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Positive selection

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A Novel Combination of Negative and Positive Selection in Artificial Immune Systems

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This process might be conducted in two ways: positive selection and negative selection. In negative selection, if a T cell detects any self protein, it is discarded;. otherwise, it is kept. By contrast, in positive selection, if a T cell fails to recognize any of the self proteins, it is removed [2].. Negative selection algorithms (NSA) and positive selection algorithm (PSA) are computational models that have been inspired by negative and positive selection of the biological immune system.

De novo transcriptome assembly and positive selection analysis of an individual deep-sea fish

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The phylogenetic tree with the highest bootstrap value was used in subsequent positive selection analysis. Indeed, including a greater number of the shallow-water species would increase the statistical significance of the result. maculatus) can provide the subsequent positive selection analysis with the greatest number of single-copy orthologs. Therefore, these three species of fish were referred to the subsequent positive selection analysis of A. Positive selection analysis.

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

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Our structure-modeling revealed charac- teristics of positive-selection in the intrinsically disordered protein regions in some circadian clock proteins (Additional file 19: Figure S6). The Ka/Ks profile of each of these circadian rhythm pro- teins showed multiple positive selection regions with signifi- cant fluctuations in Agave (data not shown).

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

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Positive selection on orthologous genes in 13 L.. 1 this was interpreted as evidence of positive selection. Phipack and GENECOV were used to identify genes under positive selection with recombin- ation [71, 72]. A binomial test was used to estimate associations between each of the COG and VFDB categories and the frequency of positive selection.. Mapping of positive selection on protein tertiary structure.

Contrasting genetic variation and positive selection followed the divergence of NBSencoding genes in Asian and European pears

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Positive selection drives the evolution and selection of NBS-encoding genes in Asian and European pears Ka/Ks ratio of several paralogous gene pairs were greater than one, indicating a positive selection on NBS-. b Distribution of F ST values across the whole NBS- encoding gene family of Asian pears. bretschneideri, with the lat- ter showing comparatively stronger selection and more rapid evolution of NBS-encoding genes.

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral

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Positive natural selection in the human lineage. Journal of the Royal Statistical Society. https://doi.org/10.2307/

Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

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Positive and negative selection analysis coupled with structure-based mapping of amino acidic changes shows most genetic variation occurs in the unstructured N-terminal cytoplasmic domain suggesting a. 6 Positive and negative selection analysis of the chIFITM proteins. 7 Structural modelling of the chIFITM proteins. b Secondary structure prediction of the three chIFITM proteins according to PSIPRED. 8 Electrostatic surface potential of the chIFITM3 model.

Landscape genomics: Natural selection drives the evolution of mitogenome in penguins

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The concentration of codons under positive selection in specific domains of the mito- genome are very likely to be related to protein function [20, 88] and a meta-analysis of 237 vertebrates showed that most of the genes under positive selection were lo- cated in Complex I [89].

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds

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Detecting recent positive selection in the human genome from haplotype structure. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever. Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. Genome-wide scans for footprints of natural selection. Genome-wide detection and characterization of positive selection in human populations.

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

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The majority of genes evolving under positive selection have been identified in the longest branches. However, the branch- site test for positive selection is more powerful on longer branches, and the position of a branch in the tree might affect the power [67]. However, this observation also could be explained by the greater power in detecting strong neg- ative selection in longer genes, similarly to the increase in the power when detecting positive selection for longer genes [67]..

Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping

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Recent and ongoing selection in the human genome. https://doi.org/10.1038/nrg2187.. Signatures of natural selection in the human genome. Mapping signatures of positive selection in the genome of livestock. https://doi.org/10.1016/j.. Detecting recent positive selection in the human genome from haplotype structure. https://doi.org . https://doi.org/10.1101/. https://doi.org/10.1093/.

Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

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We found a region on BTA Mbp containing three SLAMF (signaling lymphocytic activation molecule fam- ily) genes ( SLAMF1 , CD84 and SLAMF6 ) that showed a strong signal of positive selection in Jiaxian Red.

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae

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Effects of positive selection can be investigated by analyzing nucleotide sequences of the loci of interest. The objectives of this work were to study the nucleotide sequence diversity of exon 2 of the MHC class II DRB and DQB loci in the family Equidae, and to assess signatures of positive and nega- tive selection on this functionally important domain of the antigen-presenting MHC class II molecules.

Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle

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Candidate selection signatures and genes under positive selection. Signatures of selection — the d i approach. Totally, we identified the top 1% with highest average di values in the empir- ical distribution as candidate selection regions for each group. The genome-wide distribution of the standard- ized di values were generated for these groups (Fig.

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

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Next, within the synonymous mutations, we found that the tAI-up mutations have significantly higher DAF than the tAI-down mutations (Fig. 3, Wil- coxon rank sum tests), supporting the positive selection for synonymous mutations that increase the tAI and puri- fying selection on mutations that decrease the tAI..

Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

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All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered.. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.. Willows (genus Salix) are widely distributed in the northern hemisphere, ranging around the North Tem- perate Zone, and are the most important source of wood in forests [1–3].

Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

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Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role. Background: Polar bears are uniquely adapted to an Arctic existence. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage..

Population genomics identifies patterns of genetic diversity and selection in chicken

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It seems that positive selection of game fowls leads to convergence of neural activity, and defects in relevant genes have been implicated in the pathogenesis of Alzheimer’s and Parkin- son’ s diseases. For example, APP , SNCA and PPT1 are in- volved in neural activity, and defects in those genes have been implicated in the pathogenesis of Alzheimer’s disease, Parkinson’ s disease, and infantile neuronal ceroid lipofusci- nosis, respectively [33–35].

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data

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Overlapping of the putative sweep regions identified from the top 1% of the cross-population DCMS statistic with candidate regions under positive selection previously reported in other cattle populations.. of the within-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations.. of the cross-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations..

Identification of selection signatures involved in performance traits in a paternal broiler line

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Detecting recent positive selection in the human genome from haplotype structure. A map of recent positive selection in the human genome. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Integrative genomic analysis reveals extended germline homozygosity with lung cancer risk in the PLCO cohort.. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.