Some Housekeeping

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Lecture 14

• Some Housekeeping
• Review
• Phylogenetic Inference
• What can we learn from phylogenetics?
• Of trees and bushes
• How to read a tree
• Reconstructing phylogenies
• Tree building methods
• Types of characters
• Bootstrapping

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Some Housekeeping

• 2nd written assignment
• 10 of final mark
• If omitted split up marks
• Term paper 15 ? 20
• Final Exam 30 ? 35
• Mid-term exam
• Grades
• Not yet
• 1st written assignment
• Grades

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Review

• Any questions?
• Any answers?
• Phylogeography
• Molecular Clock
• Assumption and problems
• Did Adam meet Eve?
• Gene trees vs. species trees
• Lineage sorting
• Why use mtDNA?
• Three times rule
• Demography and phylogeography
• Geographic patterns

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Two typical questions

• 1st To float or to breathe?
• What was there first?
• Swim bladder or lung
• Darwin lung derived
• More fish ? ancestral
• Fish earlier than tetrapods
• Whatever is derived
• How often evolved?

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Two typical questions

• 2nd Homology or Convergent Evolution
• African cichlids
• 3 lakes
• Speciation within lakes?
• Colonization between lakes?

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True phylogenies
mtDNA
nuclear
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Species tree and gene trees
Time
Ancestor (root)
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How to read a tree

• Can be rotated freely

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Rooted and unrooted trees

• Root by outgroup
• Species that is equally distant to all OTUs
• Tricky need to test several different outgroups

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Quiz are these two trees the same?
Ellasochirus tenuimanus
Pagurus acadianus
Pagurus bernhardus
Labidochirus splendescens
Lithodes aequispina
Paralithodes camtschatica
Pagurus pollicaris (NE)
Pagurus pollicaris (GU)
Pagurus longicarpus (NE)
Pagurus longicarpus (GU)
Clibanarius vittatus
Coenobita sp.
Artemia salina
0.05
Pagurus bernhardus
Pagurus acadianus
Ellasochirus tenuimanus
Labidochirus splendescens
Lithodes aequispina
Paralithodes camtschatica
Artemia salina
Clibanarius vittatus
Coenobita sp.
Pagurus longicarpus (NE)
Pagurus longicarpus (GU)
Pagurus pollicaris (NE)
Pagurus pollicaris (GU)
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Unfortunatelywe werent there to watch

• Dont have true phylogeny
• Need to infer from data
• Have data from A, B and C
• Morphological
• Genetic
• Reconstruct phylogeny
• How many possibilities?

5 possibilities
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An (almost) infinite forest

• Exponential increase in number of possible trees
• Only one is true
• Impossible to check all
• Have to search for right tree
• Exhaustive search
• Only if lt 10 OTUs
• Statistical algorithms
• Constrain likely tree space
• Different criteria for finding best tree

Number of electrons in visible universe
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Phylogenetic Inferenceensuring homology
DNA (observed sequences)
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Tree Building Methods

• Distance based
• Calculate distance between OTUs
• Construct tree
• Advantages
• Computationally efficient
• Can use more characters
• Can include biases
• Base composition bias
• Transitions / transversions
• Codon position bias
• Disadvantage
• Information loss
• reduced to distance
• Examples
• UPGMA
• Neighbor-joining
• Minimum Evolution

• Character based
• Use ind. characters to construct trees
• Advantages
• Fewer assumptions
• Direct use of data
• No loss of information
• Disadvantages
• Computationally intensive
• Can only use shared derived characters
• Examples
• Maximum Parsimony
• Maximum Likelihood

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Types of characters

• Informative for Maximum Parsimony and distance
  methods
• Synapomorphies
• Informative for distance methods
• Autapomorphies
• Uninformative
• Symplesiomorphies

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Genetic distance trees
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Homoplasy and Saturation

• Saturation of mutations
• Third codon positions
• Transitions
• Problem
• Underestimation of longer branch lengths
• Solution
• More taxa
• Consideration pf part of variability
• Corrections

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Maximum Parsimony

• Parsimony
• Simplest explanation is the best
• Choose tree which can be explained by fewest
  steps
• For example lungs and swim bladders

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Maximum Parsimony
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Bootstrap analysis

• Resampling of characters
• With replacement
• Characters may be sampled several times
• Repeat 1000 times
• Reconstruct phylogeny
• 1000 trees
• Construct consensus tree
• Indicate how often specific groups occur

Second replicate
First replicate
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Bootstrap analysis
Indicates how well a tree is supported by data
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Key Concepts

• Phylogenetic Inference
• Two typical problems
• Genealogies ? species trees
• How to read a tree
• Parts of a tree
• Rotation
• Rooting
• Reconstruction
• Lots of possible trees
• Alignment

• Tree building methods
• Distance based
• UPGMA, Neighbor Joining, Minimum Evolution
• Character based
• Maximum parsimony
• Maximum likelihood
• Types of characters
• Synapomorphies
• Autapomorphies
• Symplesiomorphies
• Potential problems
• Homoplasy and saturation
• Bootstrapping