Phylogenies

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Phylogenies Classifying species (AKA Cladistics
Taxonomy)

• What are phylogenies?
• How do we read them?
• How do we estimate them?

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Carolus LinneausSystema Naturae (1735)

• Swedish botanist natural theologist
• Hierarchical classification based on ideal of
  unchanging types.
• Binomial nomenclature - replaced polynomials
• Categories
• K, P,C, O, F, G, S
• Assumes a static, unchanging Universe

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Charles Darwin and Fig. 1

• Origin of Species (1859)
• Species diverge they do so gradually
• Articulated idea of shared ancestry, branching of
  lineages (cladogenesis) and change along branches
  (anagenesis)
• Only figure in OS a dendrogram

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Problems with Linnean system

• It does NOT represent evolutionary history.
• Hierarchical categories do not imply degree of
  evolutionary change or divergence.
• Are Rabbits as different from Rodents as they are
  from Elephants?
• When and how should we split groups into separate
  categories? - splitting vs. lumping
• How different is different enough to warrant
  separate groupings?
• Ex Dogs wolves

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Dendrogram Phylogenies

• Phylogeny Interpretation of the evolutionary
  history and relationships between a group of
  organisms
• Phylogenetic tree Hypothesis of
  ancestor-descendent relationships among
  populations, species, or larger groups

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Why construct phylogenies?

• Understand evolutionary history
• System of classifying organisms organizing
  diversity
• Most biologists agree most efficient way to
  classify organisms is based on phylogenetic
  relatedness

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All species coalesce to a common ancestor

• Recall our lab
• Just as all genes coalesce to a single ancestral
  gene, all individuals coalesce to a single
  ancestor.
• Like tracing a family tree

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• Tips
• Branches
• Nodes
• Root
• Most Recent Common Ancestor (MRCA)

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Phylogeny of Vertebrates
Name another tip Name another node
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Monophyletic groupings
Who is the MRCA of Mammals and Crocodiles?
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Monophyletic groupings
Nodes name monophyletic groups An ancestor and
ALL of its descendents
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Reading phylogenies

• 5 of these are identical
• Which one is not the same?

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Paraphyletic groupings
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Tree of Life
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What data should we use to generate trees?

• What data do you use?
• Often do it without understanding why

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What data should we use to determine evolutionary
relationships?

• Characters distinguishable variations of an
  organism
• Morphologic
• Developmental
• Genetic
• Quantifiable
• Independent of each other
• Homologous due to common ancestry

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Phenetic approach

• Sokal (1950) Made classification rigorous. Based
  groupings on many characters rather than few
  important ones.
• Calculated overall SIMILARITY. Generated
  phenograms (Basically, phylogenetic trees)
• Characters Vary independently of other features.
  Homologous among ingroups.
• Character states alternative versions of
  character.
• Presence/absence
• 1/2/3/4etc.

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Characters

• Are the bones of the upper limb homologous
  structures?
• Are wings of bats, birds and pterosaurs
  homologous structures?

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PitfallsWhen Similarity ? Close Relationship!

• 2 taxa may share a derived character state
• OR may share an ancestral character state
• OR may share a character state due to convergence
  to same phenotype (MRCA did not have the
  character) These are analogous traits
• Bird and bat wings
• Dermopterans, Flying squirrels, Sugar gliders
• Only if first case is true will you ALWAYS infer
  correct phylogenetic relationship.

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Anura Caudata Caecilians Mammals Turtles
Crocs Birds Tuatara Lizards
Snakes
Diapsida
Where is the MRCA of Tuatara and Crocs?
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Anura Caudata Caecilians Mammals Turtles
Crocs Birds Tuatara Lizards
Snakes
A
B
C
D
The Monophyletic group that includes Birds, Crocs
Turtles begins at node
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Willi Hennig and Cladistics

• Grouping scheme based ONLY on phylogenetic
  relationships
• Not on degree of similarity and adaptive
  divergence
• Used presence of shared derived characters
  (synapomorphies) to infer evolutionary
  relationships
• Based trees upon total weight of ALL
  synapomorphies

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Phylogenetic terms

• Plesiomorphy Ancestral character state
• Symplesiomorphy Ancestral character state shared
  by many taxa - phylogenetically uninformative
• Apomorphy Derived (novel) character -
  phylogenetically uninformative
• Synapomorphy Shared derived character - GOLD
• Hennig has indeed emphasized and defined some
  procedures of phylogenetic analysis that have
  long been used by systematists. He might even
  have clarified them if he had not unnecessarily
  replaced the usual plain-language terms by a
  bizarre and idiosyncratic new terminology."
  (1978) G. G. Simpson

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Similarity ? Relationship

• 2 taxa may share a derived character state
• OR may share an ancestral character state
• OR may share a state due to convergence
• Bird and bat wings
• Dermopterans, Flying squirrels, Sugar gliders
• Only if first case is true will you infer the
  phylogenetic relationship correctly.

synapomorphy
symplesiomorphy
analogy
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Synapomorphies identify monophyletic groups

• Unite groups with shared, (only among each other)
  derived (from some ancestral group) characters

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Problems

• What characters (traits) are best for assessing
  evolutionary relationships?
• Skull length, body size, pelage color, limb
  modification and specialization, chromosome ?
• When and how should we split groups into separate
  categories? - splitting vs. lumping
• How different is different enough to warrant
  separate groupings?
• Can/should hierarchical categories imply degree
  of evolutionary change or divergence?
• Are Hyraxes as different from Manatees as they
  are from Bats?
• Are dogs as different from cats as they are from
  humans?

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Problems with characters

• Which characters are phylogenetically
  informative?
• How do we quantify of possible states
  frequency of change among them?
• How do we establish polarity?
• How do we deal with continuous traits Quantify
  or discard them?

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Ideal character

• States are discrete
• of states are knowable (across taxa)
• Transition frequencies (rates of change) are
  estimable

DNA ONLY 4 states A C G T No polarity Can
measure transition frequencies
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Method of inferring a tree

• Choose the most parsimonious one
• Parsimony Methodological reductionism
  Explanation which requires the fewest
  undocumented assumptions is probably correct.
• Occams Razor The easiest explanation is
  probably the correct one.
• William of Occam 14th century Franciscan monk
• In cladistics/phylogeny The tree which requires
  us to postulate the least evolutionary change
  fewest homoplasies is probably correct

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Parsimony

• Find all possible tree topologies calculate
  total number of changes required to produce each
  topology.
• Topology with fewest changes the most
  parsimonious tree

C A B D
A B C D
Taxa A, B, C, D Characters
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Placement of Cetaceans

• Morphology of astragalus unites Artiodactyls
• Most parsimonious placement one gain of
  pulley-shaped astragalus

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Placement of Cetaceans

• Mounting genetic evidence suggests Hippos have
  shared genes with Cetaceans more recently than
  they have with other Artiodactyls (e.g. deer)

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Placement of Cetaceans

• Appearance of SINEs (mutations) throughout the
  genome suggests that Cetaceans Hippos are close
  relatives
• Rare Selectively neutral Once established, lost
  only via drift