Phylogeny

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Chapter 25

• Phylogeny Systematics

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Phylogeny

• the evolutionary history of a species or a group
  of related species
• the construction of phylogenies is based on
• the fossil record (the sequence in which fossils
  appear in the layers of sedimentary rock)
• morphological molecular homologies
• an analytical approach to understanding the
  diversity relationships of organisms
• traditional systematics uses morphological
  homologies to infer evolutionary relationships
• molecular systematics uses molecular homologies
  (similarities in DNA, RNA, proteins, other
  molecules) to infer evolutionary relationships

Systematics
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What are homologies?

• similarities between two species due to
  shared ancestry
• result of divergent evolution
• can be
• shared derived characters features that are
  unique to a particular taxon (classification
  group)
• shared primitive characters features that a
  group of organisms may share with other organisms
  outside their taxon (ie with organisms that they
  are not as closely related to)

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Analogies

• similarities between two unrelated species that
  evolved independently of each other as 2 lineages
  adapted to similar lifestyles
• result of convergent evolution
• (ex) 4-chambered heart of birds
  mammals
• NOTE the more points of resemblance 2
  characteristics (ex skulls, DNA sequences) have
  the less likely they are analogies (? the more
  likely they are homologies)

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Taxonomy

• the science of classification
• ordered division of organisms into categories
  based on a set of characteristics used to assess
  similarities (shared derived characters)
  differences
• features of taxonomy useful in phylogenetic
  systematics
• binomial nomenclature
• Genus species names used to describe species
• hierarchical classification
• includes 8 taxa DKPOCFGS

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Phylogenetic Trees

• diagrams that depict hypotheses about
  evolutionary relationships
• the branches of phylogenetic trees reflect the
  hierarchical classifications of groups nested
  within more inclusive groups
• the sequence of the branching is NOT related to
  the age of the species

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Cladograms

• diagrams that depict patterns of shared
  characteristics among taxa
• do not imply evolutionary history but if the
  shared characteristics are due to common
  ancestry, can form the basis of a phylogenetic
  tree

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Clades

• groupings within a cladogram
• clades can be
• monophyletic made up of an ancestral species
  and all of its descendents
• paraphyletic made up of an ancestral species
  and only some of its descendents
• polyphyletic a grouping that leaves out the
  common ancestor of the species included

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Cladistics

• the analysis of how species may be grouped into
  clades
• monophyletic clades (valid clades) are defined by
  characteristics that are unique to the group
  (shared derived characteristics)
• these characteristics are identified by comparing
  ingroup species with an outgroup species that
  does not have the shared derived characteristic

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Phylogenetic Trees Rate of Evolution

• by varying the lengths of the branches in a
  phylogenetic tree, we can show the rate at which
  a homologous gene (a shared gene due to common
  ancestry) has evolved in different lineages
• this type of diagram is called a phylogram

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Phylogenetic Trees Geologic Time

• another way phylogenetic trees can be altered is
  to place evolutionary branch points in the
  context of geologic time
• this type of diagram is called an ultrametric
  tree
• the ultrametric tree to the right shows us that
  invertebrates chordates diverged during the
  Neoproterozoic Era and the two groups have had an
  equal amount of type to evolve since then (even
  if the rates of evolution within the lineages are
  different)

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Which phylogenetic tree is most accurate?

• as we increase the number of species included in
  a phylogenetic tree, the number of ways to
  arrange them also increases leading to many
  different phylogenetic hypotheses
• the 1st step in evaluating phylogenetic
  hypotheses is to follow the principle of maximum
  parsimony
• the simplest explanation that is consistent with
  the facts should be investigated first
• in other words, investigate the phylogenetic tree
  that requires the fewest evolutionary changes
  first
• the 2nd step is to apply the principle of maximum
  likelihood
• investigate the phylogenetic tree that reflects
  the most likely sequence of evolutionary events
  (based on certain rules about how DNA changes
  over time)

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Types of Homologous Genes

• orthologous genes
• genes that are passed in a straight line from one
  generation to the next but have ended up in
  different gene pools because of speciation
• often shared by distantly related species
• (ex) 99 of the genes of humans mice and 50 of
  the genes of humans yeast are orthologous
• paralogous genes
• genes found in multiple copies within the same
  genome
• results from gene duplication
• may lead to gene families that have related
  functions
• (ex) the ?-globin ?-globin gene families (which
  both produce subunits of hemoglobin) diverged
  from an ancestral globin gene that likely
  duplicated and, then, mutated
• often shared by closely related organisms
• studying both types can give us clues to an
  organisms evolutionary history

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Molecular Clock

• method used to measure the absolute time (ie the
  numerical age in mya) of evolutionary change
  based on the observation that some genes other
  regions of the genome appear to evolve at
  constant rates
• based on the assumption that the number of
  nucleotides substituted in genes is proportional
  to the amount of time since
• a species branched from its common ancestor
  (orthologous)
• the genes duplicated (paralogous)

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Preview Universal Tree of Life

• consists of 3 domains
• Bacteria
• Archaea
• Eukarya
• early history unclear