GTS354 Semester Test 2 Preparation

Scope: L10 - L17

Answers to tasks at end of each lecture:

Lecture 10: Viral genome evolution

Core concepts
• Co-evolution: the process of reciprocal evolutionary change that occurs
between pairs of species or among groups of species as they interact with
one another.
• Host adaptation: hosts = ability to adapt to protect themselves against
pathogens. Example: the innate and acquired immune responses are
adaptations of the human body that exist for the sole purpose of warding off
disease
• Mutation (antigenic drift) = a change in the DNA sequence of an organism.
Mutations can result from errors in DNA replication during cell division,
exposure to mutagens or a viral infection.
• Reassortment (antigenic shift) = another form of genetic exchange that can
occur in segmented viruses—viruses that have their genome split into multiple
segments. Reassortment only occurs when multiple viruses co-infect the
same cell and replicate their progeny segments in the same cytoplasm.
• Recombination = process by which pieces of DNA are broken and
recombined to produce new combinations of alleles. This recombination
process creates genetic diversity at the level of genes that reflects differences
in the DNA sequences of different organisms.

• Selection pressure = are external agents which affect an organism's ability

to survive in a given environment
What are the most important selective pressures on virus genome evolution?
Selective pressure = forces that drive evolution via natural selection
➢ Host immune system
➢ Host Range
➢ Viral transmission
➢ Replication efficiency
➢ Genetic diversity
➢ Antiviral therapeutics
➢ Environmental factors
➢ Co-infection
➢ Genetic drift
➢ Reproductive strategy

1. Host immune system:

• Viruses that can evade or escape the host immune response have a
better chance of replicating and thus spreading within and between
hosts.
• Viruses thus evolve various mechanisms to counteract or escape the
host immune system to ensure their persistence.

2. Host Range:
• Host range= diversity of species that viruses can naturally infect.
Determined mainly by the receptors on both the virus and cells they
want to infect.

• Some viruses = broad host range (e.g. virus that can infect different
types of mammals as well as insects or virus that can infect multiple
plant species – Cucumber mosaic virus and Influenza A virus)
• Other viruses = narrow host range (e.g. virus that can inly infect one
host – most studied phages)
 • The ability of viruses to adapt to different hosts and expand their host
range can be a strong selective pressure. What does this mean? The
genome encodes all the parts of the virus such as the viral receptors.
Some viruses adapt their receptors to different host than their original
host, meaning that the encoding of the receptor in the genome
changed. This allows the virus to enter more host cells than it could
originally.
• Especially a problem in zoonotic viruses → where viruses that could
previously only infect non-human animals or insects adapted to infect
humans. We call this host-jumping.

3. Viral transmission:
• The success of a virus is affected by modes of transmission.
• Modes of transmission: airborne, vector-borne, direct contact (contact
with bodily secretions such as kissing, blood droplets, and saliva).
• Viruses that can adapt efficient modes of transmission have an
advantage.

4. Replication efficiency:
• Viruses that replicate quickly and efficiently within their host cells =
competitive advantage.
• Example: Poliovirus has a rapid replication cycle (~8hrs between
infection and release of viral progeny)
• Mutations within the viral genome that enhances replication are
favoured above mutations that does not enhance replication.

5. Genetic diversity:
• Genetic diversity within a viral population = provide reservoir of
variants with properties different than the rest of the population.
• This diversity helps the virus to adapt to changing conditions and find
more successful strategies for survival.
• Example HIV-1, Group M, Subtype C and Influenza virus.

6. Antiviral therapeutics:
• Use of antiviral drugs/therapies = exert selective pressure on viruses.
• Where viruses develop resistance mechanisms
• Example HIV and Hepatitis C

7. Environmental factors:
• Environmental conditions = temperature, pH, humidity
• Can impact virus stability and survival outside the host
• Viruses can evolve to be more resistant under various environmental
conditions. If virus can survive under more environmental conditions =
better chance of infecting a particular host.
8. Co-infection:
• When a host is simultaneously infected with multiple strains or species
of a virus → competition among the viral strains or species drive the
evolution of the more successful variants.
• Example: Flaviviruses (arbovirus that infects animals and mosquitoes):
when mosquitoes are infected with flavivirus that replicates in human
cells and mosquito cells → mosquito flaviviruses persist because they
are better adapted to replicate in the mosquito cell lines.
• Example: Co-infection of Influenza viruses (segmented genome) can
lead to reassortment of the viral genome and a new virus persists.

9. Genetic drift:
• Genetic drift = the change in frequency of an existing gene variant in
the population due to random chance.
• Without strong selective pressures, random genetic changes can
accumulate in a virus population over time.
• Leads to genetic diversity
• Which means there is a potential for adaptations and allows the more
frequent variants to persist.

10. Reproductive strategy:

• Viruses have different reproductive strategies
• Some viruses = chronic infections and others = latent infections
• Chronic infection = continued presence of infectious virus following the
primary infection (virus continuously replicates in host and host shows
symptoms)
• Latent infection = pathogenic virus remains dormant within the cell
(virus not actively replicating and host not showing symptoms).
 • The reproductive strategy affects the long-term evolutionary dynamics
of viruses

Lecture 11: Prokaryotic genome evolution

Core concepts

• Reductive genome evolution = the process by which genes and their

corresponding functions are lost, resulting in the downsizing of the genome
• Endosymbiosis = one organism (endosymbiont) living inside of cell of
another organism (host) for their mutual benefit.
• Black Queen hypothesis = is reductive evolution theory which seeks to
explain how natural selection (as opposed to genetic drift) can drive gene
loss.
In a microbial community, different members may have genes which produce
certain chemicals or resources in a "leaky fashion" making them accessible to
other members of that community. If this resource is available to certain
 members of a community in a way that allows them to sufficiently access that
resource without generating it themselves, these other members in the
community may lose the biological function (or the gene) involved in
producing that chemical.
Put another way: the black queen hypothesis is concerned with the conditions
under which it is advantageous to lose certain biological functions.
By accessing resources without the need to generate it themselves, these
microbes conserve energy and streamline their genomes to enable faster
replication.
• Muller’s ratchet = a process which, in the absence of recombination
(especially in an asexual population), results in an accumulation of irreversible
deleterious mutations.

Lecture 12:
Core Concepts:
• Adaptation
Is any heritable trait that helps an organism, such as a plant or animal, survive
and reproduce in its environment
• Phylogeny
Is the representation of the history of the evolution of a species or group,
especially in reference to lines of descent and relationships among broad
groups of organisms
• Horizontal Gene Transfer
Is the non-sexual movement of genetic information between genomes.
Three types:
Lecture 14 & 15:
Core concepts:
• What is a species concept and what is speciation?
Species are separated from one another by prezygotic and postzygotic
barriers, which prevent mating or the production of viable, fertile offspring.
Speciation is the process by which new species form.
It occurs when groups in a species become reproductively isolated and
diverge
• Biological species concept
• Phylogenetic species concept
• General lineage species concept
defines species as groups of organisms that share a pattern of ancestry and
descent and which form a single branch on the tree of life
• Barriers to gene flow
• Geographic barriers
• Reproductive isolation
• Prezygotic barrier
• Postzygotic barrier
• Models of speciation
o Allopatric, sympatric, parapatric, peripatric, ecological
 • The speed of speciation
is a measurement of how many new species appear in an interval of time
within a given taxon and a given habitat, region, or ecosystem. A rate of
speciation can also be a comparative measure, less dependent on time,
relating to how one taxon seems to diversify relative to another
• Polyploidy
is the heritable condition of possessing more than two complete sets of
chromosomes. Polyploids are common among plants, as well as among
certain groups of fish and amphibians.
• Hybridization
the breeding of two different organisms from genetically diverse groups or
species
• Cryptic species
are phenotypically highly similar species. Species complexes resulting from
taxonomic artefacts should not be considered as cryptic species. To identify
cryptic species, first one should establish species boundaries and only then
study processes resulting in phenotypic similarity.
• Microbial species
A microbial species is a concept represented by a group of strains from a
variety of sources, or by a population of strains, that contains freshly isolated
strains, stock strains maintained in vitro for varying periods of time, and their
variants

Critique the applicability of the BSC and PSC to microbes.

Biological Species Concept (BSC)
Reproductive isolation:
• Relies on the concept of
reproductive isolation to define
species
• Considers organisms to be part
of the same species if they can
interbreed and produce fertile
offspring
• Concept is less applicable to
most microbes → because many
of them reproduce asexually (e.g.
fission, budding, HGT)
Temporal and Spatial Limitations:
• BSC may not be suitable for
microbes with complex life cycles
or those that exist in different
forms under different conditions.
Phylogenetic Species Concept (PSC)
Genetic Divergence:
• The PSC defines species based
on shared ancestry and genetic
divergence.
• Can be highly relevant to
microbes, because: doesn’t
depend on the reproductive
isolation criterion.
• Microbes can be identified and
classified based on their genetic
differences (indicates distinct
evolutionary lineages).
Molecular Tools:
• Advances in molecular biology →
easier to generate phylogenetic
trees based on genetic make-up
of microbes
 • BSC may not account for the • Useful for studying microbial
diversity of life cycles and forms diversity
exhibited by many microbes • PSC suited for modern methods
of microbial characterisation
Genetic Exchange: Horizontal Gene Transfer (HGT):
• In microbes: significant genetic • PSC challenges: HGT
exchange even between distantly • HGT can blur the lines of genetic
related organisms (e.g HGT) divergence and make it difficult to
• This exchange → challenges the define species boundries
clear demarcation of species
based on reproductive isolation
(genes can move between
lineages more fluidly)
Critique
Microbial Diversity:
• Microbes = incredibly diverse group of organisms (Bacteria, Archaea,
Eukaryotic microorganisms)
• One approach = not fit ALL microorganisms (microbial groups have different
and unique characteristics)
Practicality:
• Applying BSC or PSC to microbes → may be practical in research and
laboratory
• Not same real-world implication (conservation and ecology) as it has for
macroorganisms
Hybrid Approaches:
• In practice: microbial characterisation uses combination of approaches
• using strategies based on both the BSC and the PSC
Discuss the role of isolating barriers in speciation.

Prezygotic isolating barriers: barriers BEFORE (pre-) mating

Geographic Isolation:
• Geographic barriers physically separate populations, preventing them from
interbreeding.
• For example, a river, mountain range, or body of water can isolate
populations.
• Over time → isolated populations may accumulate genetic differences that
lead to speciation.
Ecological Isolation:
• Different populations occupy distinct ecological niches within the same
geographic area.
• They do not encounter each other because they are adapted to different
habitats or food sources, reducing the chances of interbreeding.
Temporal Isolation:
• Populations may have distinct mating seasons, times of day when they are
active, or periods of reproductive receptivity.
• This temporal difference can prevent the mating of individuals from different
populations.
Behavioural Isolation:
• Populations may have different mating behaviours, courtship rituals, or
preferences for specific traits in potential mates.
• These behavioural differences can lead to reproductive isolation.
Mechanical Isolation:
• Differences in genitalia or reproductive structures can physically prevent
mating or hinder successful copulation between individuals from different
populations.

Postzygotic isolating barriers: barriers AFTER (post-) mating

Hybrid Inviability:
• Hybrids resulting from the mating of individuals from different populations may
not develop properly or have reduced fitness
• making them less likely to survive and reproduce.
Hybrid Sterility:
• Even if hybrids are viable, they may be sterile and unable to produce
offspring.
• This is common in interspecies crosses between closely related species
• Example: mules (horse × donkey).
Hybrid Breakdown:
• In some cases, first-generation hybrids may be viable and fertile,
• but when they mate with each other or with individuals from the parent
populations, their offspring may have reduced fitness or other problems.

Isolating barriers are essential for the process of speciation for several reasons:
• Isolating barriers prevent the exchange of genes between populations.
• This allows genetic differences to accumulate over time, eventually leading to
the divergence of the populations into distinct species.
• Isolation barriers can allow populations to adapt to their specific environments
more effectively. Over time → this adaptation can lead to the development of
unique traits and characteristics that contribute to speciation.
• Isolating barriers help maintain the genetic integrity of species by preventing
the dilution of unique genetic combinations.
• This is important for the stability and survival of species in their respective
niches.
• The presence of multiple species within an ecosystem enhances biodiversity
and contributes to the overall evolutionary dynamics.
• Speciation is a driving force of diversity in the natural world.

So….
• isolating barriers are crucial in the formation of new species by preventing
gene flow between populations
• allowing them to evolve independently and adapt to their specific
environments.
• The various types of prezygotic and postzygotic barriers collectively contribute
to the rich tapestry of life on Earth.

Lecture 17:
Core Concepts:
Hypotheses of the ancestry of modern humans
Homo sapiens
• Phase 3 Expansion outside Africa
“Recent African Origin”
Supported by:
➢ Mitochondrial DNA
➢ Fossils
➢ Genome evidence of introgression outside Africa
➢ Genomic ancestry outside Africa nested in African ancestry
 • Phase 2 African origins
Ancestors of modern humans originated in Africa and then dispersed to the
rest of the world
Replacing (rather than interbreeding) with archaic hominins that were resident
outside Africa at the time

• Phase 1 Divergence from MRCA

Hominins diverged from most recent common ancestor (0.3-1 MYA)
Critically evaluate the evidence that modern humans originated in Africa
1. Fossil Evidence:
• Oldest known fossils of anatomically modern humans (Homo sapiens) →
found in Africa
• Particularly: East Africa
• Date back to approx. 200 000 years ago

2. Lack of intermediary fossils:

➢ Lack of transitional fossils between archaic Homo sapiens and anatomically
modern Homo sapiens found outside Africa
➢ Supports idea of single origin in Africa

3. Genetic Evidence:

• Mitochondrial DNA:
• mtDNA passed from mothers to all offspring
 • show that all non-African populations have a common African ancestry
• consistent with the migration of a small African population that gave rise to all
modern humans
• Y-chromosomal DNA:
• Passed from all fathers to sons
• Research: evidence of single ancestral lineage of African origin

4. Archaeological Evidence:
• Cultural and Technological advances:
• Evidence of advanced cultural and technological development (symbolic
artifacts and complex toolmaking) emerged in Africa
• Consistent with the development of modern human behaviour and cognition
• Out of Africa dispersal:
• Archeological findings outside Africa dated to 70 000 – 100 000 years ago
• Coincides with the timing of the suggested Out-Of-Africa migration

5. Climate and Environmental context:

• Paleoclimatic data and evidence from African environmental history suggest
that Africa provided a stable and habitual environment for hominin evolution
AND emergence of Homo sapiens

Argue whether modern humans are still evolving

IN SHORT: Yes. WHY? evolution is an ongoing process, and it does not cease.
Genetic Adaptations:
• Human populations are still subject to natural selection and genetic drift.
• In some cases, we can observe genetic adaptations to changing
environments.
• Example: there is evidence of genetic adaptations to high-altitude
environments, such as the Andes and the Himalayas, where populations have
evolved traits that help them thrive at low oxygen levels.
Disease Resistance:
• The coevolution of pathogens and human immune systems continues, leading
to the development of new genetic variations that provide resistance to
diseases.
• This is particularly evident in populations with a long history of exposure to
specific pathogens, such as malaria or HIV.
Lactase Persistence:
• Lactase persistence, the ability to digest lactose in adulthood, has evolved in
some human populations in response to the practice of dairy farming.
• This adaptation is a relatively recent example of ongoing human evolution.

Cultural Practices and Genetic Evolution:

• Human culture and technology can influence genetic evolution.
• Example: practices like agriculture and animal domestication have influenced
the human diet and the selection of genetic traits related to food consumption.

Environmental Changes:
• Human-induced environmental changes, such as climate change, may exert
selective pressures on populations.
• Populations in regions affected by climate change → shifts in allele
frequencies related to temperature adaptation or disease resistance.

Gene Flow:
• Gene flow between human populations is more extensive today due to
globalization
• can introduce new genetic variation and facilitate the spread of advantageous
genetic traits.
• Gene flow is a key factor in the evolution of populations.

Recent Genetic Studies:

• Advances in genetic research, including whole-genome sequencing and the
ability to track genetic changes over time → insights into ongoing human
evolution.
• These studies reveal that human populations are continually accumulating
new genetic variations.

Microevolution:
• Microevolutionary changes, which involve small-scale genetic shifts within a
population
• can accumulate over time and lead to the development of distinct traits or
characteristics.
• These changes, while small, contribute to the overall process of evolution.