Classification

• Taxonomy is the branch of biology that names and groups organisms according to their characteristics and evolutionary history.

• Organisms were first classified more than 2,000 years ago by the Greek philosopher Aristotl
• Organism’s were grouped into land dwellers, water dwellers and air dwellers
• Plants were placed into three categories based on the differences in their stems
• As new organism’s were discovered, his system became inadequate.
  • Categories were not specific enough.
  • Common names did not describe a species accurately.
  • Names were long and hard to remember.

• Carolus Linnaeus (mid-1700’s) Swedish biologist - established simple system for classifying and naming organisms.

• Hierarchy (a ranking system) for classifying organisms the basis for modern taxonomy.
• He is considered to be “father” of modern taxonomy
• Linnaeus used an organisms morphology (form and structure) to categorize it - organisms grouped with similar organism
• First - divided all organisms into two Kingdoms, Plantae (plants) and Animalia (animals). These are the same as Aristotle’s main categories.
• Modern System:
  • Kingdom (plant and animal) was divided into Phyla* (division for plants)
  • Phyla divided into smaller groups - Classes
  • Class divided into Orders
  • Order divided into Families
  • Family divided into Genera
  • Genus divided into Species (scientific name)
• *Note: Phyla and Family were not in Linnaeus’s classification system but were added by modern scientists.

• Species can be subdivided:
  • Zoologists refer to closely-related species that are reproductively isolated due to genetic drift in geographically separate areas ‘subspecies’.
  • Botanists use the term ‘varieties’ for similar taxons.
• To classify organisms, modern taxonomist consider the phylogeny (evolutionary history) of the organism.

• Varieties: 
  • Peaches and nectarines come from different varieties of the peach tree, Prunus persica.
  • Genetic variant of common peach, nectarines probably bred in China >4,000 years ago. Trees virtually identical. Expression of a recessive allele thought responsible for smooth skin of nectarines, lack fuzzy trichomes (plant hairs) characteristic of peaches.

• Names based on Latin or Ancient Greek words - scientist everywhere understood these languages. 
• FIRST word of the scientific name (‘species’ name) is the genus to which the organism belongs.
  • The genus name refers to the relatively small group of organisms to which a particular type of organism belongs.
• SECOND word of the name is the species. (Species identifier)
  • The species name is usually a Latin description of some important characteristic of the organism

• Style of Latin name for an organism: capitalize the genus (first part) but NOT the species identifier (second part). 
• Use italics or underline to indicate these are species names: Acer rubrum or Acer rubrum (‘scientific’ or ‘species’ name)  red maple tree (‘common’ name)
  • Acer - Latin name for Maple (genus)
  • rubrum - Latin word for Red (species)

the name can be abbreviated as: A. rubrum or A. rubrum

• Humans:
  • Homo sapiens nHomo because of our large brain and upright posture.
  • sapiens because of our intelligence and ability to speak

Objectives

• Explain what information can be gathered from a phylogenetic tree.
• What is systematic taxonomy and what are four kinds of evidence used organize organisms
• How can the embryological evidence be used to show phylogenetic relationships that are not evident from either the study or morphology or the study of the fossil record?
• Explain cladistic taxonomy and identify one conclusion that is in conflict with classical systematic taxonomy. 
• What are two flaws of the molecular clock model on determining relatedness between species?

• Systematics is a system that organises the tremendous diversity of organisms into a phylogenetic tree.
  • Phylogenetic tree shows the evolutionary relationships thought to exist between organisms.
  • Hypothesis based on lines of evidence, such a the fossil record, morphology, embryological patterns of development and chromosomes and macromolecules.

• The fossil record often provides clues to evolutionary relationships
• It is not a continuous record - some fossil records are incomplete
• Systematic taxonomists consider other evidence to confirm information contained within the fossil record with other lines of evidence.

• Taxonomists study an organism’s morphology and compare it to other living organisms.
  • Homologous features are important, but must separate features that are truly ‘homologous’ with those the seem homologous but are actually ‘analogous’.
  • The more homologous features two organisms share, the more closely related they are thought to be.

• Early patterns in embryological development provide evidence of phylogenetic relationships.
• They also provide means of testing hypotheses about relationships that have developed from other lines of evidence

• Taxonomists compare ‘macromolecules’ - such as DNA, RNA and proteins as a kind of “molecular clock”.
• Compare amino acid sequences for homologous protein molecules of different species.
• Amino acid differences provide clues to how long ago two species diverged from a shared evolutionary ancestor.
• Compare ‘karyotypes’ (patterns of chromosomes) of two related species.
• Regions of chromosomes that have the same pattern of banding are clues to the relatedness of organisms.
• The chromosomes of humans and chimpanzees show a surprising degree of similarity.

• Cladistics - system of taxonomy that reconstructs phylogenies by inferring relationships based on similarities.
• Used to determine the sequence in which different groups of organisms evolved.
• To do this, it focuses on a set of unique characteristics found in a particular group of organisms.
• These unique characteristics are called derived traits or derived characters.

•  Patterns of shared derived traits used in cladistics to construct branching diagrams called cladograms.
• Cladograms show sequences in which different groups of organisms likely to have evolved.
• Key to cladistics is identifying morphological, physiological, molecular or behavioral traits that differ among the organisms being studied and that can be attributed a common ancestor

Objectives

• Distinguishing features of the six kingdoms system of classification. 
• Characteristics that distinguish archaebacteria from eubacteria.
• Why are protists grouped together in the six kingdom system in spite of having differences that are greater than those between plants and animals?
• Evidence that prompted the creation of the three-domain system of classification.
• Principal differences between the six kingdom system and the three-domain system of classification.
• Characteristics that place fungi, plants and animals in the Eukarya domain.

• The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization.
• Prokaryotes - microscopic single-celled organism which has neither a distinct nucleus with a membrane nor other specialised organelles; include bacteria and cyanobacteria.
• Eukaryotes - organisms whose cells have a well defined membrane-bound nucleus (containing chromosomal DNA) and organelles

• Modern Archaebacteria likely descended from at least very similar to the first organisms on Earth. 
• Unicellular prokaryotes - distinctive cell membranes and biochemical and genetic properties differ from all other life forms. 
• Some are autotrophic - producing food by chemosynthesis. ‘chemosynthetic bacteria’
• Many Archaebacteria live in harsh environments such as sulfurous hot springs, very salty lakes and anaerobic environments, such as the intestines of mammals.

• They are UNICELLULAR PROKARYOTES.  Most of the Bacteria (Germs) that affect your life are members of the Kingdom Eubacteria. 
• Eubacteria are both autotrophic and heterotrophic.
• Includes the disease-causing bacteria such as tooth decay or food poisoning.
• The combined Kingdoms, Archaebacteria and Eubacteria include the greatest number of living things on Earth. 
• ALL OF THE PROKARYOTES ARE IN THESE TWO KINGDOMS.
• Both reproduce by binary fission, but they do have some ways to recombine genes, allowing evolution to occur.

• These organisms are placed here more because of What They Are Not than What They Are.
• Kingdom Protista contains all eukaryotes that are NOT plants, animals or fungi; includes unicellular and simple multicellular eukaryotes.
• Eukaryotic cells have nuclei and organelles that are surrounded by membranes.
• The cells of multicellular protists are not specialized to perform specific functions in the organisms.
• Includes Euglena and Amoeba.

• Fungi are eukaryotes, and most are multicellular.
• The cells of fungi have cell walls that contain a material called chitin.
• These organisms are heterotrophic and obtain their nutrients by releasing digestive enzymes into a food source.
• They absorb their food after it has been digested by the enzymes.
• Fungi act either as decomposers or as parasites in nature.
• Kingdom Fungi includes molds, mildews, mushrooms, and yeast

• Eukaryotic, multicellular and carry out photosynthesis. They are autotrophs.
• Plant cells have cell walls, that contain the polysaccharide cellulose.
• Plant cells specialized for different functions, such as photosynthesis, the transport of materials and support.
• Kingdom Plantae includes mosses, ferns, cone-bearing plants (gymnosperms), and flowering plants (angiosperms).

• Animals are multicellular, eukaryotic, and heterotrophic.
• Animal cells have no cell walls.
• Most members of the Animal Kingdom can move from place to place.
• Some are permanently attached to surfaces such as sponges and barnacles.
• Fish, Birds, Reptiles, Amphibians, and mammals-including humans belong to the Kingdom Animalia.
• This Kingdom also includes sponges, jellyfish, worms, sea stars, and insects.

• Living things fall into three broad groups called domains. n
  • Domain Archaea (archaebacteria) n
  • Domain Bacteria (eubacteria)
• Domain Eukarya (eukaryotes)-true nuclei with linear chromosomes and membrane—bound organelles.
  • This Includes Protista, Plantae, Fungi, and Animalia

• Viruses have no nucleus, cytoplasm, organelles, or cell membrane, so can not carry out cellular functions.
• Only able to replicate by infecting cells and using the organelles and enzymes within
• very small, size ranges form 20nm to 250 nm (size of small bacteria)
• Consists of two parts: a nucleic acid and a protein coat called a capsid
• Nucleic acid may be DNA or RNA but not both
• Some viruses have a membrane-like structure outside the capsid called an envelope

a) attachment of virus to host cell

b) injection of viral DNA

c) Integration of the viral DNA into host genome, and

d)  Multiplication of the host cell with the viral DNA.

a) HIV attaches to the cell surface

b) Virus core enters cell and its RNA is converted to DNA (reverse transcription)

c) Viral DNA enters nucleus and combines with host cell DNA

d) RNA copies of virus are made (viral assembly)

e) The assembled viral particles leave the cell through lysis or budding