Introduction Adaptation – a change that improves an organisms chances of survival and reproduction

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Introduction

Adaptation – a change that improves an organisms chances of survival and reproduction
Mutations are not necessarily beneficial.
In order to examine the tempo and mode of genomic evolution, 40,000 generations of E.coli were sequenced.
The genomes were sequenced at 2K, 5K, 10K, 15K, 20K and 40K generations.
These genomes were compared to the ancestral stain.
Almost 20 year long experiment.
Glucose was limiting nutrient.
12 populations

Introduction

Deletion – nucleotide removed
Insertion – nucleotide added
IS insertion – insertion sequence – entire sequence added
Inversion – section removed, inverted, reinstalled
45 mutations in 20K generation
Include 29 single-nucleotide polymorphisms SNPs inserted
Include 16 deletions, insertions and other polymorphisms DIPs

Mutations Found

Rates of Genomic and Fitness Improvement

Discussion

Genomic evolution is near-linear.
Normally this would suggest neutral evolution, mutations do not matter.
Fitness is not linear and the rate of improvement slows down over time.
Indicates that the rate beneficial mutations are occuring is declining and/or their their average benefit is becoming smaller.
These effects should cause the rate of genomic evolution to decelerate but, it remains the same.

Discussion

Hypothesis: only a small fraction of all substitutions are beneficial and most are neutral. The beneficial substitutions occur in early generations and adapt to the conditions of the experiment. The neutral mutations occur later and the rate of fitness improvement slows down.
Evidence to reject hypothesis:
1. You would expect to find mutations that did not change the protein sequence but, all 26 point mutations found in coding regions (22 in 20K) changed the protein sequence.
2. You would not expect to see mutations in the same genes in the other 11 populations if due to random drift but if by selection then same genes would be mutated because they evolved in same environments.

Discussion

3 cases where all 11 populations have substitutions in same gene
9 genes have mutations in other lines
Only 2 cases where no mutation has occured

Discussion

3. You would expect many mutations would not become fixed but, almost all mutations that occur early are present in the rest of the generations.
4. Strains with neutral mutations would have no fitness advantage but, isogenic strains with ancestral and derived alleles show a significant advantage.

40K Genome Analysis

After 26K generations a greatly elevated rate of genomic evolution occured.
40K genome contained 627 SNP and 26 DIP mutations
40K genome 1.2% smaller than ancestor.
Unlike the mutations before 20K, only a small number of these later mutations are beneficial

References

1. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF; Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. October 2009, 461:1243-1247.

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Introduction Adaptation – a change that improves an organisms chances of survival and reproduction

Introduction

Adaptation – a change that improves an organisms chances of survival and reproduction

Mutations are not necessarily beneficial.

In order to examine the tempo and mode of genomic evolution, 40,000 generations of E.coli were sequenced.

The genomes were sequenced at 2K, 5K, 10K, 15K, 20K and 40K generations.

These genomes were compared to the ancestral stain.

Almost 20 year long experiment.

Glucose was limiting nutrient.

12 populations

Introduction

Deletion – nucleotide removed

Insertion – nucleotide added

IS insertion – insertion sequence – entire sequence added

Inversion – section removed, inverted, reinstalled

45 mutations in 20K generation

Include 29 single-nucleotide polymorphisms SNPs inserted

Include 16 deletions, insertions and other polymorphisms DIPs

Mutations Found

Rates of Genomic and Fitness Improvement

Discussion

Genomic evolution is near-linear.

Normally this would suggest neutral evolution, mutations do not matter.

Fitness is not linear and the rate of improvement slows down over time.

Indicates that the rate beneficial mutations are occuring is declining and/or their their average benefit is becoming smaller.

These effects should cause the rate of genomic evolution to decelerate but, it remains the same.

Discussion

Hypothesis: only a small fraction of all substitutions are beneficial and most are neutral. The beneficial substitutions occur in early generations and adapt to the conditions of the experiment. The neutral mutations occur later and the rate of fitness improvement slows down.

Evidence to reject hypothesis:

1. You would expect to find mutations that did not change the protein sequence but, all 26 point mutations found in coding regions (22 in 20K) changed the protein sequence.

2. You would not expect to see mutations in the same genes in the other 11 populations if due to random drift but if by selection then same genes would be mutated because they evolved in same environments.

Discussion

3 cases where all 11 populations have substitutions in same gene

9 genes have mutations in other lines

Only 2 cases where no mutation has occured

Discussion

3. You would expect many mutations would not become fixed but, almost all mutations that occur early are present in the rest of the generations.

4. Strains with neutral mutations would have no fitness advantage but, isogenic strains with ancestral and derived alleles show a significant advantage.

40K Genome Analysis

After 26K generations a greatly elevated rate of genomic evolution occured.

40K genome contained 627 SNP and 26 DIP mutations

40K genome 1.2% smaller than ancestor.

Unlike the mutations before 20K, only a small number of these later mutations are beneficial

References

1. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF; Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. October 2009, 461:1243-1247.