Chapter 18 How Genomes Evolve

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Chapter 18How Genomes Evolve
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• To see the evolutionary histories of genomes
• We must combine our understanding of mutation and
  recombination with comparisons between the
  genomes of different organisms in order to infer
  the patterns of genome evolution that have
  occurred.
• Clearly, this approach is imprecise and
  uncertain, but it is based on a surprisingly
  large amount of hard data and we can be
  reasonably confident that, at least in outline,
  the picture that emerges is not too far from the
  truth.

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18.1 Genomes the First 10 Billion Years
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18.1.1 The origins of genomes

• The first biochemical systems were centered on
  RNA ribozymes, and recently Riboswitches.
• In the test tube, synthetic RNA molecules have
  been shown to carry out other biologically
  relevant reactions such as synthesis of
  ribonucleotides, synthesis and copying of RNA
  molecules and transfer of an RNA-bound amino acid
  to a second amino acid forming a dipeptide, in a
  manner analogous to the role of tRNA in protein
  synthesis.

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The first DNA genomes

• How did the RNA world develop into the DNA world?
  The first major change was probably the
  development of protein enzymes, which
  supplemented, and eventually replaced, most of
  the catalytic activities of ribozymes
• Maynard Smith J. and Szathmáry E. 1995. The Major
  Transitions in Evolution. WH Freeman, Oxford.
• Forterre, P. 2005. The two ages of the RNA world,
  and the transition to the DNA world a story of
  viruses and cells. Biochimie 87 793-803.

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How unique is life

• Life arose on more than one occasion, even though
  all present-day organisms appear to derive from
  single origin.
• The single origin is indicated by the remarkable
  similarity between the basic molecular biological
  and biochemical mechanisms in bacterial,
  archaeal, and eukaryotic cells.
• Advantage in natural selection.
• A pyranosyl (????) version of RNA and peptide
  nucleic acid are more stable.

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18.2 Acquisition of New Genes

• Morphological evolution was accompanied by genome
  evolution.
• There seem to have been two sudden bursts when
  gene numbers increased dramatically.
• The first of these expansions occurred when
  eukaryotes appeared about 1.4 billion years ago,
  and involved an increase from the 5000 or fewer
  genes typical of prokaryotes to the 10 000 or
  more seen in most eukaryotes.
• The second expansion is associated with the first
  vertebrates, which became established soon after
  the end of the Cambrian, with each
  protovertebrate probably having at least 30 000
  genes, this being the minimum number for any
  modern vertebrate, including the most 'primitive'
  types.

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The origin of new genes

• By duplicating some or all of the existing genes
  in the genome.
• By acquiring genes from other species.
• By recombination of different genes.
• By do novo creation of genes from non-gene
  sequences like repetitive sequences.

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18.2.1 Acquisition of new genes by gene
duplication
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Genome sequences provide extensive evidence of
past gene duplications

• Concerted evolution by gene conversion.
• Britten, R.J. 2006. Almost all human genes
  resulted from ancient duplication. PNAS 103
  19027-19032.

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Whole genome duplication is possible
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Genome evolution also involves rearrangement of
existing genes
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18.2.2 Acquisition of new genes from other species

• Lateral gene transfer
• Horizontal gene transfer
• Ways?

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18.3 Noncoding DNA and genome evolution

• A function that has not jet been identified.
• A possibility is that noncoding DNA has no
  function but is tolerated by a genome because
  there is no selective pressure to get rid of it.

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18.3.1 Transposable elements and genome evolution
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18.3.2 the origin of introns

• Length energy and time cost, genomic design,
  mutational forces
• Number mRNA-mediated intron loss

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18.4 The human genome the last five million years
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15.4. The Human Genome the Last 5 Million Years
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• The genome data confirm our close kinship with
  chimps We differ by only about 1 in the
  nucleotide bases that can be aligned between our
  two species, and the average protein differs by
  less than two amino acids. But a surprisingly
  large chunk of noncoding material is either
  inserted or deleted in the chimp as compared to
  the human, bringing the total difference in DNA
  between our two species to about 4.
• The traits that make us human sparse body hair,
  upright gait, the big and creative brain.
• This year, several groups published evidence that
  natural selection has recently favored a handful
  of uniquely human genes expressed in the brain,
  including those for endorphins and a sialic acid
  receptor, and genes involved in microcephaly.

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Evolutionary studies beneift your health

• Such evolutionary breakthroughs are not just
  ivory-tower exercises they hold huge promise for
  improving human well-being.
• Take the chimpanzee genome. Humans are highly
  susceptible to AIDS, coronary heart disease,
  chronic viral hepatitis, and malignant malarial
  infections chimps arent.
• Darwin focused on the existence of evolution by
  natural selection the mechanisms that drive the
  process were a complete mystery to him.
• But today his intellectual descendants include
  all the biologistswhether they study morphology,
  behavior, or geneticswhose research is helping
  reveal how evolution works.

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Questions for further study

• Translate the following reviews
• Long, M., E. Betrán, K. Thornton, and W. Wang
  (2003). The origin of new genes glimpses from
  the young and old. Nature Reviews Genetics 4
  865-875.
• Li, W.H., J. Yang, X. Gu (2005). Expression
  divergence between duplicate genes. Trends in
  Genetics 21 602-607.