Common Bottle neck

1. COMMON BOTTLENECKS AND
ISSUES
BY
Assist. Prof.
Dr. Berciyal Golda. P
VICAS

2. In production and project management, a bottleneck is
one process in a chain of processes, such that its limited
capacity reduces the capacity of the whole chain. The result of
having a bottleneck are stalls in production, supply overstock,
pressure from customers, and low employee morale.
Definition:
The bottleneck effect, also known as a
population bottleneck, is when a species goes through an event
that suddenly and significantly reduces its population. Think
about how only so much stuff can come out of the neck of a
narrow bottle at a time.
INTRODUCTION

3. Genetic Drift
• Genetic drift is the change in allele frequencies
that occurs by chance events. In essence, it is
identical to the statistical phenomenon of
sampling error on an evolutionary scale.
• It is a random process.
• Because sampling error is greatest in small
samples and smallest in large samples, the
strength of genetic drift increases as
populations get smaller.

4. Effects of chance in small populations - genetic drift
The smaller the population, the less genetic variety it has.
▪ In a very small population, alleles can be lost from one
generation to the next, simply by random chance.
▪ When a population evolves only because of this type of
random sampling error, GENEC DRIFT is taking place.
▪ The smaller a sample, the greater the chance of deviation
from a predicted result
▪ Genetic drift is the change in allele frequencies that occurs by
chance events. In essence, it is identical to the statistical
phenomenon of sampling error on an evolutionary scale.
▪ It is a random process.
▪ Because sampling error is greatest in small samples and
smallest in large samples, the strength of genetic drift
increases as populations get smaller.

5. BOTTLENECK EFFECT

6. Effects of Genetic Drift
1. significant in small populations
2. causes allele frequencies to change at
random
3. can lead to a loss of genetic variation within
populations
4. can cause harmful alleles to become fixed
© 2011 Pearson Education, Inc.

7. Effects of Genetic drift:
• Populations lose genetic variation
• With little variation, a population is less likely to have some
individuals that will be able to adapt to a changing
environment
• Any lethal alleles may be carried in the population by
heterozygous individuals, and become more common in the
gene pool due to chance alone
• significant in small populations
• causes allele frequencies to change at random
• can lead to a loss of genetic variation within populations
• can cause harmful alleles to become fixed
There are two types of Genetic Drift:
1. Bottleneck Effect
2. Founder Effect

8. 1. The Bottleneck Effect
• sudden reduction in population size due to a change in
the environment
• New gene pool may not reflect original
• If the population remains small, it may be further
affected by genetic drift
• Bottlenecks are periods of very low population size or
near extinction. This is another special case of genetic
drift.
• The result of a population bottleneck is that even if the
population regains its original numbers, genetic variation
is drastically reduced

9. What could cause bottlenecks?
A population bottleneck is an event that drastically
reduces the size of a population. The bottleneck may
be caused by various events, such as an environmental
disaster, the hunting of a species to the point of extinction, or
habitat destruction that results in the deaths of organisms
Some disaster strikes the original population ……

10. Original
population
Bottlenecking
event

11. Original
population
Bottlenecking
event
Surviving
population

12. • A population bottleneck event can lead to
genetic drift.
– It occurs when an event
drastically reduces
population size.
Original population
–The bottleneck effect is genetic drift
that occurs after a bottleneck event.
Leaves very little genetic variation

13.  sudden reduction in population size due to a change in the
environment
 New gene pool may not reflect original
 If the population remains small, it may be further affected by
genetic drift
 Examples:
 Cheetahs -nobody knows exactly why it occurred, but cheetahs
underwent an extreme population bottleneck several thousand
years ago. As a result, they have very little genetic variation.
 Northern Elephant Seal-underwent an extreme population
bottleneck resulting from fur hunting in the nineteeth century.
 Endangered Species

14. Cheetahs
• Populations may suffer a dramatic
drop in numbers.
• This could be due to a chance
event, such as a volcanic eruption,
earthquake, flood, fires etc
• The few survivors will contain a
much smaller variety of alleles than
the original population.
• The genetic diversity of the new
population will remain restricted.

15. –During the 1800s the over hunting of Northern Elephant seals
reduced the population to about 20 individuals
–The 20 seals did not represent the genetic diversity of the original
population
–Since hunting stopped, the population has grown to over 100,000
–However the population has little genetic diversity
Northern Elephant Seals

16. Why is the bottleneck effect bad?
The bottleneck effect, also known as a
population bottleneck, is when a species goes through an
event that suddenly and significantly reduces its population.
Think about how only so much stuff can come out of the
neck of a narrow bottle at a time.
What is the bottleneck effect in genetics?
The bottleneck effect is an extreme example
of genetic drift that happens when the size of a population is
severely reduced. Events like natural disasters (earthquakes,
floods, fires) can decimate a population, killing most
individuals and leaving behind a small, random assortment
of survivors

17. 2. Founder Effect
The founder effect is genetic drift that occurs when
when a few individuals, representing a fraction of
the original allele pool, invade a new area and
establish a new population.
• The founder effect occurs when a few individuals
become isolated from a larger population
• Allele frequencies in the small founder population
can be different from those in the larger parent
population

18. The founder effect is genetic drift that occurs after the start of new population.
– It occurs when a few individuals start a new population

19. Founder effect: the small initial
number of Amish colonists
included an individual carrying
the recessive allele for six-
fingered dwarfism

20. 1. THE IMPACT OF BOTTLENECKS ON BACTERIAL
GENETIC DIVERSITY
The evolution and spread of infectious disease agents
are underpinned by an ability to generate high levels of
genetic variation enabling rapid acquirement of novel
adaptive traits.
A key on-going paradigm shift in our understanding of
genetic variability in pathogenic bacteria was the
demonstration that localised hypermutation (LH) due to
hypermutable DNA elements was responsible for the phase
variation (PV) phenomenon of rapid ON and OFF switches in
surface antigens and restriction-modification systems (RM).

21. We now recognise that LH and PV are widely
distributed across bacterial pathogens and commensals but
with significant diversity in the numbers of loci and in the
types of functions encoded by these loci .

22. The importance of genetic variability to infection has been recognised
by careful epidemiological investigations whose ability to detect genetic
determinants of disease has been enhanced by the genomics revolution. An
under-appreciated conundrum of the infectious disease lifestyle is that genetic
diversity is severely impacted by bottlenecks during transmission between and
within-hosts.

23. Impact of selective and non-selective bottlenecks on the
genetic diversity of bacterial populations during transmission
between hosts.
This figure depicts transmission of a bacterial species
from one host to another by the faecal-oral route with an initial
step of excretion from a large genetically diverse population,
consisting of seven genotypes, of a small subset of the
population into the environment followed by a subsequent step
of acquisition by and colonisation of a second host by a less
diverse population, consisting of three genotypes.
The genotypes represent different combinations of
alleles or phase variants of multiple genes.

24. Bottlenecks are a short-hand to describe the
phenomenon of a rapid reduction in the number of organisms in
a population leading to loss of genetic variants . Conceptually,
two opposing types of bottlenecks can be defined, selective and
non-selective.
While these differing types of bottlenecks may occur in
isolation and have defining features, biological situations are
often complex and these two types of bottlenecks may occur
simultaneously or, due to varying strengths of selection,
overlap.
In this case, the degree of bottlenecking is directly
linked to the strength of selection with differences in the fitness
advantages of the genetic variants for surviving the bottleneck
altering the genetic structure of the whole surviving population.

25. The genotypes represent different combinations of
alleles or phase variants of multiple genes
(a) Non-selective bottlenecks.
(b) Mixed bottlenecks.
(c) Selective bottlenecks.
(a) Non-selective bottlenecks.
In this mode, there is random inclusion of particular
genotypes from the starting population into the transmitted
population during both the initial excretion and secondary
acquisition steps.
These bottlenecks strongly skew the population structure
without any selection such that dominant genotypes occur by
chance with no guarantee of the same pattern being observed
during another similar transmission event.

26. Non-selective bottlenecks occur when a population is
reduced in size, sometimes to only a few cells, through
chance, non-selective events such as a physical reduction in
the population during transmission to a new host.
In non-selective bottlenecks, the effect on the genetic
variants within the surviving population is random.
This effect may be observed as each biological
replicate of the same experiment having a different
population structure and hence high genetic divergence
from the starting population and between biological
replicates

27. (b) Mixed bottlenecks.
In this model, the purple, yellow and blue variants are
weakly adaptive for survival in the environment.
However, due to the non-selective excretion bottleneck,
only the adaptive yellow and non-adaptive red variants pass
through the initial bottleneck and colonise the second host
Thus selective and non-selective bottlenecks create
changes in population structure that can be extreme when a
single cell bottleneck occurs.

28. (c) Selective bottlenecks.
In this case, the red variant type has a much higher fitness
for survival in the environment than other variants.
Hence only this variant is transmitted. In this selective
bottleneck, selection of the red variant produces a significant
reduction in population diversity of the transmitted population that
would be reproducible during another similar transmission event.
High mutation rates allow for recovery of some additional
genetic variation during colonisation of the second host in both B
and C.
Contrastingly, selective bottlenecks, particularly when
selection is strong, may lead to high divergence from the starting
population but low divergence between biological replicates of the
output populations due to selection of a common genotype.

29. Spread of a bacterial pathogen within a host is subject to
multiple selective and non-selective bottlenecks that impact on
disease outcome.
A phase-variable bacterial species is depicted that exists
in two phase variation states (blue and yellow) in the
gastrointestinal tract of a host.
This organism penetrates the mucosal lining of the gut
and replicates in the bloodstream and subsequently spreads to
internal organs.
The yellow variants are able to replicate at fast rates in
internal organs but are rapidly cleared by immune effector cells
and/or antibiotic treatment.

30. In contrast, the blue variants invade hosts in the organs
where they replicate slowly and are able to resist antibiotic
clearance due to poor intracellular penetration of antibiotics and
slow growth rates.
These organisms provide a reservoir for relapse of an
infection due to the generation of antibiotic resistance or
cessation of treatment.
Each stage of this process introduces either narrow non-
selective bottlenecks (i.e. dissemination to blood and tissue
macrophages) or a stringent selective bottleneck (i.e. survival of
antibiotic therapy) such that disease only occurs in a subset of
hosts following the stochastic effects of sorting between the two
variants as they pass through each of the bottlenecks.

32. Conclusion
• significant in small populations
• causes allele frequencies to change at random
• can lead to a loss of genetic variation within
populations
• can cause harmful alleles to become fixed

33. Genetic drift results from random sampling
error
Sampling error is higher with smaller sample