pastpaperbd/ Biology/ Notes/ Species and Taxonomy
T4

Species and Taxonomy

AQA spec ref: 3.4.6 - Investigating diversity

Classifying living organisms into groups has been a central task of biology since Aristotle, but the modern understanding of classification is based on evolutionary relationships rather than just physical similarity. Understanding how species are defined and classified, and why this matters, is fundamental to ecology, evolution, and conservation.

The Species Concept

A species is defined by AQA as: a group of organisms that share similar morphology, physiology and behaviour, and can interbreed to produce fertile offspring.

The critical part of this definition is fertile offspring. Two organisms might look similar and even mate, but if their offspring are sterile, they belong to different species. The classic example is the horse (Equus caballus) and donkey (Equus asinus): they can interbreed to produce a mule, but mules are sterile (due to the chromosomal mismatch - horses have 64 chromosomes, donkeys have 62, giving mules 63 - which prevents proper meiosis). Therefore horses and donkeys are separate species.

This is called the biological species concept and it has limitations:

  • It cannot be applied to asexually reproducing organisms (bacteria, some plants, some animals)
  • It cannot be applied to fossils
  • Ring species challenge it (adjacent populations can interbreed but geographically separated end populations cannot)
  • Some apparently different species can hybridise and produce fertile offspring

For AQA, the biological species concept (interbreeding + fertile offspring) is the required definition.

Why Species Are Hard to Define in Practice

The boundaries between species are often not sharp, especially when populations are diverging. Taxonomy is therefore sometimes subjective - biologists disagree on whether particular populations constitute separate species. The number of recognised species changes as new genetic data becomes available. Many species previously distinguished by morphology alone have been found (by DNA analysis) to be multiple cryptic species; conversely, some morphologically distinct populations are genetically very similar.

Taxonomy and Classification

Taxonomy is the science of classifying organisms into groups. The hierarchical classification system, developed by Carl Linnaeus in the 18th century, groups organisms at increasingly inclusive levels:

Domain→Kingdom→Phylum→Class→Order→Family→Genus→Species

Mnemonic: Do Kings Play Chess On Fine Green Silk.

Each level is called a taxon (plural: taxa). At each level, organisms in the same group share more features. The genus and species together form the binomial name.

Binomial nomenclature: every species has a unique two-part Latin name: Genus species (e.g. Homo sapiens, Canis lupus, Quercus robur). Rules:

  • Genus name starts with a capital letter
  • Species name starts with a lower case letter
  • Both are italicised (or underlined in handwriting)
  • The genus name may be abbreviated after first mention (e.g. H. sapiens)

The reason for Latin: a universal language that is understood by scientists worldwide, regardless of their native language, and prevents confusion from common names (which vary by region and language).

Organisms in the same genus share a more recent common ancestor than organisms in the same family but different genera.

The Three Domains

The three-domain system, developed by Carl Woese in the 1970s and 1980s, fundamentally revised our understanding of life's history. Based on ribosomal RNA (rRNA) sequence analysis, all life was reclassified into three domains:

1. Bacteria

  • Prokaryotes (no membrane-bound nucleus)
  • Cell wall of peptidoglycan (murein)
  • Circular DNA, no histones
  • 70S ribosomes
  • Diverse metabolic strategies
  • Include most pathogenic organisms

2. Archaea

  • Prokaryotes (no membrane-bound nucleus)
  • No peptidoglycan in cell wall (different chemical composition)
  • Often found in extreme environments (thermophiles, halophiles, methanogens) - but many archaea are in ordinary environments
  • Circular DNA with some histone-like proteins
  • 70S ribosomes, but different structure from bacterial 70S
  • Metabolically and genetically more similar to Eukarya than to Bacteria - particularly in DNA replication and transcription machinery

3. Eukarya

  • Eukaryotes (membrane-bound nucleus)
  • Includes all protists, fungi, plants, and animals
  • 80S ribosomes
  • Linear chromosomes, histones
  • Complex internal membrane system

Why Archaea were separated from Bacteria: rRNA sequences showed that Archaea share many molecular features with Eukarya that are absent in Bacteria - including similar transcription and translation machinery, similar DNA polymerases, and similar histones. This suggests Archaea and Eukarya share a more recent common ancestor than either does with Bacteria. The traditional two-kingdom system (prokaryotes vs eukaryotes) obscured this important evolutionary division.

Phylogenetics and Evolutionary Classification

Modern taxonomy is based on phylogenetics - the study of evolutionary relationships. Two organisms are classified together if they share a recent common ancestor. Organisms that are more closely related are placed in the same (lower) taxon.

Phylogenetic trees (cladograms) show the branching pattern of evolutionary relationships. Each branch point (node) represents a common ancestor. The more recent the common ancestor, the more closely related the organisms.

Evidence used in classification:

Traditional evidence:

  • Morphology - body structure, anatomical features (homologous structures indicate shared ancestry)
  • Physiology - metabolic processes, enzyme structure
  • Behaviour - courtship, communication, social structure

Molecular evidence (increasingly dominant):

  • DNA sequence comparison - the more similar the DNA sequences of two species, the more closely related they are. A difference in DNA sequence represents accumulated mutations since the two species last shared a common ancestor.
  • Amino acid sequence comparison - comparing sequences of conserved proteins (e.g. cytochrome c, haemoglobin) across species. Closely related species have more similar amino acid sequences.
  • Ribosomal RNA sequences - especially useful for very distantly related organisms (rRNA is highly conserved and changes slowly). This is what Woese used to establish the three-domain system.
  • Immunological comparisons - antibodies raised against proteins of one species cross-react more strongly with proteins of closely related species.

Why molecular evidence is superior to morphological:

  • Convergent evolution can make distantly related organisms look similar (e.g. dolphins and ichthyosaurs - similar body shape but very different ancestry)
  • Molecular data is more objective and can provide quantitative measures of relatedness
  • DNA is present in all organisms, allowing universal comparisons

Classification Example

The classification of modern humans:

  • Domain: Eukarya
  • Kingdom: Animalia
  • Phylum: Chordata
  • Class: Mammalia
  • Order: Primates
  • Family: Hominidae
  • Genus: Homo
  • Species: Homo sapiens

Sharing the family Hominidae with Homo sapiens are the great apes (gorillas, chimpanzees, orangutans). Sharing the genus Homo were extinct species like Homo neanderthalensis and Homo erectus. The closer the shared taxon, the more recent the common ancestor.

Summary

  • Species: organisms that share morphology/physiology/behaviour and can interbreed to produce fertile offspring
  • Taxonomy hierarchy: Domain→Kingdom→Phylum→Class→Order→Family→Genus→Species
  • Binomial nomenclature: italicised, Genus species (capital G, lower s)
  • Three domains: Bacteria (peptidoglycan wall), Archaea (no peptidoglycan, more similar to Eukarya), Eukarya (nucleus, 80S ribosomes)
  • Phylogenetics: classification based on evolutionary relationships (shared ancestry)
  • Evidence: morphology, physiology, behaviour; DNA sequences, amino acid sequences, rRNA sequences (Woese → three domains)
  • Molecular evidence superior: avoids confusion from convergent evolution; quantitative; universal

AQA Exam Tips

  • Species definition: must include both "can interbreed" AND "produce fertile offspring" - mules show why both are needed.
  • Binomial name rules: italics (or underline), capital genus, lower species. AQA will ask you to correctly format a name or identify errors.
  • Why Archaea are a separate domain: their rRNA sequences are more similar to Eukarya than to Bacteria, suggesting a different evolutionary lineage. Do not say Archaea are just unusual bacteria.
  • Molecular vs morphological: AQA may ask why molecular evidence is more reliable. State: convergent evolution can produce similar morphology in unrelated organisms; molecular data is more objective; DNA sequences can be quantitatively compared.
  • Shared genus = shared recent ancestry: if two species share a genus name, they share a more recent common ancestor than two species in the same family but different genera. AQA tests this logic.
  • Cytochrome c: a commonly cited example of molecular evidence. The amino acid sequence of cytochrome c differs by 1 position between humans and chimpanzees, but by 45 positions between humans and yeast - consistent with the much greater evolutionary distance to yeast.