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CSU BZ 220 - Population Genetics

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BZ220 1st Edition Lecture 6Outline of Previous LectureI. Structure of DNA and genetic codeII. Causes of MutationsIII. Types of MutationsA. Nucleotide mutationsB. Chromosomal mutationsIV. Effects of mutationsOutline of Current LectureI. Mutation RatesA. Genome Mutation RatesB. Human Nucleotide Mutation RatesC. Men vs. WomenD. Variable Mutation RatesII. Population GeneticsIII. Patterns of Allelic DiversityIV. HeterozygosityA. CalculationV. Allele FrequencyVI. Genotype FrequencyVII. Calculation Allele FrequenciesCurrent LectureMutation rate can be calculated in two different ways. You can use easily recognized phenotypes to calculate the new number of phenotypes per generation, or you can identify nucleotide changes from DNA sequences. Both extrapolations should give you the same answer.The second way can only be used if the number of nucleotides in the genome are known. We are able to extrapolate per gene mutation rates per genome per individual mutation rates if we have an estimate of the number of genes in a specific genome. A few organisms that we know the number of genes in the haploid genome are humans, Drosophila (fruit fly), C.Elegans (worm), Arabidopsis (plant), Yeast, E.coli, and HIV. The number of genes in a haploid genome forthese organisms are 20,000-25,000, 14,404, 19,971, 25,500, 5,773, 5,379, and 9 respectively. These numbers are still only estimates but based on these estimates it can be hypothesized thatthe complexity of an organism is not solely controlled by the number of genes but could also be These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.due other biological areas including protein folding. As the years and science progress the estimated number of genes in haploid genomes have steadily decreased since scientists now accept that humans (arguably the most complex) do not have to have extremely large genomes nor do they have the biggest genomes known. Based on these gene numbers it is estimated thateach human has about 1.6 mutant proteins that differ from their parents. As expected due to our highly efficient DNA polymerase and repair enzymes, human nucleotide mutation rate is very low: only 1 in 40 million nucleotides are copied incorrectly. To put this into perspective, humans have about 7 million nucleotides in the diploid genome. When this number is taken into account, each human on average has 175 nucleotide mutations;however, due to the redundancy of genetic code, most of the mutations are silent. Although as stated in the last lecture women have a higher rate of chromosomal mutations, men forming gametes are 2 to 5 times more likely to experience DNA replication mistakes. This is due to the fact that spermatogonal stem cells are continually replicating in males while females are born with the number of eggs they will have in their lifetime. Since sperm is constantly being replicated there is a better opportunity for mistake that could accumulate as men age. Mutation rate among species and especially individuals vary due to variable environments, variation in number of cell divisions prior to gamete formation (generation time),and variation in accuracy of DNA polymerase and repair enzymes. To some up mutation, there are many forms of mutations, mutation is an evolutionary force that creates genetic variability, most mutations are neutral or slightly deleterious, and the effect of the mutation depends on the environment. Population genetics can be defined as the genetic variation in natural populations which includes allelic frequency and heterozygosity. When looking at population genetics we must remember that mutation can occur in several different places in a gene and can come in many forms. Because of varying factors, sometimes patterns of allelic diversity can be formed.Allelic diversity is having multiple alleles for a given gene at the population level. An example of a pattern of allelic diversity is that populations of the Mummichog fish that live in the northern, colder climates have a much different allelic frequency than the same population of fish in the warmer southern environment. Heterozygosity is the fraction of individuals in a population that are heterozygous for average gene. Another definition is the fraction of genes in a population that are heterozygous in the average individual. Both of these definitions mean and lead to the same result: asummary of allelic diversity in a population. In order for heterozygosity to exist, more than one allele must be present in the population.In order to calculate the heterozygosity of a population you must look at each individual genotype and determine what fraction of the genotype is heterozygous. For example in a population of 5, gene 1 and 2 were looked at. Individuals 1, 2,3,4,5 had the following genotypes:aaBB, AaBB, aaBB, AABB, AaBb respectively. Individuals 1, 3, and 4 have a heterozygosity of 0 since they are homozygous at both genes. Individual 2 has a heterozygosity of 0.5 because it is heterozygous at gene 1 only. Individual 5 has a heterozygosity of 1 since it is heterozygous at both genes. The heterozygosity of the entire population then can be determined by dividing the added number of heterozygous genes in individuals 2 and 5 to get 1.5 and then dividing by the number of individuals in the population (in this case 5). 1.5 divided by 5 is 0.3, so thirty percent of the genes in this population are heterozygousAllele frequency is the number of copies of a given allele divided by the total number of copies of all alleles. Genotype frequency is the number of individuals with a given genotype divided by the total number of individuals. As a result, one can calculate the allele frequencies based on the genotype frequencies mathematically. In order to do so we use the following formulas: p(the dominant allele) = (the number of dominant homozygotes) + half of the numberof heterozygotes. The same formula can be used to find the q(the number of recessive alleles) ifwe change the number of dominant homozygotes to the number of recessive homozygotes. For example the frequencies of blood types M, MN, and N are 0.29, 0.50, and 0.21 respectively. P (or the frequency of M [the dominant] allele, is 0.54 because the number of genes homozygous for M was 0.29 and the number of heterozygotes in the population was 0.5. When we add 0.29 to half of 0.5 (0.25) we get 0.54 as the M allele


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