dNdS ratios reflect patterns of genetic divergence that have accumu.pdf

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dN/dS ratios reflect patterns of genetic divergence that have accumulated between species over time. A dN/dS ratio of 1.0 is consistent with a neutral model of evolution. Look back at the relationship between dN and dS for both the lysin and VERL genes. What is the most likely hypothesis explaining the pattern that species with more distantly related gene sequences tend to have lower dN/dS ratios? Additional info: using MEGA software, it was found that the dN/dS ratio for lysin was 1.237 (positive selection) and the dN/dS ratio for VERL was about 1 (neutral selection). Solution dN/dS ratio is a statistical test to quantify selection pressure on protein coding regions of microbes. Two things taken into consideration here, rate of substitution at silent sites (dS- assumed neutral) and rate of substitution at non-silent sites(dN- positive). Because both the species are divergent from each other we observe lower dN/dS ratio. The sequesence which are present in the exsisting species are essential for their survival, so they can not afford to change the sequence. They have more distantly related gene sequences, so they do not have any similarity and do not need significant changes in the sequence..

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allele distribution: In population genetics, allele frequencies are used to describe the amount of variation at a particular locus or across multiple loci. When considering the ensemble of allele frequencies for a large number of distinct loci, their distribution is called the allele frequency spectrum. Distribution of Allele Frequency Investigation of the distribution of minor-allele frequencies (MAF) suggests that for all traits, except possibly for HDL level, the distribution of observed susceptibility SNPs is skewed toward higher minor-allele frequencies (MAF >20%) rather than intermediate frequencies (MAF 5–20%) in comparison with SNP allele-frequency distributions in general human populations or among tagging SNPs that have been included in common genotyping platforms. Overall, out of 387 SNPs included in the analysis for all traits combined, the fraction of SNPs with intermediate- frequency categories was only 23.0%, which was significantly lower than the corresponding fraction of 55.0% among independent representative SNPs (any pairwise r2 0.1) from the HapMap (hapmap.ncbi.nlm.nih.gov) database (P = 2.05 × 1030). The power-weighted analysis also estimated a relatively small fraction (26.4%) of susceptibility SNPs for the intermediate- frequency category, and thus indicated that the observed clustering of common susceptibility SNPs toward higher frequencies is unlikely to have resulted from the artifacts of study power. Distribution of Effect Sizes for Susceptibility SNPs. We define “effect size” for susceptibility SNPs using two alternative criteria. In one, we define it as the coefficient () for a SNP when its association with the outcome is modeled through a regression model, such as linear regression for a quantitative trait or logistic regression for a qualitative trait, assuming a linear trend per copy of an allele. In our analysis, the regression coefficients for quantitative traits are presented in units of standard deviation (SD) of the trait so that they are comparable across traits. In a second criterion, we define effect size as the contribution of the SNP to genetic variance of the trait, that is, gv = 22f(1 f), where f is the allele frequency for either of the two SNP alleles (4). It is noteworthy that the power for detection of a susceptibility SNP for most commonly used association tests that assume linear trend depends on and f only through the quantity gv (4) Determining allele and genotype frequencies can be done two slightly different ways. One method involves converting the initial numbers of each genotype to frequencies and then doing all calculations as frequencies. In this case the frequency of the p allele = the frequency of the p/p homozygotes + 1/2 the frequency of the heterozygotes. The frequency of the q allele = the Determining allele and genotype frequencies can be done two slightly different ways. One method involves converting the initial numbers of each genotype to frequencies and then doing all calcul.

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The capacity of an animal to produce differs between species, breeds and strains as a result of genetic factors. However, a complex of inter-related factors in the animal husbandry will influence the animal's ability to utilize that capacity for growth, development and production. Progress in breeding and feeding for further increase in production and efficiency can be limited by environmental factors. Research into these factors has therefore been increasing in recent years, especially in countries having intensive animal production. Animal housing design is mainly concerned with the physical environment, in particular climatic and mechanical factors, but all other factors should also be considered in order to create a good layout, where healthy, high yielding animals can be provided with correct feeding, can be easily handled and can produce without stress or suffering physical harm. Heat Regulation All domestic livestock are homeotherms; that is, they maintain relatively constant internal body temperatures, usually within a 1 to 2° C range. Normal body temperatures of some domestic animals and humans are given The body temperature of most domestic animals is considerably higher than the environmental temperature to which they are exposed most of the time. They maintain their body temperatures by balancing internal heat production and heat loss to the environment. The hypothalmus gland acts as a body thermostat by stimulating mechanisms to counteract either high or low ambient temperatures. For example, increased conversion of feed to-heat energy is used to counteract low ambient temperatures, while for example increased respiration (rate and volume) and blood circulation in the skin counteracts high ambient temperatures. Varying temperature also results in changed behaviour. Most animals reduce their level of activity in a hot environment and, for example, pigs lie clustered in a heap at low temperatures, while they lie spread out with extended limbs at high temperatures. This would suggest increased space requirement for pigs held in a warm, tropical climate. The body can tolerate short periods of heat stress, but if the ambient temperature exceeds the body temperature for an extended period, it may prove fatal. When feed is converted by the animal's metabolism for the production of milk, eggs, meat, off-spring etc., heat is produced as a by-product. An increased production level and thus feed requirement will therefore result in increased internal heat production. High yielding animals are consequently more likely to suffer from heat stress in a hot climate than are low yielding ones. Feeding fibre-rich, low digestible feed stuffs like hay will result in high heat-production because of increased muscular activity in the alimentary tract and, in ruminants, increased micro-organism activity in the rumen. An increased share of concentrates in the feed may therefore reduce heat stress in an animal under hot climatic conditions. Heat is produced

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