Every cell protects the integrity of the genome. DNA is chemically stable, and the cell defends it with various protective and repair devices. When genes are altered, the consequences for the cell might not be disastrous: the system as a whole is robust, and the redundancy of the genetic code provides a buffer. So, in eukaryotes, does the abundance of "junk" DNA. Nevertheless, DNA can change in a number of ways.

  • Point mutations are additions, deletions or substitutions of single bases, or inversions of pairs of bases. These are the most common kind of gene alteration, and the kind with (generally) the least far-reaching effects in terms of evolution.
  • Whole genes can be excised and deleted. Sometimes excised genes are re-inserted back to front (inverted). These are much less common changes but have greater evolutionary impact.
  • Genes can be moved to a different part of the genome (transposed), perhaps because of old retrovirus residues. They can even be moved from one organism to another, crossing species boundaries. These are rare events but their effects are cumulative and potentially dramatic.
  • Numerous repeats of a single gene, or of a short DNA sequence, can be inserted into the genome. This is known as amplification. When a short, meaningless DNA sequence is reiterated the result is a length of simple-sequence DNA. Simple-sequence DNA is "junk", but amplified genes can be essential for the cell's viability, for example ribosomal and histone genes.
  • Most eukaryotic genes consist of one or more coding sequences (exons) separated by non-coding segments (introns). Exons might sometimes be moved from one gene to another to create novel genes and hence novel proteins. This process is known as exon shuffling.

These changes can alter organisms subtly or markedly. If a developmental "master gene" is modified, the effect can be particularly dramatic. These "master genes" encode transcription factors and control the expressions of many other genes, so significant changes in them can alter the entire course of development, perhaps creating a novel sort of organism.

Over thousands of millions of years, cumulative changes in DNA have resulted in the diversification of countless species. One result of the revolutionary progress in molecular biology during the last quarter of the twentieth century was a revision of the "tree of life". Before the 1970s, the historical connections among species were reconstructed mainly from comparative anatomical and embryological evidence and the fossil record. Now there is ever-increasing reliance on comparative gene sequencing. This modern, molecular biological, approach gives results that are reassuringly consistent with those of the traditional approach. However, comparative gene sequencing allows greater refinement of detail and has provided insights into early life on Earth, even into times before the fossil record began.

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