Why phylogeny should be considered

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Why phylogeny should be considered
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Sperm competition in primates
But, species are not independent!
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Major Available Methods

• Linear/square-change Parsimony
• Independent contrasts
• Phylogenetic Autocorrelation
• Generalized Least Squares
• Bayesian stochasic mapping

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Linear/Square-change parsimony
b
c
d
a
Tips n Branches 2n-2
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Independent contrasts
b
c
d
a
Tips n Contrasts n-1
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Independent Contrasts
value of x
value of y

24
30
40
20
9
14
20
7
22
35
8
17
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Independent Contrasts

• Calculations
• by convention, contrasts for independent variable
  are positive
• contrasts for dependent variable may be positive
  or negative
• correlate contrasts
• no correlation no causal relationship
• significant correlation causal relationship
  (negative or positive)

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Independent Contrasts
value of x

value of y
30
40
24
20
20
9
14
7
22
35
8
17
x y d1 2 4 d2 6 10 d3 9 13
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Independent Contrasts
10
x y d1 2 4 d2 6 10 d3 9 13
y contrast
0
15
x contrast
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Assumptions of independent contrasts

• We know branch lengths
• Traits values evolve by Brownian motion
• Needed to calculate ancestral states
• Needed to accommodate error in the estimation of
  ancestral states

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Expected change in time, t, is 0 with var. t
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Assumptions of independent contrasts

• We know branch lengths
• Traits values evolve by Brownian motion
• Strength of correlation is the same across the
  tree

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Broader objections

• The tip correlation may be what we care about
• No characters evolve by Brownian motion
• The assumption of a constant correlation is
  biologically unrealistic

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