Altklausuren & Quiz

What is not true about UPGMA and Neighbor-joining approaches?

A) Neighbor-joining clusters sequences which minimise total tree-branch length

B) UPGMA clusters OTUs that are most similar

C) Neighbor-joining begins with a “star” tree

D) Neighbor-joining requires a distance matrix while UPGMA does not

In protein evolution, what does the statistic D tell us?

A) the rate of substitution

B) the expected proportion of differences between two protein sequences

C) the proportion of sequences not changing over time

D) the proportion of differences between two protein sequences

What is the effective population size of humans?

A) Approximately 12,500

B) Approximately 1,250,000

C) Approximately 125,000,000

D) Approximately 125,000

Which of the following could explain the obeserved correlation between DNA polymorphism and recombination rate?

A) Dominance

B) Neutral theory

C) Overdominance

D) Genetic hitchhiking

What is the main difference between Mycobacterium leprae and M. tuberculosis?

A) M. tuberculosis has half the genes of M. leprae

B) M. leprae affects humans while M. tuberculosis does not

C) M. leprae has half the genes of M. tuberculosis

D) They are descended from different ancestors

What do we call a codon where a base change causes no change in the amino-acid produced?

A) a stop codon

B) non-degenerate

C) four-fold degenerate

D) two-fold degenerate

What is not true about the domestication of dogs?

A) Domestication of dogs began at least 15,000 years ago.

B) Dogs are most closely related to wolves.

C) Mitochondrial DNA suggests East Asian dogs are probably the oldest clade of domesticated dogs.

D) Most studies suggest dogs were domesticated independently in the Americas.

Variation in which human gene is supposedly associated with the “risk taking”?

A) LCT

B) AMY

C) DRD4

D) CCR5

What does Tajima’s D test for?

A) differences in the ratio of polymorphism to divergence

B) differences in the ratio of polymorphism to divergence at synonymous and nonsynonymous sites

C) frequency spectrum of segregating sites

D) expected proportion of differences

What does observed F_ST range between in humans?

A) 0.05 - 0.15

B) 0.025 - 0.05

C) 0.5 - 1

D) 0.15 - 0.3

The expected proportion of changes (k) between two DNA sequences can be calculated as (note: d = observed proportion of differences):

A) k = 3/4 ln (1-4d/3)

B) k = 3/4 ln (1+4d/3)

C) k = -3/4 ln (1-4d/3)

D) k = -3/4 ln (1+4d/3)

What is the “Fast-X effect”?

A) suppression of X expression in the male germline

B) an enrichment in loci that cause hybrid incompatibilities on the X chromosome

C) an increase in the rate of adaptive evolution on the X chromosome

D) upregulation of the single X chromosome in male somatic tissue approximately two-fold

Which of the follwing is expected for a pseudogene?

A)Ka/Ks = 0

B) Ka/Ks = 1

C) Ka/Ks < 1

D) Ka/Ks > 1

Invertebrates have … Hox genes?

A) 16

B) 4

C) 1

D) 8

On average, the least divergent proteins between human and chimpanzee are those expressed in the:

A) brain

B) blood

C) testes

D) kidneys

Suppression of the X chromosome occurs:

A) in males and females

B) in females, in the ovaries

C) in males, thorughout the entire body

D) in males, in the testes

According to Haldane’s rule, which sex suffers more from hybrid incompatibilities?

A) heterogametic

B) female

C) male

D) homogametic

The homeobox is a highly conserved region of … bp?

A) 40

B) 120

C) 60

D) 180

The fact that genome length is not correlated with organismis complexity is known as:

A) Haldane’s rule

B) the c-value paradox

C) the g-value paradox

D) the genomic paradox

When was protein sequencing first invented?

A) 1960s

B) 1950s

C) 1970s

D) 1980s

What does a positive value of Tajima’s D indicate? (D > 0)

A) An excess of high-frequency variants

B) An excess of intermediate-frequency variants

C) Neutrality

D) An excess of low-frequency variants

Which of these organisms has the largest genome?

A) onion

B) diatom

C) amoeba

D) gorilla

How many haplotypes are present in the following sequence data?

A) 3

B) 2

C) 4

D) 1

Which order best represents the current understanding of human migration, from earliest presence of humans to latest presence of humans?

A) Africa > Europe > North America > South America > SE Asia / Australia

B) Europe > Africa > SE Asia / Australia > North America > South America

C) SE Asia / Australia > Europe > Africa > South America > North America

D) Africa > SE Asia / Australia > Europe > North America > South America

Match the models of human evolution with their assumptions

A) 1-C, 2-B, 3-A

B) 1-B, 2-A, 3-C

C) 1-A, 2-C, 3-B

D) 1-A, 2-B, 3-C

The homeodomain is a protein domain of … amino acids?

A) 60

B) 120

C) 40

D) 180

What is true about “Mitochondrial Eve”

A) She is the last common ancestor of our mitochondrial genome

B) She was European

C) She was the only woman of her time to have children

D) She is our last common ancestor

What amino acid do all proteins begin with?

A) Proline (Pro)

B) Glycine (Gly)

C) Methionine (Met)

D) Tryptophan (Trp)

The mutation responsible sickle-cell anaemia (and malaria resistance) occurs in:

A) an exon

B) a 3’ UTR

C) a 5’ UTR

D) an intron

Which of the following represents a typical value of the transition/transversion ratio for DNA substitutions?

A) 0

B) 0.25

C) 0.50

D) 1.00

E) 2.00

What is the “large-X effect”?

A) upregulation of the single X chromosome in male somatic tissue approximately two-fold

B) an enrichment in loci that cause hybrid incompatibilities on the X chromosome

C) suppression of X expression in the male germline

D) an increase in the rate of adaptive evolution on the X chromosome

Which of these techniques uses a distance matrix?

A) maximum likelihood

B) Bayesian interference

C) neighbor-joining

D) maximum parsimony

On average, the most divergent proteins between human and chimpanzee are those expressed in the:

A) testes

B) kidneys

C) blood

D) brain

What is the following result in a MK (McDonald-Kreitman) test indicative of?

A) Balancing selection

B) Neutral protein evolution

C) Weak purifying selection

D) Positive selection for amino-acid changes

What is the definition of a paralogue?

A) a sequence that is homologous due to gene duplication

B) a sequence that is similar due to shared ancestry

C) a sequence that is homologous due to speciation

D) a sequence that evolved in parapatry

Flower development in plants is controlled by which gene?

A) mc1r

B) homeobox (Hox)

C) MADS-box

D) Pax6

Ovary-specific genes are:

A) over-represented on the X chromosome

B) up-regulated in the female germline

C) under-represented on the X chromosome

D) only present on the X chromosome

What is the following result in a MK (McDonald-Kreitman) test indicative of?

A) Positive selection for amino-acid changes

B) Neutral protein evolution

C) Balancing selection

D) Weak purifying selection

If the observed proportion of differences (D) between two protein sequences is 0.42, the expected proportion of differences (K) is:

A) 0.32

B) 0.40

C) 0.42

D) 0.54

E) 0.84

How many base pairs (bp) are in 1 Gb?

A) 1000,000

B) 1000,000,000

C) 10,000

D) 1000

What is a clade?

A) a paraphyletic group

B) a phenetic taxon

C) a monophyletic group

D) a polyphyletic group

Mexican and South American dog breeds:

A) Were domesticated in the Americas from American wolves

B) Were brought to the Americas by Europeans after 1492

C) Were brought to the Americas by Vikings before 1492

D) Were derived from domesticated dogs brought to the Americas from Asia

E) Are hybrids between modern Asian and European dog breeds

Given the distance matrix below, use the UPGMA method to draw a tree and then order sequences A, B, C and D from least derived (basal) to most derived.

A) B, C, D, A

B) D, C, B, A

C) A, B, C, D

D) A, D, C, B

Which statement is true regarding the differences between cis-acting and trans-acting factors?

A) cis-acting factors usually encode transcription factors, trans-acting factors do not

B) cis-acting factors usually affect many genes, trans-acting factors usually affect only one gene

C) cis-acting factors are physically linked to the gene they regulate, trans-acting factors are not

D) trans-acting factors are more free to evolve, cis-acting factors are more evolutionary constrained

Which of the following DNA sequence changes is a transition?

A) A -> T

B) C -> T

C) C -> A

D) G -> C

E) G -> T

What type of species has the largest known genome?

A) Bacteria

B) Amoeba

C) Diatom

D) Insect

E) Vertebrate

What type of genetic variation is associated with number of children in the Icelandic population?

A) Gene copy number

B) Synonymous SNP

C) Nonsynonymous SNP

D) Microsatellite repeat number

E) Chromosomal inversion

What is not a possible cause of a negative value of Tajima’s D? (D < 0)

A) Population admixture

B) Purifying selection

C) Recovery after a selective sweep

D) An expanding population

Which of the following is expected for a pseudogene?

A) dN/dS < 0

B) dN/dS = 0

C) 0 < dN/dS < 1

D) dN/dS = 1

E) dN/dS > 1

Which of the following methods are used for gene expression profiling?

A) Shotgun sequencing and primer walking

B) RAD-seq and mass spectrometry

C) RNA-seq and microarrays

D) CRISPR-Cas and RNAi

E) Microsequencing and cDNA-probing

Methods for determining the amino acid sequence of proteins were developed in the:

A) 1920’s

B) 1930’s

C) 1940’s

D) 1950’s

E) 1960’s

Which pair of species/taxa are male-heterogametic?

A) Drosophila and honeybee

B) Drosophila and human

C) Honeybee and chicken

D) Human and chicken

E) Anolis lizard and sea turtle

The most parsimonious tree is the one that:

A) Requires the fewest sequence changes

B) Minimizes the distance matrix

C) Maximizes the distance matrix

D) Has the lowest p-value

E) Has the lowest bootstrap value

Which type of site is expected to show the least divergence between species?

A) non-degenerate

B) 2-fold degenerate

C) 3-fold degenerate

D) 4-fold degenerate

E) 5-fold degenerate

According to the fossil record, which was the first hominin to leave Africa?

A) Homo sapiens

B) Homo neanderthalensis

C) Homo denisovensis

D) Homo erectus

E) Homo habilis

The Drosophila homologue of the mammalian Pax6 gene is known as:

A) Dax6

B) eyeless

C) white

D) Fmr1

Which of the following represents a rare genetic change (RGC)?

A) Point mutation

B) Transition

C) Transversion

D) Intron gain

E) Parsimony informative site

The defining feature of a cis-regulatory variant is that it:

A) Alters the tissue is which a gene is expressed

B) Only has an effect in heterozygotes

C) Affects expression differently in males and females

D) Is genetically linked to the gene it regulates

E) Leads to the creation of a new splicing site

Which of the following statements about mammalian mitochondrial DNA is true?

A) It has a higher recombination rate than nuclear DNA

B) It is paternally inherited

C) It is maternally inherited

D) It cannot be used for phylogenetic analysis

E) It is transmitted horizontally among individuals

Connect the possible outcomes of gene duplication with the correct terms.

A) 1-C, 2-D, 3-A, 4-B

B) 1-B, 2-C, 3-D, 4-A

C) 1-D, 2-A, 3-B, 4-C

D) 1-A, 2-B, 3-C, 4-D

If all nucleotides are used with equal frequency, the maximum divergence we expect between two DNA sequences is:

A) 0%

B) 25%

C) 50%

D) 75%

E) 100%

If all amino acids are used with equal frequency, we expect two random protein sequences to be … identical:

A) 1%

B) 5%

C) 12%

D) 20%

E) 25%

What is not true about protein evolution when compared to DNA evolution?

A) proteins are generally more conserved

B) protein evolution is typically simpler than DNA evolution

C) proteins are easier to align and compare between species

D) protein sequences are simpler than DNA sequences

Who is known for the hypothesis “ontogeny recapitulates phylogeny”?

A) Charles Darwin

B) R. A. Fisher

C) Motoo Kimura

D) Thomas Hunt Morgan

E) Ernst Haeckel

What is the major difference between the HKA (Hudson-Kreitman-Aguade) and the MK (McDonald Kreitman) tests?

A) The HKA test requires an outgroup species

B) The MK test requires a protein-coding gene

C) The HKA test requires a distance matrix

D) The MK test requires a pseudogene

E) The HKA test requires a pseudogene

Which one of the following statements about the great apes is correct?

A) Because they are so closely related, it is not possible to determine the phylogeny of the great apes.

B) Bonobo is an outgroup to human and chimpanzee.

C) Gorilla is more closely related to chimpanzee than to human.

D) Human is more closely related to gorilla than to chimpanzee.

E) Some parts of the human genome are more similar to gorilla than they are to chimpanzee.

The key genes that control flower development in plants are:

A) OR genes

B) NB-LRR genes

C) Hox genes

D) MADS-box genes

E) FLORETTE genes

Which of the following statements about Mitochondrial Eve is true?

A) She was the first female Homo sapiens

B) She was the only female to survive the last ice age

C) She had a great granddaughter

D) She was the only female of her generation to reproduce

E) She was the only female of her generation to have a daughter

In the male germline of Drosophila melanogaster:

A) Expression of the X chromosome is suppressed relative to the autosomes

B) The X chromosome is enriched with male-biased genes relative to the autosomes

C) The X chromosome is completely inactivated

D) X-chromosomal gene expression is up-regulated approximately two-fold

E) X-chromosomal gene expression is up-regulated approximately four-fold

What is not true about the H2 form of the polymorphic chromosome 17 inversion in humans?

A) H2 is probably the derived form

B) H2 is rare in most populations, except for in Europe

C) Women with H2 have more children, on average

D) H2 is probably the ancestral form

According to the molecular clock, sequence divergence between species depends on:

A) The number of generations since their last common ancestor

B) The number of years since their last common ancestor

C) The average mutation rate of the species

D) The average effective population size of the species

E) The harmonic mean of the census population size of the species

Clone-by-clone genome sequencing is also known as … genome sequencing?

A) Hierarchical

B) Next-generation

C) Long-read

D) Sanger

E) Shotgun

What is not true about synonymous substitutions?

A) Ks is the number of synonymous substitutions divided by the total number of synonymous sites

B) they are also calles “replacements”

C) synonymous codons are not used with equal frequency

D) they change the DNA sequence but not the amino-acid produced

Variation in the level of starch in the human diet is positively correlated with what kind of variance in the amylase enyme gene?

A) copy number variation

B) inversion

C) single-nucleotide polymorphism

D) deletion

The ratio dN/dS is also sometimes referred to as:

A) Alpha

B) Delta

C) Kappa

D) Tao

E) Omega

A mutation in the CCR5 gene is associated with:

A) Risk-taking behavior

B) Alcohol tolerance

C) Nomadic lifestyle

D) Body Mass Index (BMI)

E) Resistance to HIV/AIDS

According to the neutral theory of molecular evolution, both divergence between species and polymorphism within species depend on:

A) The census population size

B) The effective population size

C) The recombination rate

D) The neutral mutation rate

E) The generation time

Methods to determine the sequences of DNA were first developed in the:

A) 1960s

B) 1950s

C) 1970s

D) 1980s

Which of the following statements is true of background selection?

A) It has the greatest effect in regions of low recombination

B) It has the greatest effect in regions of high recombination

C) It has the greatest effect when there is strong positive selection

D) It does not affect levels of genetic variation

E) It relies solely on genetic drift

Which sequencing method involves the use of mapped BAC clones?

A) clone-by-clone

B) Sanger sequencing

C) RNA sequencing

D) shotgun sequencing

A negative value of Tajima’s D is expected when there is:

A) Population expansion

B) Pseudogenization

C) Non-disjunction

D) Whole genome duplication

E) Balancing selection