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BIO404 – FINAL – 09.01.2023 (150 min)

You need to explain your answers when you are asked to. Please write clearly and comply with word limitations.

Q1. The article by Tong et al. (2022, Nat Comm) that we

discussed in class suggested that sociality led to relaxation of
selection in spider lineages. Indicate whether the
characteristics listed below would increase or decrease so as
to cause relaxation of selection. Simply write “increase” or
“decrease” next to each. 3 pt
• Reproductive skew (i.e. unequal distribution of
offspring): inc
• Effective population size: dec
• Rate of genetic drift: inc
Indicate whether the characteristics listed below would increase or decrease due to relaxation of selection (hint:
check the article figure above). 3 pt
• Average dN/dS of genes under positive selection: dec
• Average dN/dS of genes under negative selection: inc
• The frequency of slightly deleterious polymorphisms: inc

Q2. Suggest and briefly explain two mechanisms through which sociality increases fitness of a lineage. Max 10
words each.
1) Division of labor and more specialized functions = increased efficiency / More effective avoidance of predators
/ more effective food gathering / etc
2)

Q3. Describe the last universal common ancestor (LUCA) for the below properties. Each time choose the best of
the 3 answers in parentheses. Assume parsimony. 8 pt.
Habitat (terrestrial, marine, or unpredictable): Marine
Explain your answer in 1 sentence: Because life evolved first in the oceans

Genetic material (RNA, DNA, or unpredictable): DNA

Explain your answer in 1 sentence: Because all modern-day life forms use DNA as genetic material

Energy production (chemoautotrophic, phototrophic, or heterotrophic): Chemoautotrophic

Mutation rate (faster than today’s bacteria, slower than today’s bacteria, unpredictable): Unpredictable

Prokaryotic cell wall (present, absent, unknown): Present

When did LUCA live, approximately? 3.5 billion years ago / >3.5 billion years ago

Q4. The figure on the right is from Zeng et al.

(2018, Nat Comm) who estimated past effective
population sizes (Ne) for chromosome Y and
mitochondrial DNA of human populations.
Provide a reasonable explanation for the
observed differences in Ne between chrY and
mtDNA in max 30 words. (ignore changes in time)
2 pt.
In humans there is a trend for higher
reproductive skew in males, therefore we observe lower effective population size in chrY than mtDNA.
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Q5. The figure on the right shows results from an article by King et al. (2009, Current Biology), who studied a
freshwater snail species in shallow and in deep parts of two lakes. The snail populations can include asexual
females, as well as sexual males and sexual females. The authors also
note that different habitats within lakes (shallow or deep) can differ in
their parasite intensity. Given this information, the results in the figure,
and theories on the evolution of sex, suggest which habitat (shallow or
deep) may have higher parasite load. Explain your answer, referring to
coevolution and adaptation rate. 4 pt

… Shallow environments must have higher parasite load. This is because

we expect sex to be more common … when hosts are coevolving with
rapidly evolving parasites

and because the figure shows that … in shallow environments, sex is

more common,

This is because sexual reproduction allows for … faster adaptation of the host.

Q6. The figure on the left shows a phylogeny of molluscs based on genomic
data. “bs” stands for bootstrap support, and “pp” is another measure of
branch support.

a. Does this imply that annelida is the ancestor of molluscs? 1 pt. No [it is an
outgroup]

b. Are cephalopoda closer to gastropoda or to bivalvia? 1 pt. Equally distant

c. Are cephalopoda closer to neomeniomorpha or to bivalvia? 1 pt. Bivalvia

d. Given the figure, are mollusca a monophyletic group? 1 pt. Yes

e. One of the branching patterns within mollusca is ambiguous (is not strongly supported) – which one? 2
pt. Scaphopoda clustering with gastropoda and bivalvia

Q7. The formula H = 4*N*mu describes heterozygosity (i.e. the proportion of mismatches between two copies of
a locus) for autosomal loci as a function of the mutation rate and effective population size. Estimate the following,
assuming a nuclear mutation rate of 10-9, and taking into account the effect of haploidy and diploidy. 3 pt

a1. The number of breeding males, if chrY heterozygosity is 0.002.

0.002=2*Nm*10-9. Nm =106 [You need to use 2 in the formula because the locus is haploid]

a2. The total number of breeding individuals, if autosomal heterozygosity is 0.01.

0.01=4*Nt*10-9. Nt =2.5*106

b. Estimate mitochondrial heterozygosity using your answers in (a1) and (a2) and assuming an mtDNA mutation
rate of 10-7. (Hint: Do not use the Ne formula based on breeding male and female numbers, but simply assume
that a total breeding population is composed of breeding males and breeding females. The answer then should be
0.3) 3 pt
Nf =Nt – Nm = 2.5*106 - 106 = 1.5*106
H = 2*Nf*mu = 2*1.5*106*10-7 = 0.3
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Q8. The figure on the left describes allopatric the speciation in a

beetle lineage.

Imagine we calculate Fst (genetic differentiation) between the two

groups at neutral loci at time points 2, 3 and 4. How would Fst
change in time? 1 pt
Increase over time

Name the forces that could contribute to change in Fst at neutral loci? 2 pt
Mutation and drift [saying selection loses 1 pt – this is a neutral locus]

Q9. The figure on the left shows stigma widths measured by

Cozzolino and colleagues (Cozzolino et al. 2022 Evol Ecol) in
two orchid species, Ophrys normanii (dark grey) and O.
chestermanii (light grey).
Explain the difference in stigma width distributions between
allopatric (non-overlapping) populations and sympatric
(overlapping) populations based on the reinforcement
model, referring to hybrid fitness, phenotypic divergence,
and post- and/or pre-zygotic reproductive isolation. Use
max. 3 sentences / 40 words. 4 pt

The sympatric populations show higher phenotypic divergence than allopatric populations, which suggests that in
the past, the two sister species could hybridize, but hybrid fitness was low. Therefore there was selection against
hybridization leading to pre-zygotic isolation. [see slides 70 and 71 in Chp 14 slides]

Q10. Humans and chimpanzees diverged around 6 million years ago, and the average genome-wide distance
between the two species is 0.01. Estimate the divergence time between gorilla and macaque given an average
genome-wide distance of 0.05, assuming the same mutation rate and same generation time among primates. 2 pt
0.05 diff / (0.01 diff/ 6 my) = 30 my

Now estimate the divergence time between goat and sheep given an average genome-wide distance of 0.05,
assuming the same mutation rate, but also given that Caprini (goat, sheep and relatives) have a generation time
of ~5 years, while Hominini have a generation time of ~20 years. Bonus 3 pt.
0.01 diff/ 6 my / 20 y/gen = (0.01/6/20) diff / gen
0.05 diff / (0.01/6/20) diff / gen * 5 gen/y = 7.5 my
[OR simply 30 my / 4 = 7.5 my]

Q11. Imagine an eye-color variant X1 that is at 0.25 frequency today in Asian humans, known to be under
negative-frequency dependent selection.
In which type of tissue did the mutation creating this variant happen? 1 pt
Germ-line
What is the probability that X1 will fix in the future, given the above information? Explain in 1 sentence. 2 pt
0, because neg freq dep sel creates balancing selection

What is the expected long-term frequency of X1, given the above information? 1 pt 0.5 [or between 0 and 1]

If all humans started wearing lenses tomorrow and selection stopped, what would be the probability that X1 will
fix in the future? State the probability and explain in 1 sentence. 2 pt
0.25 because it would become neutral
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Q12. Based on what observation do we infer that multicellularity evolved convergently in eukaryotes? Explain in
max 30 words. 4 pt

Multicellular eukaryote lineages, such as plants and fungi, have close relatives which are not multicellular. We can
therefore see that multicellular did not evolve once, but evolved convergently.

Q13. Order the events by writing 1-24 on the right side. 8 pt

Events No. Events No.
300 thousand years ago 20 RNA world 2
Interbreeding with Neanderthals 22 The last common ancestor of 14
humans and lemurs
3.5 billion years ago 3 Accumulation of organic matter 1
First oxidative phosphorylation 5 Split between apes and Old World 15
Monkeys
First complex cells with organelles 6 6 million years ago 16
The evolution of tool use and larger brains 18 The evolution of bipedalism in hominins 17
The first land invertebrates 10 The first land plants 9
The last common ancestor of Neanderthals 19 First human writing systems 24
and Homo sapiens
Neanderthal extinction 23 Earliest photosynthesis 4
The last common ancestor between 12 Endosymbiosis between an eukaryotic 7
elephants and kangaroos lineage and cyanobacteria
Homo sapiens groups migrating into 21 500 million years ago 8
Eurasia
The first placental mammals 13 The last common ancestor between 11
salamanders and dinosaurs

Accumulation of organic matter 1

RNA world 2
3.5 billion years ago 3
Earliest photosynthesis 4
First oxidative phosphorylation 5
First complex cells with organelles 6
Endosymbiosis between an eukaryotic lineage and cyanobacteria 7
500 million years ago 8
The first land plants 9
The first land invertebrates 10
The last common ancestor between salamanders and dinosaurs 11
The last common ancestor between elephants and kangaroos 12
The first placental mammals 13
The last common ancestor of humans and lemurs 14
The split between ape and Old World Monkey lineages 15
6 million years ago 16
The evolution of bipedalism in hominins 17
The evolution of tool use and larger brains 18
The last common ancestor of Neanderthals and Homo sapiens 19
300 thousand years ago 20
Homo sapiens groups migrating into Eurasia 21
Interbreeding with Neanderthals 22
Neanderthal extinction 23
First human writing systems 24