Lecture 20.docx

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Ecology & Evolutionary Biology
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Stephen Wright

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Lecture 20:  Identification of Genes Subject to Adaptive Evolution (HKA Test):  Different genes are compared to each other, and for different genes is the ratio of divergence to polymorphism.  Contrasts the ratio of polymorphism to divergence at silent sites for two or more genes.  Neutral theory: P and D ratio should give an estimate of Ne, the Ne should be the same under neutral model ratio. Is the Ne the same throughout the genome? Selective sweep will reduce the Ne and coalesce time  Significant departure from neutral expectation consistent with selection acting at one or more genes  Positive selection: P/D < neutral genes, selective sweep, reduced diversity surrounding the selected site  Balancing selection: P/D > neutral genes, increase diversity surrounding the selected site. However if it persist for really long time, that means a lot of time for recombination to happen and that means that any linked neutral sites that are with the functional allele should eventually recombine with the background, balancing selection is hard to detect. Since time can break down the hitchhiking effect.  Balancing Selection is really rare  Balancing Selection at the ABO blood group: Look at the functional regions where the AA polymorphisms are. Human B allele is more similar to gorilla B allele than to the human A and O allele, elevated diversity where polymorphism is maintained ever since we diverged from the species. Look at narrow regions.  Role of recombination rate in structuring genetic diversity: Natural selection at linked loci  High recombination: if there is an advantageous mutation, it is going to spread however there is not much sweep signal. Spread  Sweep  Recombine  Low recombination: if there is an advantageous mutation, there will be more selective sweep.  Thus if positive selection is happening often enough, there will be a positive correlation between the rate of recombination and amount of neutral variants. High recombination = higher diversity, lower recombination = lower diversity  Signal of Genome-Wide Linked Selection: higher recombination will have 1) slight correlation divergence between species, 2) stronger correlation with diversity and 3) positive correlation with diversity/divergence  Divergence produce a control to the neutral mutation rate, to make sure that high recombination are not due to higher mutation rate  Signal of Genome-Wide Linked Selection:  If genes are subject to a lot of positive selection, as you get closer to the genes we expect neutral diversity to drop. Selective sweep for NS AA changes, stronger regions of low recombination and as it gets closer to genes. Positive selection?  Purifying selection: an alternative to positive selection. If deleterious mutations appearing every generation, high recombination are eliminating deleterious mutations and that should have little effect on linked neutral diversity. Low recombination and deleterious mutation that will eliminate all the linked neutral variation. Purifying selection in low recombination is reducing the Ne of alleles, and neutral variation and negative selection can lead to this correlation in diversity also.  Purifying and Positive Selection can both lead to a correlation with Ne and recombination  Recent study examining patterns of diversity in relation to recombination rates suggests that it can be explained by purifying selection  Testing Genome-Wide Positive Selection: Linking M-K type tests with hitchhiking  M-K: Excess of NS divergence between species  Hitchhiking: signals of low diversity  Sella: Lineage specific changes in one species, the AA fixations that
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