lecture_notes:05-01-2015
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| - | ==== BME 235 notes 5/1/2015 ==== | + | ===== BME 235 notes 5/1/2015 ===== |
| + Can learn species demographic info from a single genome | + Can learn species demographic info from a single genome | ||
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| + Amount of heterozygosity is directly proportional ... | + Amount of heterozygosity is directly proportional ... | ||
| - | + Wright-Fischer model of reproduction | + | ==== Wright-Fischer model of reproduction ==== |
| - Finite and constant population (N) | - Finite and constant population (N) | ||
| - Random mating with respect to the gene of the locus you are looking at | - Random mating with respect to the gene of the locus you are looking at | ||
| - Non-overlapping / discrete generations | - Non-overlapping / discrete generations | ||
| - | + Genetic drift | + | ==== Genetic drift ==== |
| - Allele frequency (p) changes over generations via process of random mating | - Allele frequency (p) changes over generations via process of random mating | ||
| - Changes till it reaches fixation (non-segregating) or extinction | - Changes till it reaches fixation (non-segregating) or extinction | ||
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| - pi(p) = p : the probability an allele with frequency p will go to fixation | - pi(p) = p : the probability an allele with frequency p will go to fixation | ||
| - | + Heterozygosity, H | + | ==== Heterozygosity, H ==== |
| - rate of differences per base pair in the genome | - rate of differences per base pair in the genome | ||
| - can be measured extremely precisely | - can be measured extremely precisely | ||
| - Ht = H0*(1 - (1/(2N)))^t : heterozygosity over time | - Ht = H0*(1 - (1/(2N)))^t : heterozygosity over time | ||
| - | + Mutation | + | ==== Mutation ==== |
| - Adds genetic variation to a population | - Adds genetic variation to a population | ||
| - Works to counter allele fixation through genetic drift | - Works to counter allele fixation through genetic drift | ||
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| - Independent of population size | - Independent of population size | ||
| - | + Mutation - drift equilibrium | + | ==== Mutation - drift equilibrium ==== |
| - deltaH = -(1/(2N))*H + 2mu*(1 - H) | - deltaH = -(1/(2N))*H + 2mu*(1 - H) | ||
| - to determine stable heterozygosity, assume deltaH is 0 and solve for H (assuming mutation - drift equilibrium) | - to determine stable heterozygosity, assume deltaH is 0 and solve for H (assuming mutation - drift equilibrium) | ||
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| - becomes H ~= 4Ne*mu where Ne is the effective population size | - becomes H ~= 4Ne*mu where Ne is the effective population size | ||
| - | + Molecular evolution | + | ==== Molecular evolution ==== |
| - what is rate of fixation of new mutations over evolutionary time? | - what is rate of fixation of new mutations over evolutionary time? | ||
| - 2N*mu new alleles per generation, each of which starts life at frequency 1/2N | - 2N*mu new alleles per generation, each of which starts life at frequency 1/2N | ||
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| - molecular clock | - molecular clock | ||
| - | + PMSC | + | ==== PMSC ==== |
| - pairwise sequentially Markovian coalescent model | - pairwise sequentially Markovian coalescent model | ||
| - used to predict local time to the most recent common ancestor (TMRCA) based on local density of heterozygotes | - used to predict local time to the most recent common ancestor (TMRCA) based on local density of heterozygotes | ||
| - hidden markov model where observations is diploid sequence, hidden states are discretized TMCRA, and transitions represent ancestral recombination events | - hidden markov model where observations is diploid sequence, hidden states are discretized TMCRA, and transitions represent ancestral recombination events | ||
lecture_notes/05-01-2015.txt ยท Last modified: 2015/05/01 20:25 by nsaremi
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