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EVOLUTION OF GENOMES C-value paradox: - in certain cases, lack of correlation between morphological complexity and genome size “[For] some commonly cited extreme values for amoebae... considerable uncertainty about the accuracy of these measurements and the ploidy level of the species...” Gregory Nature Rev. Genet. 6:699, 2005 Table 8.3 & Alberts Fig.1.38 Genic fraction vs. genome size Function of non-genic DNA in eukaryotes? Composition of human genome Gregory Nature Rev. Genet. 6:699, 2005 Fig. 8.15 Genic contribution to expansion in genome size Hartwell Fig. 21.11 Scenario showing possible events following whole genome duplication 26 genes on 2 chromosomes 36 genes on 4 chromosomes Figure 8.7 Evidence for whole genome duplication in ancestor of yeast ~ 100 million years ago? Kellis Nature 428:617, 2004 see also Fig.8.7 Duplication of entire genome much more common in plant evolution than in animal evolutionary history For chromosome number >12, even numbers much more common than odd numbers Frequency distribution of haploid chromosome numbers in dicot plants Griffiths 7th ed, Fig. 26-12 Evolution of tandem arrays of eukaryotic genes Over evolutionary time expect independent mutations to accumulate … but often observe all copies identical (or nearly so) - evolve “in concert” Fig. 6.25 Concerted evolution - maintenance of homogeneous nt sequences among multi-gene family members (especially when in tandem arrays) - exchange of sequence info so members kept very similar - eg. eukaryotic ribosomal RNA gene copies Fig. 6.26 Possible evolutionary scenarios resulting in “homogenized” tandem array 1. Beneficial mutations fixed by positive selection -but spacers with no known function show concerted evolution 2. Recent amplification 3. Mutation in one repeat “spreads” to others Fig. 6.27 Unequal crossing over - homologous recombination between misaligned arrays - change in number of repeats Fig. 6.31 Example of unequal crossing over in human b-globin array “Lepore” b - thalassemia misalignment (of sister chromatids during mitosis in germ cell or homologous chromosomes during meiosis…) Page & Holmes Fig. 3.15 Gene conversion - non-reciprocal recombination - no change in gene copy number - can occur in dispersed as well as tandem repeats - example of yeast mating-type switching Fig. 6.29 Watson Fig. 10-21 Example of concerted evolution in primate b -globin gene cluster Exon 3 Exons 1 & 2 How do you interpret these data? ... and panel 3 of Fig.6.33 ? Fig. 6.33 Resurrection of ribonuclease pseudogene by gene conversion PR pancreative ribonuclease SR seminal ribonuclease … in some bovine species, gene conversion of y SR with PR gene, so functional again What is predicted status of SR gene in giraffe? or sheep? Fig. 6.33 Factors affecting rate of concerted evolution (p. 317-320) 1. Number, arrangement, structure of repeats - non-coding regions evolve more rapidly, and if divergent enough may “escape” homogenization 2. Functional requirement - selective advantage of high amount of same gene product vs. diversity 3. Population size - time for variant to be fixed or eliminated Evolutionary implications of concerted evolution (p.320-322) “molecular drive” 1. Spread of advantageous mutations (or removal of deleterious ones) 2. Retards paralogous gene divergence (preventing redundant copy from becoming non-functional) 3. Generates increased genetic variation at a particular locus within a population Methodological implications - degree of sequence divergence of paralogous genes undergoing concerted evolution is not correlated with evolutionary time so gene duplications can appear younger than they really are…