Common Bottle neck.pptx

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 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 © 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 Non-selective bottlenecks. Mixed bottlenecks. 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.

31. 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

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