scholarly journals Pervasive selection pressure in wild and domestic pigs

2020 ◽  
Author(s):  
J. Leno-Colorado ◽  
S. Guirao-Rico ◽  
M. Pérez-Enciso ◽  
S. E. Ramos-Onsins
Keyword(s):  
Low Frequency ◽  
Deleterious Mutations ◽  
Large White ◽  
Domestic Pigs ◽  
Behavior Development ◽  
Median Proportion ◽  
Frequency Changes ◽  
Nearly Neutral Mutations ◽  
Approximate Bayesian ◽  
Neutral Mutations

ABSTRACTAnimal domestication typically affected numerous polygenic quantitative traits, such as behavior, development and reproduction. However, uncovering the genetic basis of quantitative trait variation is challenging, since they are caused by small allele-frequency changes. To date, only a few causative mutations related to domestication processes have been reported, strengthening the hypothesis that small effect variants have a prominent role. So far, approaches on domestication have been limited to the detection of the global effect of domestication on deleterious mutations and on strong beneficial variants, ignoring the importance of variants with small selective effects. To overcome these difficulties, here we propose to estimate the proportion of beneficial variants based on the asymptotic MacDonald Kreitman (MK) method, according to estimates of variability based on frequency spectrum. We applied this approach to the pig species, analyzing 46 complete genome sequences from 20 European wild boars, 6 Iberian and 20 Large White pigs at different molecular scales: gene, metabolic pathway and whole-genome.Descriptive variability analyses on pig populations indicate that domestic and wild pig populations do not differ in nonsynonymous fixed mutations. Instead, most variants are shared among them, despite that the phenotypes of wild and domestic individuals are clearly divergent. Additionally, asymptotic MK plots based on summary statistics show that small effects variants may affect the final calculation of α, the proportion of beneficial mutations. The distribution of fitness effects inferred with Approximate Bayesian Computation analysis indicates that both wild and domestic pigs display an important quantity of deleterious mutations at low frequency (~83% of total mutations) and a high number of nearly-neutral mutations (~17%) that may have a significant effect on the evolution of domestic and wild populations. Exclusive mutations show that recent demographic changes have severely affected the fitness of populations, especially of the local Iberian breed. Finally, the median proportion of the strong favorable mutations are very scarce in all cases (≤ 0.2%). The median estimated alpha values (weak and strong favorable) are 0.9% for wild and domestic pigs.

scholarly journals The effects of weak selection on neutral diversity at linked sites

2021 ◽  
Author(s):  
Brian Charlesworth
Keyword(s):  
Theoretical Models ◽  
Population Variation ◽  
Deleterious Mutations ◽  
Weak Selection ◽  
The Mean ◽  
Frequency Changes ◽  
Site Diversity ◽  
Neutral Mutations ◽  
Approximate Expressions

The effects of selection on variability at linked sites have an important influence on levels and patterns of within-population variation across the genome. Most theoretical models of these effects have assumed that selection is sufficiently strong that allele frequency changes at the loci concerned are largely deterministic. These models have led to the conclusion that directional selection for new selectively favorable mutations, or against recurrent deleterious mutations, reduces nucleotide site diversity at linked neutral sites. Recent work has shown, however, that fixations of weakly selected mutations, accompanied by significant stochastic changes in allele frequencies, can sometimes cause higher diversity at linked sites when compared with the effects of fixations of neutral mutations. The present paper extends this work by deriving approximate expressions for the mean times to loss and fixation of mutations subject to selection, and analysing the conditions under which selection increases rather than reduces these times. Simulations are used to examine the relations between diversity at a neutral site and the fixation and loss times of mutations at a linked site subject to selection. It is shown that the long-term level of neutral diversity can be increased over the equilibrium expectation in the absence of selection by recurrent fixations and losses of linked, weakly selected dominant or partially dominant favorable mutations, and by linked recessive or partially recessive deleterious mutations. The results are used to examine the conditions under which associative overdominance, as opposed to background selection, is likely to operate.

SEM image sharpness analysis

1996 ◽  
Vol 54 ◽  
pp. 142-143
Author(s):  
M. T. Postek ◽  
A. E. Vladar
Keyword(s):  
High Frequency ◽  
Low Frequency ◽  
Quantitative Information ◽  
Primary Electron ◽  
Image Sharpness ◽  
Critical Dimensions ◽  
Sem Image ◽  
Frequency Changes ◽  
Electron Microscopes ◽  
Scanning Electron

Fully automated or semi-automated scanning electron microscopes (SEM) are now commonly used in semiconductor production and other forms of manufacturing. The industry requires that an automated instrument must be routinely capable of 5 nm resolution (or better) at 1.0 kV accelerating voltage for the measurement of nominal 0.25-0.35 micrometer semiconductor critical dimensions. Testing and proving that the instrument is performing at this level on a day-by-day basis is an industry need and concern which has been the object of a study at NIST and the fundamentals and results are discussed in this paper.In scanning electron microscopy, two of the most important instrument parameters are the size and shape of the primary electron beam and any image taken in a scanning electron microscope is the result of the sample and electron probe interaction. The low frequency changes in the video signal, collected from the sample, contains information about the larger features and the high frequency changes carry information of finer details. The sharper the image, the larger the number of high frequency components making up that image. Fast Fourier Transform (FFT) analysis of an SEM image can be employed to provide qualitiative and ultimately quantitative information regarding the SEM image quality.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

scholarly journals Experimental Estimate of the Abundance and Effects of Nearly Neutral Mutations in the RNA Virus ϕ6

Genetics ◽  
2007 ◽  
Vol 176 (1) ◽  
pp. 467-476 ◽  
Author(s):  
Christina L. Burch ◽  
Sebastien Guyader ◽  
Daniel Samarov ◽  
Haipeng Shen
Keyword(s):  
Rna Virus ◽  
Experimental Estimate ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations

Dynamic modulation of cerebrovascular resistance as an index of autoregulation under tilt and controlled Pet CO2

2002 ◽  
Vol 283 (3) ◽  
pp. R653-R662 ◽  
Author(s):  
Michael R. Edwards ◽  
J. Kevin Shoemaker ◽  
Richard L. Hughson
Keyword(s):  
Transfer Function ◽  
Function Analysis ◽  
Low Frequency ◽  
Mean Flow ◽  
Low Frequencies ◽  
Cerebrovascular Autoregulation ◽  
Cerebrovascular Resistance ◽  
Arterial Blood ◽  
Transfer Function Analysis ◽  
Frequency Changes

Transfer function analysis of the arterial blood pressure (BP)-mean flow velocity (MFV) relationship describes an aspect of cerebrovascular autoregulation. We hypothesized that the transfer function relating BP to cerebrovascular resistance (CVRi) would be sensitive to low-frequency changes in autoregulation induced by head-up tilt (HUT) and altered arterial Pco 2. Nine subjects were studied in supine and HUT positions with end-tidal Pco 2(Pet CO2 ) kept constant at normal levels: +5 and −5 mmHg. The BP-MFV relationship had low coherence at low frequencies, and there were significant effects of HUT on gain only at high frequencies and of Pco 2 on phase only at low frequencies. BP → CVRi had coherence >0.5 from very low to low frequencies. There was a significant reduction of gain with increased Pco 2 in the very low and low frequencies and with HUT at the low frequency. Phase was affected by Pco 2 in the very low frequencies. Transfer function analysis of BP → CVRi provides direct evidence of altered cerebrovascular autoregulation under HUT and higher levels of Pco 2.

scholarly journals Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Hao Chen ◽  
Min Huang ◽  
Bin Yang ◽  
Zhongping Wu ◽  
Zheng Deng ◽  
...  
Keyword(s):  
Geographic Origin ◽  
Whole Genome Sequencing Data ◽  
Biological Functions ◽  
Sequencing Data ◽  
Phenotypic Characteristics ◽  
Large White ◽  
Wild Boars ◽  
Domestic Pigs ◽  
Southern Chinese ◽  
History Of

Abstract Background Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Results Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs. Conclusions This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

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