Topic : Phylogenetic Reconstruction

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Topic Phylogenetic Reconstruction

• I. Systematics Science of biological diversity.
  Systematics uses taxonomy to reflect phylogeny
  (evolutionary history).
• - Based on cladistic analysis (will define
  shortly)
• II. Taxonomy identify, name and classify
  organisms.
• Carl Linneaus (Swedish Prof. 1707-1778)
• Binomial nomenclature, Genus species

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III. Hierarchial Taxonomic Grouping Plants

• Kingdom
• Phylum
• Class
• Order - names end in ales
• Family - names end in aceae
• Genus
• species

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Table. Classification of Large Ground Finch and
Common Buttercup
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Figure The connection between classification and
phylogeny
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IV. Classification and Phylogeny

• After the publication of Charles Darwins book On
  the Origin of Species (1859) differences and
  similarities among organisms became to be seen as
  the result of their evolutionary history
  phylogeny.
• Phylogenetic Trees trace evolutionary
  relationships among taxa.
• taxa (plural) taxon (singular) named taxonomic
  unit at any level.

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V. Types of Phylogenetic Trees

• Monophyletic members of taxa result from single
  common ancestor. Only legitimate taxa derived
  from cladograms!
• Polyphyletic members of taxa result from more
  than one common ancestor.

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Figure Monophyletic versus and polyphyletic
groups
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VI. Homology vs. Analogy

• Homologous Traits Common origin.
• Similarity in structure reflects common
  ancestry
• Characters reflect ancestral past.
• Examples

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Figure  Homologous structures anatomical signs
of evolution
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VI. Homology vs. Analogy

• Analogy similarity in gross appearance and
  function DOES NOT reflect common ancestry.
• traits or characters exhibit a common
  function BUT different evolutionary origins.
• Analogy DOES reflect similar selective pressures
  ----gt Convergent Evolution.
• Ex., bird and insect wings,
• succulence in plants,
• Monotremes, marsupial, placental mammals

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Figure Convergent evolution and analogous
structures cactus and euphorb
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Three types of Mammals
Monotremes Marsupials Placental
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VII. Molecular Markers aid Systematics

• Two Approaches
• 1) Sequence of amino acids in proteins of human
  genome only 2
• 2) Sequence of nucleotides in nucleic acids DNA
  and RNA comparisons via sequencing, restriction
  mapping and hybridization.
• Much data now held in electronic data bases.
• Goal Identify and compare homologous DNA
  sequences among taxa.

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How to identifying homologous nucleotide
sequences

• 1. Select appropriate portion of genome to
  compare.
• Often mtDNA segments for recently diverged taxa.
• Often rRNA genes for distantly related taxa
  evolves slowly.
• Example Aligning segments of DNA
• Today utilize sophisticated computer programs to
  analyze differences between sequences.

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Figure Aligning segments of DNA
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Molecular Clock utility

• Goal is to provide an independent assessment for
  the origin of taxonomic groups in time.
• Based on the fact some proteins, cytochrome C
  and some mitochondrial genomes evolve at a
  constant rate of evolution over time.
• Thus, Molecular clocks are calibrated in actual
  time graphing differences in sequences against
  time.
• However, some proteins and nucleic acids evolve
  at different rates.
• Molecular clocks also assume constant Mutation
  Rate?
• Utility may be minimal

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Figure Dating the origin of HIV-1 M with a
molecular clock In 2000 estimated invasion of
aids into humans in 1930s. Evidence also for
multiple origins of AIDs invading humans as well.
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VIII. Science of Phylogentic Systematics B.
Cladistics - uses novel homologies to define
branch points.

• Location of branch point relative time of
  origin between taxa.
• Location of branch point extent of divergence
  between branches or how different 2 taxa have
  become since diverging from a common ancestor.
• Recent branch versus deeper branch

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VIII. Science of Phylogentic Systematics C.
Cladistic Analysis

• Clade evolutionary branch
• Cladistic analysis groups organisms by order in
  time, clades arose along a dichotomous tree.
• Each branching point indicates a novel homology
  unique to the species on the branch.
• Uses ONLY homologies to construct trees!!!
• DOES NOT use level of divergence.

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Figure Cladistics and taxonomy
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Figure Constructing a cladogram
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VIII. Science of Phylogentic Systematics C.
Cladistic Analysis

• Uses outgroup comparison to recognize primitive
  traits members of the study group AND to
  establish a starting point for the tree.
• Outgroup Species or a group of species
  relatively closely related to study group BUT
  clearly NOT as related as any study group members
  are to each other.
• Outgroup study group may share primitive
  characters, likely shared a common ancestor.

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VIII. Science of Phylogentic Systematics C.
Cladistic Analysis

• First, outgroup determines shared primitive
  character states.
• Next, examine synapomorphies shared derived
  character states to construct the tree.
• Synapomorphies novel homologous traits that
  evolved in an ancestor common to all species on
  ONE branch BUT not on other branch.
• Parsimony simplest tree using the fewest
  changes to show evolutionary relationships.

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Figure Constructing a cladogram
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Figure Parsimony and the analogy-versus-homolog
y pitfall 4 chambered heart is analogous NOT
homologous
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VIII. Science of Phylogentic Systematics C.
Cladistic Analysis Limitations

• Since focus solely on phylogenetic branching
  cladistic analysis accepts ONLY monophyletic
  study groups.
• Preferred approach is to use a combination of
  characters to design trees for study groups
  including molecular, morphological, anatomical,
  ultrastructural, and developmental.

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Figure When did most major mammalian orders
originate?
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• The END FOR NOW