Introduction
McVicker et al. used a different approach for detecting natural selection in the human genome than any that we discussed in lecture. Specifically, they
Used a hidden Markov model to identify genome segments that are highly conserved across placental mammals. Some of the segments are in exons, and some lie outside exons.
Compared the amount of nucleotide sequence diversity (within humans) and the amount of nucleotide sequence divergence (between humans and chimps, humans and macaques, and humans and dogs) at the 10 percent of sites closest to the conserved segments with the diversity and divergence at the 50 percent of sites that were farthest away.
Compared sequence divergence along the branch leading to humans with divergence along the branch leading to chimps and the branch leading to macaques.
Here are figures taken from the paper that illustrate the main patterns.
Conclusions in McVicker et al.
McVicker et al. (2009) conclude that
[O]ur analyses reveal a dominant role for selection in shaping genomic patterns of diversity and divergence
Questions
As with Project #2, I am not asking you to analyze any data or run any simulations. I’m asking that you apply what you’ve learned about drift, selection, and evolution at the nucleotide sequence level to answer several questions related to the analyses they present and the conclusions that they draw.
What type of selection would explain nucleotide sequence conservation (i.e., lack of variation) in those genome segments where it is observed?
How might focusing on sequences that are conserved affect the conclusions that McVicker et al. (2009) reach?
Why would the amount of divergence and diversity at (presumably neutral) sites depend on whether they are close to conserved segments or distant from them?
What evidence do the data provide that the SNPs identified as neutral are evolving in a way that is effectively neutral?
Are the patterns McVicker et al. found consistent with my claim that natural selection is primarily purifying? http://darwin.eeb.uconn.edu/eeb348-notes/molevol-patterns.html#revising-the-neutral-theory
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