Population genetics midterm study guide

What is population genetics?

The study of genetic variation within and among populations.

What are genetic markers?

Detectable genetic differences used to identify or compare individuals and populations. Examples include SNPs, microsatellites, and mitochondrial DNA.

What are the four types of genetic diversity?

Allelic diversity is the variety of alleles; genotypic diversity is the variety of genotypes; heterozygosity is the proportion of heterozygotes; nucleotide diversity is the average DNA sequence difference between pairs.

What is Hardy-Weinberg equilibrium?

A model that predicts genotype frequencies when allele frequencies are not changed by evolutionary forces. The formulas are p plus q equals 1 and p squared plus 2pq plus q squared equals 1.

What are the five assumptions of Hardy-Weinberg equilibrium?

A large population, random mating, no mutation, no migration or gene flow, and no natural selection.

What are the four major evolutionary processes?

Mutation, natural selection, genetic drift, and gene flow.

What does FST measure?

Genetic differentiation among populations. A value near zero means little differentiation.

What is the difference between the island model and the stepping-stone model?

The island model has migration among populations broadly; the stepping-stone model has migration mainly between neighboring populations.

What is a mutation?

A change in a DNA sequence. A transition switches purine for purine or pyrimidine for pyrimidine; a transversion switches a purine and a pyrimidine.

What is the difference between synonymous and nonsynonymous mutations?

A synonymous mutation does not change the amino acid; a nonsynonymous mutation changes the amino acid.

What is genetic drift?

A random change in allele frequencies caused by sampling. It has a stronger effect in small populations.

What is the difference between a bottleneck and the founder effect?

A bottleneck occurs when a population suddenly becomes very small. The founder effect occurs when a small group starts a new population.

What is Lewontin's paradox?

Species with very different population sizes can have surprisingly similar levels of genetic diversity.

What is the difference between migration and gene flow?

Migration is the movement of individuals. Gene flow is the movement of alleles between populations through reproduction.

What is the difference between census population size and effective population size?

Census size is the actual number of individuals. Effective population size is the size of an idealized population experiencing similar genetic drift and inbreeding. Effective size is usually smaller.

What factors can reduce effective population size, Ne?

Unequal sex ratios, unequal reproductive success, population-size changes, overlapping generations, population subdivision, and nonrandom mating.

What is the extinction vortex?

A small population experiences more drift and inbreeding, loses genetic diversity and fitness, declines further, and faces greater extinction risk.

Why do we estimate effective population size, Ne?

To predict genetic drift, inbreeding, loss of genetic diversity, and population viability.

What is linkage disequilibrium, LD?

A nonrandom association between alleles at two or more loci. For two loci, D equals P of AB minus P of A times P of B.

What does recombination do?

It exchanges DNA between homologous chromosomes and creates new combinations of existing alleles. It generally breaks down linkage disequilibrium.

Why are beneficial mutations rare?

Most new mutations are neutral or harmful. Only a small subset provides an advantage in a particular environment.

What is coalescent theory?

It traces sampled genetic lineages backward in time to find their common ancestors.

What is the most recent common ancestor, MRCA?

The most recent ancestral copy shared by all the sampled genetic lineages being studied.

What is the probability that two gene copies coalesce one generation back in a diploid population?

The probability is approximately one divided by two times Ne, written 1 over 2Ne.

What are the basic assumptions of coalescent methods?

Assumptions can include constant population size, random mating, discrete generations, selective neutrality, and no immigration, depending on the model.

Where does uncertainty in coalescent analyses come from, and how can it be reduced?

Uncertainty comes from random genealogies, limited sampling, mutation rates, and model assumptions. Using multiple independent loci is especially helpful.

How are mutation rate and DNA differences used to estimate divergence time and effective population size?

DNA mutations accumulate through time. With mutation rates and a model, sequence differences help estimate divergence time and population parameters. Theta equals 4Ne times mu for diploid populations.

What is Markov Chain Monte Carlo, MCMC?

A method that samples many possible parameter values or genealogies to estimate probability distributions that are difficult to calculate directly.

What is a posterior distribution?

A probability distribution of parameter values after combining prior information with observed data.

What is Bayes' theorem, and how is it used in population genetics?

Bayes' theorem combines the prior and the likelihood of the data to produce a posterior distribution. It can help estimate parameters such as Ne, migration, and divergence time.