BIOB51 FINAL EXAM QUESTIONS
WITH CORRECT DETAILED
ANSWERS
molecular clock case study: origins of HIV - Answer- - four independent origins:
separate intros from primates
- all four types have mutation leading to same amino acid in same position in same
protein
why is studying the origins of HIV important? - Answer- can be used to predict when a
zoonotic virus will jump to human populations
types of mutations - Answer- synonymous (silent), nonsynonymous, pseudogene
synonymous (silent) mutation - Answer- - amino acid sequence of the protein is
unchanged
- selectively neutral
nonsynonymous mutation - Answer- - amino acid sequence of the protein is changed
- likely subject to selection
pseudogene mutation - Answer- non-functional, mutations accumulate by genetic drift
evidence of selection dependent on LD between selected traits and markers - Answer-
selective sweeps & genetic hitchhikers, Fat outliers across thousands of loci, SNP
analysis
evidence of selection where predictions of neutral evolution are violated - Answer- ratio
of nonsynonymous to synonymous mutations (dN/dS)
selective sweep - Answer- adaptive allele spreads through a population more quickly
than recombination acts to separate it from neighbouring alleles
genetic hitchhiking - Answer- - alleles in LD with selected alleles increase in frequency
along with selected alleles
- selected alleles frequently surrounded by same set of alleles at neighbouring locations
(hitchhikers)
effect of selective sweep on beneficial mutations - Answer- - strong selection in favour
of an allele leads to an increase in frequency faster than recombination
,- creates LE and beneficial mutation spreads to fixation along with the other alleles
located nearby on the same chromosome (hitchhikers)
how to identify selective sweep in a genome? - Answer- A region of decreased
polymorphism relative to the rest of the genome can indicate a selective sweep
how will evidence of selective sweeps decrease over time? - Answer- recombination
proceeds over generations and LD will decrease
F_ST - Answer- measure of population differentiation - reduction in heterozygotes at a
locus attributed to effects of population subdivision
how is F_ST use in GWAS? - Answer- - scale up to estimate F_ST from thousands of
loci
- compare F_ST between subpopulations to identify regions under selection (outliers)
what do F_ST outliers indicate? - Answer- more difference between populations than
expected by chance
F_ST outliers case study: human adaptation to high altitudes - Answer- - low
environmental O2 availability, observed variation in blood oxygen content of village
women
human adaptation to high altitudes: effects of natural selection - Answer- AA genotype
with highest blood O2 saturation level linked to highest # of offspring and lowest
offspring mortality
what is the agent of natural selection in the Tibetan altitude case study? - Answer- high-
altitude hypoxia is acting as an agent of natural selection in the population
which allele was responsible for high altitude adaptation in Tibetan people? - Answer-
EPAS1 allele
how were the effects EPAS1 allele determined? - Answer- GWAS comparing Han
Chinese and Tibetan people saw EPAS1 as a F_ST outlier: more difference than
expected and very rapid allele frequency change
how did the high altitude adaptation gene arise? - Answer- interbreeding with extinct
hominid
what is the source of the EPAS1 allele - Answer- introgression
convergent adaptation to high altitude in Asia and America - Answer- two independently
evolved biological pathways countering negative effects of hypoxia: fatty acid
metabolism & neuronal protection
, how is evidence of selection dependent on LD between selected traits and markers
used? - Answer- - differences degrade over time
- useful for tracking more recent evo events
how is evidence of selection where predictions of neutral evolution are violated used? -
Answer- - differences maintained in genome for longer
- reveals ancient histories and recent events
dN/dS ratio - Answer- rate of nonsynonymous to synonymous substitutions
when dN/dS > 1 - Answer- positive selection
when dN/dS < 1 - Answer- purifying selection
when dN/dS = 1 - Answer- neutral evolution
what happens to mutations when dN/dS > 1 - Answer- many N differences between
species are fixed by positive selection
what happens to mutations when dN/dS < 1 - Answer- most N mutations are deleterious
and are removed (purifying selection)
what happens to mutations when dN/dS = 1 - Answer- N and S mutations evolving
neutrally
why does the BRCA1 gene undergo positive selection? - Answer- Evidence suggests:
also serves role in DNA damage repair and cell division, may protect against viruses
Possible Trade off = pleiotropic effects
what type of selection is artificial selection? - Answer- directional - humans favouring a
certain trait and breeding it to an extreme
why were gray wolves domesticated? - Answer- • Initial selection for behaviour
• More recent selection for morphological & physiological traits
example of extreme phenotypic variation - Answer- dogs - more phenotypic variation
than any other species with >400 breeds (sub-species)
case study: evolution by artificial selection - Answer- bull terrier - Breeders selected
desirable phenotypic traits (e.g., head shape), over generations, choose to mate only
those dogs with traits closer to trait goal
genetic basis of bull terrier artificial selection - Answer- selection for tandem repeat
tandem repeat - Answer- • selection on phenotype leads to selection on tandem repeat
loci associated with development genes
WITH CORRECT DETAILED
ANSWERS
molecular clock case study: origins of HIV - Answer- - four independent origins:
separate intros from primates
- all four types have mutation leading to same amino acid in same position in same
protein
why is studying the origins of HIV important? - Answer- can be used to predict when a
zoonotic virus will jump to human populations
types of mutations - Answer- synonymous (silent), nonsynonymous, pseudogene
synonymous (silent) mutation - Answer- - amino acid sequence of the protein is
unchanged
- selectively neutral
nonsynonymous mutation - Answer- - amino acid sequence of the protein is changed
- likely subject to selection
pseudogene mutation - Answer- non-functional, mutations accumulate by genetic drift
evidence of selection dependent on LD between selected traits and markers - Answer-
selective sweeps & genetic hitchhikers, Fat outliers across thousands of loci, SNP
analysis
evidence of selection where predictions of neutral evolution are violated - Answer- ratio
of nonsynonymous to synonymous mutations (dN/dS)
selective sweep - Answer- adaptive allele spreads through a population more quickly
than recombination acts to separate it from neighbouring alleles
genetic hitchhiking - Answer- - alleles in LD with selected alleles increase in frequency
along with selected alleles
- selected alleles frequently surrounded by same set of alleles at neighbouring locations
(hitchhikers)
effect of selective sweep on beneficial mutations - Answer- - strong selection in favour
of an allele leads to an increase in frequency faster than recombination
,- creates LE and beneficial mutation spreads to fixation along with the other alleles
located nearby on the same chromosome (hitchhikers)
how to identify selective sweep in a genome? - Answer- A region of decreased
polymorphism relative to the rest of the genome can indicate a selective sweep
how will evidence of selective sweeps decrease over time? - Answer- recombination
proceeds over generations and LD will decrease
F_ST - Answer- measure of population differentiation - reduction in heterozygotes at a
locus attributed to effects of population subdivision
how is F_ST use in GWAS? - Answer- - scale up to estimate F_ST from thousands of
loci
- compare F_ST between subpopulations to identify regions under selection (outliers)
what do F_ST outliers indicate? - Answer- more difference between populations than
expected by chance
F_ST outliers case study: human adaptation to high altitudes - Answer- - low
environmental O2 availability, observed variation in blood oxygen content of village
women
human adaptation to high altitudes: effects of natural selection - Answer- AA genotype
with highest blood O2 saturation level linked to highest # of offspring and lowest
offspring mortality
what is the agent of natural selection in the Tibetan altitude case study? - Answer- high-
altitude hypoxia is acting as an agent of natural selection in the population
which allele was responsible for high altitude adaptation in Tibetan people? - Answer-
EPAS1 allele
how were the effects EPAS1 allele determined? - Answer- GWAS comparing Han
Chinese and Tibetan people saw EPAS1 as a F_ST outlier: more difference than
expected and very rapid allele frequency change
how did the high altitude adaptation gene arise? - Answer- interbreeding with extinct
hominid
what is the source of the EPAS1 allele - Answer- introgression
convergent adaptation to high altitude in Asia and America - Answer- two independently
evolved biological pathways countering negative effects of hypoxia: fatty acid
metabolism & neuronal protection
, how is evidence of selection dependent on LD between selected traits and markers
used? - Answer- - differences degrade over time
- useful for tracking more recent evo events
how is evidence of selection where predictions of neutral evolution are violated used? -
Answer- - differences maintained in genome for longer
- reveals ancient histories and recent events
dN/dS ratio - Answer- rate of nonsynonymous to synonymous substitutions
when dN/dS > 1 - Answer- positive selection
when dN/dS < 1 - Answer- purifying selection
when dN/dS = 1 - Answer- neutral evolution
what happens to mutations when dN/dS > 1 - Answer- many N differences between
species are fixed by positive selection
what happens to mutations when dN/dS < 1 - Answer- most N mutations are deleterious
and are removed (purifying selection)
what happens to mutations when dN/dS = 1 - Answer- N and S mutations evolving
neutrally
why does the BRCA1 gene undergo positive selection? - Answer- Evidence suggests:
also serves role in DNA damage repair and cell division, may protect against viruses
Possible Trade off = pleiotropic effects
what type of selection is artificial selection? - Answer- directional - humans favouring a
certain trait and breeding it to an extreme
why were gray wolves domesticated? - Answer- • Initial selection for behaviour
• More recent selection for morphological & physiological traits
example of extreme phenotypic variation - Answer- dogs - more phenotypic variation
than any other species with >400 breeds (sub-species)
case study: evolution by artificial selection - Answer- bull terrier - Breeders selected
desirable phenotypic traits (e.g., head shape), over generations, choose to mate only
those dogs with traits closer to trait goal
genetic basis of bull terrier artificial selection - Answer- selection for tandem repeat
tandem repeat - Answer- • selection on phenotype leads to selection on tandem repeat
loci associated with development genes
