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Bottleneck Vs Founder Effect

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Last Updated: 02 July 2021

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Genetic drift is a random process of alleles being passed from parents to offspring. Increasing genetic diversity in the population requires introducing a greater number of alleles, which can only occur through mutations or addition of unrelated members to the population. Genetic drift only affects how already-existing alleles are passed down. If an allele has high frequency at baseline, chance of it being passed down to subsequent generations is higher than alleles of lower frequency. Through random chance, high-frequency alleles can eventually have a frequency of 100%, becoming fixed in the population. Conversely, low-frequency allele can eventually disappear from the population if none of the few parents who possess that allele happen to pass it onto their offspring. Genetic drift describes random selection of alleles that are passed from one generation to the next due to independent assortment in gametogenesis. Genetic drift cannot create new alleles, so it cannot increase genetic diversity. It can, however, decrease genetic diversity if allele of low frequency is not passed down to subsequent generations due to pure chance. There is no hard and fast rule for whether genetic drift or natural selection have had greater effect on shaping populations. Both have greatly shaped populations present on Earth today, but their relative importance varies between species and has also varied over time. Conditions of the Hardy-Weinberg equilibrium require that both natural selection and genetic drift be negligible. If genetic drift is occurring, then the population cannot be in Hardy-Weinberg equilibrium. Bottleneck effect is a term used to describe loss of genetic variation that occurs after outside forces destroy most of the population. Few individuals leave to reproduce and pass their traits on to all of their offspring, which then may thrive without competition of large population. Eventually, there may be large, very genetically similar population based on the traits of a few original survivors. Founder effect describes low genetic variation of population derived from small groups of individuals in new geographic location. Genetic drift is random change of allele frequency in the population. The Bottleneck effect describes a phenomenon when the population has a sudden reduction in gene pool due to natural environmental events, natural disasters, disease, or human involvement. This reduction in gene pool will likely cause bias that did not exist in the original population. For example, suppose the population of birds has small numbers with mutations making them unable to fly. If a disease reaches this population that kills all birds when they reach altitude above 50m, then the gene pool of the population will suddenly shift to favor flightless birds. Bottleneck effect, after a long time, could potentially lead to speciation, but this is not the defining factor of effect. Introducing new species can increase pressures of natural selection, but does not directly relate to the bottleneck effect.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

Bottleneck Effect

Bottleneck effects happen when some catastrophe, like an earthquake or tsunami, kills off most of the population at random and leaves only a handful of survivors. A catastrophe has to be something that strikes at random, however, and kills individuals irrespective of the genes they carry. A Plague that only kills individuals lacking particular gene would be an example of natural selection, and not a bottleneck effect, because it kills individuals with specific genetic makeup, rather than striking at random. Bottleneck effects dramatically reduce genetic diversity because most of the population dies and genes carried by diverse individuals perish with them. Northern elephant seals, for example, were hunted almost to extinction in the late 19th century; at one point there were as few as 20 left alive. Their population rebound to more than 30 000 over the following century, but there is much less genetic variation among northern elephant seals than among southern populations, which do not undergo such intense hunting.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

Introduction

The major histocompatibility complex is one of the most important genetic systems for infectious disease resistance in vertebrates. Characteristically, MHC genes show high allelic diversity, long allelic persistence times and high heterozygosity. High levels of polymorphism of MHC genes is believed to be the result of balancing selection leading to long-term maintenance of allelic lineages as well as positive / diversifying selection for amino acid replacement identified at molecular level by increased ratio of nonsynonymous over synonymous substitutions at functionally important antigen-binding sites. This diversity allows binding of a variety of pathogen-derive antigens that initiate appropriate immune response. A number of studies have underscored the influence of MHC diversity patterns on individual fitness and long-term persistence of populations and species. Mechanisms responsible for maintaining polymorphism at MHC genes include negative frequency dependent selection and heterozygote advantage, which are not mutually exclusive. Frequency dependence arises because carriers of common alleles are more likely to be invaded by coevolving parasites while new and thus rather rare MHC alleles cause temporary advantage. Heterozygosity allows presentation of a wider range of pathogen-derive peptides, and thus provides greater resistance to infection. Disassortative mating, mother-fetus interaction, and spatio-temporal variations in pathogen-mediate selective regimes also contribute to the maintenance of high MHC diversity. It is well known that isolation and large demographic declines affect the ability of the population to maintain genetic diversity over time due to increased action of genetic drift. Genetic drift may overcome balancing selection, leading to reduced variation at MHC loci. A number of studies have documented severely reduced MHC variation in small, bottlenecked populations and endangered species. These species may be more susceptible to disease and thus more prone to extinction. Therefore, understanding the role of selection in maintaining MHC variation in bottlenecked populations has implications for conservation of endangered species. Arctic fox has circumpolar distribution. Most mainland populations have no apparent borders and show pronounced gene flow. Commander Islands populations live at the southern edge of the species geographic range in the Pacific Ocean and have been isolated since the Pleistocene. They are thought to represent two endemic subspecies. Islands were discovered in 1741, and at that time Arctic foxes were abundant on both islands. Subsequently, both populations were hunted heavily for their fur, and up to half of each island's population was killed annually. However, up to the middle of the 20th century, numbers remained relatively stable with about 2000-4000 foxes on Bering and up to 1000 on Mednyi. In 1970-1980, Mednyi population crashed due to epizootic mange. Nowadays, population of Mednyi Arctic foxes is < 100 individuals, 10-15% of its former abundance. Cases of disease also occur on Bering Island, but there it had no appreciable effect on the population size, which remains stable.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

Materials and methods

When analysing anonymous markers, absence of co-migration must be assume. Each locus is supposed to be di-allelic and alleles are assumed to be induced by identical mutations. These assumptions are not testable without time-consuming segregation analyses but seem to provide negligible bias. Statistical analysis of dominant markers is not as straightforward and powerful as analysis of co-dominant markers. However, lack of statistical power can be circumvented by generating numerous markers. Without analysing multiple generations, Hardy-Weinberg equilibrium must classically be postulate, which is usually unrealistic, especially in the case of small sample size and intra-population analysis. Lynch and Milligan offer statistical background and recommendations to investigate population structure with classical F analogues. Roughly, analysis must be limited to fragments whose frequency is less than 1 and F estimations with small sample size should be correct following Weir and Cockerham methods of calculation. These recommendations have been followed and have been calculated using RAPDFst software. These estimates have been performed at both regional and local scale, and to estimate pairwise F-statistics between groups. To avoid strict Hardy-Weinberg equilibrium postulation, it is permissible to adopt phenetic analysis, where each PCR product is assumed to represent a profile. The most frequently applied phenetic method to estimate population structure is certainly the use of Shannon's diversity index to partition diversity among populations. Unfortunately, these estimations seem particularly bias in the case of small and unequal samples and are thus not present here. Considering RAPD product as phenotype, multivariate analyses based on Euclidian distances are particularly promising to reveal the structure of genetic variability. Although correspondance analysis is the most frequently used method to analyse binary data, it simultaneously maximizes inertia among individuals and loci. This property could potentially hide relationships between loci. Thus, in order to provide a genome-wide variability point of view summarized in few synthetic variables, principal component analysis based on covariance matrix was preferred here. Then, between-group eigenanalysis can be processed to partition this variability into within-and between-group components. The statistical significance of this partition is assessed by the Romesburg randomization test. Multivariate analyses have been performed using ADE-4 software. In addition, Bayesian statistical procedures have been proposed to investigate population structure with dominant markers. This hierarchical approach aims to investigate genetic data by incorporating effects of uncertainty about fixation index and inbreeding coefficient into estimations of these parameters, through use of Markov Chain Monte Carlo. Mcmc is run 250 000 times to ensure convergence of Markov Chain to its stationary distribution and, after initial 50 000 simulations are discard, estimations every five steps are retained to avoid autocorrelation among samples. The Deviance information criterion is a measure that takes into account both how well the model fits data and how many parameters are required to do it. Running different models on the same dataset, DIC is model choice criterion.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

4.2 Viral population bottlenecks

Rad sequencing resulted in a total of 628. 4 million gray seal reads and 111. 5 million harbor seal reads, with an average of 2. 4 million reads per individual, following implementation of sequence quality filters. Systematic evaluation of Stacks parameters, following Paris et al., Identify similar optimal parameters for both species. As expect, and previously demonstrated in Paris et al., Mean coverage per locus increases and the number of assembled loci per individual decreases as M increases for both species. The number of polymorphic loci and SNPs for both gray and harbor seals was greatest at M = 2, which was therefore selected as the optimal value for both datasets. Changing the M parameter had little impact on the number of assembled loci, although we observe a slight drop after M = 1. The number of polymorphic loci and SNPs jumps from M = 1 to 2 and then continues to rise to greater values of M. After transition from M = 1 to 2, number of polymorphic loci rises by fewer than 150 loci with each incremental increase of M, and we therefore select M = 2 and N = M = 2 as optimal value for both datasets. Interestingly, it was clearly apparent in our evaluation of Stacks parameters that the gray seal data set was significantly more polymorphic than the harbor seal dataset. Gray seals had more than twice the number of polymorphic loci and SNPs than harbor seals at select M = 2 for any tested value of r, and this trend remains across all test values of M and r. Similarly, across all test values of M and r, gray seals had twice, or nearly twice, number of polymorphic loci and greater number of SNPs. Using select, optimal parameters and following removal of highly repetitive stacks, gray and harbor seal RAD catalogs contain 244 822 and 195 906 de novo loci, respectively. Rad loci of two species were compared through alignment to reference Weddell seal genome. For gray seals and harbor seals, respectively, 187 696 and 145 591 loci align to Weddell seal genome, and 100 251 loci were sequence in both study species. We identify, genotyped, and further analyzed 8 716 and 3 761 polymorphic r80 loci containing 10 097 and 4 312 SNPs that were sequence in at least 80% of individuals in at least one sample group in gray and harbor seals, respectively. Polymorphisms were largely special Although 9 211 of these loci were present in sequence data of both species, only 560 of loci were polymorphic in both species. Intrahost variants were used to analyze population structures and to assess population bottlenecks during transmission. Virus genetic diversity increases during mouse infection, and decreases during horizontal transmission to both larvae and nymphs. Initial point of tick infection during bloodfeeding also introduces fixed or nearly fixed POWV mutations into populations.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

Sources

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions.

* Please keep in mind that all text is machine-generated, we do not bear any responsibility, and you should always get advice from professionals before taking any actions

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