BOI 101/3 Organisms Biodiversity Notes

BOI 101/3 Organisms Biodiversity Notes

Course Information

• Course Name: Organisms Biodiversity (Biodiversiti Organisma)

• Semester: 2

• Academic Session: 2024/2025

• Lecturers:

  • Dr Nurul `Ain Elias (NAE) - nurulain.elias@usm.my

  • PM Dr. RAHMAD ZAKARIA (RZ) - rahmadz@usm.my

  • Dr Norhafiz Hanafi Ahmad Shah (NHAS) - hafizhanafi@usm.my

• Lecture/Class Info:

  • Monday 10-11am (DK U, Physical)

  • Tuesday 2-3pm (DK U, Physical)

  • Friday 3-4pm (E48A, Physical)

Course Synopsis

This course covers elements of biodiversity involving genes, species, and ecosystems, with emphasis on biological diversity including characteristics of various biological groups of fauna & flora. It also addresses the problems of loss of species, habitats, and ecosystems, the importance of biodiversity conservation, and efforts by the government. Topics include legislation, international agreements for biodiversity protection, and biodiversity hotspots.

Course Outcome

Upon completion of this course, students should be able to:

1. Discuss the diversity of plant and animal life and its economic value, ecological significance, and conservation relevance.

2. Identify and classify plant and animal species based on specific traits.

3. Explain basic biodiversity concepts to raise awareness about biodiversity, particularly in the tropics.

4. Apply acquired knowledge to discuss biodiversity conservation at the national and international levels.

5. Describe the relationship between natural selection and evolutionary processes in the formation of biodiversity.

References

• Bidlack, J.E. and Jansky, S.H. (2017). Stern’s Introductory Plant Biology, 14th edition. Mc Graw Hill, New York.

• Hickman, Jr. C.P., Keen, S. L. A. and Eisenhour, D. (2018). Animal Diversity, 8th edition. McGraw Hill, New York.

• Hashim, Z. H., Omar, W. M. W., Yahaya, Z. S. & Convey, P. 2019. Tropical Biodiversity and Ecology, 2nd Edition. School of Biological Sciences, Universiti Sains Malaysia, Penang.

• Raven, P., Johnson, G., Mason, K., Losos, J., and Duncan, T. (2020). Biology, 12th Edition. Mc Graw Hill, New York.

• Urry, L. A., Cain, M.L., Wasserman, S. A., Minorsky, P. V., and Reece, J. B. (2017). Campbell Biology Edition 11. Pearson International Edition.

Assessments

• Test (20%)

  • Test 1 (Plants): 10%, 9th May 2025 (Friday), 1 hour, Week 7

  • Test 2 (Animals): 10%, 24th June 2025 (Tuesday), 1 hour, Week 13

• Quiz (20%)

  • Quiz 1 (Plants): 10%, Spontaneous

  • Quiz 2 (Animals): 10%, Spontaneous

• Assignment (20%)

  • Assignment 1 (Plants): 10%, Dateline: 9th May 2025 (Friday), Week 7, before 5pm, eLearn

  • Assignment 2 (Animals): 10%, Dateline: 20th June 2025 (Tue), Week 12, before 5pm, eLearn

• Final Exam (40%)

  • Part 1: MCQ compulsory (25 marks)

  • Part 2: Essay: 3 questions out of 4 (25marks/question)

  • Synchronous exam. Date & Location: July 2025 TBA. Duration: 2 hours

Grades

• A : 80-100%

• A- : 70-79%

• B+ : 64-69%

• B : 58-63%

• B- : 52-57%

• C+ : 46-51%

• C : 40-45%

• C- : 36-39%

• D+ : 32-35%

• D : 28-31%

• D- : 25-27%

• F : 0-24%

Teaching Schedule

• Week 1

  • 24th Mar (M): Course Briefing (Assessments, Rules & Regulation, Group formation)

  • 25th Mar (T): Introduction to biodiversity

  • 28th Mar (F): Evolution, plant origins & plant classifications – Part 1

• Week 2

  • 31st Mar (M): No Lecture - Public Holiday (Eid – Fitr)

  • 1st Apr (T): No Lecture - Public Holiday (Eid – Fitr)

  • 4th Apr (F): Evolution, plant origins & plant classifications – Part 2

• Week 3

  • 7th Apr (M): Plant tissue systems (Plant cells)

  • 8th Apr (T): Plant identification 1) 1-Plant structure & functions: Roots

  • 11th Apr (F): Plant identification 1) 1-Plant structure & functions: Stems

• Week 4

  • 14th Apr (M): Plant identification 1-Plant structure & functions: Leaves

  • 15th Apr (T): Plant identification 1-Plant structure & functions: Flowers

  • 18th Apr (F): Plant identification 2) 2-Plant Organs: Fruits. Due for topic approval for Assignment 2 (Animal) 18th Apr 2025, before 5pm

• Week 5

  • 21st Apr (M): Plant identification 2-Plant Organs: Seeds

  • 22nd Apr (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Algae

  • 25th Apr (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Bryophytes.

• Week 6

  • 28th Apr (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Angiosperms Part 1

  • 29th Apr (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Angiosperms Part 2

  • 2nd May (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Pteridophytes

• Week 7

  • 5th May (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Gymnosperms Part 1

  • 6th May (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Gymnosperms Part 2

  • 9th May (F): TEST 1 - PLANTS, Assignment 1 (Plants) Submission (eLearn, 9th May 2025, before 5pm)

• Mid Semester Break (11th – 18th May 2025)

• Week 8

  • 19th May (M): Introduction to Animal Biodiversity

  • 20th May (T): The importance of biodiversity, threats & conservation

  • 23rd May (F): Animal body plans

• Week 9

  • 26th May (M): Classification of Invertebrates and Vertebrates

  • 27th May (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Cnidarians)

  • 30th May (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Porifera)

• Week 10

  • 2nd June (M): No Lecture - Public Holiday (DYMM Agong`s Birthday)

  • 3rd June (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Platyhelminthes)

  • 6th June (F): No Lecture - Public Holiday (Eid – Adha)

• Week 11

  • 9th June (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Nematodes)

  • 10th June (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Mollusca)

  • 13th June (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Annelids)

• Week 12

  • 16th June (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Arthropods)

  • 17th June (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Invertebrates (Echinoderms)

  • 20th June (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Vertebrates (Fishes). Assignment 2 (Animals) Submission (eLearn, 20th June 2025, before 5pm)

• Week 13

  • 23rd June (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Vertebrate (Amphibians)

  • 24th June (T): TEST 2 – ANIMALS

  • 27th June (F): No Lecture - Public Holiday (Muharram)

• Week 14

  • 30th June (M): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Vertebrate (Reptilians)

  • 1st Jul (T): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Vertebrate (Birds)

  • 4th Jul (F): Characteristics of each phylum, classification, habitat, ecology, and distribution, economic importance, and conservation: Vertebrate (Mammals)

• Study Week (6th – 13th Jul 2025)

• Exam Week (14th July – 1st Aug 2025)

Introduction to Biodiversity

Biological diversity refers to the variety of plants, animals, and other living things in a specific area or region.

• The term biodiversity is derived from the Greek word bios (life) and the Latin word diversitas (variety), literally meaning variety of life.

• Biodiversity encompasses the number and abundance of different species within a particular region.

• The Convention on Biological Diversity defines biodiversity as the variability among living organisms from all sources, including terrestrial, marine, and other aquatic ecosystems, as well as the ecological complexes of which they are part.

Components of the Environment

• Biotic factors: The living components of the environment.

• Abiotic factors: The non-living components of the environment.

Types of Biodiversity

1. Ecosystem diversity: The variety of habitats, ecosystems, and communities within a biosphere.

2. Species diversity: The variety of species in a given area.

3. Genetic diversity: The variety of genetic makeup within a species.

Ecosystem Diversity

Deals with variations in ecosystems within a geographical location and their overall impact on human existence and the environment. Examples include:

• Forest ecosystems

• Ocean ecosystems

• Grassland ecosystems

• Tundra ecosystems

• Wetland ecosystems

• Desert ecosystems

Species Diversity

Refers to the variety of life forms and the number of individuals of each species within a biological community. It includes the full range of species on Earth, from unicellular microorganisms to multicellular plants and animals.

• Species richness refers to the number of species in an ecosystem.

What is a Species?

Species are a set of individuals with the same distinct characteristics that can mate and produce fertile offspring.

• Species are the basic units of life classification and building blocks for grouping all living things on Earth.

• Millions of species exist on our planet, with new discoveries still being made, especially in tropical rainforests and deep oceans.

• Species are part of a taxonomic hierarchy.

Genetic Diversity

Definition: The total number of genetic characteristics in the genetic makeup of a species.

• Different types (varieties or strains) within a species can have slight differences in:

  • Size

  • Shape

  • Disease or pest resistance

  • Ability to survive in difficult conditions

• High genetic diversity makes a species stronger and more capable of surviving in changing environments.

Heritable variation is the basis for evolution by natural and artificial selection.

• New genetic variation arises through:

  • Gene and chromosome mutation in individuals

  • Recombination of genetic material during cell division preceding sexual reproduction in populations of sexually reproducing organisms.

Natural vs Artificial Selection

Evolution by natural selection and artificial selection, relies on heritable variation. Example: Brassica oleracea, where different parts are selected for such as terminal buds for cabbage, lateral buds for brussels sprouts, stems for kohlrabi, leaves for kale, flower buds for broccoli, flower clusters for cauliflower.

Importance of Biodiversity

• Protect freshwater resources

• Speed recovery from natural disasters

• Maintaining balance of the ecosystem

• Sustainability and growth

• Provision of food security

• Adaptation to different habitats

• Provision of biological resources

• Promote soils formation and protection

• Maintain food chain in the nature

• Protect freshwater resources

• Speed recovery from natural disasters

• Maintaining balance of the ecosystem

• Protect freshwater resources

• Speed recovery from natural disasters

• Maintaining balance of the ecosystem Sustainability and growth

Threats to Biodiversity

• Climate Change: Rising temperatures affect seasons, sea levels, and glaciers.

• Habitat Loss & Degradation: Caused by natural events or human activities like deforestation and climate change.

• Pollution: (water, air, or land) threatens all life forms.

• Invasive Species: Introduction of exotic species can harm native species.

• Overexploitation: Over-harvesting species and natural resources faster than they can sustain themselves.

• Other Potential Threats: Epidemics and infectious diseases.

Value of Biodiversity

• Economical Value: Provides basic necessities such as food, raw materials for medicines, shelter, and clothing.

• Ecological Value: Organisms are interconnected, playing specific roles in the environment.

• Aesthetic Value: Natural beauty encourages us to preserve the environment for future generations.

History of the Earth and Life

• $4.567$ billion years ago: Formation of the Solar System

• $4.56$ billion years ago: Formation of the Earth

• $4.37-4.20$ billion years ago: Formation of the atmosphere and ocean

• $4.10 (4.20?)$ billion years ago: Birth of first proto-life

• $2.90$ billion years ago: Emergence of photosynthetic life

• $2.10$ billion years ago: From prokaryotes to eukaryotes

• $640$ million years ago: Origin of Multicellular Life

• $540$ million years ago (The Paleozoic Era): The Co- evolution of Planets and Insects

• $550-540$ million years ago: The Evolution of Vertebrates

• $66$ million years ago: Dinosaur extinction

Life of Land

• The origin of vascular tissue allowed plants to colonize land.

• Life on land offered opportunities like:

  • Unlimited sunlight

  • Abundant $CO_2$

  • Few pathogens or herbivores initially

• Disadvantages included:

  • Maintaining moisture

  • Supporting their body

  • Reproducing and dispersing offspring without water

  • Obtaining resources from soil and air

Biological Diversity Figures

• Approximately $8.7$ million species of plants and animals in existence

• $391,000$ species of vascular plants

• $369,000$ or $94$ percent) are flowering plants

• Over 1 million animal species have been identified, mostly insects

Kingdoms and Domains

Linnaeus System

• 2 kingdoms

Haeckel System

• 3 kingdoms

Copeland system

• 4 kingdoms

Whittaker system

• 5 kingdoms

Woese et al.

• 6 kingdoms (3 domains)

Cavalier-Smith

• 2 empires (8 kingdoms)

Based on molecular data and ultrastructure kingdom Protista is regarded as a paraphyletic group.

Six Kingdom System

• Bacteria

• Archaea

• Protista

• Plantae

• Fungi

• Animalia

Characteristics of Plants

1. Plants are highly organized, composed of cells, tissues, and organs.

2. Plants take in and use energy through photosynthesis.

3. Plants respond to stimuli through differential growth.

4. Plants have cell walls.

5. Plants reproduce sexually or asexually.

Plants Origins

• Both green algae and plants contain chlorophylls $a$ and $b$, and carotenoids.

• Molecular data shows plants evolved from streptophyte algae.

• The green lineage originated when a heterotrophic eukaryotic host cell captured a cyanobacterium. This happened 1 to 1.5 billion years ago.

Plants Adaptations

• Adaptations are characteristics that enable an organism to better survive in a certain environment.

• Adaptations may involve changes in structure, form, or function.

• Obtaining Enough Water: Adaptations include roots that anchor them and absorb water and dissolved minerals.

• Preventing Excessive Water Loss/Dessication: Plants have a waxy cuticle over their epidermal cells to prevent water loss.

• Getting Enough Energy + Structural support: Must absorb sunlight for photosynthesis.

• Tolerating High Temperatures: Plants rely on evaporative cooling, though they do not produce sweat.

• Tolerating Low Temperatures: Many plants also overwinter in a dormant state

• Reproduction: Some have complex systems to employ wind, water, and different organisms for both fertilization and dispersal.

Taxonomy

Taxonomy is the science of describing, naming, and classifying organisms.

Linnaeus

Developed a classification system based on visual observations of flower parts. Introduced Binomial nomenclature, a system of naming organisms based on a unique two-part name for each.

• The first part of the name designates the genus

• The second part of the name, the specific epithet, designates the species.

Classification hierarchy

• Species

• Genus

• Family

• Order

• Class

• Phylum

• Kingdom

• Domain

Soil

Composed of mineral particles (sand, silt, and clay), organic material (humus), soil air, and soil water.

Cation Exchange

Clay particles have negative electric charges that attract cations, such as $K^+$ and $Mg^{2+}$.

• Roots secrete protons ($H^+$), which are exchanged for other positively charged mineral ions.

• Anions are repelled by clay particles and tend to remain in solution.

• 19 elements are essential for most plants. Carbon, oxygen, hydrogen, and nitrogen—come directly or indirectly from soil water or from gases in the atmosphere.

Plants obtain elements from the soil as dissolved mineral ions.

Plant structure

• Composed of basic building blocks called cells

• Cells organized into tissues

• Tissues organized into organs

Plant tissues

• Epidermis, the protective tissue that covers the plant’s surface

• Xylem, the water-conducting tissue

Plant cell

Plant cells have cell walls composed largely of cellulose, a long-stranded polysaccharide consisting of linked glucose molecules.

Function: water-insoluble waxy coating, the cuticle, over their epidermal cells.

Response to stimuli

respond to stimuli by the differential growth of parts of their bodies. Examples gravity, sunlight and luminosity, temperature and chemical composition. Roots, for example, normally grow in the direction of gravity.

Plant reproduction characteristics

• Asexual reproduction

• Sexual reproduction in plants involves the union of gametes that may or may not come from two separate individuals.

Plant Structure and Life Span

The plant body is organized into a root system and a shoot system: leaves, stem with flowers and fruits. Types include herbaceous or woody.