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 |

- | + Not sequencing 1 genome but 2 (for a diploid organism), so can compare genomes to each other | + | |

+ | Not sequencing 1 genome but 2 (for a diploid organism), so can compare genomes to each other | ||

- Each is composed of a segment of the genome of an individual from previous generations | - Each is composed of a segment of the genome of an individual from previous generations | ||

- Looking further and further back you are sampling 1000s of individuals | - Looking further and further back you are sampling 1000s of individuals | ||

- | + 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 | ||

- More generations reduce genetic variation in a population | - More generations reduce genetic variation in a population | ||

- | + rate it goes down is inversely proportional to population size (N) | + | - Rate it goes down is inversely proportional to population size (N) |

- | - lose variation faster with small N | + | - lose variation faster with small N |

- | - lose variation slower with large N | + | - lose variation slower with large N |

- Markov chain with absorbing boundary (math model) | - Markov chain with absorbing boundary (math model) | ||

- 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/05-01-2015.1430511652.txt.gz · Last modified: 2015/05/01 13:20 by nsaremi