Unit 2: Section 7

Classification is the act of arranging organisms into groups based on their similarities and difference. This makes it easier for scientists to identify and study them. Taxonomy is the study of classification. There are a few different classification systems in use, but they all involve placing organisms into groups in a taxonomic hierarchy:

• There are eight levels of groups (called taxonomic groups) used in classification.
• Similar organisms are first sorted into one of three very large groups called domains, e.g. animals, plants and fungi are in the Eukarya domain.
• Similar organisms are then sorted into slightly smaller groups called kingdoms, e.g. all animals are in the animal kingdom.
• Similar organisms from that kingdom are then grouped into a phylum. Similar organisms from each phylum are then grouped into a class, and so on down the eight levels of the taxonomic hierarchy.
• As you move down the hierarchy, there are more groups at each level but fewer organisms in each group.
• The hierarchy ends with species - the groups that contain only one type of organisms.

The Five Kingdoms

• Prokaryotae (Monera) - e.g. bacteria. Prokaryotic, unicellular, no nucleus, less than 5um.
• Protoctista - e.g. algae, protozoa. Eukaryotic cells, usually live in water, single-celled or simple multicellular organisms.
• Fungi - e.g. moulds, yeasts, mushrooms. Eukaryotic, chitin cell wall, saprotrophic (absorb substances from dead or decaying organisms).
• Plantae - e.g. mosses, ferns, flowering plants. Eukaryotic, multicellular, cell walls made of ceullulose, can photosynthesise, contain chlorophyll, autotrophic (produce their own food).
• Animalia - e.g. nematodes (roundworms), molluscs, insects, fish, reptiles, birds, mammals. Eukaryotic, multicellular, no cell walls, heterotrophic (consume plants and animals).

The Binomial Naming System

• The nomenclature (naming system) used for classification is called the binomial system - all organisms are given one internationally accepted scientific name in Latin that has two parts.
• The first part of the name is the genus name and has a capital letter. The second part is the species name and begins with a lower case letter. 
• The binomial system helps to avoid the confusion of using common names.

Phylogeny

• Phylogeny is the study of the evolutionary history of groups of organisms.
• All organisms have evolved from shared common ancesters (relatives).
• Phylogeny tells us who's related to whom and how closely related they are.
• Closely related species diverged away from each other most recently.
• Classification systems now take into account phylogeny when arranging organisms into groups.

• Early classification systems only used observable features to place organisms into groups.
• But this method has problems. Scientists don't always agree on the relative importance of different features and groups based solely on physical features may not show how related organisms are.
• Classification systems are now based on observable features along with other other evidence.
• The more similar organisms are, the more related they are. We now use a wide range of evidence to see how similar, and therefore how related, organisms are. E.g:
  - Molecular evidence: the similarites in proteins and DNA. More closely related organisms will have more similar molecules. You can comopare things like how DNA is stored, the sequence of DNA bases and the sequences of amino acids in proteins from different organisms.
  - Embryological evidence: the similarities in the early stages of an organism's development
  - Anatomical evidence: the similarities in structure and function of different body parts
  - Behavioural evidence: the similaries in behaviour and social organisation of organisms.

Five Kingdoms vs Three Domains

• In the older system the largest groups were the five kingdoms - all organisms were placed into one of these groups.
• In 1990, the three domain system was proposed. This new system has three domains - large superkingdoms that are above the kingdoms in the taxonomic hierarchy.
• In the three domain system, organisms with cells that contain a nucleus are placed in the domain Eukarya (this includes four of the five kingdoms). Organisms that were in the kingdom Prokaryotae are separated into two domains - the Archae and Bacteria.
• The lower hierarchy stays the same - Kingdom, Phylum, Class, Order, Family, Genus, Species.
• The three domain system was proposed because of new evidence, mainly molecular:
  - Molecular evidence - the enzyme RNA polymerase is different in bacteria and archaea. Archaea, but not Bacteria, have similar histones to Eukara.
  - Cell membrane evidence - The bonds of the lipids in the cell membranes of Bacteria and Archaea are different. The development and composition of flagellae are also different. 
• Most scientists now agree that Archaea and Bacteria evolved separately and that Archaea are more closely related to Eukarya than Bacteria. The three-domain system reflects how different the Archaea and Bacteria are.

• Dichotomous keys provide a way to identify organisms based on observable features.
• They consist of a series of questions, each with only two possible answers. Each answer leads to the name of the organism or another question, and so on, until the organism is identified.