Molecular evolutionary analysis
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Molecular Evolutionary Analysis. Dan Graur. 1959. Q: We may ask the question where in the now living systems the greatest amount of information of their past history has survived and how it can be extracted? A: Best fit are the macromolecules which carry the genetic information.

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Molecular Evolutionary Analysis

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Molecular evolutionary analysis

Molecular Evolutionary Analysis

Dan Graur


Molecular evolutionary analysis

1959


Molecules as documents of evolutionary history

Q: We may ask the question where in the now living systems the greatest amount of information of their past history has survived and how it can be extracted?

A: Best fit are the macromolecules which carry the genetic information.

Molecules as documents of evolutionary history


Molecular evolutionary analysis

Palimpsest


Molecular evolutionary analysis

“Searching for an objective reconstruction of the vanished past is surely the most challenging task in biology.”

“In one sense, everything in biology has already been ‘published’ in the form of DNA sequences of genomes.”

1991

Sydney Brenner


Molecular evolutionary analysis

Assumption:

Life is monophyletic


Molecular evolutionary analysis

ancestor

descendant 1

descendant 2

Any two organisms share a common ancestor in their past


Molecular evolutionary analysis

(5 MYA)

ancestor

Some organisms have very recent ancestors.


Molecular evolutionary analysis

(18 MYA)

ancestor

Some have less recent ancestors…


Molecular evolutionary analysis

(120 MYA)

ancestor

…and less recent.


Molecular evolutionary analysis

(1,500 MYA)

ancestor

But, any two organisms share a common ancestor in their past


Molecular evolutionary analysis

The differences between 1 and 2 are the result of changes on the lineage leading to descendant 1+those on the lineage leading to descendant 2.

descendant 1

descendant 2

ancestor


Step 1 sequence alignment

Step 1:Sequence Alignment


Step 2 translating number of differences into number of changes ste p s

Step 2: Translating number of differences into number of changes (steps).


Molecular evolutionary analysis

Example:

1. the number of nucleotide substitutions per site between two non-coding sequences (K) according to Kimura’s two parameter model


Molecular evolutionary analysis

Example:

2. the number of synonymous nucleotide substitution per synonymous site between two coding sequences (KS) according to Jukes and Cantor’s one parameter model


Molecular evolutionary analysis

Example: the number of nonsynonymous nucleotide substitution per nonsynonymous site between two coding sequences (KA) according to Jukes and Cantor’s one parameter model


Molecular evolutionary analysis

Ki = number of substitutions (or replacements) of type i per number of sites of type i per 2T

Ki


Molecular evolutionary analysis

r = rate of substitution = number of

substitutions per site per year

Ki


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