Cons Gen -- Final Exam

list one proximate cause, or driver, of genetic erosion

list one proximate cause, or driver, of genetic erosion

reduced population size

because of their resolution and ability to capture fine-scale structure, population delineation should be conducted with genetic/genomic data to the exclusion of other data types (e.g., demographic, behavioural, etc.)

false

the earliest stages of speciation often begin with gradual genetic differentiation (the sundering of a gene pool), but the entire process typically takes hundreds of thousands or millions of years

true

over time, hybrid zones change in three ways. what are they?

reinforcement, fusion, stability

genetic rescue can occur when two inbred populations are crossed if outbreeding depression goes down and overall genetic relatedness goes up.

false

genetic erosion refers to the overall loss of genetic diversity, which includes the loss of individual genes and their combinations

true

genetic rescue can affect the community through all of the following except

- increasing individual niche partitioning
- adapting to the current habitat and reducing dispersal
- reversing the direction of genetic Allee effect
- higher resilience to demographic stochasticity
- reinforcing predator-prey dynamics

adapting to the current habitat and reducing dispersal

peripheral populations are generally more prone to extinction than are core populations. Which of the following statements about populations is untrue?

• peripheral populations may contain important genetic variants that are not present in core populations

• peripheral populations are often subject to reduced gene flow

• core populations usually contain unique genetic variants that are deleterious

• peripheral populations are often subject to reduced efficiency of selection because of small population sizes

• peripheral populations always have higher genetic diversity

peripheral populations always have higher genetic diversity

the ___ defines species to include “any species of fish or wildlife or plants and any ___ of any species of fish or wildlife which interbreeds when mature.”

Endangered Species Act, distinct population segment

hybridization can be assessed with genetic markers, and such marker data are commonly used to define new subspecies irregardless of geography

false

genetic tools reflect evolutionary timescales (millenia) whereas environmental niche modeling reflects ecologicla timescales (tens or hundreds of years)

true

as long as a founding captive population is large enough, captive breeding and subsequent reintroduction programs will be successful as the effects of inbreeding, drift and selection ill be mitigated

false

greater habitat connectivity can decrease the odds of outbreeding depression and local adaptation by increasing gene flow, thus decreasing genetic differentiation between and among populations

true

adaptations to captivity can be maladaptive in the wild because captive animals will dominate when released/reintroduced into the natural population

false

habitat loss can occur even without a concomitant loss in its geographic footprint if barriers to movement (powerlines) emerge

true

which of the following is the least likely outcome of vertebrate road mortality?

• reduced gene flow

• decreased genetic diversity

• decreased hybridization

• reduced effective population size

• increased genetic structure

decreased hybridization

zoos contribute to conservation in several ways, including (choose all that apply):

• sustaining captive individuals to increase genetic diversity

• recovery of endangered species

• exhibition of animals not locally common

• research (animal husbandry)

• conservation policy insights

• recovery of endangered species

• exhibition of animals not locally common

• research (animal husbandry)

For the associated Figure, pick the 3 plots (i.e., from choices a, b, c, d, e, and/or f) that best correspond to the answer choices below:

• isolated by distance

• random mating population

• fragmented cline

b, a, e

Which statement best describes A) heterozygote(s), B) homozygote(s), and C) genotype(s)? (1 point each)

The alleles a person has are called  (Blank 1) ____________.

(Blank 2) ___________ have two identical alleles at a gene locus.

(Blank 3) ____________ have two different alleles at a gene locus.

genotypes; homozygotes; heterozygotes

What is the ultimate source of genetic diversity in every population?

Mutation

There are exceptions to most, if not all, scientific Laws. For example, Newton's Law of Gravity (describing the force of gravitational attraction between two bodies as the product of the masses and inversely as the square of the distance between them) breaks down at the quantum level. Pick two of Mendel's three laws and describe how they are often violated in nature (in the future, provide explanation).

Law of Dominance: incomplete dominance, codominance, multiple alleles, multifactorial traits)

Law of Independent Assortment: linked genes

Explain the "semi-conservative" process of DNA replication.

Each new DNA molecule comprises one original strand and one newly synthesized strand that complements the original.

Which of the following statement is NOT true about dosage compensation in mammals?

• Dosage compensation accounts for the observation that the amount of product formed by two copies of a gene is the same as that formed by having only one copy of that gene.

• The X-chromosome displays dosage compensation.

• One of the two X chromosomes in each cell is randomly inactivated early in development.

• Females heterozygous for X-linked traits are the homogametic sex.

Females heterozygous for X-linked traits are the homogametic sex.

Allelic variation among loci is "shuffled" through independent assortment of chromosomes. Using a single word, how else is allelic variation shuffled within a chromosome?

Recombination

Eukaryotic genes consist of introns (A), exons (B) and regulatory sequences (C).  Choose the correct answers. (1 point each).

(Blank 1)__________ are coding sequences that specify a polypeptide or protein.

(Blank 2)_________ are non-coding sequence that serve in part as spacers to facilitate copying/cutting/pasting new forms of genes or gene products (i.e., RNA or proteins). 

(Blank 3)_________ are molecular tuning knobs that are used to increase or decrease gene expression. 

exons; introns; regulatory sequences

Which of the following statements is correct?

• Edwin Chargaff found that the amount of A and C are proportional to G and T, respectively, and this empirical fact helped scientists elucidate the double-helical structure of DNA.

• Multifactorial traits are the same as quantitative traits and such traits are influenced by multiple genes.

• Genes can assort independently among gametes even if they are on the same chromosome.

• There are so few Y-linked traits because the Y chromosome contains a very small number of genes, far fewer than any autosome or the X chromosome.

There are so few Y-linked traits because the Y chromosome contains a very small number of genes, far fewer than any autosome or the X chromosome.

Gaucher's disease, an autosomal recessive condition, is much more common in Ashkenazi Jews than in the general population. Charles, a Jewish man without the disease, has a sister with Gaucher's as does his father. His mother is unaffected. Charles's wife, Rachel, does not show the disease but knows she carries a disease allele. What is the probability that the first child of Charles and Rachel will not show Gaucher's disease, but has a disease allele?

1/4

Polydactyly (extra fingers) is a rare, monogenic condition inherited as an autosomal dominant trait. A man with six fingers on each hand and his unaffected wife seek genetic counseling. Their first son has six fingers on each hand, but the second son has five fingers. What is the probability that their next child will have polydactyly?

1/2

More than 98% of genomic DNA codes for proteins

False

If your favorite species' genome has a (high) mutation rate of 1 x 10^-4 per gene per generation then, on average, a mutation at any given gene occurs once every            generations.

10,000

During (Blank #1)__________, the information encoded in DNA is copied into mRNA (i.e., from nucleic acid to nucleic acid). The process of (Blank #2)__________ then converts the mRNA sequences into a sequence of amino acids called a polypeptide (i.e., from a nucleic acid to a protein). This information flow, from DNA->RNA->protein, is the basis of the (Blank #3)__________ of molecular biology.

transcription; translation; central dogma

The eminent evolutionary biologist, Theodosius Dobzhansky, said "nothing in biology makes sense except in the light of evolution." List two pieces of scientific evidence from molecular biology that support this contention.

(any of the following)

• Homology of genes from bacteria to man

• common informational macromolecule (DNA)

• functional macromolecules (proteins)

• mutation as driving force for natural selection

The phenomenon termed (Blank #1)__________ silences the great majority of genes on one of the two X chromosomes. In contrast, (Blank #2)__________ silences one gene at a time across many different autosomes. (Blank #1)__________ is random in that either the paternally derived chromosome or the maternally derived chromosome is affected. In (Blank #2)__________, either the allele transmitted by the father or the one transmitted by the mother will be silenced in an ordered non-random fashion from one generation to the next.

X-inactivation; imprinting

Which of the following statement is incorrect about mutation in protein-coding genes?

• A nucleotide substitution could be silent if it produces no change in the amino acid sequence (i.e., a silent substitution).

• A nucleotide substitution could produce a change in the amino acid, but this single amino acid change could be neutral (e.g., an exchange of two similar amino acids like a valine for an alanine).

• A synonymous nucleotide substitution in an exon could produce a functional change in the resulting protein.

• A nucleotide substitution could occur in an intron and therefore be removed during splicing of the primary transcript.

A synonymous nucleotide substitution in an exon could produce a functional change in the resulting protein.

It is reported that the human genome has ~25,000 protein-coding genes that have the capacity to produce several hundred thousand gene products. What can directly account for the vast difference in gene number and product number? Choose all that apply.

• tRNA transformation

• Alternative promoters

• Post-translational modification

• Alternative splicing of immature mRNA

• mRNA editing

• Alternative promoters

• Post-translational modification

• Alternative splicing of immature mRNA

  • mRNA editing

A spontaneous mutation is a heritable alteration in the nucleotide sequence (or structure) of the genome of an organism. Which of the following does not represent a causative mechanism underlying a spontaneous mutation? Choose all that apply.

• Proofreading errors associated with DNA polymerase

• Replication slippage

• Base misincorporation errors associated with DNA polymerase

• Diet (e.g., aflatoxins)

• Replication slippage

• Base misincorporation errors associated with DNA polymerase

• Diet (e.g., aflatoxins)

The base sequence of the template DNA strand is 5'-AATCAGACATGCGTC-3'. What is the base sequence of the primary transcript of this template DNA strand?

5'-GACGACUGUCUGAUU-3'

(Blank #1)           of the genetic code means that the same amino acid can be encoded by more than one codon. It occurs most often due to changes in the (Blank #2)           position of codons.

degeneracy; third

What type of mutation should (in general) be the most deleterious in terms of the probability of "protein" change?

Frameshift mutation

In a screening program to detect a-thalassemia in Sri Lanka, the heterozygote "carrier" frequency was 4%. What is the fraction of Sri Lankan population that does not show a-thalassemia? Assume that there are three alleles including a normal allele, a dominant mutant allele, and a recessive mutant allele, and the recessive mutant allele's frequency is a half of the normal allele's frequency. 

0.08

A population cannot have low heterozygosity and high allelic diversity at the same time.

False

(Blank)__________ is one of three levels of biodiversity—the others being species diversity and ecosystem diversity--recommended for conservation by the International Union for Conservation of Nature as well as the Convention on the Biological Diversity.

genetic diversity

Inbreeding changes genotype frequencies by increasing homozygosity, but it does not change allele frequencies.

True

The rate of mutation exceeds the rate of genetic drift in the absence of gene flow.

False

Sexual selection, including male-male competition and female choice, can lead to deviations from Hardy-Weinberg equilibrium for reasons such as nonrandom mating.

True

Positive assortative mating for a given trait increases homozygosity at the loci responsible for the trait.

True

Because natural selection favors well-adapted genotypes, it always acts to decrease genetic diversity.

False

Which of the following best describes the relationship among population size, drift, inbreeding, fixation, and fitness decline?

• The harmful alleles that ultimately contribute to inbreeding depression are less likely to be fixed by mutation and drift in smaller populations.

• The harmful alleles that ultimately contribute to inbreeding depression are more likely to be fixed by mutation and drift in larger populations.

• The harmful alleles that ultimately contribute to inbreeding depression are less likely to be fixed by mutation and drift in larger populations.

The harmful alleles that ultimately contribute to inbreeding depression are less likely to be fixed by mutation and drift in larger populations.

In a field study by Meagher et al. (2000), the reproductive success of field mice was measured in part by survival of weaned offspring.  In outdoor enclosures, the male inbred mice showed a weaned offspring survival rate of 22%, while the outbred male mice had a weaned offspring survival rate of 50%.  Using the equation from the lecture notes and/or the textbook, what is the general measure of inbreeding depression (δ)?

δ = 0.56

In the following graphic of the extinction vortex, match each number to the correct word or phrase below:

Inbreeding (1 or 2), Loss of genetic variability (3), Random genetic drift (1 or 2), Higher mortality (4 or 5), Lower reproduction (4 or 5).

(Blank)__________ describes the proportion of total phenotypic variation in a population due to genetic factors.

heritability

What principle is a null model for population genetics and states that populations following idealized conditions will have the same allele frequencies from one generation to the next?

Hardy-Weinberg Equilibrium

Among the options below, which are the correct assumptions necessary for Hardy-Weinberg Equilibrium? Select all that apply.

• Allelic frequencies may not be the same in males and females

• No genotype provides any advantages for viability and fertility

• Mating is not random

• The population is sufficiently large that allele frequencies do not change across generations

• The number of alleles per locus should not exceed four

• Mutation regularly occurs to generate new alleles

• Immigration exceeds emigration

• No genotype provides any advantages for viability and fertility

• The population is sufficiently large that allele frequencies do not change across generations

A diploid, sexual organism has a locus with 4 alleles:  the frequency of the A allele is f(A) = 0.3, the frequency of the B allele is f(B) = 0.2, the frequency of the C allele f(C) = 0.1, and the frequency of the D allele f(D) = 0.4. What are the expected genotype frequencies for AB, BC, CD, and AD?

f(AB) = 0.12; f (BC) = 0.04; f (CD) = 0.08; f(AD) = 0.24

(Blank #1): a change from one allele to another resulting from additions, deletions, or substitutions of nucleotides in the original DNA sequence. Increases variation in a population. 

(Blank #2): the effective exchange of genetic material from one population to another via migration; homogenizes the two populations. 

(Blank #3): Nature's "preference" for/against phenotypes through the process of differential survival and reproduction due to heritable characteristics. 

(Blank #4): sampling error resulting from the random change in allele frequencies from one generation to the next; greater effect in small populations, which may cause alleles to be more rapidly fixed or lost; decreases genetic variation. 

mutation; gene flow; natural selection; genetic drift

Go to the AlleleA1 web site (https://faculty.washington.edu/herronjc/a1/) and simulate a single population with a starting A1 frequency of 0.7, a finite population of size = 50, no migration, no selection, unidirectional mutation rate from A1 to A2 = 0.001, and an inbreeding coefficient = 0.7. What happens to the allele A1 over 5000 generations?

decreasing to nearly zero

Repeated generations of self-fertilization can increase autozygosity to the theoretical maximum of 100%.

True

In any given species, the potential severity of outbreeding depression is generally higher than inbreeding depression.

False

Individuals polymorphic at functional Major Histocompatibility Complex (MHC) loci usually suffer more seriously from pests, parasites, and infectious diseases than do inbred individuals.

False

Compared to a single large population of the same total size, completely isolated and fragmented populations experience all of the following except:

• Inbreeding depression

• Increased inbreeding

• Elevated extinction risk

• Loss of genetic diversity over generations

• Increased ability to evolve

Increased ability to evolve

In a hypothetical study on five Canadian populations of moose (Alces alces), the average observed heterozygosity for 21 microsatellite loci was 0.42. The average of expected heterozygosity within these populations was 0.63. The expected heterozygosity across all five populations was 0.75. Provide the answers below to two decimal places.

A) Calculate the inbreeding within populations

B) Calculate the inbreeding due to population differentiation

C) Calculate the total inbreeding due to both inbreeding within populations and differentiation among them.

A) 0.33

B) 0.16

C) 0.49

Fill in the blanks regarding zygosity and fitness.

The (Blank #1)           hypothesis posits that a heterozygote advantage is specifically due to the assayed loci.

The (Blank #2)           hypothesis claims that marker loci are closely linked to fitness loci.

The (Blank #3)          hypothesis claims that a heterozygote advantage is conveyed not by the scored loci or tightly linked loci but by genome-wide effects (heterosis).

direct effect; local effect; general effect

The genetic effects of habitat fragmentation depend upon (choose all that apply):

• distribution of individuals in fragments

• time since fragmentation

• effective migration rates

• geographic distribution of fragments

• All of the choices

• predator-prey dynamics

• distribution of individuals in fragments

• time since fragmentation

• effective migration rates

• geographic distribution of fragments

What is not a common mechanism underlying Outbreeding Depression?

• Maladaptation

• Genetic compatibility

• Physiological incompatibility

• Chromosomal inversions

• Reproductive isolation

Genetic compatibility

Which of the following statements is incorrect?

• Genetic rescue effects typically persist to at least the F3 generation and, in outbreeding species, are expected to stabilize by this time

• Genetic rescue is not impacted by the mating system

• Use of augmented gene flow between populations of outbreeding species is recommended when the risk of outbreeding depression is low

• The beneficial effects of genetic rescue generally far outweigh the negative effects of outbreeding depression (which are often predictable)

• Crossing of an inbred population to an unrelated population reduces inbreeding, and increases genetic diversity

Genetic rescue is not impacted by the mating system

Among vertebrates, an individual's sex can be determined genetically (by XY chromosomes or ZW chromosomes), by environmental conditions such as embryo incubation temperature, or by behavioral factors (e.g., dominance or agonistic interactions). 

True

The number of different proteins of a species is strictly determined by the number of genes whereby there is a 1:1 relationship between an individual gene and its singular protein product.

False

The Central Dogma of Molecular Biology states that genic information moves from DNA to RNA to protein in the direction of DNA replication -> translation -> transcription.

False

Using a hypothesis testing statistical framework, scientists can reject the null model based on goodness-of-fit tests with empirical data but doing so does not prove the alternative hypothesis.

True

Homologous sequences are orthologous if they are derived from a speciation event.

True

Microsatellites, often used as genetic markers in conservation efforts, occur in tens of thousands of locations in eukaryotic genomes and consist of di-, tri-, or tetra- nucleotide tandem repeats in DNA sequences. 

True

Genetic distance (i.e., recombination rate) is equivalent to physical distance at a chromosome level such that 1Megabase (Mb) = 1centiMorgan (CM).

False

In eutherian mammals, small portions of the X and Y chromosomes can cross-over because they share a homologous region

True

The term "genome" includes protein-coding genes, intergenic regions (i.e., gene deserts), non-functional pseudogenes, and repetitive regions such as telomeres, satellite DNA, and transposable elements.

True

Eukaryotic genes consist of exons, introns, and associated regulatory sequences such as promoters and enhancers.

True

List two characteristics of RNA which indicate it could be considered as the earliest replicator molecule.

• RNA can encode information

• RNA molecules can function as enzymes

Genome size does not correlate with organismal complexity; this phenomenon is called the (Blank)                      and is illustrated by the fact that some salamanders have genomes >10x the size of the human genome.

C-value paradox

A(n)         is any specific physical location in the genome, in a gene or chromosome. 

A(n)          is a part of the genome sequence that encodes an RNA or protein product.

A(n)          is a particular variant at a locus that may or may not result in phenotypic differences.

locus; gene; allele

The (Blank)                                Theory of Inheritance states that inherited traits are controlled by genes residing on chromosomes and are transmitted through gametes.

Chromosomal

During replication, the enzyme (Blank #1)____________ elongates the daughter strand in the 5' to 3' direction and the enzyme (Blank #2)____________ fuses the replicated DNA fragments into a contiguous molecule.

DNA polymerase; DNA ligase

The (Blank #1)             can be described as an organism's (Blank #2)             DNA content, which refers to the information in a single set of chromosomes.

genome; haploid

Which of the following is NOT a cost/problem associated with sexuality?

• Physiological and/or energetic expenses associated with rearing offspring of two different sexes

• Physiological and/or energetic expenses associated with finding a mate

• Physiological and/or energetic expenses associated with aggressive intrasexual competition

• Sexually transmitted diseases

Physiological and/or energetic expenses associated with rearing offspring of two different sexes

The nitrogenous bases (adenine, guanine, cytosine, and thymine) in DNA molecules are arranged in complementary pairs. Which nucleotide pairs with ADENINE in DNA? Which nucleotide pairs with it in RNA? If 22% of the DNA extracted from a shark genome is found to be ADENINE, what percentage will be represented by guanine, cytosine and thymine respectively?

thymine, uranine, 33, 33, 22 %

How many DNA duplex molecules are obtained from an initial single DNA duplex after 7 cycles of the polymerase chain reaction (PCR)?

128

A geneticist found that a specific mutation—a nucleotide substitution--has no effect on the polypeptide encoded by a given gene. Fill in the blanks for all possible reasons.

The substitution could be (Blank #1)          , meaning that it produced no change in the amino acid sequence.

The substitution could produce a change in the amino acid, but this single amino acid change would be (Blank #2)           .

The substitution could occur in an (Blank #3)            and therefore would be removed during splicing of the primary transcript.

synonymous; neutral; intron

If a trait is polygenic, determined by three biallelic genes with equally additive contributions to the phenotypic trait, what is the probability of the offspring phenotype having two dominant and four recessive alleles when the parental genotypes are AaBbCc and AaBbCc?

15/64

Which of the following terms is incorrectly matched with the definition?

• linkage: the co-inheritance of two genes because they are in close proximity on a chromosome and have little or no recombination between them

• none of them

• charged tRNA: a tRNA molecule to which an amino acid has been attached

• polygenic: One phenotypic trait influenced by many genetic loci

• transversion: substitution of one purine for another purine

• a and c are incorrect

• genotype: the alleles intrinsic to an individual

transversion: substitution of one purine for another purine

Is Mendel's law of independent assortment true for all pairs of genes? Why or why not?

No, not all pairs of genes follow the law of independent assortment because genes near each other (i.e., linked) on the same chromosome do NOT assort independently

Color blindness is a common X-linked recessive trait. Assume a female with a color blindness allele mates with a normal male. Denote the color blindness allele as X^b, and the normal allele as X^B.  What are the possible genotypes of the offspring? What is the probability that the offspring is color blind?

X^BX^B, X^bX^B, X^BY, X^bY. The probability the offspring is color blind is 0.25.

Among the following choices, which is usually organized in a single circular haploid chromosome and inherited maternally?

• Mitochondrial DNA

• Autosomal chromosomes

• The mammalian Y chromosome

• The mammalian X chromosome

Mitochondrial DNA

In the context of "genotype x environment interaction", what will happen if a crop strain from A region is planted in B region where the environment varies?

The crop strain may maintain a constant genotype, but its phenotype may differ due to varying environmental conditions.

Sarah and Ben have two children (Christopher, and Sue). Sarah and Sue suffer from an allergic response to caffeine characterized by hives and facial swelling. Ben and Christopher do not have this problem. The two children grow up and some have children of their own. One out of Sarah's three daughters is affected, whereas all of Christopher's two sons are not. What is the most likely mode of inheritance of this condition by a recessive mutation?

Autosomal inheritance

The genetic code is degenerate, which means

Multiple codons correspond to one amino acid

For DNA replication, cells must solve at least three problems. Select 3 of these problems from the 5 choices below.

• addition of the RNA primers

• manage coiling stress generated during unwinding

• unwinding of the helix

• post-translational modification of the nascent DNA chain

• ligation of Okazaki fragments

• manage coiling stress generated during unwinding

• unwinding of the helix

• ligation of Okazaki fragments

Which of the following terms is not matched properly with the definition?

• Spontaneous mutation: A mutation due to an internal mutagen 

• Missense mutation: Nucleotide change that results in a single amino acid substitution

• Synonymous mutation (substitution): A mutation that has a phenotypic effect on the protein. 

• Nonsense mutation: Nucleotide change that results in a premature stop codon

Synonymous mutation (substitution): A mutation that has a phenotypic effect on the protein. 

DNA is organized into chromatin, a nucleoprotein structure of eukaryotic chromosomes. Histon octamers facilitate this process by making nucleosomes. Which one is not a member of histones that participated in the histone octamer?

• H4

• H3

• H2A

• H1

• H2B

H1

A coding/sense strand has the sequence 5' AGCATTTCGACG 3'. What is the template/anti-sense strand that matches this DNA sequence (label the 5' and 3' ends)? What is the resulting mRNA sequence (label the 5' and 3' ends)?

5'-CGTCGAAATGCT-3', 5'- AGCAUUUCGACG-3'.

A coding/sense strand has the sequence 5' AGCATTTCGACG 3'. After translation, assuming a start codon is immediately upstream of the given sequence, what will be the resulting amino acid sequence?  

Ser-Ile-Ser-Thr

What is the amino acid sequence if "CG" is inserted like so: 5' AGGAA[CG]AACTTTAG 3'. What is the name for this type of mutation?

Arg-Asn-Glu-Leu-Stop, frameshift mutation

Select "three" proper descriptors of each type of RNA molecule from the five options below. tRNA (Blank #1)               , rRNA (Blank #2)               , mRNA (Blank #3)               . 

A. is generally a single-stranded molecule

B. is a template for protein synthesis

C. is one component of the ribosome

D. can carry one type of amino acid per molecule

E. is the product of RNA polymerase.

AED; AEC; AEB