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This chapter explores how genomes evolve through mutation, recombination, and comparisons between different organisms. It discusses the origins of genomes, acquisition of new genes, noncoding DNA, and the human genome's evolution over the past five million years.
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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.
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.
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.
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 (吡喃糖基) version of RNA and peptide nucleic acid are more stable.
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.
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.
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.
Genome evolution also involves rearrangement of existing genes
18.2.2 Acquisition of new genes from other species • Lateral gene transfer; • Horizontal gene transfer • Ways?
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.
18.3.2 the origin of introns • Length: energy and time cost, genomic design, mutational forces • Number: mRNA-mediated intron loss
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.
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 aren’t. • 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 biologists—whether they study morphology, behavior, or genetics—whose research is helping reveal how evolution works.
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 Genetics4: 865-875. • Li, W.H., J. Yang, X. Gu (2005). Expression divergence between duplicate genes. Trends in Genetics 21: 602-607.
