Name:
Score: /100
Name:
Question #1 (30 points)
Genotype
Observed
Expected
Chi-square
AA
210
205.71
AC
60
1.0714
CC
10
Total
280
280
Test for Hardy-Weinberg proportions by filling in the five missing values in the above table (10 points).
Is this population at Hardy-Weinberg equili
ium? Explain your reasoning (5 points).
Name four different reasons why departures from Hardy-Weinberg proportions might be observed (20 points).
Question #2 (5 points)
The black line in this plot shows a simulated allele frequency trajectory. Allele A is beneficial, and it increases in frequency over time. Does the above plot show evolution for a small population (100 individuals) or a large population XXXXXXXXXXindividuals)?
Question #3 (15 points)
Explaining how novel characters can evolve. Use this as a chance to demonstrate your understanding of evo-devo (three to five sentences in total).
Question #4 (25 points)
The neutral theory holds that the amount of genetic diversity found in a species should be proportional to effective population size and mutation rate (i.e., in the shaded gray region of the above figure). However, real-world genetic data paints a different picture. Give two different explanations why the above pattern might arise. Explain your reasoning (four to eight sentences in total).
Question #5 (25 points)
Many human genomes contain traces of Neanderthal ancestry. However the autosomes of non-Africans contain approximately five times as much Neanderthal DNA per base pair as X chromosomes. Hypothesize why there is a relative lack of introgressed Neanderthal DNA in human X chromosomes, and explain your reasoning. Use this as a chance to demonstrate your comprehensive understanding of evolutionary biology (four to eight sentences in total).
1/4
4/4
µ = 10−8 µ = 10−9
Acyrthosiphon pisum
Aedes aegypti
Ailuropoda melanoleuca
Allolobophora chlorotica
Amphimedon queenslandica Anopheles arabiensis
Anopheles gambiae
Apo
ectodea icterica
Aquila clanga
Bactrocera depressa
Balaenoptera bonaerensis
Bos taurus
Bostrycapulus aculeatus
Caenorhabditis elegans
Callithrix jacchus
Camponotus ligniperdus
Ceratitis capitata
Chelonoidis nigra
Cichla pleiozona
Ciona intestinalis
Ciona savignyi
Crassostrea gigas
Culex pipiens
Cystodytes dellechiajei
Daubentonia madagascariensis
Drosophila americana Drosophila ananassae
Drosophila arizonae
Drosophila bipectinata
Drosophila buzzatii
Drosophila kikkawai
Drosophila malerkotliana
Drosophila melanogaste
Drosophila miranda
Drosophila mojavensis
Drosophila novamexicana
Drosophila parabipectinata
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila subobscura
Echinocardium cordatum
Eschrichtius robustus
Eudyptes filholi
Eudyptes moseleyi
Eulemur mongoz
Eunicella ve
ucosa
Gorilla gorilla
Gulo gulo
Halictus scabiosaeHippocampus kuda
Homo sapiens
Leptogorgia sarmentosa
Lynx lynx
Mytilus edulis Mytilus galloprovincialis
Mytilus trossulus
Nasonia vitripennis
Nomascus ga
iellae
Ostreola stentina
Ovis canadensis
Pan paniscus
Pheidole pallidulaPongo abelii
Propithecus coquereli
Reticulitermes flavipes
Reticulitermes grassei
Reticulitermes lucifugus
Sistrurus catenatus
XXXXXXXXXX XXXXXXXXXX
10−4
10−3
10−2
10−1
100
pa
irw
is
e
di
ve
s
ity
(d
iff
e
en
ce
s
pe
p)
approximate population size
Echinodermata
Arthropoda
Chordata
Annelida
Porifera
Mollusca
Nematoda
Cnidaria
Nemertea
Ne Nc
log10(π) = log10(θ) − log XXXXXXXXXX4θ/3) θ = 4Ncµ µ = 10−8
µ = 10−9
[0.08, 0.12]
10−3.5
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the autho
funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted Fe
uary 3, 2021. ; https:
doi.org/10.1101/ XXXXXXXXXX429633doi: bioRxiv preprint
https:
doi.org/10.1101/ XXXXXXXXXX
http:
creativecommons.org/licenses
y-nd/4.0
m=10
−8
m=10
−9
Acyrthosiphon pisum
Aedes aegypti
Ailuropoda melanoleuca
Allolobophora chlorotica
Amphimedon queenslandica
Anopheles arabiensis
Anopheles gambiae
Apo
ectodea icterica
Aquila clanga
Bactrocera depressa
Balaenoptera bonaerensis
Bos taurus
Bostrycapulus aculeatus
Caenorhabditis elegans
Callithrix jacchus
Camponotus ligniperdus
Ceratitis capitata
Chelonoidis nigra
Cichla pleiozona
Ciona intestinalis
Ciona savignyi
Crassostrea gigas
Culex pipiens
Cystodytes dellechiajei
Daubentonia madagascariensis
Drosophila americana
Drosophila ananassae
Drosophila arizonae
Drosophila bipectinata
Drosophila buzzatii
Drosophila kikkawai
Drosophila malerkotliana
Drosophila melanogaste
Drosophila miranda
Drosophila mojavensis
Drosophila novamexicana
Drosophila parabipectinata
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila subobscura
Echinocardium cordatum
Eschrichtius robustus
Eudyptes filholi
Eudyptes moseleyi
Eulemur mongoz
Eunicella ve
ucosa
Gorilla gorilla
Gulo gulo
Halictus scabiosae
Hippocampus kuda
Homo sapiens
Leptogorgia sarmentosa
Lynx lynx
Mytilus edulis
Mytilus galloprovincialis
Mytilus trossulus
Nasonia vitripennis
Nomascus ga
iellae
Ostreola stentina
Ovis canadensis
Pan paniscus
Pheidole pallidula
Pongo abelii
Propithecus coquereli
Reticulitermes flavipes
Reticulitermes grassei
Reticulitermes lucifugus
Sistrurus catenatus
10
4
10
6
10
8
10
10
10
12
10
14
10
16
10
18
10
−4
10
−3
10
−2
10
−1
10
0
p
a
i
w
i
s
e
d
i
v
e
s
i
t
y
(
d
i
f
f
e
e
n
c
e
s
p
e
p
)
approximate population siz e
Echinodermata
Arthropoda
Chordata
Annelida
Porifera
Mollusca
Nematoda
Cnidaria
Nemertea
N
e
N
c
log
10
(Ï€)=log
10
(θ)−log
10
(1+
4θ
3)θ=4N
c
µ µ=10
−8
µ=10
−9
[0.08,0.12]
10
−3.5
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the autho
funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted Fe
uary 3, 2021. ; https:
doi.org/10.1101/ XXXXXXXXXX429633doi: bioRxiv preprint
Name:
Score: /100
Name:
Question #1 (30 points)
Genotype
Observed
Expected
Chi-square
AA
210
205.71
AC
60
1.0714
CC
10
Total
280
280
Test for Hardy-Weinberg proportions by filling in the five missing values in the above table (10 points).
Is this population at Hardy-Weinberg equili
ium? Explain your reasoning (5 points).
Name four different reasons why departures from Hardy-Weinberg proportions might be observed (20 points).
Question #2 (5 points)
The black line in this plot shows a simulated allele frequency trajectory. Allele A is beneficial, and it increases in frequency over time. Does the above plot show evolution for a small population (100 individuals) or a large population XXXXXXXXXXindividuals)?
Question #3 (15 points)
Explaining how novel characters can evolve. Use this as a chance to demonstrate your understanding of evo-devo (three to five sentences in total).
Question #4 (25 points)
The neutral theory holds that the amount of genetic diversity found in a species should be proportional to effective population size and mutation rate (i.e., in the shaded gray region of the above figure). However, real-world genetic data paints a different picture. Give two different explanations why the above pattern might arise. Explain your reasoning (four to eight sentences in total).
Question #5 (25 points)
Many human genomes contain traces of Neanderthal ancestry. However the autosomes of non-Africans contain approximately five times as much Neanderthal DNA per base pair as X chromosomes. Hypothesize why there is a relative lack of introgressed Neanderthal DNA in human X chromosomes, and explain your reasoning. Use this as a chance to demonstrate your comprehensive understanding of evolutionary biology (four to eight sentences in total).
1/4
4/4
µ = 10−8 µ = 10−9
Acyrthosiphon pisum
Aedes aegypti
Ailuropoda melanoleuca
Allolobophora chlorotica
Amphimedon queenslandica Anopheles arabiensis
Anopheles gambiae
Apo
ectodea icterica
Aquila clanga
Bactrocera depressa
Balaenoptera bonaerensis
Bos taurus
Bostrycapulus aculeatus
Caenorhabditis elegans
Callithrix jacchus
Camponotus ligniperdus
Ceratitis capitata
Chelonoidis nigra
Cichla pleiozona
Ciona intestinalis
Ciona savignyi
Crassostrea gigas
Culex pipiens
Cystodytes dellechiajei
Daubentonia madagascariensis
Drosophila americana Drosophila ananassae
Drosophila arizonae
Drosophila bipectinata
Drosophila buzzatii
Drosophila kikkawai
Drosophila malerkotliana
Drosophila melanogaste
Drosophila miranda
Drosophila mojavensis
Drosophila novamexicana
Drosophila parabipectinata
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila subobscura
Echinocardium cordatum
Eschrichtius robustus
Eudyptes filholi
Eudyptes moseleyi
Eulemur mongoz
Eunicella ve
ucosa
Gorilla gorilla
Gulo gulo
Halictus scabiosaeHippocampus kuda
Homo sapiens
Leptogorgia sarmentosa
Lynx lynx
Mytilus edulis Mytilus galloprovincialis
Mytilus trossulus
Nasonia vitripennis
Nomascus ga
iellae
Ostreola stentina
Ovis canadensis
Pan paniscus
Pheidole pallidulaPongo abelii
Propithecus coquereli
Reticulitermes flavipes
Reticulitermes grassei
Reticulitermes lucifugus
Sistrurus catenatus
XXXXXXXXXX XXXXXXXXXX
10−4
10−3
10−2
10−1
100
pa
irw
is
e
di
ve
s
ity
(d
iff
e
en
ce
s
pe
p)
approximate population size
Echinodermata
Arthropoda
Chordata
Annelida
Porifera
Mollusca
Nematoda
Cnidaria
Nemertea
Ne Nc
log10(π) = log10(θ) − log XXXXXXXXXX4θ/3) θ = 4Ncµ µ = 10−8
µ = 10−9
[0.08, 0.12]
10−3.5
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the autho
funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted Fe
uary 3, 2021. ; https:
doi.org/10.1101/ XXXXXXXXXX429633doi: bioRxiv preprint
https:
doi.org/10.1101/ XXXXXXXXXX
http:
creativecommons.org/licenses
y-nd/4.0
m=10
−8
m=10
−9
Acyrthosiphon pisum
Aedes aegypti
Ailuropoda melanoleuca
Allolobophora chlorotica
Amphimedon queenslandica
Anopheles arabiensis
Anopheles gambiae
Apo
ectodea icterica
Aquila clanga
Bactrocera depressa
Balaenoptera bonaerensis
Bos taurus
Bostrycapulus aculeatus
Caenorhabditis elegans
Callithrix jacchus
Camponotus ligniperdus
Ceratitis capitata
Chelonoidis nigra
Cichla pleiozona
Ciona intestinalis
Ciona savignyi
Crassostrea gigas
Culex pipiens
Cystodytes dellechiajei
Daubentonia madagascariensis
Drosophila americana
Drosophila ananassae
Drosophila arizonae
Drosophila bipectinata
Drosophila buzzatii
Drosophila kikkawai
Drosophila malerkotliana
Drosophila melanogaste
Drosophila miranda
Drosophila mojavensis
Drosophila novamexicana
Drosophila parabipectinata
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila subobscura
Echinocardium cordatum
Eschrichtius robustus
Eudyptes filholi
Eudyptes moseleyi
Eulemur mongoz
Eunicella ve
ucosa
Gorilla gorilla
Gulo gulo
Halictus scabiosae
Hippocampus kuda
Homo sapiens
Leptogorgia sarmentosa
Lynx lynx
Mytilus edulis
Mytilus galloprovincialis
Mytilus trossulus
Nasonia vitripennis
Nomascus ga
iellae
Ostreola stentina
Ovis canadensis
Pan paniscus
Pheidole pallidula
Pongo abelii
Propithecus coquereli
Reticulitermes flavipes
Reticulitermes grassei
Reticulitermes lucifugus
Sistrurus catenatus
10
4
10
6
10
8
10
10
10
12
10
14
10
16
10
18
10
−4
10
−3
10
−2
10
−1
10
0
p
a
i
w
i
s
e
d
i
v
e
s
i
t
y
(
d
i
f
f
e
e
n
c
e
s
p
e
p
)
approximate population siz e
Echinodermata
Arthropoda
Chordata
Annelida
Porifera
Mollusca
Nematoda
Cnidaria
Nemertea
N
e
N
c
log
10
(Ï€)=log
10
(θ)−log
10
(1+
4θ
3)θ=4N
c
µ µ=10
−8
µ=10
−9
[0.08,0.12]
10
−3.5
.CC-BY-ND 4.0 International licenseavailable under a
(which was not certified by peer review) is the autho
funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprintthis version posted Fe
uary 3, 2021. ; https:
doi.org/10.1101/ XXXXXXXXXX429633doi: bioRxiv preprint