Parsimony methods

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# Parsimony methods - PowerPoint PPT Presentation

Parsimony methods. the evolutionary tree to be preferred involves ‘ the minimum amount of evolution ’. Reconstruct all evolutionary changes along any possible tree Find tree with least number of changes. Edwards &amp; Cavalli-Sforza 1963. . A simple example.

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Presentation Transcript

Parsimonymethods

the evolutionary tree to be preferred involves ‘the minimum amount of evolution’

• Reconstruct all evolutionary changes along any possible tree
• Find tree with least number of changes

Edwards & Cavalli-Sforza 1963.

A simple example

Evolutionary changes: 0 1 and 1  0

Root: 0 or 1

A simple example

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A simple example

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A simple example

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A simple example

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A simple example

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A simple example

this first hypothesis requires a total of 9 evolutionary changes

total number of changes required = 9.

A simple example

colour indicates

derived status ( =0, =1)

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A simple example

this alternative hypothesis requires but 8 evolutionary changes.

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homoplasy: the same status arises more than once on the tree

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A simple example

homoplasy: the same status arises more than once on the tree

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Rooted and unrooted trees

yet ‘another’ hypothesis requiring but 8 evolutionary changes

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A simple example

the two rooted hypotheses requiring 8 changes yield similar unrooted trees

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Rooted and unrooted trees

unrooting trees reduces the number of alternative solutions

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Rooted and unrooted trees

unrooting trees reduces the number of alternative solutions

Methods of rooting a tree

Use an outgroup

Use a molecular clock

Methods of rooting a tree

Use an outgroup

Ape3

Ape4

Ape1

root must be along this lineage

Ape2

Monkey

Methods of rooting a tree

only the root is equidistant to all tips

Use an outgroup

Use a molecular clock

Branch lengths

branch lengths are computed as the sum of all character changes (each divided by # alternatives)

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the sum of all branch lengths is called the ‘length’ of the tree

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But how to…

count the number of changes in large datasets

reconstruct states at interior nodes

search among all possible trees for the most parsimonious one

handle DNA sequences (4 states)

handle complex morphological characters

justify the parsimony criterion

evaluate statistically different trees