Restriction enzyme analysis
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Transcript of Restriction enzyme analysis
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Restriction enzyme analysis
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The new(ish) population genetics
Old view New view
Allele frequency changelooking forward in time; alleles
either the same or different
Shape of gene tree lookingbackward in time; alleles are
related phylogenetically
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The first ‘gene tree’, 1979
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Diploid individuals Dissolved individuals
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Wright, Kingman and the coalescentSewell Wright
J. F. C. Kingman
Probability of common ancestry of two Randomly chosen alleles in previous generation
€
1
2N
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Probability that 10 sequences have j ancestors in previous generation
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Probability that all k copies from a sample came from differentcopies in the preceding generation
So, the time it takes for two copies from a sample to come from thesame copy in the preceding generation is:
€
E(uk ) ≈4N
k(k −1)€
1− Gkk ≈k(k −1)
4N
And, the total time it takes for all copies from a sample to come from acommon ancestral copy is:
€
4N 1−1
k
⎛
⎝ ⎜
⎞
⎠ ⎟
With large k
(units in generations)
4N generations
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Expected fixation time of neutral allele in population of size N
(Kimura)
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Shape of gene trees from a random mating population
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How to draw a coalescent tree
1. Sample k copies from a population of 2N chromosomes2. Go back in time, drawing from an exponential distribution,
with the average being
3. Combine two lineages4. Decrease k by 15. If k-1, stop; otherwise, go back to step 1, using k-1 as a starting
point €
4N
k(k −1)
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Root of a gene tree captured in very few samples
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Stochastic nature of the coalescent process
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Estimating genetic diversity within populations
€
θ =Sn
1
jj=1
n−1
∑=
θ= 4N average number ofdifferences between two randomly sampledsequences from a population
“Watterson’s theta”
or θ = observed number of differences between all pairsof sequences from a population. Also called “”
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past present
Genetic diversity (θ) or
population size
Signatures of stable and expanding populations
Long internal branchesShort external branches
Short internal branchesLong external branches
Stable population Expanding population
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• Mycoplasma is transmitted horizontally, often at bird feeders
• Expanded throughout the eastern US in just five years
• Has now crossed the Rockies and is spreading south through California.
Rapid spread of Mycoplasma in House Finch populations
Courtesy Cornell Lab of Ornithology
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Serially-sampled phylogeny of 12 Mycoplasma strains
Years before present 30 20 10 0
Estimated coalescence of chickenand finch strains, (611 yrs.)(95 % c.i. 484-753 yrs.)
Numerous fixed SNP and indeldifferences, including CRISPR deletion
Estimated mutation rate:~9.3 x 10-10 per site per year;24 homoplasious sites suggestrecombination
Phylogeny obtained using BEAST, strict clock, 10 million cycles, sampling every 1000 cycles743,011 aligned sites
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200 150 0100 50
051015
MonthsYears
Time before present
Effective
population
size
Inferred Mycoplasma expansion 17 years ago
104
103
102
10
2.57.512.5
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Shape (node depths) of higher level trees depend on extrinsic factors
Interordinal molecular phylogeny of mammals
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“Lucky Mother” conceptfor mtDNA