It is now common to score many thousands of SNPs in numerous individuals sampled

Question

It is now common to score many thousands of
SNPs in numerous individuals sampled from several popqllations. Many of these SNPs are neutral and therefore provide information about rates of migration among population. SNPs that show unusual patterns of genetic variation may indicate regions of the genome that are subject to selection.

A) Will loci involved in local adaptation, such
that different alleles are favored in different
populations, show unusually high or unusu-
ally low values of Fst between populations?
Explain your answer.

B) What could account for SNPs that show
high heterozygosity within populations,
but unusually low values of Fst between
populations?

C) Even when thousands of SNPs are scored.
many of the SNPs that are the actual targets of
selection are often not genotyped. However,
even SNPs that are selectively neutral can be
used to detect regions of the genome that
are locally adapted. Why?

Explanation / Answer

Part A-

Loci play an important role to make changes in alleles. In between population, the locus of a single allele may be different. These differences come through crosses. That is one of the reasons that SNPs have unusual patterns. For a particular allele locus plays an important role for the stability of the allele. Linked alleles have fewer tendencies to be separate and so the SNPs have. SNPs closer to an allele have less chance to separate. Therefore, this also affects fixation values (fst).

Part B-

SNPs are alleles therefore; alone they cannot make high values of fst. If SNPs shows heterozygosity, but alleles not, then it will not affect positively.

Part C-

The main reason behind this the conservation of the nucleotides. Locally adapted SNPs can conserve for several generations but they remain neutral because they do not exhibit any change in gene performance.

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