scholarly journals Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos

2014 ◽  
Author(s):  
João C. Teixeira ◽  
Cesare de Filippo ◽  
Antje Weihmann ◽  
Juan R. Meneu ◽  
Fernando Racimo ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Intermediate Frequency ◽  
High Genetic Diversity ◽  
Protein Coding ◽  
Missense Change ◽  
Linear Iga Disease ◽  
Filament Protein

Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 million years of independent evolution. While the majority of these trSNPs were found in three genes of the MHC cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.

scholarly journals Novel Astroviruses in Insectivorous Bats

2008 ◽  
Vol 82 (18) ◽  
pp. 9107-9114 ◽  
Author(s):  
D. K. W. Chu ◽  
L. L. M. Poon ◽  
Y. Guan ◽  
J. S. M. Peiris
Keyword(s):  
Virus Detection ◽  
High Genetic Diversity ◽  
Insectivorous Bats ◽  
Detection Rates ◽  
Human Astroviruses ◽  
Wide Range ◽  
The Family ◽  
Apparently Healthy

ABSTRACT Bats are increasingly recognized to harbor a wide range of viruses, and in most instances these viruses appear to establish long-term persistence in these animals. They are the reservoir of a number of human zoonotic diseases including Nipah, Ebola, and severe acute respiratory syndrome. We report the identification of novel groups of astroviruses in apparently healthy insectivorous bats found in Hong Kong, in particular, bats belonging to the genera Miniopterus and Myotis. Astroviruses are important causes of diarrhea in many animal species, including humans. Many of the bat astroviruses form distinct phylogenetic clusters in the genus Mamastrovirus within the family Astroviridae. Virus detection rates of 36% to 100% and 50% to 70% were found in Miniopterus magnater and Miniopterus pusillus bats, respectively, captured within a single bat habitat during four consecutive visits spanning 1 year. There was high genetic diversity of viruses in bats found within this single habitat. Some bat astroviruses may be phylogenetically related to human astroviruses, and further studies with a wider range of bat species in different geographic locations are warranted. These findings are likely to provide new insights into the ecology and evolution of astroviruses and reinforce the role of bats as a reservoir of viruses with potential to pose a zoonotic threat to human health.

scholarly journals A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

2017 ◽  
Vol 4 (2) ◽  
pp. 160805 ◽  
Author(s):  
Yann X. C. Bourgeois ◽  
Boris Delahaie ◽  
Mathieu Gautier ◽  
Emeline Lhuillier ◽  
Pierre-Jean G. Malé ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Intermediate Frequency ◽  
Chromosome 1 ◽  
Ancestral Population ◽  
Naturally Occurring ◽  
Plumage Polymorphism ◽  
Phenotypic Diversification ◽  
Colour Patterns ◽  
Colour Morphs

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis -regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.

scholarly journals Detecting Long-term Balancing Selection using Allele Frequency Correlation

2017 ◽  
Author(s):  
Katherine M. Siewert ◽  
Benjamin F. Voight
Keyword(s):  
Complex Traits ◽  
Balancing Selection ◽  
Population Data ◽  
Intermediate Frequency ◽  
Summary Statistic ◽  
Computationally Efficient ◽  
Multiple Alleles ◽  
Demographic Models ◽  
Project Data

AbstractBalancing selection occurs when multiple alleles are maintained in a population, which can result in their preservation over long evolutionary time periods. A characteristic signature of this long-term balancing selection is an excess number of intermediate frequency polymorphisms near the balanced variant. However, the expected distribution of allele frequencies at these loci has not been extensively detailed, and therefore existing summary statistic methods do not explicitly take it into account. Using simulations, we show that new mutations which arise in close proximity to a site targeted by balancing selection accumulate at frequencies nearly identical to that of the balanced allele. In order to scan the genome for balancing selection, we propose a new summary statistic, β, which detects these clusters of alleles at similar frequencies. Simulation studies show that compared to existing summary statistics, our measure has improved power to detect balancing selection, and is reasonably powered in non-equilibrium demographic models or when recombination or mutation rate varies. We compute β on 1000 Genomes Project data to identify lo ci potentially subjected to long-term balancing selection in humans. We report two balanced haplotypes - localized to the genes WFS1 and CADM2 - that are strongly linked to association signals for complex traits. Our approach is computationally efficient and applicable to species that lack appropriate outgroup sequences, allowing for well-powered analysis of selection in the wide variety of species for which population data are rapidly being generated.

scholarly journals Signatures of long-term balancing selection in human genomes

2017 ◽  
Author(s):  
Bárbara Domingues Bitarello ◽  
Cesare de Filippo ◽  
João Carlos Teixeira ◽  
Joshua M. Schmidt ◽  
Philip Kleinert ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Theoretical Perspective ◽  
Human Populations ◽  
Protein Coding ◽  
Human Genomes ◽  
Genome Wide ◽  
Higher Power ◽  
Genome Wide Data ◽  
Immune Related Genes

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

Abusive head trauma (AHT) outcome at long-term follow-up and the role of elective neurosurgical approach: A report of 22 cases

2013 ◽  
Author(s):  
Francesca Menegazzo ◽  
Melissa Rosa Rizzotto ◽  
Martina Bua ◽  
Luisa Pinello ◽  
Elisabetta Tono ◽  
...  
Keyword(s):  
Head Trauma ◽  
Abusive Head Trauma ◽  
Long Term Follow Up

The Second Start of Transformation in Ukraine?

2014 ◽  
pp. 30-52 ◽  
Author(s):  
L. Grigoryev ◽  
E. Buryak ◽  
A. Golyashev
Keyword(s):  
Economic Growth ◽  
Armed Conflict ◽  
Political Crisis ◽  
Investment Climate ◽  
Institutional Reforms ◽  
Personal Consumption ◽  
Governance Quality ◽  
Political Turmoil

The Ukrainian socio-economic crisis has been developing for years and resulted in the open socio-political turmoil and armed conflict. The Ukrainian population didn’t meet objectives of the post-Soviet transformation, and people were disillusioned for years, losing trust in the state and the Future. The role of workers’ remittances in the Ukrainian economy is underestimated, since the personal consumption and stability depend strongly on them. Social inequality, oligarchic control of key national assets contributed to instability as well as regional disparity, aggravated by identity differences. Economic growth is slow due to a long-term underinvestment, and prospects of improvement are dependent on some difficult institutional reforms, macro stability, open external markets and the elites’ consensus. Recovering after socio-economic and political crisis will need not merely time, but also governance quality improvement, institutions reform, the investment climate revival - that can be attributed as the second transformation in Ukraine.

Thoughts on the Long-Term Strategy, Science and Democracy

2006 ◽  
pp. 4-19 ◽  
Author(s):  
L. Abalkin
Keyword(s):  
Strategy Development ◽  
Russian Science ◽  
Global Trends ◽  
The World ◽  
World Development ◽  
Crucial Condition

The article covers unified issues of the long-term strategy development, the role of science as well as democracy development in present-day Russia. The problems of budget proficit, the Stabilization Fund issues, implementation of the adopted national projects, an increasing role of regions in strengthening the integrity and prosperity of the country are analyzed. The author reveals that the protection of businessmen and citizens from the all-embracing power of bureaucrats is the crucial condition of democratization of the society. Global trends of the world development and expert functions of the Russian science are presented as well.

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