Genetic variation, HW equilibrium, Inbreeding, and Effective Population Size Flashcards
What does population genes answer?
Questions that can’t be answered by molecular genetics
When is a single base change called an SNV?
If only present in one individual, or if rare
When is a single base change called a mutation?
If rare and observed in disease context
When is a single base change called a SNP?
If common in the population
Non-synonymous mutation
AA change occurs
Frameshift mutation
Insertion or deletion of nucleotide bases in numbers that are not divisible by 3. Changes the subsequent AAs and can cause premature stop codon
Name 4 methods for detecting genetic variation in DNA
- PCR + electrophoresis
- Sanger sequencing
- Whole-genome SNP genotyping
- Next-generation sequencing
Steps of PCR
- Denaturation - heat DNA strand to 95C to break the hydrogen bonds
- Primer annealing - After first step with end up with 2 separate strands. Cool back down to 50-65C and primers anneal to the template strand by forming H bonds at the exact position they compliment the DNA
- Extension - Heat to 72C which is optimal temp for thermal Taq polymerase enzyme to synthesis new strands of DNA in 5’ to 3’ direction
repeat about 25 times
After how many rounds is the first target length strand found?
2
Why does DNA migrate slowly to positive charge in a gel electrophoresis
Phosphates carry a slight negative charge
Why does DNA migrate slowly to positive charge in a gel electrophoresis
Phosphates carry a slight negative charge
Steps in Sanger sequencing
- Amplify region by PCR
- Dye-terminator PCR - DNa polymerase is added with chain terminators ddNTPS in a ratio of 100:1 respectively. PCR extension finishes when ddNTP bonded with template strand. Each ddNTP iis fluorescently labelled with a colour corresponding to the base
- Capillary electrophoresis - To read the sequence we measure the mass of each DNA fragment at single basepair resolution and detect the fluorescence signals
Whole-genome sequencing
- Genomic DNA is fragmented into regions of 200bps
- SNP probes complementary to the sequence upstream of SNP added
- We get base pairing between fragmented DNA and complementary probe
- Like Sanger sequencing there are chain terminator ddNTPs
- SNP chips read sequence
What do the colours of an SNP chip mean?
Green = homozygous A/A
Red = homozygous B/B
Yellow = heterozygous A/B
Next generation sequencing
- Genomic DNA is fragmented into pieces of 400/500bps
- Ligases add sequence adapters - extra pieces of DNA on either side of template DNA
- On a flow cell there are oligonucleotides complimentary to adapter 1 and adapter 2
ddNTP chain terminators are reversible
Hardy-Weinberg definition and equation
genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors
p^2 + 2pq +q^2 = 1
What are the 5 principles of Hardy-Weinberg equilibrium?
- No mutation
- Random mating
- No gene flow (migration)
- Infinite population size
- No selection
What is the inbreeding coefficient (F) for the offspring of half-sibilings?
0.125
What is the F for full siblings?
1/4
What is the F for half siblings?
1/8
What is the F for first cousins and double first cousins?
1/16 and 1/8 respectively
What is the F for Uncle-niece
1/8
What is the probability of being homozygous at a locus for unrelated individuals?
p^2 + q^2
What is the probability of being homozygous at a locus for related individuals?
p^2 + q^2 + 2pqF
What does assortative mating lead to?
Increase homozygosity
What does negative assortative mating (disassortative mating) lead to?
Increase in heterozygosity
What is another name for inbreeding?
Endogamy
What is an effective population size (Ne)
Size of idealised population required to see same genetic variation
Estimating Ne via inbreeding
Inbreeding reduces heterozygosity
Panmixia
Random mating
Panmictic index
Pt = 1 - Ft (where Ft is the inbreeding coefficient at generation t)
What is the modern method of estimating Ne?
Identity-by-descent (IBD) in SNP-chip data
Length distribution between all paris of individuals in a cohort can be used to estimate Ne of previous generations
Estimating Ne further back in time
Pairwise sequential Monte Carlo (PSMC) method
8 Factors affecting Ne
- Division into two sexes
- Variation in offspring numbers
- Inbreeding
- Mode of inheritance
- Age and stage structure
- Changes in population size
- Spatial structure
- Genetic structure
How does division into two sexes affect Ne?
A small number of individuals of one sex can greatly reduce effective population size below the total number of breeding individuals
How does variation in offspring number effect Ne?
A larger variance in offspring number than expected with random variation reduce Ne below N
How does inbreeding affect Ne?
The correlation between the maternal and paternal alleles of an individual caused by inbreeding reduces Ne
How does mode of inheritance affect Ne?
The Ne experienced by a locus depends on its mode of transmission
How does age and stage structure affect Ne?
Ne is much lower than N
How does changes in population size affect Ne?
Episodes of low population size have a disproportionate effect on the overall value of Ne
How does spatial structure affect Ne?
Limited migration between populations greatly increase Ne for the whole population, whereas high levels of local extinction greatly decrease Ne
How does genetic structure affect Ne?
Balancing selection increases Ne
Directional selection reduces Ne
