Evolution - Exam 3

Suppose that you study a rare human genetic disease and find that the mutation rate for this disease is (μ = 0.00012), while the selection (s) acting against this allele is 0.7. What would be the estimated equilibrium frequency for the recessive allele in question?

0.00050

The approximate number of coding genes in the human genome is:

22,500

Among the oldest fossils on Earth are the microfossils from the Agnes gold mine of South Africa, which are __________ years old.

3.2 billion

In both prokaryotes and eukaryotes, when we look at the protein-coding regions within a genome, we observe the codon usage bias, in which some codons occur more frequently than others yet specify the same amino acid. Which of the following is a possible explanation of this phenomenon?

A codon for which complementary tRNAs are common can be translated more quickly.

A ribozyme is:

A piece of RNA that is also a catalyst.

A transitional fossil that documents the evolution of birds from dinosaurs is:

Archaeopteryx

Suppose that you collected the allele and genotype frequency data from a natural population. If you found that the expected genotype frequencies were considerably different from your observed genotype frequencies, what would be your first conclusion regarding this population?

At least one of the evolutionary processes is operating in this population.

The human parasite Mycoplasma genitalium, with one of the smallest genomes of any organism that can be grown, as well as Chlamydia trachomatis, an obligate intracellular parasite, are examples of the types of organisms that functional genomics researchers have focused on. What is the main purpose of the study of such genomes?

By studying such genomes, researchers try to discover the basic and essential cellular functions of early life.

In order to understand the origin of life on Earth, evolutionary biologists collaborate with:

Chemists, geologists, atmospheric scientists

In light of recent achievements in the field of genomics, would it be reasonable to expect that the use of comparative genomics might shed light on the extinct genomes of early life?

Comparative genomics and studies of the bacteria with very small genomes do shed light on a common ancestor and researchers can estimate the minimal characteristics that a cell would need to operate as a living organism.

An estimated 95% of the human genome

Consists of different kinds of non-coding DNA.

What is the most relevant hypothesis for the benefit of making the switch from the RNA- to a DNA-based genetic system during the evolution of life?

DNA is a more stable molecule because deoxyribose is less reactive than is ribose.

Horizontal Gene Transfer has never played an important role in evolution of either prokaryotes or eukaryotes.

False

Random genetic drift refers to how allele and genotype frequencies change over generations in very large populations.

False

Which of the following molecules involved in membrane structure was likely favored by selection in the evolution of early cells?

Fatty acids

Which of the following is not true for recombination across the genomes, including the human genome?

Genomes are broken up into a series of discrete haplotype blocks with a great genetic diversity and high genetic recombination within them.

What do we know about horizontal gene transfer (HGT) in the evolution of early life?

HGT was probably a powerful force during early cell evolution, leading to complex cellular organisms.

Which of the following are not transposable elements in the human genome?

Histones

The human genome:

Is mostly non-coding DNA

The Hardy-Weinberg equilibrium serves as a null model for studies of allele frequencies and genotype frequencies in populations. This model begins with a number of basic assumptions about the individuals and population under study, as well as the evolutionary processes in operation. Which of the following is not an assumption of this model?

Mating in the population is not random with respect to the locus in question.

The earliest bird and mammal fossils are found in

Mesozoic Era rock strata

The origin of cell structures might be hypothesized to have involved a hypercycle, based on mutualism at the molecular level. Which of the following is correct regarding the hypercycle model?

Natural selection will favor a hypercycle that is enclosed in a membrane.

Which gas was most likely the least abundant in early Earth's atmosphere?

O2

Which scientists first formulated the "prebiotic soup hypothesis" to explain the abiotic origin of life on earth?

Oparin and Haldane

Which two scientists elaborated on Darwin's idea of the "warm little pond" and formulated the "prebiotic soup hypothesis" as the first hypothesis for the abiotic origin of life on earth?

Oparin and Haldene

In 1977 Sidney Fox tested the prebiotic synthesis of biological molecules and produced:

Peptide-like structures with only weak and unstable bonds between the amino acids.

What is an important difference between individual and population genetics thinking?

Population-level thinking tends to focus on changes in populations across generations. Individual-level thinking asks questions such as: what offspring are produced, and in what frequencies, from a given pair of parents? Individual- and population-level approaches ask different questions.

Which of the following is true regarding prophage DNA in a prokaryotic genome?

Prophage often encodes virulence factors.

The first genetic material was most likely:

RNA

Alu repeats are examples of

SINES (Short Interspersed Nuclear Elements)

Which scientists found that small pieces of RNA in laboratory conditions were capable of changing length over 70 generations, and that this length change was under the influence of natural selection?

Spiegelman and his colleagues

What is the role of telomerase, a protein-based enzyme with an RNA template, in eukaryotic DNA replication?

Telomerase extends the 3' end of a chromosome, adding a specific repeat sequence.

When testing for selection, evolutionary biologists often use the McDonald-Kreitman test. What can we learn from this test?

The McDonald-Kreitman test compares ratios of dN:dS by comparing the pattern of allele substitutions between species to the pattern of allelic polymorphisms within species. This test provides a powerful tool for detecting the selective advantage of non-synonymous mutations (positive selection). If a locus is under positive selection for different traits in different populations, this will lead to fixation of a beneficial mutation and low levels of polymorphism within populations but high levels of divergence between populations (pN/pS < dN/dS).

Which of the following statements about the Lincoln and Joyce experiment on self-replicating ribozymes is most likely correct?

The self-replicating ribozymes that had more efficient catalytic activities would soon began to dominate their populations.

Which of the following statements refers to the C-value paradox?

There is an enormous variation in genome size, but the organismal complexity does not correlate well with genome size.

Long interspersed elements (LINES) make up about 17% of human genome. What type of transposable elements are they?

They are retrotransposons

The recently-discovered intermediate fossil between early bony-finned air breathing fish and tetrapod vertebrates is:

Tiktaalik

DNA is a more stable molecule than RNA

True

In order to understand the origin of life on Earth evolutionary biologists collaborate with chemists, geologists, and atmospheric scientists.

True

The genes of most prokaryotes lack introns, while the genes of most eukaryotes have introns.

True

The genomes of Mycoplasma genitalium have been used to discover the basic gene sets that may have been present in early life forms.

True

Miller and Urey developed and conducted some experimental tests for a "prebiotic soup" model of the origin of life, which had been proposed a few decades earlier by Oparin and Haldane. What did Miller and Urey show could be synthesized abiotically?

amino acids

Syntenic dot plots:

are tools for comparing the gene order of two different strains or species of bacteria. provide us with a picture of the genomic reorganizations that have occurred. plot gene position in the clockwise direction beginning at the origin of DNA replication (ORI).

The major genetic effect of inbreeding in a population is to:

decrease the number of loci at which the average individual is heterozygous.

Which of the following molecules involved in membrane structure was likely favored by selection in the evolution of early cells?

fatty acids

Which of the following can be found in the genome of the severe acute respiratory syndrome (SARS) coronavirus, which was responsible for an epidemic in 2002-2003?

gene segments for the replicase region gene segments for the structural proteins

Viral genomes tend to be extremely compact due to the effects of strong selection on genome size. Such a remarkable degree of compression is achieved by the fact that:

multiple genes may overlap in the same reading frame but only partially overlapping. multiple genes of a virus may be packed with different reading frames.

In the southern European plains, a species of flowers comes in two distinct colors, purple and light pink. Botanists noticed that when the pink variant takes over the field, bees more often visit the purple ones, and vice versa. Such unusual switch of the pollinator's preference is probably an example of:

negative frequency dependent selection.

In one species of cichlid fish in Lake Tanganyika, two mouth morphs (the "right-handed" or dextral and "left-handed" or sinistral) show an interesting association between morph type and fitness. Regarding the relative frequencies of the two mouth genotypes, the higher the frequency of either type, the lower is its fitness because of the rapid adaptation of their prey. This frequency-dependent selection on the mouth morphs in cichlids is an example of:

negative frequency-dependent selection

Small, circular DNA molecules in bacterial cells, which often code for resistance to one or more antibiotics and have the ability to move by the process of conjugation, are called:

plasmids.

All of the following may be found in prokaryotic genomes except:

spliceosomal introns

All of the following is true regarding Spiegelman's experiment on the origins of life except that:

there was no selection for any of the variations in length.

One of the problems in hospitals is that some human pathogens, such as S. pneumoniae, H. influenzae, and N. gonorrhoeae, have active mechanisms for acquiring DNA from the environment (which is released when other cells die). Such DNA can subsequently be incorporated into the genome by recombination and confer resistance to multiple antibiotics. This process of gene transfer is known as:

transformation.

In a mouse population that contains hybrid New Zealand Black (NZB)/New Zealand White (NZW) mice, NZW homozygotes are phenotypically normal, whereas NZB homozygotes exhibit a number of autoimmune defects. The NZB/NZW heterozygotes experience even more severe autoimmune disease, and they are used as a medical model of the human autoimmune disease lupus. This is an example of:

underdominance and unstable equilibrium.

Human populations are polymorphic for the gene coding for the myoglobin protein. There are two different alleles of this gene (A1 and A2). In a 2002 study, Takata et al. found that in a small Japanese population, the frequency of the A1 allele was p = 0.755, while that of the A2 allele was q = 0.245. Calculate the genotypic frequencies for A1A1, A1A2, and A2A2 (in the same order) under the Hardy-Weinberg equilibrium. Choose the best answer.

0.57, 0.37, 0.06

In a population of birds, wing feather pigmentation is determined by a single gene with a codominant pair of alleles (A1 and A2). Suppose genotype A1A1 has a dark brown wing color, genotype A1A2 is light brown, and birds with the genotype A2A2 have a light beige color. In a population of 1,000 birds, 350 have dark wings, 500 have light brown wings, and 150 have light beige wings. What is the A1 allele frequency in this population?

0.60

Which of the following statements regarding the eukaryotic genome structure is not correct?

A very large fraction of eukaryotic genomes codes for proteins.

During which geological period was there a rapid diversification (explosion) of animal taxa in a relatively short time geologically speaking (several million years)?.

Cambrian

The C-value paradox leads to the questions of why there is such enormous variation in genome size and why organismic complexity does not correlate with genome size. Which of the following statements resolves this paradox to some extent?

Genome size variation results in part from a balance between the proliferation of transposable elements and selection for replication speed. There is an association between C-value and cell size, which may be one of the important aspects of selection as it affects genome size. In most cases, the genome size differences result largely from differences in the quantity of noncoding DNA.

In eukaryotes, protein-coding genes are typically composed of exon regions that code for protein products, interspersed with intron regions that are spliced out before translation. The exon theory of genes proposes an evolutionary explanation for this feature of eukaryotic genomes. Choose the best summary of this theory.

In the presence of introns, unequal recombination is likely to occur between the exons, creating new combinations of protein domains without disrupting the structure of the individual domains.

Which of the following statements about LUCA is not correct?

It is meant to be a single organism.

In a recent study (2006), Voight and his colleagues applied a genomics approach to explore how evolutionary processes have shaped the human genome. One of the interesting haplotypes was associated with the human gene responsible for the persistence of lactose tolerance into adulthood. Which of the following is true regarding this gene?

Lactase persistence has been under strong positive selection in human populations that traditionally consume milk and its products.

Choose the statement that best describes evolution when selection is acting against a rare dominant or a recessive allele.

When a dominant allele is rare, natural selection will drive its frequency down very fast, whereas when a recessive allele is rare, it practically remains hidden from selection.

In some studies, the quantities Ka and Ks are replaced with the similar quantities dN and dS, where dN is the rate of non-synonymous substitutions at non-synonymous sites and dS is the rate of synonymous substitutions at synonymous sites. If dN/dS > 1, we could say that replacements:

are advantageous.

In 1977 Sidney Fox tried a different approach to testing the prebiotic synthesis of biological molecules. He mixed a number of different amino acids together at a high temperature (120°C) in an environment lacking water. When he subsequently placed the mixture into water to investigate what the amino acids would form, he:

found some peptide-like structures, but the bonds between the amino acids were weak and unstable.

Which of the following types of prokaryotes are known to have the smallest genomes?

obligate symbionts

Ka is defined as the number of non-synonymous substitutions per site, and Ks is defined as the number of synonymous substitutions per site. What type of selection might be indicated with the following ratio: Ka/Ks << 1?

purifying selection