What is population genetics?
the study of how genetic variation is distributed within species - the change of allele frequencies, genotype frequencies, and phenotype frequencies - genetic analysis of how evolution occurs, on a variet of timescales
What can population genetics tell us?
the contemporary and historical biology of species
What is the first stage of population genetics research?
collect fin clips from many fish from each river and extract DNA from them
Why is DNA used in population genetics research?
best, least complicated way to study genetic variation
Why are phenotypes bad to study in population genetics research?
most phenotypic traits have a complicated basis (ex: skin colour in humans influenced by many genes, natural selection…)
What was the first widely-used molecular genetic marker?
proteins - only genetic markers available were enzyme loci
How were variations in amino acid sequences detected when proteins were sued as molecular genetic markers?
variations in amino acid sequences could produce differences in electric charge that could be detected by electrophoresis
What are microsatelites?
tandem arrays of 2, 3, or 4 bp repeats embedded within non-repetitive DNA sequences on chromosomes
Why are microsatellites useful as genetic markers?
- mutate relatively faster than most DNA sequences - highly polymorphic (many alleles)
- are widely distributed in and abundant in genomes
- are inherited according to Mendelian rules - each microsatellite is a genetic locus
- selectively neutral (not influenced by natural selection)
- easy to study using PCR and gel electrophoresis
What hapens when a microsatellite undergoes an insertion mutation?
1) daughter strand slips and loops out
2) repair mechanisms assume daughter strand is correct; so add bases to template strand
3) microsatellite now has +1 mutation
What hapens when a microsatellite undergoes a deletion mutation?
1) template strand slips and loops out
2) repair mechanicsms assume daughter strand is correct; cut out looped out bases in template strand
3) microsatellite now has -1 mutation
Compare the rates of mutation accumulation in microsatellites and most other DNA sequences.
microsatellites mutate faster (~10^(-4)) than most DNA sequences (10^(-6)-10^(-9))
What does polymorphic mean?
show much allelic variation
What are alleles?
variations of the same DNA (originally variations of the same gene)
What does PCR do?
amplifies particular DNA sequences of choice, such as a particular microsatellite array
What technique can be likened to “DNA photocopying”?
PCR (polymerase chain reaction)
What is gel electrophoresis used for?
separating fragments of DNA according to size
What charge is carried by DNA fragments?
How does gel electrophoresis work?
in presence of electric field, fragments of DNA in gel matrix migrate toward positive electrode; small fragments move faster than big fragments
How does the rate of migration of a DNA fragment in gel electrophoresis relate to its size?
How are microsatellites inherited?
co-dominant Mendelian inheritance
What purpose do microsatellites serve in organisms?
What is the second stage of population genetics research (after DNA extraction)?
amplify microsatellite loci and determine genotypes via gel electrophoresis
How does gel electrophoresis allow one to determine the microsatellite genotype of an organism?
two bands are produced when heterozygous; one if homozygous (and position allows inference of length)
What is done in population genetics after gel electrophoresis has been performed (stage 3)?
observed heterozygosity (Ho) and observed homozygosity are calculated; then allele frequencies are estimated
How are observed heterozygosity and homozygosity calculated?
count number of heterozygotes and homozygotes; divide each number by total number of organisms; multiply by 100%
How are alelle frequencies estimated using the results of gel electrophoresis?
each allele is assigned some identifier (based on position in gel); then are counted up (taking into account homozygotes) and divided by total number of alleles
What do p and q represent in the Hardy-Weinberg equilibrium?
the frequency of each allele (p = one allele; q = the other)
Why must p + q = 1?
since there are only 2 alleles - their frequencies must add up to the total
What do p^(2) and q^(2) represent?
the probabiliies of each homozygous genotype
What does pq represent?
the probability of a heterozygous genotype
What equation relates the probabilities of each genotype?
p^2 + 2pq + q^2 = 1
What equation relates the frequencies of each allele?
p + q = 1
How does the expected heterozygosity (HE) relate to the expected homozygosity (Ho)?
HE = 1 - HO… or 2pq = 1 - (p^2 + q^2)
What does the Hardy Weinberg equlibrium allow one to do?
predict the expected frequency of any genotype if we know the frequency of the alleles
What are the assumption of the Hardy-Weinberg Equilibrium?
organism is diploid; reproduction is sexual; mating occurs at random; population size is very large; migration is 0; mutation is 0; natural selection does not affect the gene in question (7)
What assumption of the H-W equil. are we often testing for?
mating occurs at random
Why is a large population size better for H-W?
gives better fit to randomness
Why is the assumption that natural selection doesn’t affect the gene in question important in the H-W?
if some genotypes make it more likely for an organism to die, it distorts the genotype frequencies
Does natural selection affect microsatellites?
Which H-W assumptions are more like guidelines than necessary?
large population size;
migration and mutation are 0;
natural selection doesn’t affect gene
How can the H-W equilibrium be used to test the hypothesis that a certain population mates randomly?
compare (chi square/exact test) observed genotype frequencies to expected genotype frequencies, assuming HWE
Why might someone compare allele frequencies in different populations if trying to determine if shad home to natal rivers?
if they do, each river populaiton is reproductively isolated; and in reproductively isolate dpopulations, allele freuqnceis change over time
Why do allele frequencies change over time in reproductively-isolated populations?
mutations (but this is slow, even for microsatellites); natural selection (doesn’t affect microsatellites); GENETIC DRIFT
What does genetic drift do?
produces a “random walk” in allele frequencies - the freq. of a given allele will change randomly from one generation to another
What causes genetic drift?
chance variation in which individuals reproduce and which alleles they happen to pass on to the next generation
In what populations does genetic drift occur more rapidly?
What does genetic drift lead to in a completely isolated population (in the absence of new mutations)?
fixation of one allele
In general, what does genetic drift result in regarding populations?
loss of genetic variation within populations; but causes different populations to become more genetically different
Why does genetic drift result in different populations becoming more genetically different?
every population drifts independently
What affect does genetic have on heterozygosity and homozygosity within a population?
decreases heterozygosity and increases homozygosity
How can one quantify how different two (sub)populations are?
look at the loss of heterozygosity (due to drift) in the 2 subpops compared to the (expected) heterozygosity if the 2 subpops were brought back together
What are the steps to calculating genetic differences among populations?
1) calculate HE for the entire pop (HT) as if all the individuals had the opportunity to mate randomly
2) calculate HE for each subpopulation and take average across all subpops (Hs)
3) FST = HT - HS)/(HT)
What does the formula (HT - HS)/(HT) calculate?
relative loss of herozygosity due to drift = increase in fixation of alleles = fixation index (FST)
What values can the fixation index (FST) have and what do they mean?
0 = no differences between pops 1 = when there are 2 alleles per locus and all pops have become fixed for one allele or another
What value will FST eventually reach (theoretically) for 2+ populations that are completely isolated from each other
1 (more genetically different)
In many populations of one species, why might the FST be higher for some rivers and lower for others?
some rivers might share more recent coancestry (less time for drift to occur) and/or some rivers might be exchanging more migrants than other pairs of rivers
What effect does migration have on genetic differentiation?
makes them more genetically simlar (less differentiated)
How does FST relate to the number of migrants exchanged between populations?
What formula relates FST to the number of migrants?
FST = 1/(4Nm + 1), where N = pop size, m = migration rate (Nm = actual number of migrants)
What does Nm represent, if N = pop size and m = migration rate?
actual number of migrants
Where does the migration-FST equation come from?
the island model
What is the island model?
each populaiton is an island, exhanging migrnts with others
What does the island model reveal?
population diferentiation depends not on migration rate (m), but on absolute number of migrants (Nm);
very few migrants are required to greatly limit genetic differentiation (FST) due to genetic drift
How many migrants are needed to make FST 1?
How does increasing the number of migrants affect FST, according to island model?
causes FST to decrease exponentially slower at first (huge drop), then levels out
How can an indivudal be assigned to a particular population?
HWE allows one to predict the probability of any given genotype belonging to a particular population (if one knows the allele frequenceis for each potential source population)
What increases the accuracy of assignment tests?
more differing in allele frequencies among populations and more loci used
What are some applications of assignment tests?
monitoring movements/distributions of animals and populations;
catching cheaters in fishing derbies
How might an assignment test be used to catch poachers?
see if remains of a hunted animal from from a protected area
How has population genetics research helped with census of wildlife?
can use non-invasive genetic sampling (like catching bear hair on barbed wire) and microsatellite genotyping, instead of having to catch/tag/release (more expensive and invasive)
What are rapidly emerging as the “favourite” genetic markers and why?
single nucleotide polymorphisms (SNPs);
found everywhere, inccluding in genes
Why are SNPs still informative even through they have low variability and low mutation rate?
there are so many of them
What are some SNPs associated with?
particular phenotypic traits
What are SNPs?
the most common type of genetic polymorphisms
What does PCA clustering of people’s genotypes (using SNPs) do?
approximates a map of Europe
What does genetic diversity tell us about?
evolutionary, historical, and conservation status of populations
What does the genetic variability of populations (or species) reflect in the absence of migration?
a long term balance between mutations (which add genetic diversity) and drift (which diminish it) (mutation-drift equilibrium)
What is expected to be correlated with genetic diversity in the mutation-drift equliibrium and why?
long term average population size; since drift occurs slower in larger poulations
What can bottlenecks do to a population?
cause it to lose genetic variation
What is a bottleneck?
a temporary reduction in population size
Why does genetic diversity matter?
lots of evidence that animals/plants suffer a loss of fitness when genetic diversity is reduced
Why do animals/plants suffer a loss of fitness when genetic diversity is reduced?
“inbreeding depression” from mating between relatives; increased exposure to deleterious recessive mutaitons
What can potentially happen when there is too much genetic diversity - i.e. two different populations are combined?
“outbreeding depression” - loss of fitness when individuals from very different populations are interbred, perhaps due to break-up of local adaptations
Why is it important to monitor genetic diversity and gene flow between populations subject to fragmentation?
beause loss and fragmentation of habitat poses major genetic risks for many species, and increases probability of their extinction