Classification and Phylogeny: What

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Classification and Phylogeny Whats In a Name?
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Alice in Wonderland
Whats the use of their having names, the Gnat
said, if they dont answer to them? No use to
them, said Alice, but its useful to the
people that name them, I suppose.
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Whats in a name?
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Carolus Linnaeus the father of modern taxonomy
In the 1700s a Swedish physician and biologist,
Carolus Linnaeus, refined classification into a
hierarchy where groups of similar organisms can
be subdivided into smaller more distinctive
groups.
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Linnaeus classified organisms into a hierarchy of
groups

• Eventually, as one works through such a system,
  each unique form of organism is left to occupy
  its own small, but distinct category.
• Domain, Kingdom, Phylum, Class, Order, Family,
  Genus, Species

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Here are the classification hierarchies for
several different species of organisms
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A bee by any other name
Scientific name Genus species Taxonomy the
science of naming and classifying living things
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The science of taxonomy underwent a fundamental
revolution when Darwin published On the Origin of
Species
Darwin suggested organisms cluster together due
to common ancestry Species that are in the
same genus have a more recent common ancestor
than those in different genera Likewise, genera
within the same family have a more Recent common
ancestor than those in different families
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Systematics
Darwin showed that the classification of living
organisms has a natural basis their
evolutionary history
Taxonomy expanded into systematics the study of
the diversity of living organisms and their
evolutionary relationships
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How do we determine evolutionary relationships?

• Homology the same component and structures of
  organisms are repeated in many forms
• Darwin viewed homology as evidence that
  development of one structure is a modification or
  variant of the development of another (implies a
  common origin as a feature present in a common
  ancestor)

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Evolutionary Homologies
features that share common origin in a common
ancestor
humerus
Recognizing homologies position relative to
other parts and of its parts to each other
ulna
radius
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Evolutionary Homologies
features that share common origin in a common
ancestor
Recognizing homologies Transitional forms
Ex horses run on their toes (actually on the tip
of a single toe on each foot) Which toe? the
fossil record for horses is exceptional, and we
can trace the transitional stages through time to
discover that it is the third toe IN FACT, we
can trace to a common ancestor with rhinos and
tapirs (Hyracotherium) and discover that the
habit of walking on the 3rd toe is homologous in
this group
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Why do we care about homologies?
Homologies imply that the most recent common
ancestor had the trait
Nesting homologies allows us to heirarchically
classify organisms in an evolutionarily
meaningful way
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Homoplasy
Homoplasy (also analogy or analogous traits) same
or similar character in two or more taxa was not
present in the most recent common ancestor Can be
difficult to distinguish from homology
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Homoplasy results from convergent evolution
similar structure/trait has arisen in 2 or more
species, but is not possessed by a common
ancestor (and all intervening ancestors)
 cooperative hunting in canids and
felids  growth form of aloe (related to
lillies) and agave (cactus)
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Homoplasy results from evolutionary reversals
similar structure/trait has arisen in 2 or more
species, but is not possessed by a common
ancestor (and all intervening ancestors)
 secondary wing loss in birds and insects  eye
loss in cave fish and cave salamanders
Texas blind salamander Typhlomolge rathbuni
Eyed (surface dwelling) and eyeless (cave
dwelling) Astyanax mexicanus
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Evolutionary modifications
Evolutionary change (modification) is a change in
a character state
 Do not confuse character with character
state  eg., Characters include number of
digits, eye color, height Characters states
are 3, 4, 5 blue, green 2m, 2.5m,
3m Character state changes can be any
character, behavioral, physiological,
morphological, biochemical, molecular, etc. 1)
presence/absence (0,1) for any character 2)
qualitative, multistate - arbitrarily 1, 2, 3 for
any character 3) quantitative, multistate -
difficult to handle. How do you separate
variation from difference?
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Systematics
systematists infer the historical pattern of
evolutionary descent for an organism to build
a PHYLOGENY - the genealogy of a group of taxa
(the practice of developing phylogenies is called
phylogenetics)
tips- represent terminal taxa (extant species)
outgroup
A
B
C
D
1
2
Nodes - represent common ancestors that no
longer exist
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Interpretation BC evolved from a common
ancestor 1 1 is no longer present, only BC.
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Cladistics

• Cladistics is a modern approach
• Goal is to group organisms according to
  evolutionary history (phylogeny)
• Note in practice, collect data on character
  states and then reconstruct topology
• Use data to construct cladograms

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Cladistics

• cladograms can be derived by observing shared
  character states
• 3 types
• 1. shared derived character states --
  synapomorphy
• 2. shared ancestral states -- sympleisiomorphy
• 3. shared but independently evolved state --
  homoplasy
• Only 1 are useful in constructing cladograms
• SYNAPOMORPHIES DEFINE CLADES, and are evidence of
  a most recent common ancestor
• individual taxa are recognized by unique,
  unshared character states (autapomorphies)

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Ancestral vs. Derived

• If a character state was present before a clade
  split off, it is ancestral
• If a character state is new to a group, it is
  derived
• Ancestral vs. derived can be answered with
  outgroups (which define the ancestral state for a
  clade)

autopomorphy
synapomorphy
sympleisiomorphy
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Constructing a cladogram
How many synapomorphies do each pair of organisms
share?
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How many trees?
With 3 taxa, there are the following possible
trees
A
B
C
A
B
C
A
B
C
The problem that arises is that even with
complete knowledge of shared derived characters,
there are many possible phylogenies that can be
generated   of taxa bifurcating trees 3
3 4 15 5 105 6 945 How do we
chose between them?
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Choosing the correct tree
There are many possible methods for selecting
trees, most are built on the principle of
parsimony - the most likely alternative is the
simplest and least complex in the phylogenetic
context, the favored phylogeny includes the
fewest number of changes in character
state There are other ways to choose between
trees (e.g., Maximum likelihood) that weight some
kinds of character state changes differently than
others e.g., for molecular data, we know that
transversions (A, G lt--gt C, T) are less common
than transitions (Alt--gtT, Clt--gtG) - we can
calculate the probabilities for any taxon and
weight each change differently
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Defining Groups Cladistics
Monophyletic includes all taxa from a single
common ancestor
Paraphyletic does not include all taxa from a
single common ancestor
Polyphyletic includes all taxa not from a common
ancestor
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Impact of cladistics

• Cladistics argues that many traditional groups
  are paraphyletic
• Example Reptiles are not a valid group

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Reptiles are a paraphyletic group
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Cladistics would group birds with the reptiles
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Traditional and cladistic classification of
vertebrates