lecture_notes:05-01-2015
Differences
This shows you the differences between two versions of the page.
| Next revision | Previous revision | ||
|
lecture_notes:05-01-2015 [2015/05/01 20:20] nsaremi created |
lecture_notes:05-01-2015 [2015/05/01 20:25] (current) nsaremi |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ==== 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 | ||
| Line 34: | Line 35: | ||
| - 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) | ||
| Line 41: | Line 42: | ||
| - 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 | ||
| Line 48: | Line 49: | ||
| - 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 20:20 by nsaremi
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
