Richard Wolfe
CS427 PBIO 427
Abstract
May 6, 2011
Genome Evolution
Adaptation is a change that improves an organism’s chances of survival and reproduction. All
mutations, or changes, to the DNA are not necessarily beneficial. In order to examine the tempo and
mode of genomic evolution, this article looks at the genomic differences of 40,000 generations of E.
coli. The genomes of these E. coli were sequenced at 2,000, 5,000, 10,000, 15,000, 20,000 and 40,000
generations. These genomes were then compared to the genome of the ancestral strain. It took nearly 20
years to produce 40,000 generations and this experiment is still continuing. A deletion is when a
nucleotide is removed from the genome and an insertion is when a nucleotide is added. Also, an entire
sequence can be added to the genome. A section can also be removed, inverted, and then reinserted into
the genome. After 20,000 generations there were 45 mutations that had occurred, including 29 single
nucleotide polymorphisms (SNPs) and 16 deletions, insertions, and other polymorphisms. Because of
the number of mutations found in coding regions were beneficial and similar mutations were found in
the same genes of all 12 populations, it is suggested that selection is the basis of these mutations. Also,
all of the mutations that occurred in early generations remained in the later generations. Also, it was
determined that isogenic strains with ancestral and derived alleles showed a significant fitness
advantage. After 26,000 generations, a greatly elevated rate of genomic evolution occurred. At 40,000
generations the genome contained 627 SNP and 26 deletions, insertions and other polymorphisms. Also
the 40,000 generation genome was 1.2% smaller than the ancestral genome. Unlike the mutations
before 20,000 generations, 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.