describe the classification of organisms in the Eukarya domain into the taxonomic hierarchy of kingdom, phylum, class, order, family, genus and species

Objective

To describe how organisms in the domain Eukarya are classified into the hierarchical ranks of kingdom, phylum (or division), class, order, family, genus and species, and to connect classification with biodiversity, conservation, species concepts, natural selection, and modern genetic technologies – as required by the Cambridge International AS & A Level Biology (9700) syllabus.

Key Concepts (Syllabus Links)

• Cells as the basic unit of life – all eukaryotes possess membrane‑bound organelles and a nucleus.
• Biochemical processes & DNA – molecular markers (e.g., COI, rbcL) are used to infer relationships and delimit species.
• Natural selection & evolution – adaptive radiation and speciation generate the diversity that classification seeks to organise.
• Organisms in their environment – biodiversity, ecosystem services and human impacts are central to conservation.
• Observation & experiment – practical activities such as constructing dichotomous keys develop AO2 and AO3 skills.

1. The Taxonomic Hierarchy

The Linnaean system is a nested hierarchy: each successive rank groups organisms that share a greater number of characters and a more recent common ancestor.

2. Kingdoms Within the Domain Eukarya

Current consensus recognises six kingdoms (plus the green lineage often treated as a separate kingdom). The table summarises the principal distinguishing features, followed by a concise description and a representative species for each kingdom.

Brief Descriptions & Representative Species

• Protista – Plasmodium falciparum: A malaria parasite; unicellular, heterotrophic, no cell wall, possesses a remnant apicoplast.
• Fungi – Saccharomyces cerevisiae: Baker’s yeast; unicellular, chitinous cell wall, reproduces by budding, absorbs nutrients.
• Plantae – Arabidopsis thaliana: Model flowering plant; multicellular, cellulose cell walls, stores starch, exhibits alternation of generations.
• Chromista – Laminaria digitata (brown alga): Multicellular marine algae; secondary plastids with chlorophyll c, silica‑reinforced cell walls (alginate).
• Animalia – Mus musculus (house mouse): Multicellular ingestive heterotroph, lacks cell walls, true tissues and nervous system.
• Archaeplastida (green algae) – Chlamydomonas reinhardtii: Unicellular flagellate; primary chloroplasts, stores starch, used extensively in molecular studies.

3. Species Concepts and Their Molecular Basis

Understanding what constitutes a species underpins biodiversity assessment, conservation status, and modern taxonomy.

4. Biodiversity

Classification provides the framework for measuring and conserving biodiversity at three hierarchical levels.

• Genetic diversity – variation within a species (e.g., allelic differences in Arabidopsis thaliana).
• Species diversity – number and relative abundance of species in a community.
• Ecosystem diversity – variety of habitats, ecological processes and biotic interactions.

Why Biodiversity Matters

• Provides ecosystem services (pollination, nutrient cycling, climate regulation).
• Buffers ecosystems against environmental change.
• Source of medicines, food, and genetic resources.

Indicators of Biodiversity Loss

• Decline in species richness and evenness.
• Increasing proportion of threatened species on the IUCN Red List.
• Reduced genetic variability in isolated or bottlenecked populations.

5. Conservation

Effective conservation relies on accurate classification, knowledge of species status, and an understanding of human impacts.

Major Human Impacts on Biodiversity

• Habitat loss and fragmentation (deforestation, urbanisation).
• Climate change – range shifts, phenological mismatches.
• Invasive species outcompeting native taxa.
• Over‑exploitation (fishing, hunting, plant harvesting).
• Pollution (plastic, eutrophication, heavy metals).

Conservation Strategies

• In‑situ – protected areas, legislation, habitat restoration.
• Ex‑situ – seed banks, botanical gardens, zoos, cryopreservation.

6. Phylogenetics, Cladistics and Molecular Systematics

• Cladogram – a branching diagram that shows hypothesised evolutionary relationships based on shared derived characters (synapomorphies).
• Monophyly – a group containing an ancestor and all its descendants; modern taxonomy strives to recognise only monophyletic taxa.
• Parsimony principle – the simplest tree (fewest evolutionary changes) is preferred, though likelihood and Bayesian methods are also used.
• Molecular markers – DNA sequences such as COI (animals), rbcL & matK (plants), 18S rRNA (protists) provide characters for constructing robust phylogenies.
• Interpreting a cladogram – locate the root, identify synapomorphies at each node, determine sister‑group relationships, and assess monophyly of taxa.

Example Cladogram (simplified)

7. Genetic Technology – Linking DNA to Modern Classification

After studying traditional taxonomy, the syllabus expects students to understand how genetic tools refine classification.

• DNA barcoding – short, standardised gene regions (COI for animals, rbcL/matK for plants, ITS for fungi) are sequenced and compared against reference databases to identify species.
• Phylogenomics – analysis of hundreds to thousands of loci (or whole genomes) provides high‑resolution trees, revealing cryptic species and deep divergences.
• Population genetics – measures of genetic diversity (e.g., heterozygosity, F_ST) inform the Biological Species Concept and help assess the viability of small or fragmented populations.
• Practical application – DNA barcoding is routinely used in wildlife forensics, monitoring of trade in endangered species, and rapid assessment of environmental DNA (eDNA) samples.

8. Natural Selection, Speciation and the Origin of Taxa

Classification reflects evolutionary history. Adaptive radiation, driven by natural selection, generates the diversity that taxonomists organise.

• When a lineage colonises a new environment, divergent selection can lead to the evolution of distinct morphological, ecological, and genetic traits – eventually producing new species (speciation).
• Examples of adaptive radiation relevant to the syllabus:

  • Darwin’s finches (Aves) – beak morphology linked to feeding niche.
  • Lake Malawi cichlids (Actinopterygii) – colour patterns and mating behaviour.
  • Land plants on isolated islands (e.g., Hawaiian silverswords) – growth form and pollination syndromes.

• These processes explain why taxa at higher ranks (order, family) share broad adaptations, while lower ranks (genus, species) display finer, often ecologically driven differences.

9. Example Classifications – From Domain to Species

Two contrasting examples illustrate the hierarchy across kingdoms, with additional representatives to meet the syllabus requirement for a “wide range of organisms.”

9.1. Animal Example – House Mouse (Mus musculus)

1. Domain: Eukarya
2. Kingdom: Animalia
3. Phylum: Chordata
4. Class: Mammalia
5. Order: Rodentia
6. Family: Muridae
7. Genus: Mus
8. Species: Mus musculus

9.2. Plant Example – Common Sunflower (Helianthus annuus)

1. Domain: Eukarya
2. Kingdom: Plantae
3. Phylum (Division): Magnoliophyta (Angiosperms)
4. Class: Magnoliopsida (Dicotyledons)
5. Order: Asterales
6. Family: Asteraceae
7. Genus: Helianthus
8. Species: Helianthus annuus

9.3. Protist Example – Malaria Parasite (Plasmodium falciparum)

1. Domain: Eukarya
2. Kingdom: Protista
3. Phylum: Apicomplexa
4. Class: Aconoidasida
5. Order: Haemosporida
6. Family: Plasmodiidae
7. Genus: Plasmodium
8. Species: Plasmodium falciparum

9.4. Fungal Example – Baker’s Yeast (Saccharomyces cerevisiae)

1. Domain: Eukarya
2. Kingdom: Fungi
3. Phylum: Ascomycota
4. Class: Saccharomycetes
5. Order: Saccharomycetales
6. Family: Saccharomycetaceae
7. Genus: Saccharomyces
8. Species: Saccharomyces cerevisiae

9.5. Chromist Example – Brown Alga (Laminaria digitata)

1. Domain: Eukarya
2. Kingdom: Chromista
3. Phylum: Phaeophyta
4. Class: Phaeophyceae
5. Order: Laminariales
6. Family: Laminariaceae
7. Genus: Laminaria
8. Species: Laminaria digitata

9.6. Green Algal Example – Flagellate (Chlamydomonas reinhardtii)

1. Domain: Eukarya
2. Kingdom: Archaeplastida (green lineage)
3. Phylum: Chlorophyta
4. Class: Chlorophyceae
5. Order: Chlamydomonadales
6. Family: Chlamydomonadaceae
7. Genus: Chlamydomonas
8. Species: Chlamydomonas reinhardtii

10. Binomial Nomenclature

Scientific names follow a strict format:

• Italicised, with the genus capitalised and the specific epithet in lower case (e.g., Homo sapiens).
• Often followed by the authority and year of publication (e.g., Homo sapiens Linnaeus, 1758).
• Subspecies, when recognised, are added as a third italicised term (e.g., Panthera tigris altaica).

11. Practical Activities (AO2 & AO3)

11.1. Activity – Constructing a Dichotomous Key for Eukaryotic Specimens

1. Goal: Develop a usable key for ten unknown eukaryotic specimens representing at least five kingdoms.
2. Materials: Light microscopes, prepared slides, hand lenses, reference cards (cell‑wall types, plastid types, flagella), data sheets.
3. Procedure (brief):

   • Observe each specimen; record characters such as cell wall presence/composition, type of nutrition, presence of chloroplasts or flagella, storage product, and mode of reproduction.
   • Group characters into mutually exclusive pairs (couplets) to form a dichotomous key.
   • Draft the key, test it on a different set of specimens, and refine ambiguous couplets.

4. Assessment: Students must (a) produce a correctly ordered key, (b) justify each couplet with observed evidence, and (c) explain how the key reflects the hierarchical taxonomic ranks.

11.2. Activity – DNA Barcoding Simulation

1. Extract short DNA sequences (provided) from a set of organisms (e.g., COI for animals, rbcL for plants).
2. Use a simple alignment tool (e.g., BLAST‑like web interface) to identify closest matches in a reference database.
3. Discuss how sequence similarity supports or contradicts the morphological identification and which species concept is being applied.

Learning Outcomes

• Apply the Linnaean hierarchy to a range of eukaryotes.
• Explain how molecular data refine classification and species delimitation.
• Analyse the impact of natural selection and human activities on biodiversity.
• Demonstrate practical skills in observation, key construction, and basic bioinformatics.