Lecture 15: Reconstruction of Phylogeny

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Lecture 15 Reconstruction of Phylogeny

• Adaptive characters
• May indicate derived character
• (special adaptation)
• e.g. Raptorial forelegs in mantids
• May indicate convergent evolution
• e.g cacti euforbs

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Adaptive Characters

• Must ask
• Are characters independent?
• What constitutes a single character?
• e.g. paedomorphosis in salamanders
• many traits ? monophyletic
• single trait ? polyphyletic
• Different characters give different trees!

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Unrooted Trees

• no common ancestor
• no time implied
• similarity only
• compatible with
• 2(s) 3 rooted trees

A B C D
A B C D
B A C D
D C B A
C D B A
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Topologies

• total of topologies
• (2n 3)! / (2 n - 2 (n - 2)!)
• for 5 spp 105 topologies
• for 15 spp 213,458,046,676,875 topologies!!

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Rooted Trees

• Show common ancestor
• Imply time

Time
Common Ancestor
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Making a Rooted Tree

• Method 1 (morphological characters)
• 1) Choose independent characters
• 2) eliminate analogies
• 3) differentiate ancestral from derived
  homologies
• 4) parsimony
• Eliminate uninformative characters
• ? compatible with all trees

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Example Sunfish (Centrarchidae)
black crappie warmouth
outgroup largemouth bass
bluegill redear
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1) Identify independent characters transitions
Transition
a Doubling of pyloric caeca
b Reduced number of trunk scales
c Loss of 2-3 vertebral centra
d Loss of 1-2 pectoral fin rays
e Loss of subocular bar
f Enlarged levator muscle
g Addition of dorsal fin spot
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2) Construct character matrix
a b c d e f g
Bass (outgroup) 0 0 0 0 0 0 0
Crappie 1 1 0 0 0 0 0
Warmouth 1 1 1 1 0 0 0
Bluegill 1 1 1 1 1 0 1
Redear 1 1 1 1 1 1 0

• characters f g are not shared
• (not informative)

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Most Parsimonious Tree
a b c d e f g
Bass (outgroup) 0 0 0 0 0 0 0
Crappie 1 1 0 0 0 0 0
Warmouth 1 1 1 1 0 0 0
Bluegill 1 1 1 1 1 0 1
Redear 1 1 1 1 1 1 0
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Method 2

• 1) parsimony ? unrooted tree
• 2) determine polarities ? root tree (outgroup
  analysis)

outgroup analysis places root here
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Using Molecular Sequencesfor Phylogenies

• molecular sequences characters
• Direct
• 1) nucleotide sequence of homologous genes
• 2) a.a. sequence of polypeptide

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Indirect Molecular Analysis

• DNA hybridization
• stability similarity
• 2) allozyme frequency genetic distance
• 3) immunological distance
• affinity of antibody to protein of reference sp.

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Parsimony Analyses

• Similar to morphological
• Goal minimum of changes in sequence
• can estimate branch lengths (time)

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More parsimony

• Not all substitutions are equal
• Transitions
• pur? pur pyr ? pyr
• i.e. A ? G C ? T
• Transversions
• pur ? pyr
• i.e. A, G ? C, T
• Transitions gtgt Transversions
• (DNA repair mechanisms)
• Weight analysis (many options for this)

Kimura 2-parameter matrix
A C G T
A 0.6 0.1 0.2 0.1
C - 0.6 0.1 0.2
G - - 0.6 0.1
T - - - 0.6
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Maximum Likelihood

• Finding the tree mostly likely (highest
  probability) to give the character set

A
(0.25)
Assume each site evolves independently
0.2
0.1
G
0.6
0.2
C
G
A
probability 0.25 X 0.1 X 0.2 X 0.2 X 0.6
0.0006
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Neutral Theory of Molecular Evolution

• Most nucleotide substitutions polymorphisms are
  result of selectively neutral mutations (silent
  substitutions)
• Selection doesnt have to be neutral
• But, drift must be more important
• Controversy resulted but

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Molecular Clock

• Prediction from neutral theory
• single gene evolves at constant rate
• Even if neutral theory doesnt hold
• selection coefficient averaged over time ?
  linear rate
• Neutral theory important null model

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Tests of Molecular Clocks

• 1) Plot molecular divergence against fossil
  record
• 2) Relative rate test independent of fossil
  record
• - outgroup comparison all in group equal
  distance to outgroup

C to E D to E C to E c b e D to E d b
e if rate of substitution constant c d
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Substitution Rates

• Substitution rates may vary if
• selection coefficients vary
• diffns in popn size
• diffns in generation time
• diffns in exposure to mutagens
• diffns in metabolic rate etc.

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• Sometimes molecular morphological data give
  different results!
• e.g. Chachalaca
• Neotropical bird
• Morphology behaviour like a chicken
• 4 proteins like a duck??