Population Genetics:

The new way of doing research in modern genetics is different than the past. We used do manipulating the special genes and sometimes we do some varitions. We used to do Mandelian. Now, we take advantage of the natural variations of the populations. First we have to go and characterize the populations. Now we know that most traits are quantitative not discrete. Reading the peaks of the fluorescence we would know the sequence. The bees that are heterozygous they show N at the place of the nucleotide. This is read by the fluorescence by the ddNTP sequencing. Allele Frequency: The addition of all should add up to one. A is the total number of types of alleles. Another way of describing the sequence and looking ath the differences. Locus is a place that there is a mutation. So, there are 3 loci in this sequence. This consists of putting dots where there is a similar NT and we write the letter when there is a difference. Haplotype is the number of different sequences. We can just get the haplotype frequency. Haplotype is different that genotype. Genotype (combinations of alleles). Genotype is the haplotype at many site. A segregating site is the site that has segregating in the sequence. This is used for making trees based on the number of differnces in the nucleotides between species. Nucleotide Diversity measures the average heterozygocity within multiple genotypes. Pi is the NT diversity. This is the average number of differences per site between two random sequencing. Another ways of estimating pi is the number of pairwise mismatches in a sequence. Fisrt we calculate the numer of pairwise. Next, we count the mismatches between the sequences (Can also do this by multiplying the number of different kinds of NT). We tehn calculate pi=(adding the total mismatches)/(types of possible pairwise (same as (((N(N-1)/2)))) X Number of sites). Hardy Weinberg: Two people. We can predict the genotypes in the populations if we know the allele frequencies, but we have to make 9 assumptions. The bold ones are main assumptions. 2. Sexual reproduction is the equal segregation and miosis is a fair coin. 3. Means that the progenies reproduce wit heach other not with the adults. The adults ad die and the progenies continue on.5. infinite is cuz we wanna make sure that the allele frequencie wont change by sampling. This punnet square is an example of eggs and sperm that are shed to the sea. The individuals will also have the ratios of p squared, 2pq and q squared.

The next example is the male and female finding mate but it is random mating. It is 2PH since there are 2 possibilities (male can be +/+ or the female can ebe +/+ and etc.), there is or, so 2 possibilities. The highest heterozygocity happens when the requency of the alleles are equal to 0.5. As one increases, te other decreases. March 14, 2013 We can use the chi-squared toi check that they are consisteant with the hardyweinberg. We calculate the expected numbers. In the population genetic hi-square is equal to the number-1-1. The first one os the number of data and then -1 (-1-1). We estimated oen parameter from the data since the value of the p is the only thing to vbe calculated, since we can get the value of q from p (since it is p dependant. We should do the chi-squared with the number of the individuals (not the free frequencies). If we have 3 alleles, we do hardy Weinberg. First write all the genotypes. For P1P1 the frequency is (P1)2. The frequency of the P1P2 is 2P1P2. The heterozygous frequency is 2x the frequency of both alleles. The frequency of the homozygous is the value of each allele frequency squared. The df value for 3 alleles is 6-2-1=3. The 2 is the number of values calculated from the alleles. 6 genotypes in total. The number of genotypes is the same as the number of pairwise comparisons. The number of the heterozygous is n(n-1)/2. The expected value of the heterozygocity is the 1-homozygocity. It is easier to calculate the value of the homozygocity. We use hardy Weinberg to use as a null model. It does not suggest evolution. Power is how powerful the test is to detect changes in the groups. The effect size (like height size) is small, it would be harder so we would need higher sample size to have greater power. It is hard to detect mutation and selection (sudden changes) by hardy Weinberg equation. Non-random or migrtio is detected by hardy Weinberg. We can however detect easier differences (e.g., height). These questions can be addressed on the exam in a way such as 1% mutation. The carrier would be 2x the 2 frequencies. The homozygous recessive (carrying the disease) is squared Inbreeding: We will ignore (relax) this in the hardy Weinberg. Inbreeding is the mating within the related individuals. The way we calculate the individuals. One way is to get non-random mating instead of random mating, this is inbreeding. The left one is IBS and IBD. The right pic is IBS only. Everytime, theya re IBD, they are also IBS. The opposite might not be true.

Inbreeiding Coefficiet: This f value is the related by having a common ancestor with the allele. The top two are IBD since the two genes came from the mom or both from the dad. This is IBD. IBD is when the both alleles came from one parent, only. These are plants so both sexual parts on the same plant. Autozygout are homozygous that rae IBD. Allozygous can be homo or hetero that are not IBD. The heterozygous (bottom two) are not IBD since one came from the either parent. Mating with Relatives Increases IBD: We will call X (1,2), A (3,4) and Y (5,6). The only way E will be IBD is from A. The only way A will IBD is 3,3 or 4,4. The chane of E being 3,3 is 1/16. The probability of it being 4,4, is 1/16. The probablitity of E being 3,3 or 4,4 is 1/8. Allozygous means IBD. Also 3,4 or 4,3 could be IBD if the grandma herself was inbred. The probability is the probability of 3,4 or 4,3 times the probability of the gradma if she was inbred. PE inbred =1/8 + 1/8 (probability of grandma.