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5. Population Genetics.pdf

16 Pages

Biology (Sci)
Course Code
BIOL 202
Tamara Western

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Population Genetics: Population genetics analyzes the amount and distribution of genetic variation within and between populations, and seeks to infer the forces that control the variation This is the root of genetic variation and biodiversity, and the way of producing evolutionary differences Classical genetics tend to focus on what the gene does and doesnt take into account evolutionary forces At the population level, genetic variation can be seen in various recessive traits; the job of population genetics is to interpret these variations through space and time For example, sickle cell anemia is a recessive trait which is concentration in central Africa more than anywhere else in the world Albinism is another example of genetic variation which has its own characteristics Population genetics has helped prove the African roots of the human race The first map shows the sickle cell anemia proportions we discussed before The following graph shows genetic diversity among various populations around the world; the less variation, the more pure you are o The graph shows that Africa has the least genetic variations, which further solidify the argument that we have our origins in Africa o America has some of the highest genetic variation, which is to be expected as we are the furthest along the migration line and we have lost ancestral haplotypes along the way The average nucleotide difference between two random humans is about 3,000,000 nucleotides, which seems like a lot, but it actually only represents 1 different per 1000 nucleotides in the genome o The genome is approx. 3 billion base pairs, which is huge Genetic variation begins once again with classical Mendelian genetics, in which two parental types, AA and aa, are crossed to produce an Aa F1 These F1s are then selfed to produce a 1 AA: 2:Aa: 1aa genotypic ratio due to independent assortment This is a simple example involving one autosomal gene with two possible alleles; thought the principle could be extended to different numbers of alleles, loci, etc. o The principles are different for sex linked genes, mtDNA, chloroplast DNA in plants, etc. The offspring are diploid, receiving one copy of the gene from each parent Genetic variation can occur either between individuals (AA vs. aa) or within an individual (Aa) A haplotype is a unique combination of alleles at multiple loci on the same chromosomal homolog o I.e. Aa:Bb is a unique haplotype, AA:BB is another Populations can also be viewed as a gene pool model, in which the genes are separated from the individuals (not literally) Therefore, taking this literal pool of frogs as an example, we can count 5 AA, 8 Aa and 3 Aa, but we can also tally up all the alleles separately o Thus, this gene pool, contains 18A and 14a alleles (their spread amongst individuals is irrelevant here) The allele frequency, therefore, is the total number of one type of allele, either A or a in this case, and dividing by the total number of alleles (in this case two times the number of individuals) o The frequencies of A and a in this population are 0.5 each, which is not always the case o When dealing with 2 alleles, Freq A = 1 Freq a, but this idea is not limited to 2 alleles When dealing with more than 2 alleles, the sum of all of their frequencies is 1 As convention, the frequency of the dominant allele A is denoted as p and the frequency of a is denoted as q Allele frequencies can be highly spatially dependant, meaning certain regions express a certain allele more than others o In the lower left chart, eat mini-pie chart represents a population divided into allele frequencies of the alcohol dehydrogenase gene in Australian fruit flies The slow allele is much more prevalent in the North while the fast is almost completely dominant in the South; this could potentially be related to climate conditions o Another example in on the right, with a lactate dehydrogenase gene in a certain fish; each dot on the graph is a population of the type of fish There is a huge gradient in the frequency of the two alleles as you go from North to South, again hinting towards relation with climate Genetic variation can also be measured in terms of heterozygocity, which counts up the total number of heterozygotes in the population and divides it by the population number This method can also be sued to calculate the overall heterozygocity over multiple loci, or even the whole chromosome o In the graphs to the right, we can see these calculations have been done already for various types of organisms, including humans (top) invertebrates (middle) and plants (bottom) o We can see that there is between 5 and 25% percent heterozygocity in these populations, which is a lot of genetic variation Genetic diversity can therefore be predicted by using the Hardy- Weinberg equilibrium, which will be discussed later We can also measure nucleotide diversity between organisms, which calculates the diversity of a certain nucleotide with respect to all nucleotide sites in a gene Most sections of the gene are invariable, meaning that everybody has the same nucleotides there As we saw before, only 1/1000 nucleotides differ between humans which is 0.01% of the genome o We can see from the graph to the right that plants have a slightly higher diversity, while unicellular eukaryotes have a much higher diversity, but still not more than 0.1% o These 3,000,000 nucleotides in humans are the basis of DNA fingerprinting, which are used in paternity of criminal tests Hardy and Weinberg once asked what would happen to allele and genotype frequencies in the absence of any evolutionary forces, and then developed a mathematical equilibrium to explain it In generation t, a gene pool can be produced from a certain population, and then RANDOM crossing is taken out to produce generation t+1 o According to Hardy and Weinberg, the allele frequency should stay the same in the absence of evolutionary forces In technical terms, the Hardy-Weinberg principle states that genetic variation within and among populations will remain constant if: o Mutation is absent o Mating is random (with respect to genotype) o Populations are large enough to evade genetic drift o Natural selection is absent o Gene flow/immigration/dispersal is absent Basically, the HW principle only works in the absence of any evolutionary forces o Of course, this never actually happens in a real population, but its how these populations differ from the HWP thats interesting, because then we can try and see which of the forces above are acting on that population In this example, the population has 2 alleles, A and a, where p = 0.6 and q = 0.4 o The probability of getting an AA offspring is (0.6)(0.6), or p (product rule) o Similarly, the probability of getting aa is 2 (0.4)(0.4), or q o However, there are two ways of getting a heterozygote: an A egg and an a sperm, or an a egg and an A sperm Therefore, the probability of obtaining a heterozygote is 2(0.4)(0.6) or 2pq Therefore, 2he allele 2requencies for 2 alleles are p + q = 1 and the genotypic ratio is given by p + 2pq + q = 1 (they both sum up to 1) o In an offspring population of 100, we can calculate the populations of each genotype by using the formula to the right, simply multiplying the genotype frequency equation by the population number This gives, 36AA, 48Aa and 16aa o If you put these offspring into a gene pool and take a new p and q, you will see that they still sum up to one, meaning this population follows HWE The calculations on the right for p show the AA multiplies by 2 (because AA has 2 As) and 1 times the Aa (it contains one A), the same goes for q with a alleles This is not limited to two alleles: with three alleles, there are now 3 frequencies to worry about, p, q and r o Therefore, p + q + r = 1 is the allele frequency o For the genotype frequency, we simply square this to get: 2 2 2 p + 2pq + 2pr + 2qr + q + r = 1 In cystic fibrosis, the mutation is homozygous recessive and involves a buildup of mucous in the lungs o The frequency of having the disease is 0.0004, which is equal to q 2 o From this, we can take the square root to get q = 0.02, and then using the
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