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Title: Phylogeny

Chapter 25
  • Phylogeny Systematics

  • 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

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
  • 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)

  • 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
  • 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)

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

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

  • 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

  • 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

  • the analysis of how species may be grouped into
  • 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

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

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
  • 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

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
  • 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
  • the 2nd step is to apply the principle of maximum
  • investigate the phylogenetic tree that reflects
    the most likely sequence of evolutionary events
    (based on certain rules about how DNA changes
    over time)

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
  • results from gene duplication
  • may lead to gene families that have related
  • (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

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
  • the genes duplicated (paralogous)

Preview Universal Tree of Life
  • consists of 3 domains
  • Bacteria
  • Archaea
  • Eukarya
  • early history unclear