Chapter 27 - Population Genetics Flashcards
This field of genetics is concerned with genetic variation, its extent within populations, and how it changes over many generations
Population genetics
When did population genetics emerge as a branch of genetics?
1920s/1930s
The foundations of population genetics are largely attributed to these three mathematicians
Sir Ronald Fisher, Sewall Wright and J. B. S. Haldane
All of the alleles of every gene in a population make up this
Gene pool
Only these individuals contribute to the gene pool of the next generation
Individuals that reproduce
This is a group of individuals of the same species that occupy the same region and can interbreed with each other
Population
A large population is usually composed of these smaller groups
Local populations
Local populations are often separated from each other by these
Moderate geographic barriers
A population may change in these three ways
Size, geographic location and genetic composition
This term describes a gene that commonly exists as two or more alleles in a population
Polymorphic
This term describes a gene that exists predominantly as a single allele
Monomorphic
When a single allele is found in at least this percentage of cases in a population, it is considered monomorphic
99%
Genetic variation is often this, a change in a single base pair in the DNA
Single-nucleotide polymorphism (SNP)
SNPs account for this percentage of variation among people
90%
In humans, a gene that is 2,000 to 3,000 base pairs contains this many different polymorphic sites on average
10
What is the formula for allele frequency?
Allele frequency = Number of copies of an allele in a population / Total number of alleles for that gene in a population
What is the formula for genotype frequency in a population?
Genotype frequency = Number of individuals with a particular genotype in a population / Total number of individuals in a population
For a given trait, the allele and genotype frequencies are always less than or equal to this number
1 (or 100%)
What will the allele frequency be for a monomorphic gene in a population?
Equal or close to 1
For polymorphic genes in a population, the frequencies of all alleles should add up to this number
1
This equation was formed independently by Godfrey Harold Hardy and Wilhelm Weinberg in 1908 to relate allele and genotype frequencies in a population
Hardy-Weinberg equation
The Hardy-Weinberg equation states that, under a given set of conditions, allele and genotype frequencies do this
Remain unchanged over many generations
What are the five conditions that make the Hardy-Weinberg equation true for allele frequencies in a population?
- No new mutations; 2. No genetic drift; 3. No migration; 4. No natural selection; 5. Random mating
In reality, does any population completely satisfy the conditions of the Hardy-Weinberg equation?
No
These populations can nearly approximate Hardy-Weinberg equilibrium for certain genes
Large populations
What is the formula for the Hardy-Weinberg equation?
p^2 + 2pq + q^2 = 1
This statistical test can be used to see if a population really exhibits Hardy-Weinberg equilibrium for a particular gene
Chi square test
If the null hypothesis is not rejected after using a chi square test to see if a population is in Hardy-Weinberg equilibrium, is the population in equilibrium for a particular gene?
Yes
If the null hypothesis is rejected after using a chi square test to determine if a population is in Hardy-Weinberg equilibrium, is the population in equilibrium for a particular gene?
No
This describes changes in a population’s gene pool from generation to generation
Microevolution
What is the source of new genetic variation in populations?
Mutation
What are four mechanisms that alter existing genetic variation in populations?
Natural selection, genetic drift, migration, nonrandom mating
In the 1850s, these two scientists independently proposed the theory of natural selection
Charles Darwin and Alfred Russel Wallace
According to the theory of natural selection, phenotypes may vary with regard to this
Their reproductive success
This is the relative likelihood that a genotype will survive and contribute to the gene pool of the next generation
Darwinian fitness
A gene with two alleles, A and a, will have three genotypic classes that can be assigned these according to their reproductive success
Relative fitness values (w)
By convention, the gene with the highest reproductive ability is given this fitness value
1
What are three reasons why there could be differences in reproductive achievement for different genotypes?
- Fittest genotype is more likely to survive; 2. Fittest genotype is more likely to mate; 3. Fittest genotype is more fertile
What are the four patterns of natural selection?
- Directional selection; 2. Balancing selection; 3. Disruptive (or diversifying selection); 4. Stabilizing selection
This type of natural selection favors the survival of one extreme phenotype that is better adapted to an environmental condition
Directional selection
This type of natural selection favors the maintenance of two or more alleles
Balancing selection
This type of natural selection favors the survival of two (or more) different phenotypes
Disruptive (or diversifying selection)
This type of natural selection favors the survival of individuals with intermediate phenotypes
Stabilizing selection
Does the value for the mean fitness of the population have to add up to 1?
No
Which genotype (heterozygote or homozygote) has an advantage in balancing selection?
Heterozygote
This measures the degree to which a genotype is selected against
Selection coefficient
What is the formula for selection coefficient?
s = 1 - w
Heterozygote advantage can sometimes explain the high frequency of these alleles
Deleterious alleles
This is another mechanism of balancing selection in which rare individuals have a higher fitness than more common individuals
Negative frequency-dependent selection
Does disruptive selection typically act on traits that are determined by one gene or by multiple genes?
Multiple genes
Disruptive selection is likely to occur in populations that occupy these environments
Diverse environments
Does stabilizing selection tend to increase or decrease genetic diversity?
Decrease
Since 1973, these two scientists have studied natural selection in finches on the Galapagos Islands
Peter and Rosemary Grant
This refers to random changes in allele frequencies due to random fluctuations
Genetic drift
This scientist played a key role in developing the concept of genetic drift in the 1930s
Sewall Wright
What are two important consequences of the founder effect?
- Founding population expected to have less genetic variation than original population; 2. Founding population will have allelic frequencies that may differ markedly from those of original population as a matter of chance
This is the transfer of alleles from a donor population to a recipient population, changing its gene pool
Gene flow
After gene flow, the new population that forms is called this
Conglomerate
To calculate allele frequencies in a conglomerate, these two things must be known
- Original allele frequencies in donor and recipient populations; 2. Proportion of conglomerate population that is due to migrants
What is the calculation for change in allele frequency for a conglomerate population?
Δp_c = m(p_D − p_R)
What does Δp_c stand for in calculating allele frequency changes in conglomerate populations?
Change in allele frequency in the conglomerate population
What does p_D stand for in calculating allele frequency changes in conglomerate populations?
Allele frequency in donor population
What does p_R stand for in calculating allele frequency changes in conglomerate populations?
Allele frequency in original recipient population
What does m stand for in calculating allele frequency changes in conglomerate populations?
Proportion of migrants in the conglomerate population
What is the calculation for finding m (the proportion of migrants in the conglomerate population)?
m = Number of migrants in conglomerate population / Total number of individuals in conglomerate population
What are two important consequences of bidirectional migration?
- It tends to reduce allele frequency differences between populations; 2. It can enhance genetic diversity within a population
This is when individuals choose mates regardless of genotype/phenotype
Random mating
This type of mating occurs when individuals do not mate randomly
Assortative mating
What are the two types of assortative mating?
Positive and negative assortative mating
This type of assortative mating occurs when individuals are more likely to mate due to similar phenotypic characteristics
Positive assortative mating
This type of assortative mating occurs when individuals with dissimilar phenotypes mate preferentially
Negative assortative mating
This is mating between genetically related individuals
Inbreeding
This is mating between genetically unrelated individuals
Outbreeding
In the absence of other evolutionary forces, are allele frequencies affected by in- or outbreeding?
No
This scientist developed methods to quantify the degree of inbreeding
Gustave Malecot
This can be computed by analyzing the degree of relatedness within a pedigree
Inbreeding coefficient (F)
This is the probability that two alleles for a given gene in a particular individual will be identical because both copies are due to descent from a common ancestor
Inbreeding coefficient (F)
What are the two steps for determining the coefficient of inbreeding for an individual?
- Identify all common ancestors of the individual; 2. Determine the inbreeding paths (shortest path through the pedigree that includes both parents and the common ancestor)
How is the length of each inbreeding path calculated?
By adding all individuals in the path except the individual of interest
What is the formula for finding the inbreeding coefficient (F)?
𝐹 = ∑ (1/2)^𝑛 (1+𝐹_𝐴)
What does n stand for in the formula for inbreeding coefficient?
Number of individuals in inbreeding path
What does F_A stand for in the formula for inbreeding coefficient?
Breeding coefficient of common ancestor
This is another term for inbreeding coefficient
Fixation coefficient
This is the probability that an allele will be fixed in the homozygous condition
Fixation coefficient
In natural populations, as population size decreases and mate choices become more limited, does the value of F tend to increase or decrease?
Increase
This raises the proportion of homozygotes and decreases the proportion of heterozygotes
Inbreeding
This is the lowering of overall fitness in natural populations by inbreeding
Inbreeding depression
In this source of genetic variation, the independent segregation of different chromosomes may give rise to new combinations of alleles in offspring
Independent assortment
In this source of genetic variation, recombination between homologous chromosomes can also produce new combinations of alleles that are located on the same chromosome
Crossing over
In this source of genetic variation, members of different species may breed with each other to produce hybrid offspring
Interspecies cross
This source of genetic variation occurs in prokaryotes and can be in the form of conjugation, transduction or transformation
Prokaryotic gene transfer
In this source of genetic variation, point mutations can occur within a gene to create single-nucleotide polymorphisms (SNPs); genes can be altered by small deletions and additions
New alleles
In this source of genetic variation, events, such as misaligned crossovers, can add additional copies of a gene into a genome and lead to the formation of gene families
Gene duplications
This source of genetic variation involves deletions, duplications, inversions and translocations, as well as aneuploid, polyploid and alloploid offspring
Chromosome structure and number
In this source of genetic variation, new genes can be created when exons of a preexisting gene are rearranged to make a gene that encodes a protein with a new combination of domains
Exon shuffling
In this source of genetic variation, genes from one species can be introduced into a different strain of the same species or into another species and become incorporated into that species’ genome
Horizontal gene transfer
In this source of genetic variation, short repetitive sequences are common in genomes due to the occurrence of transposable elements and tandem arrays; the numbers and lengths of repetitive sequences tend to show considerable variation in natural populations
Changes in repetitive sequences
What are at least six out of ten sources of genetic variation?
- Independent assortment; 2. Crossing over; 3. Interspecies crosses; 4. Prokaryotic gene transfer; 5. New alleles; 6. Gene duplications; 7. Chromosome structure and number changes; 8. Exon shuffling; 9. Horizontal gene transfer; 10. Changes in repetitive sequences
These involve changes in genetic sequences and chromosome structure or number
Mutations
These increase mutation rate
Mutagens
This Russian geneticist was the first to suggest that mutational variability provides the raw material for evolution and new alleles
Sergei Chetverikov
Sergei Chetverikov was the first geneticist to suggest the following two ideas about genetic mutations
- Mutational variability provides the raw material for evolution (but does not constitute evolution itself); 2. Mutation can provide new alleles (but does not act as the major force dictating the final balance)
A new mutation may have one of these three effects on an individual
Beneficial, neutral, deleterious
Which of the three types of mutations (beneficial, neutral, deleterious) is least likely to occur?
Beneficial mutation
This is the probability that a gene will be altered by a new mutation
Mutation rate
How is the mutation rate expressed?
As the number of new mutations in a given gene per generation
What is the common range for mutation rate?
10^-5 to 10^-6 per generation
Many proteins have this type of structure
Modular structure
Many proteins have two or more of these, with different functions
Discrete domains
Each domain in a protein tends to be encoded by one or a series of these
Exons
This occurs when an exon and flanking introns are inserted into a gene
Exon shuffling
Exon shuffling may be promoted by these
Transposable elements
Exon shuffling can also be caused by these
Nonhomologous double crossovers
This is the incorporation of genetic material from another organism without being the offspring of that organism
Horizontal gene transfer
Horizontal gene transfer may account for this percentage range of variation in the genetic composition of modern prokaryotic species
20-30%
Can horizontal gene transfer occur from prokaryotes to eukaryotes and vice versa?
Yes
These are short sequences repeated many times in a genome
Repetitive sequences
Repetitive sequences can originate via these
Transposable elements
Repetitive sequences can be these, 1 to 6 base pair repeats, over less than a couple hundred base pairs
Microsatellites
Microsatellites are also known as these
Short tandem repeats (STR)
These repeats are 6 to 80 base pairs covering 100 to 20,000 base pairs
Minisatellites
Repetitive sequences can undergo mutation which changes this
Number of repeat units
Are the mechanisms that change micro- and minisatellite repeat numbers well understood?
No
Changes in repetitive sequences may involve these two processes
Replication errors (strand slippage) or recombination
This analyzes DNA from individuals based on the occurrence of repetitive sequences at specific sites in their genome
DNA fingerprinting (DNA profiling)
