Chapter 25 -- Systematics and the Phylogenetic Revolution

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Chapter 25 -- Systematics and the Phylogenetic
Revolution

• How to connect the dots of organisms?

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What are the traditions of classification?

• 1st classification was into plants or animals
• Traditional language used
• Grouped into general groups
• Descriptive terms followed
• Linneaus developed binomial nomenclature
• Rules?

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• Dichotomous Keys
• Organism is classified, key helps identify in the
  field
• Presence or absence of trait

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Taxonomy (arranging rules) is one of the current
sciences of classifying organisms

• 1. No two organisms have the same name.
• 2. All names are in Latin.
• 3. The first word is capitalized and refers to
  the genus.
• 4. The second word is lowercase and refers to the
  species.
• 5. The two words combined are the scientific name
  and are written in italics.
• 6. The first word can be abbreviated after the
  first use in text.

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• Taxonomy is organized in a hierarchy.
• Taxon is one level. These organisms share decided
  traits.

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What if new information does not fit the
classification models from years ago?

• Incomplete fossil record errors are being
  corrected by biochemical analysis.
• Systematics -reconstruction and study
  evolutionary relationships.
• determine common ancestor and create tree based
  on order of evolution

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There are some problems in this process that
require critical thinking while examining the
trees.

• Evolution does not occur at a constant rate
• Evolution is not unidirectional
• Location will influence the amount of selective
  pressure an organism experiences.
• Convergent evolution may independently evolve
  and appear to be similar.

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Similarities are polarized (classified) as
ancestral or derived.

• Ancestral characteristics are called
  pleisomorphic.
• The group that inherited is called
  sympleisomorphic. (Example four legs are a
  shared characteristic by many mammals)
• Derived (apomorphic) characteristics are
  characteristics that occur during speciation or a
  split. These characteristics are often states
  they are present or they arent present.

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It is difficult to tell if a similarity is
ancestral or derived.

• a. An organism that is closely related, but not a
  member of the group you are comparing is chosen
  as an outgroup.
• b. Characteristics displayed by the outgroup are
  assumed to be ancestral

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The presence or absence of a similarity can then
be recorded and used to a cladogram.

• Clades are nested inside of each other and the
  derived trait shared by the members are called
  synamorphies.
• A cladogram does not include all species and does
  not show the common ancestor at the node where
  two branched off.

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• Be aware of convergent evolution
• The principle of parsimony favors any hypothesis
  of fewest assumptions.
• The principle of parsimony does not always apply
  when evolution occurs quickly such as in DNA
  exons.
• Molecular clocks use a reliable gene to track
  mutations that have occurred to determine how
  frequently a mutuation occurs.
• (.5 changes/base pair/billion years 4 b.p.
  changes ___ years)

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Graphical explanation of basic Phylogenetic
terms 
Monophyletic taxon   A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor.   A monophyletic taxon is also called a clade. Examples   Mammalia, Aves (birds), angiosperms, insects, etc.
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Paraphyletic taxon   A group composed of a collection of organisms, including the most recent common ancestor of all those organisms.   Unlike a monophyletic group, a paraphyletic taxon does not include all the descendants of the most recent common ancestor. Examples   Traditionally defined Dinosauria, fish, gymnosperms, invertebrates, protists, etc.
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Polyphyletic taxon   A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group. Polyphyletic taxa are considered "unnatural", and usually are reclassified once they are discovered to be polyphyletic. Examples   marine mammals, bipedal mammals, flying vertebrates, trees, algae, etc.
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Comparative Anatomy

• Homologous or Analogous?
• Variation is not because of single mutations

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How is life currently grouped?

• Changes in classification
• Plants, animals
• Carl Woese

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The domain Bacteria has the largest amount of
organisms.

• a. Bacteria have important roles in the biosphere
  including nitrogen fixation and photosynthesis.
• b. Bacteria also cause many diseases.
• c. Taxonomists recognize 12-15 groups of bacteria.

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Archaea (ancient) appear to be more closely
related to eukaryotes

• It is a diverse group, but has distinct
  characteristics that separate these prokaryotes
  from other organisms.
• They have cell walls but no peptidoglycan.
• The lipids in the cell membrane are unique from
  all other organisms.
• Their ribosomal RNA sequences are distinct.
• Some archaea genes have introns.

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There are three general categories of Archaea
based on their environments or metabolic pathways.

• Methanogens are strict anaerobes
• use H2 gas to convert CO2 to CH4. They live in
  swamps, marshes, and the intestines of mammals.
• Extremophiles
• thermophiles 121 C, halophiles 15-20
  salinity Dead Sea, extreme pH (.7 11) and
  extreme pressure (must have 300 atm to survive,
  need 800 atm).
• Nonextreme archaebacteria grow in the same
  environments as bacteria, but have signature DNA
  sequences. (genome only 500 base pairs long)

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The domain Eukarya appeared 1 billion years after
prokaryotes.

• Protista
• Led to plants, fungi and animals
• Endosymbiont Theory

• Compartmentalization
• Multicellularity
• Sexuality

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Viruses dont fit into a kingdom

• Not cellular
• Infectious
• TMV