L17 - Population and conservation genetics Flashcards
What is population genetics?
The study of patterns of genetic variation in natural populations (interbreeding groups of organisms of the same species).
What is conservation genetics?
Applies population genetics to conservation situations.
What is population genetics broadly?
Variation occurs within and between populations at the phenotype and (even more) at the genotype level
What are genotype frequencies?
Number of individuals possessing the genotype divided by the total number of individuals in sample. E.g. a gene with alleles A and a gives AA Aa and aa genotypes. frequency(AA) = number of AA individuals/total number of individuals. frequency of AA + Aa + aa = 1. Note that the genotype could be a gene with a resultant phenotype or it could be a genetic locus that is not part of a gene e.g. a polymorphism in non-coding DNA.
What are allele frequencies?
Alleles (not genotypes) are passed down to subsequent gens - alleles make up the gene pool of the population. Number of copies of a particular allele present in a sample divided by total number of alleles e.g. frequency (A) = p = (2 x no of AA individuals) + number of Aa individuals/ total no of individuals x2. freq a = same but (2x no of aa individuals). Can be easily scaled up for cases when there are more than two alleles at a genetic locus.
What is Hardy-Weinberg equilibrium?
What are the effects of Mendelian inheritance and sexual reproduction on the gene pool.
What are the assumptions of the HWE?
Large (infinite) pop size, random mating, no mutation, migration or natural selection.
What can HWE be used to look for evidence of?
Population subdivision/ barriers to gene flow
Mutation, migration and natural selection
Social structure
How can we test whether a pop is in HWE?
By comparing actual allele frequencies to those expected under HWE using a CHI2 test. E.g. a gene encoding the enzyme peroxidase in pine trees growing at glacier lake, colorado has the following genotype frequencies. Is it in HWE?
HWE?
Watch youtube vid or refer to lecture slides 8-10
What are genetic markers?
Could be different alleles of genes. Or neutral markers. A microsatellite (aka short tandem repeat (STR) and simple seq repeats (SSR)) is a tract of tandemly repeated (i.e. adjacent) DNA motifs, typically repeated 5-50 times. E.g. GTCGTCGTCGTCGTCGTCGTCGTC. Highly variable in length due to slippage in DNA rep. Single nucleotide polymorphisms (SNPs) e.g. 5’ - ATTCGCGTTTG - 3’, 5’ - ATTCGGGTTTG. Many loci used in pop genetic studies
What are some applications pt1?
Detecting barriers to gene-flow. Genetic drift - within populations, allele frequencies ‘drift’ over generations due to chance differences in reproduction or survival. Populations that are genetically isolated from each other diverge over time. Happens faster in smaller populations, genetic isolation results from barriers to gene-flow (mating and migration).
What are some applications pt1 ex?
Red deer across scotland, a common pattern is that of isolation by distance i.e. individuals sample further apart are more genetically different from those sample nearby. A landscape barrier can disrupt that pattern, so pops are genetically divergent even when close together.
What are some applications pt2?
Inbreeding is a measure of the probability that two alleles are identical by descent. Inbreeding increases the proportion of homozygotes in a population. Can result from positive assortative mating of relatives or by chance (e.g. in small populations).
What are some applications pt2? Inbreeding and inbreeding depression?
Inbreeding often causes inbreeding depression e.g. isle royale wolves. Due to the expression of deleterious recessive alleles and the loss of heterozygote advantage. Extinction vortex. Genetic rescue is currently being attempted in Isle royale, with 19 wolves released in 2018/19. Pop is now ~30 wolves in 2023. Need to balance inbreeding depression with outbreeding depression and loss of adaptive alleles in reintroduction programs.
What are some applications pt3?
Reproductive success. Parentage analysis: compare genetic profiles of parents and offspring at multiple loci (usually 8-20 microsatellites, much more for SNPs). Exclusion method - mismatches at one or more loci excludes the potential parent. But genotyping is not perfect e.g. alleles can sometimes fail to amplify during PCR. Likelihoods methods usually now - calculate the likelihood of each pair being parent-offspring and assign above a threshold.
What are some applications pt3 pt2?
Allows us to look for patterns of reproductive success e.g. what are the payoffs of being dominant? Do immigrant subordinate males produce offspring.
What are some applications pt4?
Natural selection, fitness = relative average reproductive success of a genotype. Can be used to predict changes in allele frequencies over time.
What are some applications pt5?
Relatedness and social structure, close relatives share more alleles than non-relatives. E.g. siblings share an average of 1/2 of their alleles by descent. Can use measures of relatedness to investigate social structure.
What is the modern synthesis?
Cultural inheritance & Genetic inheritance -> heritable variation. <- DNA & chromosome mutations & epigenetic changes. Heritable varitation & competition -> natural selection -> evolution. Migration and genetic drift -> Evolution
