Population Genetics SA Flashcards
How does genetic drift due to inbreeding impact allele frequency?
^ fluctuation in levels due to effective smaller sample size -> loss of genetic diversity
what is another name for alleles?
variants
What is migration or outcrossing?
INtroduction of new genetic material
What is a bottleneck?
Dramatic v in population size (eg. due to mass cull) exacerbates genetic drift
What is IBD and when does it occour?
Identical by descent genes
- occurs due to inbreeding -> some shared alleles in siblings being rematched when mated
What is the inbreeding coefficient? Give some standard valus
> probability that 2 copies of a gene are IBD
- 0.25 for full sibling or parent offspring mating
- 0.125 for offspring half sibling mating
- 0.0625 for offspring of 1st cousins
- inbred strains of mice in labs may be 0.8/0.9
does NOT refer to a specific gene so must calculate for both alleles then add together
Why may IBD genes cause problems?
- random mutations in DNA mean errors and disease cuasing alleles present in every genome, but usually masked by normal alleles
- IBD ^ risk of shared mutation
Give 5 examples of inherited recessive disease
PLL - primary lens luxation PRA - progressive retinal atrophy Fucosidosis CLAD - leukocyte adhesion deficiency FIS - foal immunodeficiency syndrome
What does inbreeding depression cause?
- sick individuals
- v fitness of whole line /less robust population
What is the rate of inbreeding referred to as? How is it defined?
Delta F = change of average inbreeding coefficient over time or generations
what is the expected inbreeding rate?
natural rate of inbreeding -> v genetic diversity
usually a lot lower than popular breeds inbreeding rates, may be higher than some rare breeds Id negative assortative mating is carried out [breeding least related individuals] (cf. random matings)
What is the effective population size referred to as? How is it defined?
Ne = 1/2*DeltaF
- the number of breeding individuals in a hypothetical RANDOM mating population that would have the same rate of inbreeding as seen in the real population.
- ie. HIGH Ne =
LOW Ne =
How does Ne differ to expected in popular breed populations?
Still relatively low - probably due to population substructure eg. working v pet breeds, geographical lociation etc.
What Ne should be aimed for in a breeding population?
100 at least
What is the aim for Delta F values per generation?
< 0.5%
What will happen if Ne < 100 and Delta F >0.5%?
Population fitness will steadily decrease and become unviable in long term due to v fertility
Give 5 possible solutions to breeding populations with high rate of inbreeding
- minimise kinship./copancestry of matings
- ^ no breeding animals
- === males and females number of breeding individuals
- optimise genetic contribution (negative assortative mating, evolutionary algorithsm -> breed least related individuals)
- Outcrossing -> hybrid vigour (only in first cross, not perpetuated in subsequent crossing)
Why is optimising genetic contribution easier in some industries than others?
dairy = highly data driven, AI dogs = breed local individuals, less data
Why is affected/clear/carrier status not a helpful trichotomous distinction of individuals in some cases?
- multiple genes involved in most complex diseases
- allostatic, environmental interactions of genes mean genetic variation CURVE more useful
Why may phenotypic judgement of individuals not be useful for genetic decsions? breeding etc/
Environmental factors likely to impact phenotype eg. hip score more than purely genetics
What does heritability refer to?
Proportion of phenotype occouring due to genetics alone when environmental fators are removed
- ^ heritability means trait will respond well to selective breeding
- population specific
- relies on large database representative of the population, looking at phenotype and pedigree and taking into account relatives of each individual
Give a disease with high heritability
Osteosarcoma in Scottish deerhounds
Give a disease with low heritability
Elbow dysplasia (GSDs)
What are EBVs?
Estimated breeding value based on relatives of an individual to try and minimise impact of environment - much more reliable than phenotype alone
How have EBVs been mad more accurate?
Use of genomic information as well as dam/sire, sibling, offspring and own measurements
Which population uses GBVs and which will likely begin to use them in the future?
Dairy currently uses
Dogs - next few years
Why are EBVs useful for discrete disease? eg. bloat, epilepsy etc. (have it or don’t)
Distinguish between clear animals with high and low risk of disease (phenotype is imprecise as if animal doesn’t have disease, no further analysis can be carried out)
How does selection intensity affect success of phenotype improvement in a population?
Due to normal (ish) distribution of hip scores, exluding above a certain threshold may only eliminate 20% of population, meaning seletion pressure is not very strong
- if selection intensity is increased (eg. by selecting from only best 20% animals (excluding 80% of population) same results can be achieved in a much shorter space of time)
