Friday, November 4, 2011

Paper : genome evolution and adaptation in a long-term experiment with Escherichia coli According to Darwin, adaptation is a gradual process. The rate of adaptation is variable and diverse whose reason is unknown. It ’s well known that genomic changes are linked with adaptation, but exact relationship remain elusive. With imperfect knowledge of organism’s genetics and complicated environment, it’s difficult to make clear conclusion. Thus, this paper designed a experiment using tractable model organisms in controlled laboratory environments, in order to minimize the confounding factors and complexity. Moreover, they sequence complete genomes to find the mutations responsible for particular adaptation. In addition, it’s possible to find out whether the dynamics of genomic and adaptive evolution are coupled very tightly or only loosely.

In the first step, they sequenced the genomes of E. coli clones sampled at generations 2K, 5K, 10K, 20K and 40K. Through 20K generations , 45 mutations were identified, moreover, the number of mutational differences between accumulated in a ncestral and evolved genomes accumulated in a near-linear fashion over this period. Neutral evolution should accumulate by drift at a uniform rate and are not beneficial. However, in this experiment,they found fitness trajectory shows profound adaptation that is not linear. Particularly, the rate of fitness improvement decelerates over time indicating the rate of genomic evolution to decelerate. Under three scenarios, they explore the relationship between rates of adaptation and genomic evolution. The model predicts declining rates of both adaptive and genomic evolution or alternatively, no deceleration in either trajectory.

In the second step, they proved that the mutations are dominantly beneficial using four lines of evidence.1) The results challenged drift hypothesis : the probability of observing no synonymous substitutions is only 0.07%. On the basis of the probability, the mutations are not neutral ;2) In most cases, the evolved alleles differed between the population ;3) almost mutations in the earlier clones were transmitted in subsequent generations, which is against the drift hypothesis ;4) the derived allele is more competent in competition, which contrasts neutral drift hypothesis. Up to sum, mutations offer advantage in the same environment and beneficial substitutions are dominant. Preponderance of neutral substitutions can not explain the rate disparity.

In the study, they observed that in later generations, rate of genomic evolution is elevated, typically, the frequence of mutT gene mutation is much higher in 40K than in the earlier mutations. They sequenced the site of the mut T frameshift in clones and found the appearance of mutation took place in generation 26 500 and became dominant soon. However, unlike before 20 000 generations, only a small fraction of new mutations is beneficial. In order to verify this observation, they examine the proportion of synonymous mutations after the mutator phenotype evolved to determine if it is consistent with a random distribution across sites. Then they found in the 40 K genome the frequency of the new base substitutions is lower than the earlier genome, indicating a high proportion of late-arising no-changes are also neutral or nearly so under the conditions of the evolution experiment.

In the end, they conclude that mutations accumulated at a near-constant rate even as fitness ganis decelerated over the first 20 000 generations. On the other hand, the rate of genomic evolution accelerated markedly when a mutator lineage became established later.

Throughout the paper, I think this paper provided a good model to explore the long-term dynamic coupling between genome evolution and adaptations, such as the effects of clonal interference, compensatory adaptation, and changing mutation rates. But as far as I am concerned, the author should display more figures to demonstrate their opinion. I have impression that too much word but not vivid figure is used to present.

Barrick, J., Yu, D., Yoon, S., Jeong, H., Oh, T., Schneider, D., Lenski, R., & Kim, J. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli Nature, 461 (7268), 1243-1247 DOI: 10.1038/nature08480

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