AGRY 320 Final Exam

what is population genetics?

The study of the amount and distribution of variation in populations

what analyzes the amount and distribution of genetic variation in populations and the forces that control this variation?

population genetics

can Mendel’s laws explain the changes in alleles frequencies in a population from one generation to another?

no

what is the population genetics definition of a locus?

a location in the genome that can be independent of coding regions

what can be used to analyze any polymorphic locus in the DNA sequences of a population of organisms?

the methods of population genetics

in population genetics, is a locus a single nucleotide site or a stretch of many nucleotides?

either

what are molecular polymorphisms used to make?

broader inferences about the population, independent of functional variation or genetic analyses

one strategy for assaying molecular variations in populations:

Sequence and compare ________ as an assay for a ______ molecular marker

variation, specific

one strategy for assaying molecular variations in populations:

Sequence and compare ______ or _______ regions of interest

candidate, target

one strategy for assaying molecular variations in populations:

___________ whole individuals - generates ______ wide markers in individuals

resequencing, genome

one strategy for assaying molecular variations in populations:

Target __ chromosome, _______, and/or ________

Y, mitochondria, chloroplasts

what are the steps to analyze SNP classification?

1. Assemble discovery panel

2. Resequence individuals

3. Align and compare

4. Identify SNPs

5. Classify as rare or common

what are these: SNP, indel, microsatellite?

types of molecular markers

what does a haplotype network show?

the relationship among haplotypes

what is the gene pool?

the sum total of alleles in a population

what describes the relationship between allelic and genotypic frequencies in a random-mating population?

Hardy-Weinberg Law

what are the hardy-weinberg critical assumptions?

1. Population is random-mating.

2. Equal viability of alleles. fitness (A) = fitness (a)

3. One population, no isolation.

4. The populations is infinitely large.

what is the hardy-weinberg equation?

p2+2pq+q2=1.0

what can we use to calculate genotype frequencies in the next generation from the allele frequencies in the current generation?

the hardy-weinberg law

Genetic variation is neither created nor destroyed by the process of __________________________________________

transmitting genes to the next generation

does hardy-weinberg apply if there are more than 2 alleles per locus?

yes

what kind of populations usually deviate to a small or large degree from the Hardy–Weinberg model?

real

Depending on the type of non-random mating occurring, it can increase the frequency of _________ _______ in a population, or increase the frequency of __________ __________ in a population.

homozygous genotypes, heterozygous genotypes

what can inbreeding do?

increase the frequency of homozygous genotypes in populations

what do species show?

population structure

what is genetic drift?

a random force that can lead to the loss or fixation of an allele as a result of sampling error in finite populations

when is drift a strong force?

in small populations

when is drift a weak force?

in large populations

what is evolution?

the change in populations or species over time

Evolution is the conversion of ______ _______ _____ between individuals within populations into heritable differences between populations in time and in space by ________ ________ ________.

heritable genetic variation, population genetic mechanisms

what is darwinian fitness?

The relative probability of survival and reproduction for a genotype

what type of selection leaves a distinct signature?

positive

What forces impact diversity and modulate variation?

mutation, migration/gene flow, drift, and selection

does mutation increase or decrease genetic variation?

increase

does migration/gene flow increase or decrease genetic variation?

increase

does drift increase or decrease genetic variation?

decrease

does selection increase or decrease genetic variation?

both

what force results in new haplotypes, molecular clock, creates LD?

mutation

what force causes admixture, increases admixture, creates LD?

migration/gene flow

what force results in fixation and low diversity?

drift

what force results in selective sweep or increased heterozygosity?

selection

what are populations often rich in?

genetic variation

what is the ultimate source of all genetic variation?

mutation

how can migration add genetic variation to a population?

via gene flow from another population of the same species

what is linkage disequilibrium?

the outcome of the fact that new mutations arise on a single haplotype

why will linkage disequilibrium decay over time?

because of recombination

what do population structure and genetic bottlenecks do?

reduce variation and drive changes between populations

what signature does selection leave in the genome?

the pattern of genetic diversity surrounding the target of selection

what force can both drive favorable alleles at a locus to fixation or maintain multiple alleles at a locus in a population?

selection

____________ drives changes in allele frequencies in populations over time

selection

what are the principles of darwin’s theory of evolution?

principle of variation, principle of heredity, principle of selection

what is darwin’s principle of variation?

among individuals in a population, there is variation in morphology, physiology, and behavior

what is darwin’s principle of heredity?

offspring resemble their parents more than they resemble unrelated individuals

what is darwin’s principle of selection?

some individuals are more successful at surviving and reproducing than others in a given environment

what forces decrease variation within populations?

inbreeding/genetic drift, directional selection, and incompatability

what forces increase variation within populations?

mutation, migration, and balancing

what forces decrease variation between populations?

mutation, migration, directional selection, and balancing

what forces increase variation between populations?

inbreeding/genetic drift, directional selection, and incompatability

what is fitness?

the capability of an individual of certain genotype to survive and reproduce

how many different effects of mutations are there on fitness?

three(decrease, increase, no effect)

what is purifying selection?

the selective removal of alleles that are deleterious

what does deleterious mean?

decreases fitness

what kind of selection is associated with decreased fitness?

purifying selection

what kind of selection is associated with increased fitness?

adaptive selection

what kind of mutation is associated with no effect on fitness?

neutral mutation

what are purifying selection and adaptive selection examples of?

natural selection

what is a neutral mutation an example of?

random genetic drift

the neutral theory of molecular evolution says:

most mutations are ________

neutral

the neutral theory of molecular evolution says:

Most mutations are _________ ______ due to drift

fixed randomly

the neutral theory of molecular evolution says:

All classes of DNA sequences exhibit _____ ______ among populations and species

nucleotide diversity

the neutral theory of molecular evolution says:

molecular change ______ ____ ______ visible change

does not equal

is mutation rate higher at synonymous site or nonsynonymous sites?

synonymous

what is synonymous substitution?

A mutation that changes one codon for an amino acid into another codon for that same amino acid

what type of substitution is also called silent mutation?

synonymous

what is nonsynonymous substitution?

a type of genetic mutation where a change in a single DNA nucleotide alters the resulting amino acid in a protein

what is purifying selection?

a pervasive aspect of natural selection that reduces genetic variation and preserves DNA and protein sequences over eons of time

what is evidence for natural selection provided by?

syn sites vs nonsyn site divergence

what does the relative fitness of a new variant depend on?

the immediate selective conditions

If there is no variation within a species for some trait, there can be no _______

evolution

what is most evolution at the molecular scale?

the replacement of one protein sequence by another one of equivalent function

what is the number of amino acid differences between two different species in some molecule is directly proportional to?

the number of generations since their divergence from a common ancestor

genetic evolution is subject to ________ ________ _____ ________, but it is

constrained by the necessity of organisms to ___________ _____ ________

historical contingency and chance, survive and reproduce

what are qualitative traits?

well defined gene-determined phenotypic characteristics

what are these examples of: Mendelian traits: variation in kind, monogenic traits?

qualitative traits

what are quantitative traits?

phenotypic characteristics that vary in degree, and thus generally are measured by such units as meters, pounds, and bushels

what are these examples of: heights, lengths, weights, crop yields?

quantitative traits

what traits are controlled by multiple genes?

polygenic

what are phenotypic characteristics athe result of in polygenic traits?

the interaction of multiple genes

what kind of trait do environments play a larger role in?

quantitative

what is a Quantitative Trait Locus (QTL)?

a locus contributing to a quantitative trait

what are quantitative genetics?

the studies of inheritance of quantitative traits in different environments

what traits is complex inheritance exhibited by?

traits affected by both genetic and environmental factors—typically quantitative/continuous/complex

what does the field of quantitative genetics study?

the inheritance of complex traits using some basic statistical tools

what is the genetic architecture of a trait?

the full description of the number of genes affecting the trait

their relative contributions to the phenotype

the contribution of environmental factors to the phenotype

an understanding of how the genes interact with one another and with environmental factors

what is the mathematical model used to describe the genetic architecture of complex traits?

decomposes the phenotypes of individuals into differences that are due to genetic factors (g) and those that are due to environmental factors (e)