Lecture 19.docx

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University of Toronto St. George
Ecology & Evolutionary Biology
Stephen Wright

Lecture 19:  Testing for Adaptive Evolution: 1. Ka/Ks >1 2. Ka/Ks > Pa/Ps 3. Neutral Polymorphism: does not require recurrent adaptive evolution, for unique (a single) and recent events of adaptive evolution. Not on direct targets.  Effect of Positive Selection on Neutral Polymorphism 1. Reduction in Neutral Variation: Selective Sweep where positive mutation spreads, and genetic hitchhiking and thus reduce in neutral variations 2. Increase in linkage disequilibrium: strong haplotype set of SNPs on a single chromosome of a chromosome pair that is statistically associated. 3. Shift in SNP frequencies: excess of rare neutral polymorphisms, reduction in diversity due to elimination of common neutral variations. 4. Increased differentiation among populations: higher Fst, fraction of variation between populations. Even if the 2 populations are both experiencing positive selection , there might also be an increase in differentiation if the advantageous mutations are happening independently  Distinguishing Natural Selection vs. Demographic history: Genome-wide patterns of diversity  Demographic effects should act genome-wide in a consistent manner  Natural selection causes inconsistencies among genes in their patterns of diversity  How do we apply it? Characterize genomic distribution of patterns of genetic diversity. Are there inconsistencies across genes in their history or a historical model?  Sharp drop in level in diversity and excess of rare variants (reduced variability) and big increase in LD.  Signal of Positive Selection: Example of FOXP2  Mutations in gene within humans known to confer specific effects on language acquisition/grammar abilities  First gene possibly implicated in development of human language ability  Two AA differences from chimpanzees, one possibly functional  Human Lineage: 2/0 where the left (2) is the NS changes and the right (0) is the S changes. The other primates have no AA changes relative to humans. We are experiencing more NS changes after we diverged from chimpanzees  Unusual excess of low-frequency polymorphisms (rare variants): only 1 in 315 reference genes showed an extreme excess as the FOXP2 gene  That particular gene underwent selective sweep consistent with selection happening in the last 200,000 years, just like the FOXP2 gene  Evolution of Skin Pigmentation:  Local Adaptation Associated with UV radiation  Tradeoffs associated with light and dark pigmentation:  Less UV =reduces vitamin D synthesis. Lighter, as needing to get enough vitamin D  Higher UV: interferes with folate. Darker, prevent breaking down of folate  Positive Selection on Skin Pigmentation  SLC24A5 implicated in pigmentation  Reduction in polymorphism in European populations  Includes 1 out of 2 fixed differences between European and East Asian samples (no high levels of differentiation between human populations)  Nielsen: scanning the genome for positive selection. CLR statistic to compare probability that a region has its own SNP frequency distribution relative with the probability that its part of the genome-wide distribution. Measure of unusualness. Own allele-frequency spectrum compared to on that can fit into the gene-wide spectrum  SLC is highly differentiated and most unusual: population specific positive selection  Williamson et al: 101 regions under positive selection, as much as 10% of genome linked to regions subject to selective sweeps due to LD and positive selection.  M-K found very little evidence of positive selection. However single selection events tests have found a good amount of strong positive selection: pigmentation, immunity and olfactory  Incomplete Sweeps:  Very recent positive selection and local adaptation may often NOT show fixation events  Scans for alleles at high frequency with low diversity: SNP at high frequency, chances are
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