population genetics Flashcards
what is Population genetics
- The genetic structure of a population (a group of individuals from the same species that interbreed)
- describes how genetic transmission happens between a parents and offspring, i.e. the relationship between the genotype of the parents and the offspring in a population
what is Genetic structure a combination of
gene (allele) + genotype frequencies
- Frequencies change in time + space – results in variation in population structure
Heterozygosity definition
the proportion of individuals carrying different alleles at each loci - can be positively correlated with fitness
Allelic diversity / richness definition
number of different alleles in the population adjusted by sample size
* more sensitive of population bottlenecks + loss of genetic diversity
why is Estimating genetic diversity difficult
Loss of genetic variability is usually difficult to measure - takes place over various generations
how is homozygosity and heterozygosity shown in the equation under Hardy Weinberg equilibrium
F(A)=p F(a)=q (aleles)
Homozygotes p2, q2
Heterozygotes 2pq
Allele frequency definition
the number of each allele in the population
how are genotype and allele frequencies denoted when Describing genetic diversity
algebraically
- genotype freq : P, Q, R (AA = P, Aa = Q, aa = R)
- allele (single letter) : p, q (A = p, a = q) - p + q = 1
calculate gene/allele frequencies from genotype frequencies
p= P + ½Q
q = R + ½Q
example of how to calculate genotype + allele frequency from simple info
- Alleles: a=white A=purple (co-dominant)
- Genotypes: aa=white AA=purple Aa=light purple
- 1000 plants: 200 white, 300 purple, 500 light purple
Genotype freqs:
>aa=200/1000=0.2 - Aa=500/1000=0.5 - AA=300/1000=0.3
Allele freqs: (2000 alleles - diploid organism)
>a=400+500/2000=900/2000=0.45
>A=600+500/2000=1100/2000=0.55
example 2 of how to calculate Allele frequency from genotype frequency
- Genotype frequency: AA Aa aa
Frequency of AA = 3/8 = 0.375 (P)
Aa = 3/8 = 0.375 (Q)
aa = 2/8 = 0.25 (R) - allele frequency:
Frequency of A = 9/16 = 0.5625
a = 7/16 = 0.4375
how do genotype frequencies need to be to conform to Hardy-Weinberg equilibrium
under random mating & in the absence of selection
what is Hardy-Weinberg equilibrium
genotype frequencies in the population have reached a stable condition
what is Hardy-Weinberg model
a neutral model we fit to our data set - its assumptions in reality are rarely met - some are impossible - would violate laws of thermodynamics
what is the assumption of HWE
A single generation of random mating establishes genotype (and allele) frequencies which remain stable in future generations (HW equilibrium)
what are the 7 assumptions that variation is maintained with in the HWE
1.Diploid system
2. Sexual reproduction
3. Random mating with all other individuals in the population
4. No mutation of the alleles under consideration
5. No natural selection on the alleles under consideration
6. No migration with other populations
7. The population is infinitely large
**describes an ideal population
what are outliers
markers that appear to be under selection - high FST
values, not in HWE etc
**FST test assumes HWE - so violate the assumptions
what are neutral genetic markers
- infer NO fitness advantage (often, but not always in HWE)
- Useful investigating processes such as gene flow, migration or dispersal
what are non-neutral genetic markers
- DO infer fitness (dis)advantage may lead to divergent selection among populations (likely to be out of HWE).
- Useful for studying adaptation, sexual selection, evolution etc
- probably the stuff you all find more exciting
explain the sexual reproduction assumption in HWE
Sexual reproduction at the molecular level = production of haploid gametes (meiosis), followed by the union of two gametes from two different parents to form a new diploid offspring (syngamy)
meiosis definition
duplication of genetic material and production of haploid gametes
recombination definition
crossing over of chromatids to exchange genetic material - results in the reshuffling of genes so gametes contain a different set of alleles than either of the original parental chromosome
explain the random mating assumption in HWE
- mating pairs will form as if there were random collisions between genotypes
E.g. if a population was made up of 25% AA, 65% Aa and 10% aa, then among the females that a male could mate with: 25% will be AA, 65% will be Aa and 10% will be aa
Panmixis meaning in mating systems
Panmixis = complete interbreeding
Note: mating can be random with respect to certain genes but not with respect to others
E.g. people may mate randomly with respect to blood type, but not with respect to hair colour
what is Assortative mating in mating systems
- positive assortative mating = individuals may choose to mate with genetically similar individuals
- negative assortative mating = individuals may choose to mate with genetically dissimilar individuals
E.g. mice prefer to mate with mice with a different body odour from themselves
what is Inbreeding
non-random mating of individuals more closely related than expected by chance - depends on population size
what is Inbreeding depression
decline in the value of a trait related to fitness as a direct consequence of inbreeding
- Increase in the frequency of recessive harmful allele
- Increase of homozygosity when heterozygotes have advantage
explain the mutation assumption in HWE
- New variation is produced by mutation
- mutation is rare for 2 reasons:
>DNA repair mechanisms are efficient
>Most mutations are harmful - only mutations not harmful (or weakly harmful) will persist - Different proteins have different rates of change (mutation) & are under different selective constraints
- Mutation alone will change allele frequencies only very slowly
explain the natural selection assumption in HWE
- Natural selection = alleles that enhance survival and reproduction will increase in frequency
- For most ecological applications information from genetic loci which are not under strong selective forces is required - i.e., “neutral molecular markers”
explain the migration assumption in HWE
- Migration = movement of individuals between populations or subpopulations - potentially brings new alleles into a population
- Migration has a homogenizing effect between populations — if individuals reproduce! (gene flow)
- Gene flow limits among population genetic differences
explain the infinitely large population size assumption in HWE in terms of Effective population size (Ne)
- N = total number of individuals in a population - Simplistic representation since not all individuals may produce offspring (e.g. many may be juveniles)
- Ne of a population = the size of an “ideal” (i.e one that meet HWE assumptions) population that would lose heterozygosity (i.e inbreed) at a rate equal to the observed population
- Minimum Ne = minimum number of individuals needed to maintain genetic variability
- Traditionally: 50/500 rule
>50 refers to minimum short term Ne to avoid inbreeding effects
>500 refers to minimum Ne to avoid the loss of genetic variation and evolutionary potential
>Revised: 100/1000
what can be used to describe Population’s genetic diversity
He (expected heterozygosities)
Ar (allelic richness)
Ne (size of an “ideal” theoretical population)
