scholarly journals Agent-based modeling of DFNB1A prevalence with regard to intensity of selection pressure in isolated human population: will cochlear implantation increase the cases of hereditary deafness?

2021 ◽  
Author(s):  
Georgii P Romanov ◽  
Anna A Smirnova ◽  
Vladimir I Zamyatin ◽  
Aleksey M Mukhin ◽  
Fedor V Kazantsev ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Cochlear Implantation ◽  
Selection Pressure ◽  
Human Population ◽  
Purifying Selection ◽  
Deaf People ◽  
Hereditary Deafness ◽  
Agent Based ◽  
Assortative Marriages ◽  
Genetic Fitness

It was evidenced, that the increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) in populations of European descent was promoted by assortative marriages among deaf people. Assortative marriages become possible with a widespread introduction of sign language resulting in increased the genetic fitness of deaf individuals, thus relaxing selection against deafness. Currently, cochlear implantation is becoming a common method of rehabilitation for deaf patients, restoring their hearing ability and promoting the acquirement of spoken language. Whether the mass cochlear implantation could affect the spread of hereditary deafness is unknown. We have developed an agent-based computer model for analysis of the spread of DFNB1A. Using the model, we tested impact of different intensity of selection pressure on an isolated human population for 400 years. The modeling of the "purifying" selection pressure on deafness resulted in decrease of the proportion of deaf individuals and the pathogenic allele frequency. The modeling of relaxed selection resulted in increase of the proportion of deaf individuals and the decrease of the pathogenic allele frequency. The results of neutral selection pressure modeling showed no significant changes in both the proportion of deaf individuals and the pathogenic allele frequency after 400 years. Thus, initially low genetic fitness of deaf people can be significantly increased in the presence of assortative mating by deafness, resulting in a higher prevalence of DFNB1A. Contrary, frequency of pathogenic allele and the incidence of hereditary hearing loss will not increase in a population where all deaf individuals undergo cochlear implantation.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila

2021 ◽  
Author(s):  
Jason Bertram
Keyword(s):  
Allele Frequency ◽  
Evolutionary Biology ◽  
Polymorphic Locus ◽  
Purifying Selection ◽  
Allele Frequencies ◽  
Intermediate Allele ◽  
Genome Wide ◽  
Signature Of Selection ◽  
Basic Objective ◽  
Genomic Regions

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally-resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantial at intermediate allele frequencies, which we argue is most parsimoniously explained by positive --- not purifying --- selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as a purging of deleterious mutations.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl  Arusha virus affecting tomato plants in Kenya

2020 ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.Methods: Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated.Results: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions of the sequences.Conclusions: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals Bidirectional transcription marks accessible chromatin and is not specific to enhancers

2016 ◽  
Author(s):  
Robert S. Young ◽  
Yatendra Kumar ◽  
Wendy A. Bickmore ◽  
Martin S. Taylor
Keyword(s):  
Transcription Initiation ◽  
Human Population ◽  
Purifying Selection ◽  
Polymerase Activity ◽  
Enhancer Activity ◽  
Bidirectional Transcription ◽  
Rna Polymerase Activity ◽  
The Stability ◽  
Endogenous Loci ◽  
Accessible Chromatin

Bidirectional transcription initiating at enhancers has been proposed to represent the signature of enhancer activity. Here we show that bidirectional transcription is a pervasive feature of all forms of accessible chromatin, including enhancers, promoters, CTCF-bound sites and other DNase hypersensitive regions. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured in both enhancer assays and at endogenous loci. Bidirectional transcription initiation from accessible chromatin is therefore not sufficient for, nor specific to, enhancer activity. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect any evidence of purifying selection on the resulting enhancer RNAs within the human population. Our results suggest that transcription initiating at enhancers is frequently a by-product of promiscuous RNA polymerase activity at accessible chromatin, and may not generally play a functional role in enhancer activity.

scholarly journals Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations

2021 ◽  
Author(s):  
Keely Brown ◽  
John K. Kelly
Keyword(s):  
Allele Frequency ◽  
Plant Traits ◽  
Balancing Selection ◽  
Strong Predictor ◽  
Purifying Selection ◽  
Striking Difference ◽  
Nucleotide Polymorphisms ◽  
Mimulus Guttatus ◽  
Cis Acting ◽  
Expression Of Genes

We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the Allele Frequency Spectrum (AFS) of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with rarity disequilibrium produce a super-abundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of co-expressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high connectedness (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.

scholarly journals GENOME-WIDE DISTRIBUTION OF AUTOZYGOSITY ISLANDS IN SLOVAK WARMBLOOD HORSE

AGROFOR ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA ◽  
Marko HALO ◽  
Ondrej KADLEČÍK ◽  
Anna TRAKOVICKÁ ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Allele Frequency ◽  
Selection Pressure ◽  
Wide Distribution ◽  
Call Rate ◽  
Major Fraction ◽  
Autosomal Snps ◽  
The Past ◽  
Genome Wide ◽  
Recent Selection

The objective of this study was to estimate the distribution of autozygosity islands represented by homozygous segments (ROHs) in the genome of the Slovak Warmblood horse. The Slovak Warmblood is a very efficient breed with the excellent characteristics of a sport horse. The study included 37 animals that were genotyped by GGP Equine70k chip (71,947 SNPs). Only animals (36) and autosomal SNPs (62,439) with call rate >90% and minor allele frequency >1% were included in subsequent analyses. The homozygous segments were defined as stretches with minimum 15 consecutive homozygous SNPs of >500 kb with minimum density 1 SNP per 100 kb and maximum gap between markers of 1,000 kb. The heterozygous or missing calls were not accepted. The analysis indicated in total of 8,501 autozygosity islands in the genome of the Slovak Warmblood horse. The majority of identified segments (85.42%) were most likely derived from the remote ancestors in the past. Only 0.15% of detected segments resulted from the recent selection events affecting the genetic structure of studied population. The proportion of segments varied across chromosomes. The major fraction of autosome residing in ROH was found on ECA1 (8.30%), while ECA31 showed the lowest ROH coverage. The scan for overlapping homozygous segments shared by more than 50 % of animals demonstrated that the ECA6 autosome may be under strong selection pressure. Inside those selection signals, several genes were identified including them associated with immunity and reproduction.

scholarly journals Impact of Host Resistance to Tomato Spotted Wilt Orthotospovirus in Peanut Cultivars on Virus Population Genetics and Thrips Fitness

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1418
Author(s):  
Pin-Chu Lai ◽  
Mark R. Abney ◽  
Sudeep Bag ◽  
Albert K. Culbreath ◽  
Rajagopalbabu Srinivasan
Keyword(s):  
Population Genetics ◽  
Host Resistance ◽  
Selection Pressure ◽  
Phylogenetic Trees ◽  
Population Expansion ◽  
Purifying Selection ◽  
Recent Population Expansion ◽  
Resistant Cultivars ◽  
Tomato Spotted Wilt ◽  
Peanut Cultivars

Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) is a major constraint to peanut production in the southeastern United States. Peanut cultivars with resistance to TSWV have been widely used for over twenty years. Intensive usage of resistant cultivars has raised concerns about possible selection pressure against TSWV and a likelihood of resistance breakdown. Population genetics of TSWV isolates collected from cultivars with varying levels of TSWV resistance was investigated using five TSWV genes. Phylogenetic trees of genes did not indicate host resistance-based clustering of TSWV isolates. Genetic variation in TSWV isolates and neutrality tests suggested recent population expansion. Mutation and purifying selection seem to be the major forces driving TSWV evolution. Positive selection was found in N and RdRp genes but was not influenced by TSWV resistance. Population differentiation occurred between isolates collected from 1998 and 2010 and from 2016 to 2019 but not between isolates from susceptible and resistant cultivars. Evaluated TSWV-resistant cultivars differed, albeit not substantially, in their susceptibility to thrips. Thrips oviposition was reduced, and development was delayed in some cultivars. Overall, no evidence was found to support exertion of selection pressure on TSWV by host resistance in peanut cultivars, and some cultivars differentially affected thrips fitness than others.

scholarly journals Protein-Coding Genes of Helicobacter pylori Predominantly Present Purifying Selection though Many Membrane Proteins Suffer from Selection Pressure: A Proposal to Analyze Bacterial Pangenomes

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 377
Author(s):  
Alejandro Rubio ◽  
Antonio Pérez-Pulido
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Selection Pressure ◽  
Purifying Selection ◽  
Protein Coding ◽  
Evolutionary Selection ◽  
Protein Coding Genes ◽  
The Core ◽  
Genes Encoding ◽  
Selection For

The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of Helicobacter pylori, a bacterium that colonizes the gastric mucosa of half the world population and presents a low number of genes (around 1500 in a strain and 3000 in the pangenome). After the estimation of the pangenome, the evolutionary selection for each gene has been calculated, and we found that 85% of them are subject to purifying selection and the remaining genes present some grade of selection pressure. As expected, the latter group is enriched with genes encoding for membrane proteins putatively involved in interaction to host tissues. In addition, this group also presents a high number of uncharacterized genes and genes encoding for putative spurious proteins. It suggests that they could be false positives from the gene finders used for identifying them. All these results propose that this kind of analyses can be useful to validate gene predictions and functionally characterize proteins in complete genomes.

scholarly journals Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

2016 ◽  
Vol 113 (32) ◽  
pp. 9045-9050 ◽  
Author(s):  
Susann Wicke ◽  
Kai F. Müller ◽  
Claude W. dePamphilis ◽  
Dietmar Quandt ◽  
Sidonie Bellot ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Mechanistic Model ◽  
Reduction Process ◽  
Purifying Selection ◽  
Evolutionary Rates ◽  
Rate Variation ◽  
Functional Constraints ◽  
Turnover Rates ◽  
Parasitic Lifestyle ◽  
Functional Reduction

Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the transition from autotrophy to a nonphotosynthetic parasitic lifestyle. We show that relaxed purifying selection in all plastid genes is linked to obligate parasitism, characterized by the parasite’s dependence on a host to fulfill its life cycle, rather than the loss of photosynthesis. Evolutionary rates and selection pressure coevolve with macrostructural and microstructural changes, the extent of functional reduction, and the establishment of the obligate parasitic lifestyle. Inferred bursts of gene losses coincide with periods of relaxed selection, which are followed by phases of intensified selection and rate deceleration in the retained functional complexes. Our findings suggest that the transition to obligate parasitism relaxes functional constraints on plastid genes in a stepwise manner. During the functional reduction process, the elevation of evolutionary rates reaches several new rate equilibria, possibly relating to the modified protein turnover rates in heterotrophic plastids.

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