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Chapter Summary

  1. The development of techniques for sequencing large amounts of genetic data made whole-genome sequencing possible. With over a hundred eukaryotic genomes and over a thousand prokaryotic genomes fully sequenced as of 2010, we now have the data to study the content, structure, and organization of entire genomes and to consider how genomes themselves evolve.
  2. Genome sizes vary dramatically across organisms. Viruses tend to have the smallest genomes, followed by prokaryotes, unicellular eukaryotes, and then multicellular eukaryotes.
  3. Within multicellular eukaryotes, genome size does not correlate closely with organismal complexity. Much of the variation in eukaryotic genome size results from variation in the amount of noncoding DNA.
  4. Viral genomes may be a single chromosome or a series of chromosomal segments. They are extremely compact, ranging in size from about 2 kb to just over 1 Mb, and they often achieve additional compression by means of overlapping coding regions. Some viral genomes, particularly those of RNA viruses, encode fewer than a dozen proteins.
  5. Prokaryotic genomes are often organized as a single circular chromosome, supplemented by accessory genetic elements such as plasmids. They tend to be relatively compact, ranging in size from roughly 0.6 Mb to over 10 Mb.
  6. Bacteria engage in frequent horizontal gene transfer by the processes of transduction, transformation, and conjugation. Horizontal gene transfer is an important source of genetic variation in prokaryotic populations, and appreciable fractions of some bacterial genomes have been acquired by horizontal transfer.
  7. In most organisms, the frequencies of GC versus AT base pairs and the frequencies of alternative synonymous codon triplets are not equal. GC content and codon usage bias can tell us about the evolutionary history of genes within genomes; for example, they allow us to identify regions of the genome that have been acquired by horizontal transfer.
  8. Eukaryotic nuclear genomes vary tremendously in size, from just a few megabases in some unicellular organisms to more than 100,000 Mb in some large multicellular organisms.
  9. Typically, only a small fraction of a eukaryotic genome is composed of protein-coding sequence. The remainder is made up of introns, transposons, and other genetic elements; their distribution across the genome is the result of both selective and nonselective processes.
  10. Transposons are selfish genetic elements that facilitate their own replication and movement within the genome of their eukaryotic "hosts." By moving and replicating within genomes, transposons increase their chance of being represented in the next generation. The action of transposons is an important driver of mutation, including changes in chromosome structure.
  11. In addition to protein-coding regions and transposons, eukaryotic chromosomes include important structural regions such as centromeres and telomeres. Again, the structure of these components of the genome is fashioned by a combination of selective and nonselective evolutionary processes.
  12. Natural selection leaves a statistical signal on the genome; genes that have been under selection can be identified by genome-wide scans.
  13. The Ka/Ks ratio measures the relative frequency of nonsynonymous to synonymous substitutions. Ka/Ks values greater than 1 indicate a history of positive selection, whereas very low Ka/Ks values indicate a history of purifying selection.
  14. Recent natural selection creates extended haplotype blocks in which linkage disequilibrium has not yet been removed by recombination. These extended haplotype blocks can help us identify not only loci under selection, but also which alleles have been favored at these loci.