population genetics Flashcards
what is population genetics
the genetic structure of a population
define population
a group of individuals from the same species that interbreed
what does population genetics describe
how genetic transmission happens between a parent and offspring - the relationship between the genotype of the parents and the offspring in a population
what does genetic structure explore (2 pieces of info)
gene (allele) frequencies and genotype frequencies
why is loss of genetic variability hard to measure
usually occurs after over various generations
what is heterozygosity
proportion of individuals carrying different alleles at each of one (or several) loci
how are heterozygosity and fitness related
positively
under Hardy-Weinberg, how are heterozygotes represented
p^2 + q^2 (pp + qq)
under Hardy-Weinberg, how are homozygotes represented
2pq
what is allelic diversity (richness)
the number of different alleles in the population adjusted by sample size
example HWE:
co-dominant alleles: a=white, A = purple
genotypes: aa = white, Aa = light purple, AA = purple
plants: 200 white, 500 light purple, 300 purple
work out allele frequencies
500 + 300 + 200 = 1000 genotypes, 2000 alleles
genotype freq: aa = 0.2, Aa = 0.5, AA = 0.3
allele freq: a = 200 + 200 + 500 = 900 / 2000 = 0.45
A = 300 + 300 + 500 = 1100 / 2000 = 0.55
what are the 2 HW equations
p + q = 1
p^2 + q^2 + 2pq = 1
what are the assumptions of the HWE
diploid system,
sexual reproduction only,
random mating with all other individuals in the population,
no mutations of the alleles being considered,
no natural selection of the alleles being considered,
no migration with other populations,
the population is infinitely large
what are outliers
markers that appear to be under selection (high FST), not in HWE
what type of markers are likely to be in HWE
neutral markers that infer no fitness advantage
why are non-neutral / adaptive markers likely to be out of HWE
markers infer fitness which may lead to divergent selection among populations
what are neutral markers useful for studying
gene flow, migration or dispersal
what are adaptive markers useful for studying
adaptation, sexual selection and evolution
what is sexual reproduction (at molecular level)
production of haploid gametes (meiosis) followed by union of 2 gametes from 2 different parents to form new diploid offspring (syngamy)
what occurs during meiosis
duplication of genetic material and production of haploid gametes
what is recombination
crossing over of chromatids to exchange genetic material in the reshuffling of genes so gametes contain different set of alleles than either of the original parent chromosomes
what happens in random mating
mating pairs will form as if there were random collisions between genotypes
if a population was made up of 25% AA, 65% Aa and 10% aa then (according to random mating) what will be the genotypes of the females that a male could mate with
25% AA
65% Aa
10%aa
what is panmixis
complete interbreeding
mating can be random with respect to certain genes but not with respect to others, give an example
people may mate randomly with respect to blood type, but not in respect of hair colour
what is assortative mating
individuals may choose to mate with genetically similar individuals (positive assortative mating) or with genetically dissimilar individuals (negative assortative mating)
give an example of assortative mating
mice prefer too mate with mice with a different body odour from themselves
what is inbreeding
non-random mating of individuals ore closely related than expected by chance, dependent on population size
what is inbreeding depression
decline in the value of a trait related to fitness as a direct consequence of inbreeding
what are 2 effects of inbreeding depression
increase in freq of recessive deleterious allele
increase of homozygosity when heterozygotes have advantage
why are mutations rare
DNA repair mechanisms are efficient
most mutations are deleterious, only mutations not deleterious will persist
do all proteins mutate at the same rate
no
what happens in natural selection
alleles which enhance survival and reproduction will increase in frequency
define migration
movement of individuals between populations or subpopulations
what is the relevance of migration to allele populations
can potentially bring new alleles into a population
what does N represent in effective population size
total number of individuals in a population
what is the issue with using N
simplistic representation as not all individuals may produce offspring (e.g. juveniles)
what does Ne represent
the size of an ideal theoretical population that would show the same rate of increase in inbreeding as the population in question
what is the minimum Ne
the minimum number of individuals needed to maintain genetic variability
explain the 50/500 rule for the minimum Ne
50 = minimum short-term Ne to avoid inbreeding effects
500 = minimum Ne to avoid loss of genetic variability and evolutionary potential
who came up with the 50/500 rule and when
Franklin, 1980
what is the revised Ne rule and who / when was it established
100/1000 rule
Frankham 2014
what is He
expected heterozygosity
what is Ar
allelic richness
what is Ne
effective population size
what does it show if the heterozygosity expected is much higher than the heterozygosity observed
the population is out of Hardy Weinberg equilibrium
what is Ho
heterozygosity observed
what is Phwe
the probability of conformance to HWE
what does heterozygosity mean in terms of gene diversity
heterozygosity = gene diversity
what is loss of heterozygosity (LOH) often associated with
cancer development
what is true of BRAC1 and BRAC2 genes (regulate cell growth) in breast cancer
the genes show reduced heterozygosity
what is Fis and define
inbreeding coefficient = probability that an individual has 2 alleles at a particular locus that recently descended from a single common ancestor
what is the range of values that Fis can take on
0 (no inbreeding) - 1 (full inbreeding)
what is Fit and define
the overall inbreeding coefficient = compares heterozygosity of an individual to that of the total population under consideration; influenced by Fis and Fst
what is Fst
the probability that 2 random gametes (or genes) drawn from the same subpopulation will be identical by descent, relative to gametes taken from the entire population
what is the most common measurement used to describe the genetic differentiation of populations
Fst
what is the scale for Fst values
0 (complete panmixia) - 1 (complete genetic differentiation)
what is Hi
average observed heterozygosity across subpopulations
what is Hs
average expected heterozygosity across subpopulations
what is Ht
expected heterozygosity of total population
how do you calculate Fis
= (Hs - Hi) / Hs
how do you calculate Fit
= (Ht - Hi) / Ht
how do you calculate Fst
= (Ht - Hs) / Ht
when is inbreeding not so important
when there is no mate choice e.g. endangered species,
if a species has incredibly high genetic diversity,
can be beneficial to keep some traits e.g. seagrass is huge colony of perfectly adapted plants
who came up with F statistics
Sewall Wright, 1951
what does an Fst of 0 mean
no differentiation
what does an Fst of 1 mean
fixation for different alleles in different subpopulations
what are the Fst values for moderate genetic differentiation
0.05-0.15
what are the Fst values for great genetic differentiation
0.15-0.25
what are the Fst values for very great genetic differentiation
> 0.25
do adaptive markers often have high or low Fst
high
