Population Genetics Flashcards
Define population genetics
The study of diversity within and across populations along with its causes and implications
What is population genetics required for?
For establishing the evolutionary relationships between populations and thus, human population diversity.
What 5 things does population genetics incorporate?
Migration patterns (local, regional, global), relatedness of different populations, mating patterns, admixture, natural selection
What is admixture?
Genetic admixture occurs when individuals from two or more previously separated populations begin interbreeding.
What are the consequences of admixture?
Admixture results in the introduction of new genetic lineages into a populations..
How does admixture affect adaptation?
Admixture slows down local adaptation by introducing foreign, unadapted genotypes (gene swamping). It also prevents speciation by homogenizing populations.
T/F: Gene frequencies for traits/ diseases may be present in different freqeucnies within populations.
True
What does population genetics enable us to do?
To map susceptibility factors of a disease onto the genome and offers advantages in genetic counselling and forensics.
What three factors influence genetic diversity?
Genetic mechanisms, evolutionary forces, population characteristics.
What are the genetic mechanisms influencing genetic diversity?
Mutation and recombination
What are the evolutionary forces influencing genetic diversity?
Natural selection and genetic drift
What are the population characteristics?
Population size, geographic distribution, mating patterns and migration.
Where is the A allele predominantly distributed?
Europe
Where is the B allele predominantly distributed?
There is a block of high distribution extending from northern central Russia to the Indian subcontinent.
Where is the O allele predominantly distributed?
South America, central America
How was the distribution of the ABO alleles discovered?
Using genetic markers which are loci that are frequently heterozygous in a population.
What is the MAF of genetic markers?
> 1-5%
How can maternal lineage be traced?
Through using mtDNA
How can paternal lineage be traced?
Through Y-chromosome haplotype
T/F mtDNA is linear
False
How many genes are found on mtDNA?
37 genes, required for normal mitochondrial function.
13 mitochondrial genes encode for…
enzymes involved in oxidative phosphorylation
Why is mtDNA exclusively inherited maternally?
All spermatozoan mitochondria are metabolised upon fertilisation of the oocyte.
T/F: the majority of mtDNA is non-coding
False; the majority is coding, however the non-coding region has a high mutation rate and does not recombine.
How can mtDNA be used in gene mapping?
The high mutation rate and lack of recombination result in these mutations accumulating on the haplotype, thus enabling related haplotypes to form haplogroyps
What are haplogroups?
These are groups of mutations found on mtDNA which share defining variants at key sites.
T/F: The Y chromosome recombines with the X chromosome
Neither; only the telomeric pseudoautosomal regions recombine with the X chromosome.
Why is the Y chromosome male specific?
The Y chromosome is the chromosomal determinant of males in humans, as their sex chromosomes are XY.
What can mtDNA and Y chromosome haplogroups be used for?
To reconstruct the relationship among haplotypes through using mutations. The geographic distribution of lineages can then provide information on the history of populations such as population origin, population age.
How does population age affect mutation number?
The number of mutations increases with the age of lineages.
T/F: markers with different mutation rates are informative for different time periods
True
What type of mutations are inherited?
Germ-line mutations
How are new alleles produced?
Mutation
What is mutation pressure?
The changing of allele frequencies through mutation
How can haplotype diversity be increased?
Meiotic recombination; creates new combinations of alleles on chromosomes, i.e. new haplotypes.
What is Muller’s ratchet?
The observation that asexually reproducing species and non-recombining portions of the human genome are prone to degeneration.
Name a genetic advantage of sexual reproduction.
In sexual reproduction it takes less time to assemble the fittest genotype as alleles can be combined in parallel whereas in asexual reproduction only one allele can prevail and so combination must occur serially.
T/F: Under independent assortment, the frequency of combined alleles should be equal to the product of the two allele frequencies.
True
Name four factors of linkage disequilibrium.
Recombination, selection, migration/admixture, genetic drift
Which project utilised LD in creating association maps?
The HapMap project
Why would one population have a greater number and size of linkage blocks compared to another?
The older population the more recombination has occurred in the genome resulting in less and smaller linkage blocks.
Define Genetic Drift
The random change in allele frequencies
Why is effective population size important?
It allows us to compare the amount of genetic drift experienced by different populations. It allows us to calculate the probability and fixation for a new allele in the absence of selection and mutation.
Each generation represents….
a finite sample from the previous one and so the magnitude of genetic drift relates to population size.
What are the differences in allele frequency between a population of N=20 and N=1000?
In N=20, the allele rapidly becomes either fixed or lost from the population however when N=1000 both alleles persist in the population.
What are the two main processes of genetic drift?
Bottlenecks and the founder effect.
How does population size affect genetic drift?
Genetic drift is stronger in smaller populations, reducing population heterozygosity.
`What is the founder effect?
the founder effect occurs during the colonisation of a new territory, forming a new population with only a subset of the genetic diversity present in the original population.
What are population bottlenecks?
Bottlenecks are the reduction in size of a single, previously larger population resulting in a loss of diversity.
How do bottlenecks occur?
The occur due to a natural disaster, famine or epidemic.
What are population isolates?
These are small populations isolated from other populations by geography or social reasons.
Population isolates perform which genetic diversification process?
The founder effect
T/F: the founder effect results in a reduced genetic heterogeneity?
True
What 5 forms of information can population isolates confer?
Population-specific disease spectrum, population specific disease alleles, degree of linkage disequilibrium, mendelian disease, complex disease.
Name a country where population isolates can be found.
Finland.
T/F: in Finland is there a reduced Y chromosome diversity?
True
What four diseases are rare in Finland but prevalent in the rest of Europe?
Cystic Fibrosis, Phenylketonuria, Galactosemia, Maple Syrup disease
What are the three main “enriched” diseases of Finland?
Aspartylglucosaminuria, late infantile neuronal ceroid lipofuscinosis and progressive epilepsy with mental retardation.
In Finland 1 mutation is responsible for what percentage of disease alleles?
75-98%
`How can the differences in allele frequencies be measured?
They are measured as differences in heterozygosity using the fixation index.
What is the fixation index?
Fst is a measure of population differentiation due to genetic structure of a population.
What is assumed whilst calculating Fst?
That the population is in Hardy-Weinberg equilibrium
What does an Fst = 0 indicate?
There is no genetic differentiation
What does Fst=1 indicate?
There is complete genetic differentiation where there is a fixation of alternate alleles.
What does Fst indicate?
The proportion of genetic variance that is due to population differentiation.
Can Fst be used as a measure of genetic distance?
Yes, between pairs of populations.
What is the Darwinian definition of natural selection?
The differential reproduction of genotypes in succeeding generations.
How does natural selection manipulate diversity?
through selecting: survival into reproductive age, success in attracting a mate, the ability to fertilise, the number of progeny.
Define fitness.
The ability of an individual genotype to survive and reproduce, partly dependent on the environment.
What is negative selection?
This is the selection against variants that put their carriers at a disadvantage. This acts against change as it is essential to maintain efficient gene function as it is. This selection is seen in metabolic processes; stabilising.
What is positive selection?
This is the selection for variants that put their carriers at an advantage which therefore acts in favour of change. Spreads novel adaptations.
T/F: Positive selection leaves signatures on the genome?
True
Name two ancient adaptations which are species specific?
Bipedalism and speech
Name recent adaptations which are population specific
Resistance to infectious disease, skin colour, lactose tolerance and adaptations to altitude
What is genetic hitch-hiking and the consequences thereof?
As an allele increases in frequency, variants at a nearby location, with an absence of recombination, also increase in frequency. This results in an excess of rare variants compared to other populations.
What is another name for hitchhiking?
Selective sweeping
Name the consequence of selective sweeping.
This alters the typical pattern of genetic variation in a region, resulting in the rapid increase of the advantageous variant.
Positive selection of a trait…
creates a signature consisting of a genomic region with reduced diversity and an excess of rare alleles.
What is selective sweeping dependent on?
This is dependent on the strength of the selection pressures and therefore the time taken to complete the sweep.
What are ancestral alleles?
Those which are present in the common ancestor
What are derived alleles?
Those which are non-ancestral, arising from recent mutations
Derived alleles arise because of
mutation
What can you conclude if a derived allele is found at high frequency?
As these alleles are rare to start with, if they are found at a high frequency in a population then this is indicative of a selective sweep.
Give an example of a derived allele.
The Duffy blood group shows an excess of high frequency derived alleles at the Duffy red cell antigen gene (the FY gene)
When did population differences first arise in human populations?
less than 50-75000 years ago
Name two population differences observed in humans
Lactose tolerance and skin colour
Why did the LCT locus show a rapid increase in frequency?
There was not enough time for haplotype breakdown through recombination resulting in an increase of LD around the LCT region.
Where does the melanin pathway occur?
Melanocytes
What is tyrosine oxidised to first?
dopaquinone
What are the two possible products of the melanin pathway?
Eumelanin or pheomelanin
Which is the brown/black pigment of the melanin pathway?
Eumelanin is the brown/ black pigement
Which is the red/yellow pigment?
Pheomelanin
Which melanin pigment is found in higher concentrations in African populations?
Eumelanin
T/F: Caucasians produce pheomelanin
False
What was the selection pressure to reduce melanin production in Caucasians?
As humans migrated into cloudy, sunless regions, there was a reduction in melanin production but plasma vitamin D levels increased profoundly as the lack of sunlight made vitamin D production more efficient.
What are the two models on human origins and which is the correct one?
Multiregional and Out of Africa. Out of Africa is the correct model.
What does the multiregional model state?
Modern Homo sapiens evolved regionally with gene flow between each of these regional populations
What does the Out of Africa model state?
That modern Homo sapiens originated in Africa and then emigrated, replacing local hominids.
Why is the out of Africa model supported?
Humans lack diversity, reflecting a recent origin in a small localised population. Evidence also supports that global diversity is a subset of African diversity
The subset of African diversity implies…
that there was a founder effect or bottleneck event.
What is the relationship between LD and distance from Africa?
LD increases with increased distance from Africa as the older African populations have had more recombination events
