Population Genetics
How does inbreeding affect the genetic diversity within individuals compared to between individuals?
Inbreeding decreases genetic diversity within individuals by increasing homozygosity but increases diversity between individuals due to distinct homozygous genotypes.
What is the formula used to calculate genotype frequencies under Hardy-Weinberg equilibrium?
p² + 2pq + q² = 1, where p and q are the frequencies of two alleles.
Define mutation-drift equilibrium.
A balance where the rate of new mutations is equal to the rate of fixation or loss due to genetic drift.
What is heterozygote advantage?
A situation where heterozygous individuals have higher fitness than either homozygous form, maintaining genetic diversity.
What are transposable elements (TEs) and how do they contribute to genome diversity?
TEs are mobile DNA sequences that can insert themselves into various genome locations, increasing genetic diversity by creating mutations and rearrangements.
What is the effect of non-random mating on allele frequencies in a population?
Non-random mating does not change allele frequencies directly but can lead to an increase in homozygosity or heterozygosity, depending on the type of assortative mating.
What are the conditions required for a population to be in Hardy-Weinberg equilibrium?
Random mating, no mutation, no migration, no selection, and a large population size.
What does the molecular clock hypothesis suggest about the rate of DNA sequence changes?
It suggests that DNA sequences change at a constant rate over time, which can be used to estimate evolutionary divergence times.
What type of selection leads to a stable intermediate allele frequency?
Balancing selection, including heterozygote advantage and frequency-dependent selection.
Explain the process of gene duplication via retrotransposons.
Retrotransposons can copy mRNA and insert the cDNA back into the genome, creating a duplicate of the gene without introns.
What is the inbreeding coefficient (F) used to measure?
The inbreeding coefficient measures the probability that two alleles at a locus are identical by descent.
How does non-random mating violate Hardy-Weinberg assumptions?
Non-random mating can lead to an excess of homozygotes or heterozygotes, deviating from the expected proportions in Hardy-Weinberg equilibrium.
How does population size affect the probability of a mutation reaching fixation?
In smaller populations, the probability of fixation of a new mutation is higher due to stronger effects of genetic drift.
Explain the concept of underdominance and how it impacts allele frequencies.
Underdominance occurs when heterozygotes have lower fitness than either homozygote, leading to unstable equilibrium and fixation of one allele.
What is unequal crossing over and how does it affect chromosomal structure?
Unequal crossing over occurs between misaligned homologous chromosomes, leading to duplications or deletions of regions, which can alter chromosome structure.
Define genetic drift and how it affects allele frequencies in small populations.
Genetic drift is the random fluctuation of allele frequencies due to chance, which can lead to fixation or loss of alleles more rapidly in small populations.
What is the significance of the term "random union of gametes" in Hardy-Weinberg calculations?
It implies that all gametes have an equal chance of pairing, ensuring genotype frequencies follow the Hardy-Weinberg proportions.
Why do neutral mutations accumulate in a population over time, and what is their significance in evolutionary studies?
Neutral mutations accumulate because they neither benefit nor harm the organism, allowing them to persist without selective pressure. Their steady accumulation provides a basis for estimating evolutionary timelines and relationships, as seen in the molecular clock.
Differentiate between positive and negative selection.
Positive selection favors advantageous alleles, increasing their frequency, while negative (purifying) selection removes deleterious alleles from a population.
Define tandem duplication and its consequences for genome evolution.
Tandem duplication is when a segment of DNA is copied and placed right next to the original segment. This duplication can result in additional copies of a gene, which may evolve new functions or increase the activity of that gene, potentially leading to new traits over time.
Explain the difference between genetic diversity within populations and between subpopulations (how genetic diversity is measured).
Genetic diversity within populations is measured by heterozygosity, while genetic diversity between subpopulations reflects allele frequency differences and is quantified by FST.
Explain how deviations from Hardy-Weinberg proportions indicate evolutionary forces acting on a population.
Deviations suggest that forces such as selection, genetic drift, migration, or mutation are influencing allele frequencies, disrupting equilibrium.
Describe how the rate of fixation is independent of population size in a neutral model.
The fixation rate depends only on the mutation rate (µ) because while larger populations have more mutations, the chance of any single mutation fixing is lower, balancing out over time.
How would a dN/dS ratio close to zero for a gene inform us about the type of selection acting on that gene, and why is this significant in understanding evolutionary constraints?
A dN/dS ratio close to zero indicates strong purifying (negative) selection, meaning most nonsynonymous mutations are deleterious and removed from the population. This low ratio suggests that the gene is functionally important and under evolutionary constraint, as mutations that change the protein are not tolerated.
How do selective sweeps influence SNP diversity near an adaptive mutation?
A selective sweep fixes an advantageous mutation and reduces SNP diversity in surrounding regions by “dragging along” linked alleles to fixation.