scholarly journals Deleterious mutation load in diverse cattle breeds of the world

2021 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
High Frequency ◽  
Deleterious Mutation ◽  
East Asian ◽  
Low Frequency ◽  
Mutation Load ◽  
Cattle Breeds ◽  
The World ◽  
Low Diversity

Abstract Domestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using the whole genome data from 432 animals belonging to 54 cattle breeds of the world. Our analysis revealed a negative correlation between the genomic heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing Single Nucleotide variants (SNVs) in breeds with low diversity. Our results also showed that breeds with low diversity had more high-frequency (DAF > 0.51) deleterious SNVs than those with high diversity. A reverse trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, taurine cattle breeds had more high-frequency deleterious SNVs than indicine (or taurine-indicine hybrid) breeds. However, within taurine breeds European or Northeast Asian taurines had more high-frequency deleterious SNVs than East Asian or African taurine breeds. Similarly, within indicine breeds South Asian indicines had more high-frequency deleterious SNVs than East Asian indicine breeds. All the above observed patterns were reversed for low frequency deleterious SNVs. Some of the variation in the deleterious mutation load observed between different breeds could be attributed to the population sizes of the wild progenitors before domestication. However, the variations observed withing taurine and within indicine breeds could be due to the difference in the extent of inbreeding, strength of artificial selection and/or founding population size. The findings of this study imply that the rate of incidence of genetic diseases might vary between cattle breeds.

scholarly journals Deleterious protein-coding variants in diverse cattle breeds of the world

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Artificial Selection ◽  
High Frequency ◽  
Deleterious Mutation ◽  
Low Frequency ◽  
Mutation Load ◽  
Single Nucleotide Variants ◽  
Cattle Breeds ◽  
Low Diversity ◽  
Population Sizes ◽  
Taurine Cattle

AbstractThe domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals Harmful Mutation Load in the Mitochondrial Genomes of Cattle Breeds 

2021 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Amino Acid ◽  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract ObjectiveDomestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 252 animals belonging to 15 cattle breeds of the world. ResultsOur analysis revealed more than fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the neutral heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing variants in breeds with low diversity. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals Population size influences the type of nucleotide variations in humans

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Frequency ◽  
Genetic Diseases ◽  
Large Population ◽  
Low Frequency ◽  
Small Population ◽  
Effective Population ◽  
Genome Data ◽  
Large Populations

Abstract Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

Temporal Coding by Populations of Auditory Receptor Neurons

2010 ◽  
Vol 103 (3) ◽  
pp. 1614-1621 ◽  
Author(s):  
Patrick Sabourin ◽  
Gerald S. Pollack
Keyword(s):  
Population Size ◽  
High Frequency ◽  
Temporal Pattern ◽  
Low Frequency ◽  
Spike Trains ◽  
Afferent Input ◽  
Temporal Coding ◽  
Auditory Receptor ◽  
Receptor Neurons ◽  
High Sound

Auditory receptor neurons of crickets are most sensitive to either low or high sound frequencies. Earlier work showed that the temporal coding properties of first-order auditory interneurons are matched to the temporal characteristics of natural low- and high-frequency stimuli (cricket songs and bat echolocation calls, respectively). We studied the temporal coding properties of receptor neurons and used modeling to investigate how activity within populations of low- and high-frequency receptors might contribute to the coding properties of interneurons. We confirm earlier findings that individual low-frequency-tuned receptors code stimulus temporal pattern poorly, but show that coding performance of a receptor population increases markedly with population size, due in part to low redundancy among the spike trains of different receptors. By contrast, individual high-frequency-tuned receptors code a stimulus temporal pattern fairly well and, because their spike trains are redundant, there is only a slight increase in coding performance with population size. The coding properties of low- and high-frequency receptor populations resemble those of interneurons in response to low- and high-frequency stimuli, suggesting that coding at the interneuron level is partly determined by the nature and organization of afferent input. Consistent with this, the sound-frequency-specific coding properties of an interneuron, previously demonstrated by analyzing its spike train, are also apparent in the subthreshold fluctuations in membrane potential that are generated by synaptic input from receptor neurons.

Ritual Frequency, Emotionality, and Modes of Religiosity

2021 ◽  
pp. 53-81
Author(s):  
Harvey Whitehouse
Keyword(s):  
High Frequency ◽  
Large Scale ◽  
Low Frequency ◽  
New Guinea ◽  
Small Scale ◽  
Complex Societies ◽  
High Arousal ◽  
The World ◽  
Hierarchical Groups ◽  
To Come

Collective rituals tend to come in two kinds: frequently performed but relatively lowkey; rarely enacted but emotionally intense. According to the theory of modes of religiosity, high-frequency but low-arousal rituals produce large-scale hierarchical groups (the doctrinal mode), while low-frequency but high-arousal rituals produce small-scale highly cohesive groups (the imagistic mode). This chapter describes how that theory was first developed while carrying out fieldwork in the New Guinea rainforest. But then the author realized it could help to explain how groups throughout the world take shape and spread, and it could also help to explain how complex societies evolved.

scholarly journals Short Note on Space Wind Powered by Disorder: Dark Energy

2018 ◽  
Author(s):  
Mesut Kavak
Keyword(s):  
High Frequency ◽  
Short Note ◽  
Low Frequency ◽  
Lower Mass ◽  
Gravitational Fields ◽  
Down Low ◽  
The World ◽  
Pioneer Anomaly ◽  
Speed Up ◽  
Moving Bodies

After midnight just before sleeping, I noticed in my bed, that free space itself can cause a parachute effect on the moving bodies especially the bodies move in low gravitational fields like in Pioneer Anomaly. Because of this reason, while speed of a satellite is decreasing, speed of another one which spins around the world on different axis can increase; a satellite wandering in interstellar medium can speed up as also it can slow down; low frequency light and high frequency light behave differently; galaxies have lower mass can spin faster since mutual gravitation is not only option. These are only a few examples.

Echolocation assemblages and their effects on moth auditory systems

1982 ◽  
Vol 60 (11) ◽  
pp. 2572-2576 ◽  
Author(s):  
James H. Fullard
Keyword(s):  
High Frequency ◽  
Low Frequency ◽  
Predation Pressure ◽  
Low Diversity ◽  
Signal Diversity ◽  
Auditory Systems ◽  
Echolocation Signal ◽  
High Diversity

I analyzed the auditory characteristics of a variety of tympanate moths from areas representing low and high levels of bat (= echolocation signal) diversity. Moths sampled in two African (high diversity) sites reveal significantly higher sensitivities than those analyzed at an Ontario site (low diversity). These sensitivities are particularly pronounced at both low-frequency (5–25 kHz) and high-frequency (80–110 kHz) ranges. I suggest these auditory differences are due to the corresponding increased sensory requirements of tropical moths having to cope with a greater density and diversity of bats (predation pressure) present there.

scholarly journals The Frequency of Solitary Behaviors in Captive Odontocetesis Modulated by Environmental and Social Factors

2019 ◽  
Vol 32 ◽  
Author(s):  
Agathe Serres ◽  
Yujiang Hao ◽  
Ding Wang
Keyword(s):  
Social Factors ◽  
High Frequency ◽  
Bottlenose Dolphins ◽  
East Asian ◽  
Low Frequency ◽  
Mild Stress ◽  
Social Grouping ◽  
Solitary Play ◽  
Human Care ◽  
Neophocaena Asiaeorientalis Asiaeorientalis

The number of welfare-oriented studies is increasing in animals under human care, including odontocetes. However, validated welfare indicators are lacking for captive odontocetes. We studied the effect of several conditions (moment of the day, social grouping, public presence) and stimuli (enrichment, perturbations) on the solitary behaviour of Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis), East-Asian finless porpoises (N. a. sunameri) and bottlenose dolphins (Tursiops truncatus). The frequency of solitary play increased in the three groups in positive conditions and decreased in negative contexts, which confirms that play is a useful indicator of welfare for captive odontocetes. Jumping seem to be indicative of stress for finless porpoises but could be ambiguous for bottlenose dolphins: indicating both positive and negative excitation. Stereotypical behaviours for Yangtze finless porpoises and environment hitting behaviours for bottlenose dolphins could indicate mild stress or frustration. Vigilant behaviours are not clear indicators since a high frequency could reflect boredom, but a low frequency was observed in poor social conditions. Finally, we suggest that environmental rubbing should be investigated further since our results for this behaviour were not clear.

scholarly journals Both semantic diversity and frequency influence children’s sentence reading

2019 ◽  
Author(s):  
Ascension Pagan ◽  
Megan Bird ◽  
Yaling Hsiao ◽  
Kate Nation
Keyword(s):  
Eye Movements ◽  
Sentence Processing ◽  
High Frequency ◽  
Reading Aloud ◽  
Low Frequency ◽  
Sentence Reading ◽  
Sentence Level ◽  
Low Diversity ◽  
Independent Effects ◽  
Main Effects

Semantic diversity – a metric that captures variations in previous contextual experience with a word – influences children’s lexical decision and reading aloud. We investigated the effects of semantic diversity and frequency on children’s reading of words embedded in sentences, while eye movements were recorded. If semantic diversity and frequency reflect different aspects of experience that influence reading in different ways, they should show independent effects and perhaps even different processing signatures during reading. Forty-nine 9-year-olds read sentences containing high/low frequency and high/low diversity words, manipulated orthogonally. We observed independent main effects of both variables, with high frequency and high semantic diversity words being read more easily in target word analyses. Sentence-level analyses indicated that semantic diversity influenced the overall ease of sentence processing whereas frequency did not. These results show that variations in the amount and nature of contextual experience influence how easily words are processed during reading

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