scholarly journals Evolution of gene expression variance during adaptation to high temperature in Drosophila

2021 ◽  
Author(s):  
Wei-Yun Lai ◽  
Christian Schlötterer
Keyword(s):  
Gene Expression ◽  
Natural Populations ◽  
Selection Response ◽  
Phenotypic Variance ◽  
Adaptive Responses ◽  
Genetic Redundancy ◽  
Before And After ◽  
Polygenic Adaptation ◽  
The Impact ◽  
Expression Variance

AbstractShifts in trait means are widely considered as evidence for adaptive responses, but the impact on phenotypic variance remains largely unexplored. Here, we studied gene expression variance of Drosophila simulans males before and after 100 generations of adaptation to a novel hot laboratory environment. In each of the two independently evolved replicate populations the variance of about 150 genes changed significantly (mostly reduction). Although different genes were affected in both replicates, these genes are related to digestion in the gut. This non-parallel selection response on the gene level in combination with a convergent response at a higher phenotypic level reflects genetic redundancy, a characteristic hallmark of polygenic adaptation. We propose that the constant and simple food source in the laboratory resulted in selection for reduced variance in digestive genes. In natural populations adaptation to diverse types of food may be beneficial, resulting in higher phenotypic variance. This empirical evidence of phenotypic variance being the direct target of selection during adaptation has important implications for strategies to identify selection signatures.

scholarly journals Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

2021 ◽  
Author(s):  
Claire Burny ◽  
Viola Nolte ◽  
Marlies Dolezal ◽  
Christian Schl&oumltterer
Keyword(s):  
Drosophila Melanogaster ◽  
Experimental Evolution ◽  
Selection Response ◽  
Adaptive Responses ◽  
Genetic Redundancy ◽  
Powerful Approach ◽  
Polygenic Adaptation ◽  
Parallel Selection ◽  
Sufficient Variation ◽  
Genomic Regions

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

scholarly journals Postnatal persistence of sex-dependent renal developmentally programmed structural and molecular changes in nonhuman primates

2020 ◽  
Author(s):  
Andrew C. Bishop ◽  
Kimberly D. Spradling-Reeves ◽  
Robert E. Shade ◽  
Kenneth J. Lange ◽  
Shifra Birnbaum ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Disease ◽  
Kidney Function ◽  
Nonhuman Primates ◽  
Disease Risk ◽  
Postnatal Life ◽  
Urine Metabolites ◽  
Baboon Model ◽  
Before And After ◽  
The Impact

AbstractBackgroundPoor nutrition during development programs kidney function. No studies on postnatal consequences of decreased perinatal nutrition exist in nonhuman primates (NHP) for translation to human renal disease. Our baboon model of moderate maternal nutrient restriction (MNR) produces intrauterine growth restricted (IUGR) and programs renal fetal phenotype. We hypothesized that the IUGR phenotype persists postnatally, influencing responses to a high-fat, high-carbohydrate, high-salt (HFCS) diet.MethodsPregnant baboons ate chow (Control; CON) or 70% of control intake (MNR) from 0.16 gestation through lactation. MNR offspring were IUGR at birth. At weaning, all offspring (CON and IUGR females and males, n=3/group) ate chow. At ~4.5 years of age, blood, urine, and kidney biopsies were collected before and after a 7-week HFCS diet challenge. Kidney function, unbiased kidney gene expression, and untargeted urine metabolomics were evaluated.ResultsIUGR female and male kidney transcriptome and urine metabolome differed from CON at 3.5 years, prior to HFCS. After the challenge, we observed sex-specific and fetal exposure-specific responses in urine creatinine, urine metabolites, and renal signaling pathways.ConclusionsWe previously showed mTOR signaling dysregulation in IUGR fetal kidneys. Before HFCS, gene expression analysis indicated that dysregulation persists postnatally in IUGR females. IUGR male offspring response to HFCS showed uncoordinated signaling pathway responses suggestive of proximal tubule injury. To our knowledge, this is the first study comparing CON and IUGR postnatal juvenile NHP and the impact of fetal and postnatal life caloric mismatch. Perinatal history needs to be taken into account when assessing renal disease risk.

scholarly journals Maternal Overnutrition Programs Central Inflammation and Addiction-Like Behavior in Offspring

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Larisa Montalvo-Martínez ◽  
Roger Maldonado-Ruiz ◽  
Marcela Cárdenas-Tueme ◽  
Diana Reséndez-Pérez ◽  
Alberto Camacho
Keyword(s):  
Gene Expression ◽  
Fetal Programming ◽  
Gene Expression Pattern ◽  
Cell Types ◽  
Addictive Behavior ◽  
Adaptive Responses ◽  
Inflammatory Phenotype ◽  
Pregnancy And Lactation ◽  
Maternal Overnutrition ◽  
The Impact

Obesity or maternal overnutrition during pregnancy and lactation might have long-term consequences in offspring health. Fetal programming is characterized by adaptive responses to specific environmental conditions during early life stages. Programming alters gene expression through epigenetic modifications leading to a transgenerational effect of behavioral phenotypes in the offspring. Maternal intake of hypercaloric diets during fetal development programs aberrant behaviors resembling addiction in offspring. Programming by hypercaloric surplus sets a gene expression pattern modulating axonal pruning, synaptic signaling, and synaptic plasticity in selective regions of the reward system. Likewise, fetal programming can promote an inflammatory phenotype in peripheral and central sites through different cell types such as microglia and T and B cells, which contribute to disrupted energy sensing and behavioral pathways. The molecular mechanism that regulates the central and peripheral immune cross-talk during fetal programming and its relevance on offspring’s addictive behavior susceptibility is still unclear. Here, we review the most relevant scientific reports about the impact of hypercaloric nutritional fetal programming on central and peripheral inflammation and its effects on addictive behavior of the offspring.

scholarly journals Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective

2021 ◽  
Vol 12 ◽  
Author(s):  
Manas Joshi ◽  
Adamandia Kapopoulou ◽  
Stefan Laurent
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
Natural Populations ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Coding Sequences ◽  
The Impact

The unprecedented rise of high-throughput sequencing and assay technologies has provided a detailed insight into the non-coding sequences and their potential role as gene expression regulators. These regulatory non-coding sequences are also referred to as cis-regulatory elements (CREs). Genetic variants occurring within CREs have been shown to be associated with altered gene expression and phenotypic changes. Such variants are known to occur spontaneously and ultimately get fixed, due to selection and genetic drift, in natural populations and, in some cases, pave the way for speciation. Hence, the study of genetic variation at CREs has improved our overall understanding of the processes of local adaptation and evolution. Recent advances in high-throughput sequencing and better annotations of CREs have enabled the evaluation of the impact of such variation on gene expression, phenotypic alteration and fitness. Here, we review recent research on the evolution of CREs and concentrate on studies that have investigated genetic variation occurring in these regulatory sequences within the context of population genetics.

scholarly journals Polygenic adaptation fuels genetic redundancy in Drosophila

2018 ◽  
Author(s):  
Neda Barghi ◽  
Raymond Tobler ◽  
Viola Nolte ◽  
Ana Marija Jaksic ◽  
Francois Mallard ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genotypic Variation ◽  
Natural Populations ◽  
Genetic Redundancy ◽  
Adaptive Traits ◽  
Testing Strategies ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Phenotypic Responses ◽  
Phenotypic Convergence

AbstractThe genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic – i.e. result from selection on a large number of genetic loci – but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; mean s=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

scholarly journals Divergent patterns of selection on metabolite levels and gene expression

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander F. Kern ◽  
Grace Xiaolu Yang ◽  
Neil M. Khosla ◽  
Roy Moh Lik Ang ◽  
Michael P. Snyder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Antifungal Drugs ◽  
Ergosterol Biosynthesis ◽  
Expression Data ◽  
Yeast Strains ◽  
Genetic Cross ◽  
Polygenic Adaptation ◽  
Trait Locus ◽  
The Impact

Abstract Background Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis—an essential pathway targeted by many antifungal drugs—in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross. Results Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation. Conclusions These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways.

scholarly journals Prolactin-Like Protein-F Subfamily of Placental Hormones/Cytokines: Responsiveness to Maternal Hypoxia

Endocrinology ◽  
2007 ◽  
Vol 148 (2) ◽  
pp. 559-565 ◽  
Author(s):  
Jennifer K. Ho-Chen ◽  
Juan J. Bustamante ◽  
Michael J. Soares
Keyword(s):  
Gene Expression ◽  
Hypobaric Hypoxia ◽  
Expression Profiles ◽  
Mrna Levels ◽  
Adaptive Responses ◽  
Low Oxygen ◽  
Specific Expression ◽  
Protein F ◽  
Maternal Hypoxia ◽  
The Impact

The prolactin (PRL) family of hormones/cytokines is involved in the maintenance of pregnancy and adaptations to physiological stressors. In this report, we identify and characterize a new member of the rat PRL family, examine the impact of maternal hypoxia on placental PRL family gene expression, and investigate maternal adaptive responses to hypoxia. Perusal of the PRL gene family locus in the rat genome resulted in the identification of a putative new member of the rat PRL family. The new member is closely related to the previously reported PRL-like protein-F (PLP-F) and has been named PLP-Fβ and the originally characterized PLP-F, now termed PLP-Fα. The two proteins exhibit structural similarities but possess distinct cell- and temporal-specific expression profiles. In vivo hypoxia stimulates placental PLP-Fα and PLP-E mRNA expression in the rat and mouse, respectively. Rcho-1 trophoblast cells can differentiate into trophoblast giant cells, express PLP-Fα, and exhibit enhanced PLP-Fα mRNA levels when cultured under low oxygen tension (2%). Exposure to hypobaric hypoxia during latter part of pregnancy did not significantly impact the expression of PLP-Fβ mRNA. Finally, exposure to hypobaric hypoxia during midpregnancy led to increased maternal red blood cells, hemoglobin concentrations, hematocrit, and increased concentrations of maternal splenic mRNAs for key proteins involved in hemoglobin synthesis, erythroid Krüppel-like factor, erythroid 5-aminolevulinate synthase-2, and β-major globin. In summary, adaptive responses to maternal hypoxia include activation of placental PLP-Fα/E gene expression, which may then participate in maternal hematological adjustments required for maintaining maternal and fetal oxygen delivery.

scholarly journals Evolution of phenotypic variance provides insights into the genetic basis of adaption

2021 ◽  
Author(s):  
Wei-Yun Lai ◽  
Viola Nolte ◽  
Ana Marija Jakšić ◽  
Christian Schlötterer
Keyword(s):  
Gene Expression ◽  
Experimental Evolution ◽  
Genomic Data ◽  
Phenotypic Variance ◽  
Variance Change ◽  
Adaptive Architecture ◽  
Powerful Approach ◽  
Adaptive Architectures ◽  
Before And After ◽  
Change In Mean

AbstractMost traits are polygenic and the contributing loci can be identified by GWAS. Their adaptive architecture is, however, poorly characterized. Here, we propose a new approach to study the adaptive architecture, which does not depend on genomic data. Relying on experimental evolution we measure the phenotypic variance in replicated populations during adaptation to a new environment. Extensive computer simulations show that the evolution of phenotypic variance in a replicated experimental evolution setting is a powerful approach to distinguish between oligogenic and polygenic adaptive architectures. We apply this new method to gene expression variance in male Drosophila simulans before and after 100 generations of adaptation to a novel hot environment. The variance change in gene expression was indistinguishable for genes with and without a significant change in mean expression after 100 generations of evolution. We conclude that adaptive gene expression evolution is best explained by a highly polygenic adaptive architecture. We propose that the evolution of phenotypic variance provides a powerful approach to characterize the adaptive architecture, in particular when combined with genomic data.

Strategic Role of Zakat in Multidimensional Quality of Life in Sijunjung, Indonesia

2018 ◽  
Vol 15 (1) ◽  
pp. 55-72
Author(s):  
Herlin Hamimi ◽  
Abdul Ghafar Ismail ◽  
Muhammad Hasbi Zaenal
Keyword(s):  
Quality Of Life ◽  
Positive Impact ◽  
Wealth Distribution ◽  
Absolute Poverty ◽  
Before And After ◽  
The Status ◽  
Being There ◽  
The Impact

Zakat is one of the five pillars of Islam which has a function of faith, social and economic functions. Muslims who can pay zakat are required to give at least 2.5 per cent of their wealth. The problem of poverty prevalent in disadvantaged regions because of the difficulty of access to information and communication led to a gap that is so high in wealth and resources. The instrument of zakat provides a paradigm in the achievement of equitable wealth distribution and healthy circulation. Zakat potentially offers a better life and improves the quality of human being. There is a human quality improvement not only in economic terms but also in spiritual terms such as improving religiousity. This study aims to examine the role of zakat to alleviate humanitarian issues in disadvantaged regions such as Sijunjung, one of zakat beneficiaries and impoverished areas in Indonesia. The researcher attempted a Cibest method to capture the impact of zakat beneficiaries before and after becoming a member of Zakat Community Development (ZCD) Program in material and spiritual value. The overall analysis shows that zakat has a positive impact on disadvantaged regions development and enhance the quality of life of the community. There is an improvement in the average of mustahik household incomes after becoming a member of ZCD Program. Cibest model demonstrates that material, spiritual, and absolute poverty index decreased by 10, 5, and 6 per cent. Meanwhile, the welfare index is increased by 21 per cent. These findings have significant implications for developing the quality of life in disadvantaged regions in Sijunjung. Therefore, zakat is one of the instruments to change the status of disadvantaged areas to be equivalent to other areas.

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