# Classification

Classification is the **science of arranging organisms into groups** based on their similarities and differences, making them easier to identify and study. The study and practice of classification is called **taxonomy**, and the groups or categories within a classification system are called **taxa** (singular: taxon).

#### The Concept of Species

A **species** is generally defined as a **group of similar organisms that are able to reproduce to give fertile offspring**. This is known as the **biological species concept**. However, applying this definition can be difficult for organisms that reproduce asexually, are extinct, or cannot interbreed in captivity.

In such cases, other concepts are used:

* **Morphological species concept**: Organisms are classified as the same species if they share **identical physical features**. This is useful for single specimens, asexual species, or fossils.
* **Ecological species concept**: A population of organisms is considered a species if they share the same features and live in the same habitat at the same time, fulfilling a specific **niche**.

#### Hierarchical Classification

Organisms are organized into a **hierarchy** of taxonomic ranks, with larger groups at the top and smaller, more specific groups at the bottom. The hierarchy progresses as follows:

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

As you move down the hierarchy, there are more groups at each level, but fewer organisms in each group, and the organisms become more closely related. Organisms can only belong to one group at each level.

#### Binomial System of Naming

To avoid confusion from common names, all organisms are given a **unique, internationally accepted scientific name in Latin** with two parts, known as the **binomial system** (two-word nomenclature).

* The **first part** is the **genus name**, which starts with a capital letter.
* The **second part** is the **species name** (specific epithet or trivial name), which begins with a lower-case letter.
* Scientific names are always written in *italics* (or underlined if handwritten). For example, humans are *Homo sapiens*, dogs are *Canis familiaris*, and cats are *Felis catus*.

#### Classification Systems: From Five Kingdoms to Three Domains

Historically, organisms were often divided into two kingdoms (plants and animals), but this proved insufficient for organisms like fungi and microorganisms.

1. **Five-Kingdom System**: The five-kingdom scheme includes:
   * **Prokaryotae** (Monera): Predominantly unicellular, prokaryotic organisms (bacteria and cyanobacteria). They lack a true nucleus and membrane-bound organelles.
   * **Protoctista**: Mostly unicellular eukaryotes, resembling ancestors of fungi, plants, and animals. They have eukaryotic cells but are not differentiated into tissues.
   * **Fungi**: Eukaryotes, predominantly multicellular (except yeasts), with chitin cell walls, and heterotrophic nutrition (saprotrophic or parasitic). They do not have chloroplasts.
   * **Plantae**: Multicellular eukaryotes with cellulose cell walls, non-motile, and photoautotrophic nutrition.
   * **Animalia**: Multicellular eukaryotes, heterotrophic nutrition, motile, and without cell walls or chloroplasts. They typically have differentiated cells forming tissues and organs, and a nervous system.
2. **Three-Domain System**: Advances in molecular biology, particularly DNA sequencing and analysis of ribosomal RNA, led to a new classification scheme in 1977 by Carl Woese. This system introduced the **domain** as the highest taxonomic rank, above kingdoms. The three domains are:
   * **Bacteria** (Eubacteria): True prokaryotic bacteria. They have peptidoglycan in their cell walls.
   * **Archaea**: Extremophile prokaryotes, found in hostile environments. Molecular phylogeny revealed they are more distantly related to Bacteria than previously thought. They have unique membrane lipids and ribosomal RNA that differ from Bacteria and Eukarya, and their cell walls do not contain peptidoglycans.
   * **Eukarya**: Includes all eukaryotic cells (Protoctista, Fungi, Plantae, Animalia). Their DNA is linear (chromosomes) and associated with histones, and their cells divide by mitosis.

#### Classification of Viruses

**Viruses are not classified as living organisms** or included in the three-domain system because they are **non-cellular structures**. They do not undergo cell division, metabolism, or fulfill criteria for classification as living things. Instead, they reproduce by injecting their DNA or RNA into host cells, hijacking the host's machinery to replicate viral particles.

Viruses are classified based on:

* The **type of nucleic acid** they contain (DNA or RNA).
* Whether the nucleic acid is **single-stranded or double-stranded**.
* Their protein coat, called a **capsid**, which surrounds the nucleic acid core. Some viruses also have an outer envelope derived from the host cell membrane.

#### Criteria and Tools for Classification

Scientists use various characteristics to classify organisms, constantly updating systems as new evidence emerges. Key criteria include:

* **Morphology and anatomy**: External and internal structural features.
* **Cell structure**: Whether cells are eukaryotic or prokaryotic, and details of their organelles.
* **Physiology**: How the body works, including metabolic processes, blood composition, and renal function.
* **Biochemistry**: Comparisons of nucleic acids (DNA, RNA) and proteins. **DNA sequencing** is a powerful tool, as closely related organisms have more similar base sequences in their DNA.
* **Courtship behaviour**: This is species-specific and can be used to attract a mate of the right species, thus helping to classify species.

#### Importance of Classification

Classification is essential because it:

* **Organizes and identifies organisms**: It provides a systematic way to name and group the vast diversity of life.
* **Facilitates study**: Makes it easier for scientists to study organisms and their relationships.
* **Enables communication**: Provides a standard, internationally accepted way for scientists to communicate about species, avoiding confusion from common names.
* **Reflects evolutionary relationships**: Modern classification aims to group organisms according to their evolutionary history (phylogeny), showing who is related to whom and how closely.