The impact of natural selection on genomic variation in natural and experimental populations of Drosophila serrata

2021 ◽  
Author(s):  
◽  
Yiguan Wang
Keyword(s):  
Natural Selection ◽  
Genomic Variation ◽  
Drosophila Serrata ◽  
Experimental Populations ◽  
The Impact

scholarly journals The impact of natural selection on the evolution and function of placentally expressed galectins

2018 ◽  
Author(s):  
Zackery A. Ely ◽  
Jiyun M. Moon ◽  
Gregory R. Sliwoski ◽  
Amandeep K. Sangha ◽  
Xing-Xing Shen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Protein Structure ◽  
Genomic Variation ◽  
Human Populations ◽  
Carbohydrate Binding ◽  
Sequence Evolution ◽  
Placental Development ◽  
Human Genetic Disease ◽  
3D Protein Structure ◽  
The Impact

AbstractImmunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins both across mammals and within humans, we conducted a series of between-and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage-and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.

scholarly journals The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins

2019 ◽  
Vol 11 (9) ◽  
pp. 2574-2592 ◽  
Author(s):  
Zackery A Ely ◽  
Jiyun M Moon ◽  
Gregory R Sliwoski ◽  
Amandeep K Sangha ◽  
Xing-Xing Shen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Protein Structure ◽  
Genomic Variation ◽  
Human Populations ◽  
Carbohydrate Binding ◽  
Sequence Evolution ◽  
Placental Development ◽  
Human Genetic Disease ◽  
3D Protein Structure ◽  
The Impact

Abstract Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal–fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins, both across mammals and within humans, we conducted a series of between- and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage- and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.

Interactions Between Natural Selection, Recombination and Gene Density in the Genes of Drosophila

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 595-608 ◽  
Author(s):  
Jody Hey ◽  
Richard M Kliman
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Recombination Rate ◽  
Codon Bias ◽  
Gene Density ◽  
Drosophila Genome ◽  
Functional Variation ◽  
Subtle Effect ◽  
Efficiency Of Selection ◽  
The Impact

AbstractIn Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination—as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.

Fatal asymmetries

2021 ◽  
pp. 1-15
Author(s):  
Luis Sánchez
Keyword(s):  
Natural Selection ◽  
Artificial Selection ◽  
Political Institutions ◽  
Charles Darwin ◽  
The Impact ◽  
Descent Of Man

Abstract In Descent of Man, Charles Darwin noted the impact of political institutions on natural selection. He thought that institutions such as asylums or hospitals may deter natural selection; however, he did not reach a decisive answer. Questions remain as to whether the selective impacts of political institutions, which in Darwin’s terms may be referred to as “artificial selection,” are compatible with natural selection, and if so, to what extent. This essay argues that currently there appears to be an essential mismatch between nature and political institutions. Unfitted institutions put exogenous and disproportionate pressures on living beings. This creates consequences for what is postulated as the condition of basic equivalence, which allows species and individuals to enjoy similar chances of survival under natural circumstances. Thus, contrary to Darwin’s expectations, it is sustained that assumed natural selection is not discouraged but becomes exacerbated by political institutions. In such conditions, selection becomes primarily artificial and perhaps mainly political, with consequences for species’ evolutionary future.

scholarly journals Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage

2021 ◽  
Author(s):  
Alexander L Cope ◽  
Premal Shah
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutation Bias ◽  
Biased Gene Conversion ◽  
Intragenomic Variation ◽  
The Impact

Patterns of non-uniform usage of synonymous codons (codon bias) varies across genes in an organism and across species from all domains of life. The bias in codon usage is due to a combination of both non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most population genetics models quantify the effects of mutation bias and selection on shaping codon usage patterns assuming a uniform mutation bias across the genome. However, mutation biases can vary both along and across chromosomes due to processes such as biased gene conversion, potentially obfuscating signals of translational selection. Moreover, estimates of variation in genomic mutation biases are often lacking for non-model organisms. Here, we combine an unsupervised learning method with a population genetics model of synonymous codon bias evolution to assess the impact of intragenomic variation in mutation bias on the strength and direction of natural selection on synonymous codon usage across 49 Saccharomycotina budding yeasts. We find that in the absence of a priori information, unsupervised learning approaches can be used to identify regions evolving under different mutation biases. We find that the impact of intragenomic variation in mutation bias varies widely, even among closely-related species. We show that the overall strength and direction of selection on codon usage can be underestimated by failing to account for intragenomic variation in mutation biases. Interestingly, genes falling into clusters identified by machine learning are also often physically clustered across chromosomes, consistent with processes such as biased gene conversion. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable mutation biases on codon frequencies.

scholarly journals The ecology of ponds in the context of human activity and geography – environmental DNA and beyond

2021 ◽  
Vol 4 ◽  
Author(s):  
Karolina Bacela-Spychalska ◽  
Annette Taugbøl ◽  
Wiesław Babik ◽  
Maciej Pabijan ◽  
David Strand ◽  
...  
Keyword(s):  
Alien Species ◽  
Invasive Alien Species ◽  
Environmental Dna ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Parasitic Fungus ◽  
Detailed Knowledge ◽  
Geographic Regions ◽  
The Impact ◽  
Pond Ecosystems

Pond ecosystems are hotspots of freshwater biodiversity, often containing many rare and protected species that are not commonly found elsewhere (Harper et al. 2018;Harper et al. 2019). However, even if they constitute c.a. 30% of freshwaters by area, still not enough effort has been put into pond monitoring and management and pond ecosystems are hence relatively poorly understood. Results of ECOPOND project will lead to add valuable knowledge upon pond diversity in geographic gradient taking for consideration human impact by comparing rural and urban areas. The sample design in ECOPOND includes six geographic regions, spanning from the south of Poland to the middle of Norway, where we will sample five replicates of urban and rural ponds in close geographic proximity, making it possible to test the impact of urbanization on biodiversity and biotic homogenization across latitude. We will sample all ponds at spring and late summer, making it possible to assess also seasonality in biodiversity. ECOPOND will utilize environmental DNA and RNA to perform biodiversity screening. The extracted eDNA and eRNA fragments will be amplified with the use of several selected markers for vertebrates, invertebrates, fungi and bacteria. Comparisons between eDNA and eRNA metabarcoding are hypothesized to allow inference between present and past diversity, as eRNA is thought to be only available from live organisms in the community. Moreover, ECOPOND aims at testing the effects of selected invasives species that can have on whole ecosystems. By sampling a range of biotic and abiotic parameters describing studied ponds, we will incorporate the available data for the ponds and employ occupancy modelling methods to assess the habitat preferences of selected invasive alien species. Then we will develop a method that can contribute towards an earlywarning system of evaluating threats to ecosystem status. One of the focus species will be the parasitic fungus Batrachochytrium dendrobatidis (Bd), an infectious fungal pathogen that has caused a number of amphibian declines and extinctions. The European amphibians seem less affected by the parasite at present. However, the fungi could be a direct driver of reduced genetic variation due to selection, or directly reduce the infected amphibian’s overall fitness by reducing the microbiotic diversity on their skin, which in many cases acts as a second immune system. ECOPOND will therefore provide data on genomic variation (using RADseq) for two amphibian species: the smooth newt (Lissotriton vulgaris) and the common toad (Bufo bufo). We will investigate populations of these species inhabiting ponds that are infected and not infected by Bd as well as collect data on their skin microbes (identified using metabarcoding). We will also contrast the genomic diversity between the replicated urban/rural setup and look for repeatable genomic changes. This setup will also be compared for the genomic variation for a potential native prey, the blue-tailed dragonfly, as will ponds with and without fish and/or amphibians (possibly also comparing between native and IAS top-predators) in order to look for predatory selective sweeps in the genome and transcriptome (experimental setup). All ponds will also be analyzed for over 20 water quality parameters and include data on a range of site characteristics that will be used as explanatory variables in all models. ECOPOND will compare large datasets across large geographic regions and will provide detailed knowledge of biodiversity patterns in vertebrates, invertebrates, fungal and microbial species, as well as genomic composition and skin biodiversity for animals inhabiting the same ponds set in an urban context. As a total, ECOPOND will obtain data on the location and status of biodiversity interests, gather data that can help in preventing the establishment of invasive alien species, and eradicating or controlling species that have already become established. And finally, ECOPOND will work closely with stakeholders and develop statistical techniques that can be used for monitoring, detection and protection of biodiversity.

scholarly journals The Impact of 'Anthropotechnology' on Human Evolution

2010 ◽  
Vol 14 (2) ◽  
pp. 72-87 ◽  
Author(s):  
Sylvia Blad ◽  
Keyword(s):  
Natural Selection ◽  
Human Evolution ◽  
Common Ancestor ◽  
Biological Evolution ◽  
Genetic Effects ◽  
Evolutionary Path ◽  
Peter Sloterdijk ◽  
The Impact

From the time that they diverged from their common ancestor, chimpanzees and humans have had a very different evolutionary path. It seems obvious that the appearance of culture and technology has increasingly alienated humans from the path of natural selection that has informed chimpanzee evolution. According to philosopher Peter Sloterdijk any type of technology is bound to have genetic effects. But to what extent do genomic comparisons provide evidence for such an impact of ‘anthropotechnology’ on our biological evolution?

Impact of Privacy Issues on Successful Implementation of Personalized Medicare System

2019 ◽  
Vol 10 (3) ◽  
pp. 96-115
Author(s):  
Sandip Bisui ◽  
Subhas C. Misra
Keyword(s):  
Large Scale ◽  
Healthcare Management ◽  
Genomic Variation ◽  
Successful Implementation ◽  
Related Factors ◽  
Privacy Concerns ◽  
Novel Approach ◽  
Impact Of Technology ◽  
The Impact ◽  
Privacy Issues

Personalized medicare systems is an emerging field of research, which bears the potential to significantly reduce healthcare expenditures and treatment errors and thereby to revolutionize the entire treatment procedure. In this novel approach, genomic variation in different individuals is duly taken into consideration. However, there exist several serious issues (e.g. privacy concerns) that provide hindrance to large-scale adoption of this medicare system. The main objective of this study has been to identify the privacy issues and to evaluate their impact on successful implementation of this novel medical treatment. The methodology used is empirical and is based on a survey-based post facto procedure. The data collected from the survey are analyzed by using the method of structural modelling analysis. This is an original study in the realm of healthcare management, which reveals that the technology related factors and privacy concerns have considerable impact on the successful implementation of personalized medicare system on a large scale. But the privacy concerns have no significant moderating effect on the impact of technology related factors, so far, the success of implementation of personalized medicine is concerned.

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