.M. 2018. Mammalogy Techniques Lab Manual, Johns Hopkins University
4
Press: Baltimore [Lab practical guidebook]
5 Bleidorn, C. 2017. Phylogenomics: An introduction. Springer International Publishing AG.
Selzer, P.M., Marhöfer, R.J., Koch, O. 2018. Applied Bioinformatics: An introduction. 2nd
6
Edition. Springer International Publishing AG.
Kitching, I.J., Forey P.L., Humphries, C.J. & Williams D.M. 1998. Cladistics: The theory
7
and practice of parsimony analysis, Oxford University Press; 2nd Edition.

6
10. POLISI KURSUS / COURSE POLICY
• Registered students must follow and comply to all USM regulation from time to time.

• Due to information and assignment are based on online platform, access to

eLearning Portal is compulsory to all students

• All assignment must send through the eLearning portal.

• Attendance during WEBEX session are compulsory.

• Students must have good time management, study smart, and try to give full
commitment to achieve good grade in this course.

11. PENGESAHAN / VALIDATION

Disediakan oleh Pensyarah
Disahkan oleh Pengerusi Rancangan:
Kursus: Prepared by Course
Approved by Programme Chairperson:
Lecturer:

Dr Lim Lee Sim

Tarikh / Tarikh /
Date: 18 Okt 2022 Date: 27/10/2022

7
Appendix I
REPORT GUIDELINES
Written by Assoc. Prof. Dr Zuraini Zakaria
Modified by Lee-Sim Lim to match with this course

Your report should reflect what you want to express on the theoretical aspects that you have learned, and the
results observed during these experiments. Whether you are interested in pursuing a scientific career or in
working in other professional activities, the experience you get from writing experimental reports will be
invaluable. Report should be structured like a scientific publication in a journal and according to the following
outline. Write in simple, direct style, in THIRD person, PAST tense. Each individual experiment should be
reported to include the following sections. In the Methods, Results and Discussion sections, use topic
headings. This will help the reader understand the organization of your report.

Title

The title should be less than fifteen (15) words and reflect the factual content of the experiment. You should
produce a title for the experiment based on the main issues addressed which precisely indicate the subject
of the experiment.

Introduction

This is a section to introduce the subject you are addressing and its significance. It should explain the
importance of the experiment and give an overall background for understanding why the experiment was
performed. You should use references to present your background statements. At the end of this section, you
should indicate the purpose or objective of the experiment.

Materials and Methods

This is a list of the materials and a description of the methods used. However, the complete procedure from
the experiment manual and the list of materials need not be reproduced here. Describe tasks performed and
number of samples used. List any variations that were made in the given procedure. Do not use "command"
language.

Results

In this section you should be specific. Present your data in an organized and easy to understand form. Your
report will be easier to read if you insert tables and figures (graphs, diagrams, sketches, photos) into the text
where possible. All tables and figures should be numbered and given a descriptive title. Titles of tables should
be placed above the table, whereas titles of figures should be given below in the figure legend. The graph
axes' descriptions should include units. The explanations in this section should only be brief and indicate
important observations. Your report will be easier to read if you insert the tables and figures before your
explained text. Do not present the same data in both tables and figures, choose either one.

Discussion

This is the fun part of the report where your imagination will help you connect facts. In this section you should
state each of your results and interpret them in light of other studies published in the literature. It means that
you need to discuss by referring to literature resources or references pertaining to the subject of your
experiment. Your interpretations of the results for each variable under study should be based on facts, not
your opinion. In this section, you should also address any questions posed in the experiment manual. The
Results and Discussion sections may be combined to avoid unnecessary repetition.

Conclusion

What did you learn from the experiment? Give logical conclusions based on data and facts you obtained.
Think carefully about the interpretation of all your results, including your errors. A short paragraph of tentative
trends as well as the implications of your results and specific recommendations for further study is also
appropriate here.

8
Appendix II Rubrics for Assignment (Individual Essay)

WS/
Weight Scor W Su
Beginning Developing Accomplished Exemplary Marks
age e S m
(0-2) (3-5) (6-7) (8-10) (%)
(W) (S) WS

Introduction Introduction complete and

Introduction missing or
(General info on the completely not related to
selected study) the selected study.
Content and
Discussion There is an attempt to
(Discuss on the key complete this session but
findings of selected not answering the question
study, link key of this essay correctly. No
findings to mark is given if this session
application in life/ is skipped.
industries)
Conclusions
Conclusions missing or
irrelevant.
No mention on referred
resources as citation or
Citations and
reference at all; or no
References
citation at all but only the
Reference list.
Introduction was written but
not so relevant to the
selected study.
Briefly explain the key
findings of selected study.
Able to link the importance
of key findings to life/
selected industries, but not
so relevant and not support
with evidence.
Conclusions not accurately
made, indicating lack of
understanding and
consistency to the given
task.
Resources not cited
precisely in the text and
several cited resources did
not list in References with
correct and uniform format.
Introduction is nearly complete,
missing some minor points of
selected study.
Able to explain the key findings
of selected study but not too
detail. Able to link the
importance of key findings to
life/ selected industries
relevantly, but not support with
published evidence.
Conclusions have been
accurately made, but not
sufficient to show good
understanding on this
assignment.
Resources are cited precisely in
the text and almost all cited
resources were listed in
References with correct and
uniform format with some
technical errors.
well-written. All main points of
the selected study were
2
included.
Able to explain the key
findings of selected study
clearly. Able to link the
importance of key findings to
life/ selected industries 5
relevantly, with published
evidence.
Conclusions have been
clearly and accurately made.
Student shows good
understanding on this 2
assignment.
All resources are cited
precisely in the text and all
cited resources were listed in 1
References with correct and
uniform format.

Total Marks (%)

9
Appendix III Rubrics/Mark schemes for Lab Report
(Lab Practical 1)

1 herbarium 10 marks
• correct specimen collection 2 marks
• specimen condition 8 marks (arrangement and neatness 2 marks, drying quality 3 marks, stitch and stick 3 marks)
• label 4 marks (complete with all info: full marks, correct species 1 mark, lacking of info deduct 1 mark each, maximum 4 marks)
• picture 1 mark
Total 1 herbarium= 15%
Total 2 herbarium=30%
Report on the herbarium=5% (extra work, to add up to 30% from their existing herbarium mark, if the student submits this report)

(Lab practical 2)

 Date & time: Day-month-year format, spell the month. Exp, 9 May 2021 (2 marks)
 Location and route: as specific as possible, start from the broadest geographical category. Exp, Peninsular Malaysia, Penang Island, Universiti
Sains Malaysia, 5.3559° N, 100.3025° , route map, any information/graphics about the location etc (5 marks)
 Weather: temperature, precipitations/humidity, cloud cover, rain/no rain (2 marks)
 Habitats: info/graphic on the plant community, forest types, water sources near the site, landmarks, sketches of a map is useful (10 marks)
 Vegetation: dominant plant species, fruiting and flowering species that can be a food source for animals (5 marks)
 Commentary: unusual activities, methods descriptions, info on spotted species etc (6 marks)
 References (optional, extra 3 marks are given if this section was done properly)
TOTAL=30%

10
(Lab practical 3)
Section A- Results (7 marks)
1) Provide fish picture with correct orientation- 2 marks
2) Fish taxonomy and correct identification- 2 marks
3) Truss network measurements- 2 marks
4) Spine and rays count- 1 mark

Section B- Discussion (8 marks)

1) If many specimens were collected from the field at one time and limited jars and chemicals are available in the lab, how can we organize the
specimens during preservation? (1 mark)
2) What are the advantages and disadvantages of preserving specimens in formalin 10%? (1 mark)
3) What are the advantages and disadvantages of preserving specimens in alcohol 70%? (1 mark)
4) How can we ensure the internal organs of a big volume specimen can be preserved as well? (1 mark)
5) In your opinion, which animal species are not suitable to preserve in the solution? (1 mark)
6) Besides preserving the voucher specimens in a solution, what other preservation method can be considered? List of one or two and describe
these methods with references. (1 mark)
7) What sort of characters is used for fish identification? (1 mark)
8) What is a Truss Network and why is it important? (1 mark)

Total marks=15 marks

11
(Lab practical 4)

Beginning Developing Accomplished Exemplary Weightage Score Marks

(1-2) (3-5) (6-7) (8-10) (%)
Introduction is nearly complete,
Very little background Some introductory information Introduction complete and well-
Introduction missing some minor points.
information provided, or was provided, but missing some written. Reliable references are
References are used to support
information is incorrect. major points. used to support the content. 1
the content.
Written in paragraph format,
Not written in paragraph format, Written in paragraph format, still Well-written in paragraph format,
Experimental important experimental details are
missing important experimental missing some important all experimental details are
procedure covered, some minor details are
details. experimental details. covered. 2
missing.
Results were not reported
completely with main results All figures and tables were
No results at all or results were All figures and tables were
Results & missing. Figures and tables, if systematically produced, and
poorly reported with no figure excellently produced, and results
analysis or tables at all.
any, were not representing results were mentioned but not
were completely mentioned.
results correctly. Technical complete. Technical errors occur.
2
errors occur.
Some of the results and Some of the results and Almost all the results and Important results have been
questions (if applicable) have questions (if applicable) have questions (if applicable) have interpreted correctly and
been incorrectly interpreted and been correctly interpreted and been correctly interpreted and discussed; good understanding of
Discussion
discuss, lack of understanding discussed; partial but discussed, only minor results is conveyed. All questions
of the results. incomplete understanding of the improvements are needed. (if applicable) have been answered 3
results. correctly.
No conclusions or missing the Some important points are All important points are All important points are concluded
Conclusions 1
important points. concluded. concluded. and precisely constructed.
References Reference cited and almost All references were cited and
No reference cited Reference cited but not relevant 1
relevant highly relevant
Total Marks (%)

12
 Student Learning Activities Schedule

No Topic CLO Dalam Talian/ Berteraskan Teknologi

(Synchronous) Jumlah JPP/SLT
NF2F
Lecture Practical session
Webex

1 Pengenalan kepada CLO1 1 hour 5 hours 6 hours

sistematik CLO2
Introduction to systematics Preparation before the lecture (2 hours)
Forum/discussion (2 hours)
Exercise (1 hour)

2 Sistematik dan falsafah sains CLO1 N/A 9 hours 9 hours

Systematics and the CLO2
philosophy of science Preparation for the lecture (4 hours)
Forum/discussion (3 hours)
Exercise (2 hours)
3 Penggunaan hasil/keputusan CLO1 1 hour 8 hours 9 hours
kladistik CLO2
Application of cladistic results Preparation before the lecture (2 hours)
Exercise (1 hour)
Preparation for assignment 1 (5 hours)

4 Teknik dan kaedah CLO1 1 hour 8 hours 12 hours 21 hours

taksonomi I CLO2
Taxonomy techniques and Preparation before the lecture (2 hours)
methods I Exercise (4 hours)
Preparation for lab practical (6 hours)

5 Teknik dan kaedah CLO2 1 hour 3 hours 10 hours 14 hours

taksonomi II CLO3
Taxonomy techniques and Preparation before the lecture (2 hours)
methods II Exercise (2 hours)
Preparation for lab practical (6 hours)
6 Pengenalan kepada analisis CLO2 1 hour 10 hours 11 hours
filogenetik/kladistik CLO3
Introduction to Preparation before the lecture (2 hours)
phylogenetic/cladistic Exercise (2 hours)
analyses Preparation for lab practical (6 hours)

13
 7 Analisis filogenetik/kladistik CLO2 1 hour 2 hours 9 hours 12 hours
Phylogenetic/cladistic CLO3
analyses Preparation before the lecture (2 hours)
Preparation for Assignment 2 (2 hours)
Preparation for lab practical (5 hours)

8 Penilaian keputusan CLO2 1 hour 2 hours 9 hours 12 hours

filogenetik dan kladistik CLO3
Evaluation of phylogenetic Preparation before the lecture (2 hours)
and cladistic results Preparation for Assignment 2 (4 hours)
Exercise (3 hours)
9 Kaedah-kaedah sistematik CLO2 1 hour 5 hours 6 hours
molekul I CLO3
Molecular systematic Preparation before the lecture (2 hours)
methods I Preparation for Assignment 2 (1 hour)
Forum/discussion (1 hour)
Exercise (1 hour)
10 Kaedah-kaedah sistematik CLO2 1 hour 5 hours 6 hours
molekul II CLO3
Molecular systematic Preparation before the lecture (2 hours)
methods II Preparation for Assignment 2 (1 hour)
Forum/discussion (1 hour)
Exercise (1 hour)
11 Kaedah-kaedah sistematik CLO3 1 hour 5 hours 6 hours
molekul III
Molecular systematic Preparation before the lecture (2 hours)
methods III Preparation for Assignment 2 (1 hour)
Forum/discussion (1 hour)
Exercise (1 hour)
TOTAL SLT P&P 112

14