Bio 435C Exam2

Front 1

The null model for population genetics is

a) Newton's first law.

b) the competitive exclusion model

c) cell theory.

d) the endosymbiosis theory.

e) the Hardy-Weinberg model.

Back 1

e) the Hardy-Weinberg model

Front 2

Consider a diploid population in which a single locus has only two alleles, A1 and A2, whose respective allele frequencies equal p and q. The summation of p+q would equal:

a) 0.25

b) 0.5

c) 1

d) 1.5

e) 2

Back 2

c) 1

Front 3

The selection coefficient describes

a) the value

b) how many individuals survive to reproduction

c) the fitness difference between one genotype and an alternative genotype

d) the change in allele frequencies due to direct selection.

e) the degree of dominance of one allele relative to an alternative allele.

Back 3

c) the fitness difference between one genotype and an alternative genotype

Front 4

At an underdominant locus, how will allele frequencies change through time?

a) The homozygote with the greatest fitness advantage will have its allele fixed.

b) A balance polymorphism of both alleles will be maintained at a stable equilibrium.

c) The homozygote with the lowest fitness advantage will have its allele lost.

d) One or the other allele will be lost depending on their initial frequencies.

e) Both alleles will be lost

Back 4

d) One or the other allele will be lost depending on their initial frequenicies

Front 5

Balancing selection

Back 5

Natural selection that leads to an intermediate phenotype or to a stable equilibrium in which more than one allele is present.

Front 6

Balanced polymorphism

Back 6

A stable equilibrium in which more than one allele is present at a locus.

Front 7

Inbreeding depression is caused by

a) a reduction in fitness caused by deleterious recessives

b) random mating

c) mutation-selection balance

d) A and B

e) All of the above

Back 7

a) a reduction in fitness caused by deleterious recessives

Front 8

Two gene copies are identical by descent if

a) two individuals have the same parents

b) one allele mutates to a second allele

c) selfing occurs

d) they are both inherited from the same gene copy in a recent common ancestor.

e) balancing selection maintains two or more alleles

Back 8

d) they are both inherited from the same gene copy in a recent common ancestor

Front 9

Population bottlenecks occur when

a) a large number of genetically diverse individuals found a new population

b) population size dramatically increases

c) a consistently large population experiences a brief period of small size

d) drift in consistently small populations become fixed for a single allele.

e) inbreeding is high

Back 9

c) a consistently large population experiences a brief period of small size

Front 10

A founder event changes allele frequencies because

a) only a subset of genes in the original population are observed in the founder

b) of random sampling of alleles from the original population

c) of the coalescent process

d) A and B

e) All of the above

Back 10

d) A and B

Front 11

The neutral theory of molecular variation posits that most

a) mutations are neutral

b) substitutions are neutral

c) mutations are deleterious

d) B and C

e) All of the above

Back 11

b) substitutions are neutral

Front 12

Which of the following mutations to a codon is most likely to be selectively neutral?

a) UUG (Leu) -> CUG (Leu)

b) AUA (lle) -> AUG (Met)

c) AAC (Asn) -> AAA (Lys)

d) UGC (Cys) -> UGA (Stop)

e) AGC (Ser) -> AGA (Arg)

Back 12

a) UUG (Leu) -> CUG (Leu)

Front 13

A haplotype is

a) all of the alleles at a single locus

b) a product of epistasis

c) a set of alleles at different loci along a chromosome

d) all of the alleles in a population

e) none of the above

Back 13

c) a set of alleles at a different loci along a chromosome

Front 14

A bacteriophage was the first organism to have its genome sequenced. Sequencing of this genome was facilitated by

a) its complex genome

b) its short genome

c) previous studies of bacterial genomes

d) A and C

e) All of the above

Back 14

b) its short genome

Front 15

Eukaryotic genome size is

a) tightly correlated with organismal complexity

b) not well correlated with organismal complexity

c) largest in humans

d) typically smaller than prokaryotic genome sixe

e) approximately the same in all eukaryotes

Back 15

b) not well correlated with organismal complexity

Front 16

The C-value paradox is

a) the lack of correlation between genome size with organismal complexity

b) resolved by the identification of noncoding DNA

c) resolved by the discovery of linkage disequilibrium

d) A and B

e) All of the above

Back 16

d) A and B

Front 17

Factors that contribute to overall genome sice include

a) small genetic elements capable of self-catalyzing their movement

b) selection on cell size

c) selection on replication speed

d) A and B

e) All of the above

Back 17

e) All of the above

Front 18

The nematode, C. elegans, and humans have nearly identical numbers of protein coding genes, yethumans have much more complex organismal features. This is an example of

a) the C-value paradox.

b) the G-value paradox.

c) cell size paradox.

d) linkage disequilibrium.

e) None of the above

Back 18

b) the G-value paradox

Front 19

LUCA (last universal common ancestor)

Back 19

The population of organisms at the base of the tree of life. All living things today descended from this one lineage

Front 20

Which of the following was not a source of molecules in the prebiotic soup?

a) Meteorites

b) Comets

c) Prebiotic soup reactions

d) DNA

Back 20

d) DNA

Front 21

Why is DNA favored over RNA as genetic material?

a) DNA is more stable and thus is a more efficient transmission system

b) DNA can self-replicate

c) DNA makes chromosomes

d) DNA mutates more readily, with a weaker repair machinery

e) DNA has a more limited information storage capacity

Back 21

a) DNA is more stable and thus is a more efficient transmission system

Front 22

The two major cell types are

a) archaea and bacteria

b) Archaea and prokaryotes

c) prokaryotes and eukaryotes

d) eukaryotes and archaea

e) eukaryotes and bacteria

Back 22

c) prokaryotes and eukaryotes

Front 23

Which if the following statements regarding complexity is true?

a) evolution always progresses toward complexity

b) complexity, once gained, cannot be lost

c) modern bacteria and archaea are more complex than ancestral forms

d) complexity can be lost

Back 23

d) complexity can be lost

Front 24

The cell nucleus likely originated from a(n)

a) mitochondrion

b) archaeal cell

c) bacterium

d) eukaryote

Back 24

b) archaeal cell

Front 25

List five assumptions of the Hardy-Weinberg equilibrium.

Back 25

1) No selection

2) random mating

3) no mutation or migration

4) infinite population size

5) non-overlapping generations

6) sexual, diploid organisms

Front 26

What is the term for the condition in which the heterozygote is more fit than either homozygote?

Back 26

Overdominance or heterozygote advantage

Front 27

After one generation of inbreeding, one would expect to see a(n) ___ in heterozygotes but no change in ___ frequencies.

Back 27

decrease, allele

Front 28

What are transcription factors and how do they address the G-value paradox?

Back 28

Transcriptionfactors are proteins that bind to and regulate DNA expression. By manipulating the expression of genes,transcription factors can increase the complexity of a genome’s regulatorynetwork and the organisms phenotypic complexity.

Front 29

Describe a haplotype block.

Back 29

Ahaplotype block is a region of a chromosome in which there is little geneticdiversity, recombination is rare, and linkage disequilibrium is high.

Front 30

associative mating

Back 30

A mating pattern in which individuals with similar phenotypes or genotypes mate with one another

Front 31

balanced polymorphism

Back 31

A stable equilibrium in which more than one allele is present at a locus

Front 32

balancing selection

Back 32

Natural selection that leads to an intermediate phenotype or to a stable equilibrium in which more than one allele is present

Front 33

directional selection

Back 33

A process of selection in which selection drives phenotype in a single direction, or in which selection drives allele frequencies in a single direction toward fixation of a favored allele.

Front 34

disassortative mating

Back 34

A mating pattern in which individuals with dissimilar phenotypes or genotypes mate with one another

Front 35

fecundity

Back 35

A measure of the ability to produce offspring

Front 36

fixation

Back 36

In population genetics, an allele is said to go to fixation in a population when it replaces all alternative alleles at the same locus-that is, when its frequency reaches 1

Front 37

frequency-dependent selection

Back 37

A form of selection in which the fitness associated with a trait or genotype is dependent upon the frequency of that trait or genotype in a population

Front 38

frequency-independent selection

Back 38

A form of selection in which the fitness associated with a trait is not directly dependent upon the frequency of that trait in a population

Front 39

Hardy-Weinberg equilibrium

Back 39

Given a set of allele frequencies, the expected set of genotype that will be observed under the Hardy-Weinberg model

Front 40

Hardy-Weinberg model

Back 40

A null model for how genotype frequencies relate to allele frequencies in large populations and how they change over time in the absence of these evolutionary processes: natural selection, mutation, migration, assortative mating, and genetic drift.

Front 41

heterozygote advantage

Back 41

A form of frequency-independent selection in which heterozygote genotypes have higher fitness than the corresponding homozygote genotypes

Front 42

identical by decent

Back 42

When two or more gene copies are identical because of shared descent through a recent common ancestor

Front 43

inbreeding

Back 43

Mating with genetic relatives

Front 44

inbreeding depression

Back 44

A decrease in fitness that results from individuals mating with genetic relatives

Front 45

mutation-selection balance

Back 45

The hypothesis that senecence occurs because natural selection is not strong enough to purge deleterious mutations associated with traits that are expressed only late in life

Front 46

overdominance

Back 46

A form of frequency-independent selection in which heterozygote genotypes have higher fitness than the corresponding homozygote genotypes

Front 47

population genetics

Back 47

A subdiscipline in evolutionary biology that investigates how allele frequencies and genotype frequencies change over time

Front 48

selection coefficient

Back 48

A measure of the strength of natural selection for or against a specific phenotype or genotype

Front 49

underdominance

Back 49

A form of frequency-independent selection in which the heterozygote genotype has a lower fitness than either corresponding homozygote genotype

Front 50

Wright's F-statistic

Back 50

A statistical measure of the degree of homozygosity in a population

Front 51

Coalescent point

Back 51

The point on a gene tree that delineates the gene copy that is the most recent common ancestor of the genes being studied in a population

Front 52

coalescent theory

Back 52

A theory developed to study the gene-genealogical relationships in a population by tracing the ancestry of gene copies backward from the present through a finite population

Front 53

effective population size

Back 53

The size of an idealized population (no migration, mutation, assortative mating, or natural selection) that loses genetic variation due to genetic drift at the same rate as the population under study

Front 54

expected heterozygosity

Back 54

Denoted He, this is the fraction of heterozygotes expected under the Hardy-Weinberg model, given the allele frequencies in the population

Front 55

founder effect

Back 55

A change in allele frequencies that results from sampling effects that occur when a small number of individuals derived from a large population initially colonize a new area and found a new population

Front 56

genetic drift

Back 56

Random fluctuation in allele frequencies over time due to sampling effects in finite populations

Front 57

molecular clock

Back 57

A technique for assigning relative or absolute age based on genetic data. In their simplest form, molecular clock methods assume that substitutions at neutral loci occur in clock-like fashion, and so researchers use genetic distances between populations to estimate the time since divergence

Front 58

nearly neutral theory

Back 58

The hypothesis that most substitutions, if not strictly neutral, are only mildly deleterious

Front 59

neutral theory

Back 59

The hypothesis that at the molecular level of DNA sequence or amino acid sequence, most of the variation present within a population and most substitutional differences between populations are selectively neutral

Front 60

nonsynonymous mutation

Back 60

A mutation in a gene that changes the amino acid sequence of the protein that gene encodes

Front 61

observed heterozygosity

Back 61

The fraction of individuals in the population that are heterozgous at a given locus

Front 62

population bottleneck

Back 62

A brief period of small population size. Population bottlenecks reduce genetic diversity and can accelerate changes in allele frequencies due to genetic drift

Front 63

pseudogene

Back 63

A nonfunctional and typically untranslated segment of DNA that arises from a previously functional gene

Front 64

selectively neutral

Back 64

Alternative alleles are selectively neutral when there is no fitness difference between them

Front 65

substitutions

Back 65

The process in which a new allele arises by mutation and is subsequently fixed in a population

Front 66

Wright-Fisher model

Back 66

A population genetic model of evolutionary change in small populations with nonoverlapping generations

Front 67

adaptive landscape

Back 67

A heuristic representation of fitness as a function of genotype or phenotype. Adaptive landscapes are commonly used by biologists to envision the course of evolutionary change. Also known as fitness landscapes

Front 68

additive genetic effects

Back 68

Genetic contributions to phenotype for a polygenetic trait, in which the effects of each allele simple sum to together to determine phenotype

Front 69

background selection

Back 69

A process by which neutral or beneficial alleles are lost because they are physically linked to nearby deleterious alleles. Background selection decreases genetic variation relative to what would be expected in a neutral model

Front 70

breeder's equation

Back 70

The equation R=(h^2)s, relating the selection response R to the selection differential S and the narrow-sense heritability h^2

Front 71

broad-sense heritability

Back 71

(H^2) The fraction of the phenotypical variance that can be attributed to genetic causes and thus is potentially heritable

Front 72

clonal interference

Back 72

An overall reduction in the rate at which beneficial alleles are fixed in asexual populations due to the competition amoung alternative beneficial mutations

Front 73

coefficient of linkage disequiliribum

Back 73

A measue of nonrandom association between alleles at two different loci. The coefficient of linkage disequilibrium D between two loci is defined as the difference between the actual frequency of a haplotype and the expected frequency of that haplotype if there were no association between alleles at one locus and alleles at the other locus

Front 74

coupling

Back 74

Linkage disequilibrium in which the coefficient of linkage disequilibrium D is positive

Front 75

dominance effects

Back 75

Interactions between two alleles at the same locus in determining phenotype

Front 76

epistasis

Back 76

The phenomenon in which alleles at two or more loci interact in nonadditive ways to determine phenotype

Front 77

fitness peaks

Back 77

Combinations of trait associated with the greatest fitness values on an adaptive landscape

Front 78

fitness valleys

Back 78

Combinations of traits associated with lower fitness values on an adaptive landscape

Front 79

genetic hitchhiking

Back 79

THe process by which a neutral or even disadvantageous allele is able to "ride along" with a nearby favorable allele to which it is physically linked, and thus increase in frequency

Front 80

genotype space

Back 80

A conceptual model in which similar genotypes occupy nearby points on a plane. Adaptive landscapes are often illustrated in genotype space

Front 81

haplotype

Back 81

a set of alleles, one at each locus

Front 82

linkage disequilibrium

Back 82

The presence of statistical associations between alleles at different loci

Front 83

narrow-sense heritability

Back 83

The fraction of the total phenotypic variation that is due to additive genetic variation and this is readily accessible to natural selection

Front 84

periodic selection

Back 84

A process in which a series of clones carrying beneficial mutations successively go to fixation in an asexual population

Front 85

phenotype space

Back 85

A conceptual model in which similar phenotypes occupy nearby points on a plane. Adaptive landscapes are often illustrated in phenotype space.

Front 86

physical linkage

Back 86

The occurrence of two or more loci on the same chromosome. Physical linkage causes alleles at linked loci to segregate together (in the absense of recombination) into the gametes

Front 87

polygenic

Back 87

Traits that are affected by many genes simultaneously

Front 88

QTL mapping

Back 88

A technique for identifying the regions of the genome in which quantitative trait loci occur

Front 89

quantitative genetics

Back 89

A mathematical approach to to the population genetic study of continuously varying traits

Front 90

quantitative trait loci (QTLs)

Back 90

Loci responsible for quantitative-that is, continuously carrying- traits

Front 91

realized heritabilities

Back 91

Narrow-sense heritability values estimated by using values of the selection differential and selection response in the breeder's equation

Front 92

repulsion

Back 92

Linkage disequilibrium in which the coeffeicient of linkage disequilibrium D is negative

Front 93

selection differential

Back 93

In quantitative genetics, the difference between the mean trait value of the individuals who reproduce and the mean trait value of all individuals

Front 94

selection response

Back 94

In quantitative genetics, the difference between the mean trait value of the offspring population and the mean trait value of the parental population

Front 95

selective sweep

Back 95

A phenomenon in which a selected allele goes to fixation, carrying with it alleles at tighty linked loci

Front 96

centromere drive

Back 96

Selection at the level of the chromosome that favors mutations to centromeres that increase their chance of segregating to oocyte instead of to the polar bodies

Front 97

codon usage bias

Back 97

A bias in which certain codons occur more frequently than others that specify the same amino acid

Front 98

conservative transposons

Back 98

A transposable element that excises itself and moves to a new location while leaving the original copy in place

Front 99

C-value paradox

Back 99

The observation that differences in genome size measured in base pairs do not correlate with the number of protein-coding genes that an organism has, nor with its phenotypic complexity

Front 100

evolutionary genomics

Back 100

The study of how the composition and structure of genomes have evolved and are evolving

Front 101

GC content

Back 101

The fraction of nucleotides in a gene, chromosomes, or genome that are G or C rather that A or T

Front 102

GC skew

Back 102

A measure of whether G nucleotides or C nucleotides are overrepresented on either the leading or lagging strand of the chromosome/ Typically measures as the (G-C)/(G+C) ratio of nucleotides along one strand of the chromosome

Front 103

G-value paradox

Back 103

The observation that despite seemingly large differences in organismal complexity, multicellular eukaryotes tend to have very similar numbers of protein-coding genes

Front 104

isochores

Back 104

Extended stretches on chromosomes that have similar GC content

Front 105

LINEs

Back 105

Long interspersed Elements. A common clas of transposable elements, these autonomous transposons make up approx 17% of the human genome

Front 106

nonconservative transposons

Back 106

A transposable element that creates a duplicate copy of itself to be inserted elsewhere in the genome rather that excising its self and moving to a new location

Front 107

SINEs

Back 107

Short interspersed elements. A common class of transposable elements in humans, these non-autonomous transposons are incapable of independent replication but rather rely on genes encoded by autonomous transposons elsewhere in the genome

Front 108

transcription factors

Back 108

Proteins that bind to DNA and influence gene expression

Front 109

transposable elements

Back 109

A self-replicating genetic unit that can move or copy itself within a genome

Front 110

LUCA (last universal common ancestor)

Back 110

The population of organisms at the base of the tree of life. All living things today are descended from this one lineage

Front 111

phylogenetic event horizon

Back 111

The point in the history of life beyond which phylogenetic analysis is uninformative because there are no surviving descendants from ancestors before this point

Front 112

RNA world

Back 112

A hypothetical early stage in the history of life in which RNA was the fundamental unit which life was based, fulfilling both an informational roal and a catalytic role

Front 113

Prebiotic soup hypothesis

Back 113

The idea that the earliest life emerged in a "soup-like" liquid environment, drawing upon energy from cosmic rays, volcanic eruptions, and the Earth's own internal heat

Front 114

ribozymes

Back 114

RNA molecules with enzymatic function

Front 115

many eyes hypothesis

Back 115

The hypothesis that group living provides an advantage in the ability to detect predators