Phylogeny

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Phylogeny Domain Bacteria
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Taxonomy

• how organisms are named and classified
• Greek philosophers suggested that life might have
  changed gradually over time
• but Aristotle viewed species as fixed and said
  that life-forms could be arranged on a ladder of
  increasing complexity scalae naturae

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Taxonomy

• Carolus Linneaus developed the binomial system
  for naming species
• binomial two names
• developed a nested classification system in
  contrast to Aristotle
• grouped animals according to similar
  characteristics
• groups (taxa) known as phylum, class, order,
  family, genus, species
• thought the similarities were due to Gods
  creation

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Human being Homo sapiens -first word
Genus -second word species name -both are
usually italicized
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Phylogeny vs. Taxonomy

• taxonomical classification not only takes the
  morphological similarities of organisms into
  account it also looks at the evolutionary
  relationships
• evolutionary history of a species or a group of
  species phylogeny
• phylogenies are constructed uses data ranging
  from fossils to genetic analysis to derive
  evolutionary relationships

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Phylogeny

• classification using phylogeny depends upon
  identifying common ancestors
• physical and genetic similarities due to shared
  ancestry homology
• the relationship between common ancestors and
  their descendants can be shown as a phylogenetic
  tree
• the common ancestor is the base of a dichotomy or
  a two-way branch point
• each branch point is a divergence of two
  evolutionary lineages from a common ancestor

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• common ancestor of the fish and the human arose
  542 MYA!!
• so there has been 542 million years of evolution
  for both the fish and the human

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From Kingdoms to Domains

• earliest taxonomists just had two kingdoms
  Plants and Animals
• with the discovery of bacteria things got a bit
  more complicated
• bacteria were classified as plants since they
  were found to have a cell wall
• since algae underwent photosynthesis considered
  plants also
• fungi also classified as plants despite having
  nothing in common with plants
• organisms that consumed were considered animals
  including single celled organisms like protozoans

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• in 1969 five-kingdom classification system
  Robert Whittaker
• recognized the existence of two fundamental cell
  types prokaryotes and eukaryotes
• created a separate kingdom for prokaryotes and
  divided up the eukaryotes
• 1. Monera - prokaryotic
• 2. Protista unicellular organisms including
  algae
• 3. Fungi
• 4. Plantae
• 5. Animalia
• based on the nutritional requirements and methods
  of these domains
• plants autotrophs
• animals heterotrophs internal digestors
• fungus decomposers heterotrophs

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• this classification scheme has changed
• due to analysis of genes
• adoption of a three domain system of
  superkingdoms
• 1. Bacteria most of the currently known
  prokaryotes (or Eubacteria)
• 2. Archaea prokaryotes that inhabit a wide
  variety of environments
• 3. Eukarya - eukaryotes
• contains the old kingdoms of protists, fungi,
  plants and animals
• these kingdoms no longer exist but are still kept
  by us stubborn biologists!

gene transfer
common ancestor of all life
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Comparing Prokaryotic and Eukaryotic Cells

• Prokaryotic cells
• no nucleus
• DNA in a region of the cytoplasm called the
  nucleoid
• no membrane-bound organelles
• a Cytoplasm bound by the plasma membrane
• smaller ribosomes

• Eukaryotic cells
• membrane bound nucleus containing DNA
• membrane-bound organelles
• a Cytoplasm in the region between the plasma
  membrane and nucleus
• larger ribosomes

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Prokaryotic Cells

• usually smaller and less complex than eukaryotic
  cells
• first cells to evolve
• single-celled organisms
• 0.5 to 5um in diameter (eukaryotes 10-100um)
• some species exist as aggregates called colonies
• e.g. cyanobacteria
• defined as having no nuclear membrane, no
  mitochondria or other organelles
• divided into two domains
• Bacteria
• Archaea

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Domain Bacteria

• Bacteria
• collective biomass 10x of all eukaryotes
• vast genetic diversity among members
• physical diversity
• shapes spheres (coccus), rods (bacilli) and
  spirals

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Bacteria

• made up of numerous components
• cell capsule (slime layer) for adherence and
  protection
• cell wall
• plasma membrane phospholipid bilayer
• fimbrae for attachment conjugation
• flagella(e) for locomotion
• cytoplasm for metabolism
• nucleoid region with a single chromosome
• ribosomes for protein synthesis

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Prokaryotic Cells

• Bacterial cell components
• cell wall rigid structure outside the plasma
  membrane
• cross-linked sugars
• for protection, structural support reproduction
• gram negative bacteria have an additional layer
  of sugars and fats outside the cell wall
• this layer is responsible for the toxicity of
  these bacteria

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Prokaryotic Cells

• Bacterial cell components
• fimbrae structures involved in attachment
• shorter ones involved in reproduction pilus
• flagella made of protein filaments
• for locomotion
• cytoplasm intracellular fluid of the prokaryote
• bounded by the plasma membrane
• cytosol cytoskeleton
• no membrane-bound organelles