Chapter 25: Phylogeny and Systematics

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Chapter 25Phylogeny andSystematics
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Macroevolutionary Relatedness
Shown is a phylogenetic tree
Taxonomy is the ordered division of organisms
into categories based on similarities and
differences. p. 495, Campbell Reece (2005)
Systematics is an analytic approach to
understanding the diversity of relationships of
organisms p. 491, Campbell Reece (2005)
Phylogenies are evolutionary histories
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Microevolution is

• Any time you consider
• natural selection
• genetic drift
• mutation
• gene flow between populations
• the randomness of mating within populations
• you are considering microevolutionary processes
• Indeed, microevolution is all those evolutionary
  things up to and just about including the act of
  speciation itself

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Macroevolution is

• Any time you consider
• the likelihood of births of new species
  (speciation events)
• the likelihood of the death of species
  (extinction)
• the adaptive radiation of lineages (birth of many
  species)
• mass extinction (death of many species)
• evolutionary relationships between species
• the evolutionary history of a lineage
• biogeography, or
• shared derived characters
• you are considering macroevolutionary processes

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Connections...

• Adaptation of a species to its natural
  environment (microevolution) will not necessarily
  have a positive impact on the ability of that
  species to give rise to descendant species
  (macroevolution)
• That is, microevolution and macroevolution are
  not identical processes
• However, microevolutionary processes do impact on
  macroevolutionary processes
• For example, macroevolution is affected by the
  adaptations displayed by organisms (e.g.,
  dispersal or dormancy ability) and adaptations
  are a product of selection (a microevolutionary
  process)

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Fossils
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Classifying Organisms

• Fossils allow us to compare extinct organisms
  with modern organisms
• People study fossils to understand past
  environments plus to discover clues to
  evolutionary relationships among organisms
• Taxa (sing. taxon) are units of classification of
  organisms
• So far we have considered the taxonomic
  categories species domain
• Ideally, all taxonomic categories group organisms
  according to evolutionary (blood) relationships
• Also ideally, more closely related species should
  be grouped into more-similar taxonomic categories

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Taxonomic Categories
Do (Domain) Keep (Kingdom) Privates
(Phylum) Clean (Class) Or (Order) Forget
(Family) Getting (Genus) Sex (Species)
?
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Other Mnemonics

• Darn Kids Picking Cacti On Fridays Get Stuck
• Dumb Kids Playing Catch On Freeways Get Squished
• Did King Phillip Come Over For Great Sex?
• Do Kiss Pigs Carefully Or Face Grimy Smiles
• Do Kings Play Chess On Fine Grained Sand
• Did King Phillip Came Over From Germany Stoned?
• Did King Peter Came Over From Geneva Switzerland?
• Do Kindly Produce Credit Or Furnish Good Security
• Do Keep Peeling Cold Onions For Good Smells
• Do Keep Putting Coal On the Fire Grate Slowly
• Did King Phillip Cry, "Oh, For Goodness Sake!"?
• Do Keep Putting Cheese On Five Green Spoons
• Did Karen's Pups Chew On Furry Grey Squirrels?
• Did King Phillip Come Over For Good Spaghetti?
• Did King Phillip Court Ophelia For Good Sex?
• Did Karl Push Cliff Over Football Grand Stand?
• Did King Peter Come Over From Germany Saturday?

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Binomial Nomenclature

• Examples Escherichia coli, E. coli, Escherichia
  spp., and the genus Escherichia
• The genus name (Escherichia) is always
  capitalized
• The specific epithet (coli) is never capitalized
• The specific epithet is never used without the
  genus name (e.g., coli standing alone, by itself,
  is a mistake!)
• The genus name may be used without the specific
  epithet (e.g., Escherichia may stand alone,
  though when doing so it no longer actually
  describes a species)
• When both genus and specific epithet are present,
  the genus always comes first (e.g., Escherichia
  coli, not coli Escherichia)
• Both genus and specific epithet are always
  underlined or italicized
• Genera may be abbreviated, e.g., the E. in E.
  coli, but should be spelled out in full the first
  time they are used in a document

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Phylogenies Cladograms

• A typical goal of systematics (and paleontology)
  is the construction of phylogenies
• A phylogeny is a description of the blood (i.e.,
  evolutionary) relationships between organisms
• A phylogeny can be a description of the
  macroevolutionary history of a group of species
• A cladogram is a graphical representation of a
  phylogeny
• Cladograms show patterns of shared
  characteristics
• Cladograms come in a variety of types
• Typical among all is an attempt to properly sort
  nodes
• Nodes are speciation events
• Descendant species should be properly connected
  to their ancestral species
• Species should be grouped more closely to related
  species than they are to less-well related
  species
• The goal of a cladogram or phylogeny is to
  properly represent correct evolutionary
  relationships

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Classifying Clades
Each deeper branch point represents greater
divergence
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Classifying Proper Clades
A clade consists of an ancestral species plus all
descendant species
This is missing descendant species
The goal of systematics is to define monophyletic
taxa (a.k.a., clades)
Here is a missed ancestor species
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Monophyletic
All descendants (of the shown set, i.e., of D, E,
G, H, J, and K)
A correct grouping
A clade
Ancestor
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Synapomorphies

• Homologies are similarities between organisms
  that are present due to common descent
• Common descent means that organisms share
  ancestry / are evolutionarily related
• Clades are defined by shared derived characters
  (a.k.a., Synapomorphies)
• Synapomorphies are those homologies that are
  unique to individual taxa
• That is, the common ancestor and all of the
  descendant species share (in one form or another)
  a given homology
• And, organisms not found in a given clade do not
  share the shared derived character
• Contrast, shared primitive characters

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Polyphyletic
Convergent evolution?
This is a mistake
Polyphylies happen when species are included in
clades that they dont belong in
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Convergent Evolution

• Polyphyletic taxa occur as a consequence of
  mistaking analogies for homologies
• Analogies are two structures that superficially
  resemble each other, i.e., which appear (at least
  at first glance) to be homologous but are not
• Analogies result from convergent evolution the
  two species do similar things in similar
  environments so consequently evolve similar
  structures to perform these similar functions
• The key difference between an analogy and a
  homology are two-fold
• The common ancestor between the two species will
  have lacked the common structure
• The development of the structure will differmore
  generally, homologies predict other homologies
  between two species whereas analogies provide
  much less predictive power

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Analogies Homoplasies
Marsupial
These moles only look similar
Placental
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Analogies
This is an analogy
This is a polyphyletic grouping
This is the true clade
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Paraphyletic
This is a mistake
But one made for legitimate reasons
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Mono, Para, or Polyphyletic?
Birds are modified reptiles
Turtles may be incorrectly included here (if
mammals are excluded)
Retention of this mistake is often done
deliberately, i.e., not grouping birds with
reptiles
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Cladistics

• Cladistics is a technique by which organisms are
  assigned to different (monophyletic) taxa
• Cladistics works by identifying homologies and
  grouping together organisms such that within taxa
  individuals share more homologies than they do
  with individuals found in different taxa
• Cladistics also rejects the inclusion of
  similarities...
• that result from convergent evolution (i.e.,
  analogies)
• that are homologies that are shared with other
  taxa (i.e., shared primitive characters)
• Note, that this is not to say that it is
  necessarily easy to distinguish analogies from
  homologies
• Cladistic techniques are not able to judge
  evolutionary divergence in terms of the time
  between nodes (speciation events)
• Time information is derived from the fossil record

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Shared Derived Characters
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Cladogram based on S.D.C.
An outgroup is a species that is related to the
species being studied, but less closely they are
like a negative control
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More Familiar Synapomorphies
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Shared PrimitiveCharacters

• Not all shared characters are shared derived
  characters
• For example, a cladist would not use the fact
  that both dogs and bears have hair as a means of
  classifying both dogs and bears as carnivores,
  since the ancestor of the ancestral carnivore, a
  mammal, also had hair
• However, a cladist would use the fact that dogs
  and bears both have hair to include both among
  the mammals
• That is, hair cannot be employed to distinguish
  mammals because hair is a shared by all mammals
• However, though hair is a shared primitive
  character when comparing among mammals, it is a
  shared derived character when grouping mammals as
  distinct from other lineages

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Primitive Shared Derived Characters
These are analogies
For mammals these are primitive
For birds this is shared derived
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Molecular Systematics

• Molecular systematics has come to dominate the
  study of evolutionary relations (rather than
  supplanting other approaches, e.g., the fossil
  record, it instead serves as an increasingly
  important tool)
• Molecular systematics seeks out homologies in
  molecules, such as DNA sequences
• "One advantage of this molecular tool of
  systematics is that it is objective and
  quantitative.
• A second advantage is that it can be used to
  assess relationships between groups of organisms
  that are so physiologically distant that they
  share very few morphological similarities
• Third molecular comparisons go right to the
  heart of evolutionary relationships.

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Molecular Homologies
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Phylogram
Note differences in branch lengths (reflecting
differences in rates of sequence evolution)
In phylograms the length of the branch reflects
the degree of divergence (here in terms of
changes in DNA sequence of a gene)
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Ultrametric Tree
Note similarities in branch lengths
An ultrametric tree is a phylogram that provides
time-since-divergence information
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Maximum Parsimony
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Homologous Genes
The previous phylogenies were based on
orthologous genes
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Universal Tree
Chloroplasts
Fusion bacteria with archaea eukaryote
Mitochondria
Last common Ancestor
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The End