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Genetic diversity on squirrels

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Genetic diversity on squirrels

Postby Ph0BoLuS » Fri Sep 12, 2008 12:00 pm

Some genetics homework I have on squirrels..

1) Percentage of polymorphic loci within taxon (%P)

2) Average number of alleles per loci

3) For each locus within each taxon, calculate allele frequency of each allele at each locus.

4) Heterozygosity at each locus for each taxon.

5) Average heterozygosity per taxon.

Image

For 2, I know the average number of alleles per loci is 3 Tf A,B, and C, but that's about all I know. I would somehow have an idea how to do it if it was a simple TT: 53, Tt:36, tt:8 format, but since it's like that I have no idea how to start it.

If someone could help me get started on this one It would be greatly appreciated, because I have 10 more loci to do. Once I get started on one I would be able to finish the rest of them.
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Re: Genetic diversity on squirrels

Postby blcr11 » Fri Sep 12, 2008 1:55 pm

I’m not at all sure I’m doing this correctly—I’m not a geneticist by trade. It seems to me that the average heterozygosity is zero for douglasii (100% homozygous for TfC) and S. parryii (100% homozygous for TfA)—unless you have to take into account the possibilty of a sampling error. If the table indicates the allele frequency of TfA, B, and C then can’t you calculate the expected proportion of heterozygotes using Hardy-Weinberg statistics for the beecheyi data? It’s simpler if you can assume there are only two alleles, but I don’t know if that’s proper when you know there are three. In this case, however, since the allele frequency of TfA = 0, the three-allele calculation is the same as the two-allele case. Under Hardy-Weinberg, the proportion of TfB homozygotes would be (0.896)^2 = 0.803, the proportion of TfC homozygotes would be (0.104)^2 = 0.011, and the proportion of TfB/TfC heterozygotes would be 2(0.803)(0.011) = 0.150, making the average heterozygosity of beecheyi to be 15%. That’s how I would do it, anyway, but you can’t be sure I know what I’m talking about here.

A little too simple, perhaps. I think you have to do this kind of analysis for all ten of your loci before answering the question about percentages of polymorphic loci within taxons. The table is only for one locus.
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Re: Genetic diversity on squirrels

Postby blcr11 » Fri Sep 12, 2008 4:37 pm

Try again. I’m assuming the data in the table is the allele frequency for the three alleles of locus 1 and that each column is one taxon—and here I reveal my ignorance of genetic terms because I don’t know for certain what a taxon is and I haven’t bothered to look up the definition. For the other 10 loci there may be a fewer or greater number of alleles per locus. If the tabulated data are the allele frequencies, then the answer to 3) is just read off the table multiplied by 100 to express the proportion as a percentage. For 1) you should be able to caluclate %P for each column (taxon?) as ((# loci with multiple alleles)/11)X100. For the number of alleles/locus wouldn’t that just be (total # of alleles)/11 calculated for each column? The allele frequencies should just be read off the table, I think. Then the %heterozygosity for each locus can be calculated per taxon with Hardy-Weinberg, as above, and the average heterozygosity would be the average of the %heterozygosity per locus calculated for each column. Well, that’s my suggestion at any rate. Maybe a real geneticist can correct me.
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Postby nokok » Tue Sep 01, 2009 2:57 am

How different about DNA amplified band and polymorphic band?
I would like to calcualte %of polymorphic band after PCR and electrophoresis, please explian.
Thank you very much
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