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lecture_notes:05-01-2015 [2015/05/01 13:20]
nsaremi created
lecture_notes:05-01-2015 [2015/05/01 13:25] (current)
nsaremi
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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