Causal Genetic Variation Underlying Metabolome Differences.

PubMed

Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye; Sudarsanam, Priya; Nayler, Darcy; Staller, Max V; Cohen, Barak A

2017-08-01

An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81 , cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype. Copyright © 2017 by the Genetics Society of America.

Functional variation in the gut microbiome of wild Drosophila populations.

PubMed

Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

2018-05-26

Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

[Spatiotemporal variations of natural wetland CH4 emissions over China under future climate change].

PubMed

Liu, Jian-gong; Zhu, Qiu-an; Shen, Yan; Yang, Yan-zheng; Luo, Yun-peng; Peng, Chang-hui

2015-11-01

Based on a new process-based model, TRIPLEX-GHG, this paper analyzed the spatio-temporal variations of natural wetland CH4 emissions over China under different future climate change scenarios. When natural wetland distributions were fixed, the amount of CH4 emissions from natural wetland ecosystem over China would increase by 32.0%, 55.3% and 90.8% by the end of 21st century under three representative concentration pathways (RCPs) scenarios, RCP2. 6, RCP4.5 and RCP8.5, respectively, compared with the current level. Southern China would have higher CH4 emissions compared to that from central and northern China. Besides, there would be relatively low emission fluxes in western China while relatively high emission fluxes in eastern China. Spatially, the areas with relatively high CH4 emission fluxes would be concentrated in the middle-lower reaches of the Yangtze River, the Northeast and the coasts of the Pearl River. In the future, most natural wetlands would emit more CH4 for RCP4.5 and RCP8.5 than that of 2005. However, under RCP2.6 scenario, the increasing trend would be curbed and CH4 emissions (especially from the Qinghai-Tibet Plateau) begin to decrease in the late 21st century.

A multi-year comparison of IPCI scores for prairie pothole wetlands: implications of temporal and spatial variation

USGS Publications Warehouse

Euliss, Ned H.; Mushet, David M.

2011-01-01

In the prairie pothole region of North America, development of Indices of Biotic Integrity (IBIs) to detect anthropogenic impacts on wetlands has been hampered by naturally dynamic inter-annual climate fluctuations. Of multiple efforts to develop IBIs for prairie pothole wetlands, only one, the Index of Plant Community Integrity (IPCI), has reported success. We evaluated the IPCI and its ability to distinguish between natural and anthropogenic variation using plant community data collected from 16 wetlands over a 4-year-period. We found that under constant anthropogenic influence, IPCI metric scores and condition ratings varied annually in response to environmental variation driven primarily by natural climate variation. Artificially forcing wetlands that occur along continuous hydrologic gradients into a limited number of discrete classes (e.g., temporary, seasonal, and semi-permanent) further confounded the utility of IPCI metrics. Because IPCI scores vary significantly due to natural climate dynamics as well as human impacts, methodology must be developed that adequately partitions natural and anthropogenically induced variation along continuous hydrologic gradients. Until such methodology is developed, the use of the IPCI to evaluate prairie pothole wetlands creates potential for misdirected corrective or regulatory actions, impairment of natural wetland functional processes, and erosion of public confidence in the wetland sciences.

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster.

PubMed

Lee, Yuh Chwen G; Yang, Qian; Chi, Wanhao; Turkson, Susie A; Du, Wei A; Kemkemer, Claus; Zeng, Zhao-Bang; Long, Manyuan; Zhuang, Xiaoxi

2017-05-01

Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molecular Darwinism: The Contingency of Spontaneous Genetic Variation

PubMed Central

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions. PMID:21979160

Molecular Darwinism: the contingency of spontaneous genetic variation.

PubMed

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKown, Athena; Klapste, Jaroslav; Guy, Robert

2014-01-01

To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

Fitness variation in response to artificial selection for reduced cell area, cell number and wing area in natural populations of Drosophila melanogaster.

PubMed

Trotta, Vincenzo; Calboli, Federico C F; Ziosi, Marcello; Cavicchi, Sandro

2007-08-16

Genetically based body size differences are naturally occurring in populations of Drosophila melanogaster, with bigger flies in the cold. Despite the cosmopolitan nature of body size clines in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of body size variation are not fully understood. In particular, it is not clear what the selective value of cell size and cell area variation exactly is. In the present work we determined variation in viability, developmental time and larval competitive ability in response to crowding at two temperatures after artificial selection for reduced cell area, cell number and wing area in four different natural populations of D. melanogaster. No correlated effect of selection on viability or developmental time was observed among all selected populations. An increase in competitive ability in one thermal environment (18 degrees C) under high larval crowding was observed as a correlated response to artificial selection for cell size. Viability and developmental time are not affected by selection for the cellular component of body size, suggesting that these traits only depend on the contingent genetic makeup of a population. The higher larval competitive ability shown by populations selected for reduced cell area seems to confirm the hypothesis that cell area mediated changes have a relationship with fitness, and might be the preferential way to change body size under specific circumstances.

What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

PubMed Central

Alonso-Blanco, Carlos; Aarts, Mark G.M.; Bentsink, Leonie; Keurentjes, Joost J.B.; Reymond, Matthieu; Vreugdenhil, Dick; Koornneef, Maarten

2009-01-01

Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available. PMID:19574434

Warning signal brightness variation: sexual selection may work under the radar of natural selection in populations of a polytypic poison frog.

PubMed

Crothers, Laura R; Cummings, Molly E

2013-05-01

Though theory predicts consistency of warning signals in aposematic species to facilitate predator learning, variation in these signals often occurs in nature. The strawberry poison frog Dendrobates pumilio is an exceptionally polytypic (populations are phenotypically distinct) aposematic frog exhibiting variation in warning color and brightness. In the Solarte population, males and females both respond differentially to male brightness variation. Here, we demonstrate through spectrophotometry and visual modeling that aposematic brightness variation within this population is likely visible to two putative predators (crabs, snakes) and conspecifics but not to the presumed major predator (birds). This study thus suggests that signal brightness within D. pumilio populations can be shaped by sexual selection, with limited opportunity for natural selection to influence this trait due to predator sensory constraints. Because signal brightness changes can ultimately lead to changes in hue, our findings at the within-population level can provide insights into understanding this polytypism at across-population scales.

Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice.

PubMed

Wang, Xiao-Qiang; Yoon, Min-Young; He, Qiang; Kim, Tae-Sung; Tong, Wei; Choi, Bu-Woong; Lee, Young-Sang; Park, Yong-Jin

2015-12-01

Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, α-tocopherol (αΤ) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of αΤ content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (OsγTMT) was identified as the major factor responsible for the αΤ content among rice accessions. Nucleotide variations in the coding region of OsγTMT were significantly associated with the αΤ content variations, while nucleotide polymorphisms in the promoter region of OsγTMT also could partly demonstrate the correlation with αΤ content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying αΤ content variations in rice, which will significantly contribute the research on αΤ biosynthesis mechanisms and αΤ improvement of rice.

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition

PubMed Central

Bouain, Nadia; Saenchai, Chorpet

2018-01-01

Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating primary root length depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of growth and immune responses in plants. PMID:29608565

Development: facial makeup enhancing our looks.

PubMed

Rohner, Nicolas; Tschopp, Patrick; Tabin, Cliff

2014-01-06

A recent study in mice deciphers the complex genetic regulatory network underlying the morphogenesis of the face. The enhancer landscape underlying craniofacial development provides multiple entry points to understand what makes up the face, in natural variation or pathological conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.)

PubMed Central

Yang, Yuhua; Wang, Ying; Zhan, Jiepeng; Shi, Jiaqin; Wang, Xinfa; Liu, Guihua; Wang, Hanzhong

2017-01-01

Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP) shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79), followed by paternal effect (mean = 0.21). Analysis of the data using diploid seed embryo–cytoplasmic–maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%), followed by special combining ability of parental combination (37.0%). More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed. PMID:29163611

High individual variation in pheromone production by tree-killing bark beetles (Coleoptera: Curculionidae: Scolytinae)

NASA Astrophysics Data System (ADS)

Pureswaran, Deepa S.; Sullivan, Brian T.; Ayres, Matthew P.

2008-01-01

Aggregation via pheromone signalling is essential for tree-killing bark beetles to overcome tree defenses and reproduce within hosts. Pheromone production is a trait that is linked to fitness, so high individual variation is paradoxical. One explanation is that the technique of measuring static pheromone pools overestimates true variation among individuals. An alternative hypothesis is that aggregation behaviour dilutes the contribution of individuals to the trait under selection and reduces the efficacy of natural selection on pheromone production by individuals. We compared pheromone measurements from traditional hindgut extractions of female southern pine beetles with those obtained by aerating individuals till they died. Aerations showed greater total pheromone production than hindgut extractions, but coefficients of variation (CV) remained high (60-182%) regardless of collection technique. This leaves the puzzle of high variation unresolved. A novel but simple explanation emerges from considering bark beetle aggregation behaviour. The phenotype visible to natural selection is the collective pheromone plume from hundreds of colonisers. The influence of a single beetle on this plume is enhanced by high variation among individuals but constrained by large group sizes. We estimated the average contribution of an individual to the pheromone plume across a range of aggregation sizes and showed that large aggregation sizes typical in mass attacks limit the potential of natural selection because each individual has so little effect on the overall plume. Genetic variation in pheromone production could accumulate via mutation and recombination, despite strong effects of the pheromone plume on the fitness of individuals within the aggregation. Thus, aggregation behaviour, by limiting the efficacy of natural selection, can allow the persistence of extreme phenotypes in nature.

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification

PubMed Central

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D.; Bodrossy, Levente; Hobday, Alistair J.

2017-01-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. PMID:28148831

Coupled Effects of Natural and Anthropogenic Controls on Seasonal and Spatial Variations of River Water Quality during Baseflow in a Coastal Watershed of Southeast China

PubMed Central

Huang, Jinliang; Huang, Yaling; Zhang, Zhenyu

2014-01-01

Surface water samples of baseflow were collected from 20 headwater sub-watersheds which were classified into three types of watersheds (natural, urban and agricultural) in the flood, dry and transition seasons during three consecutive years (2010–2012) within a coastal watershed of Southeast China. Integrating spatial statistics with multivariate statistical techniques, river water quality variations and their interactions with natural and anthropogenic controls were examined to identify the causal factors and underlying mechanisms governing spatiotemporal patterns of water quality. Anthropogenic input related to industrial effluents and domestic wastewater, agricultural activities associated with the precipitation-induced surface runoff, and natural weathering process were identified as the potential important factors to drive the seasonal variations in stream water quality for the transition, flood and dry seasons, respectively. All water quality indicators except SRP had the highest mean concentrations in the dry and transition seasons. Anthropogenic activities and watershed characteristics led to the spatial variations in stream water quality in three types of watersheds. Concentrations of NH4 +-N, SRP, K+, CODMn, and Cl− were generally highest in urban watersheds. NO3 –N Concentration was generally highest in agricultural watersheds. Mg2+ concentration in natural watersheds was significantly higher than that in agricultural watersheds. Spatial autocorrelations analysis showed similar levels of water pollution between the neighboring sub-watersheds exhibited in the dry and transition seasons while non-point source pollution contributed to the significant variations in water quality between neighboring sub-watersheds. Spatial regression analysis showed anthropogenic controls played critical roles in variations of water quality in the JRW. Management implications were further discussed for water resource management. This research demonstrates that the coupled effects of natural and anthropogenic controls involved in watershed processes, contribute to the seasonal and spatial variation of headwater stream water quality in a coastal watershed with high spatial variability and intensive anthropogenic activities. PMID:24618771

Quadratic partial eigenvalue assignment in large-scale stochastic dynamic systems for resilient and economic design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Sonjoy; Goswami, Kundan; Datta, Biswa N.

2014-12-10

Failure of structural systems under dynamic loading can be prevented via active vibration control which shifts the damped natural frequencies of the systems away from the dominant range of loading spectrum. The damped natural frequencies and the dynamic load typically show significant variations in practice. A computationally efficient methodology based on quadratic partial eigenvalue assignment technique and optimization under uncertainty has been formulated in the present work that will rigorously account for these variations and result in an economic and resilient design of structures. A novel scheme based on hierarchical clustering and importance sampling is also developed in this workmore » for accurate and efficient estimation of probability of failure to guarantee the desired resilience level of the designed system. Numerical examples are presented to illustrate the proposed methodology.« less

Fitness consequences of maternal and embryonic responses to environmental variation: using reptiles as models for studies of developmental plasticity.

PubMed

Warner, Daniel A

2014-11-01

Environmental factors strongly influence phenotypic variation within populations. The environment contributes to this variation in two ways: (1) by acting as a determinant of phenotypic variation (i.e., plastic responses) and (2) as an agent of selection that "chooses" among existing phenotypes. Understanding how these two environmental forces contribute to phenotypic variation is a major goal in the field of evolutionary biology and a primary objective of my research program. The objective of this article is to provide a framework to guide studies of environmental sources of phenotypic variation (specifically, developmental plasticity and maternal effects, and their adaptive significance). Two case studies from my research on reptiles are used to illustrate the general approaches I have taken to address these conceptual topics. Some key points for advancing our understanding of environmental influences on phenotypic variation include (1) merging laboratory-based research that identifies specific environmental effects with field studies to validate ecological relevance; (2) using controlled experimental approaches that mimic complex environments found in nature; (3) integrating data across biological fields (e.g., genetics, morphology, physiology, behavior, and ecology) under an evolutionary framework to provide novel insights into the underlying mechanisms that generate phenotypic variation; (4) assessing fitness consequences using measurements of survival and/or reproductive success across ontogeny (from embryos to adults) and under multiple ecologically-meaningful contexts; and (5) quantifying the strength and form of natural selection in multiple populations over multiple periods of time to understand the spatial and temporal consistency of phenotypic selection. Research programs that focus on organisms that are amenable to these approaches will provide the most promise for advancing our understanding of the environmental factors that generate the remarkable phenotypic diversity observed within populations. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Antagonism between phytohormone signalling underlies the variation in disease susceptibility of tomato plants under elevated CO2.

PubMed

Zhang, Shuai; Li, Xin; Sun, Zenghui; Shao, Shujun; Hu, Lingfei; Ye, Meng; Zhou, Yanhong; Xia, Xiaojian; Yu, Jingquan; Shi, Kai

2015-04-01

Increasing CO2 concentrations ([CO2]) have the potential to disrupt plant-pathogen interactions in natural and agricultural ecosystems, but the research in this area has often produced conflicting results. Variations in phytohormone salicylic acid (SA) and jasmonic acid (JA) signalling could be associated with variations in the responses of pathogens to plants grown under elevated [CO2]. In this study, interactions between tomato plants and three pathogens with different infection strategies were compared. Elevated [CO2] generally favoured SA biosynthesis and signalling but repressed the JA pathway. The exposure of plants to elevated [CO2] revealed a lower incidence and severity of disease caused by tobacco mosaic virus (TMV) and by Pseudomonas syringae, whereas plant susceptibility to necrotrophic Botrytis cinerea increased. The elevated [CO2]-induced and basal resistance to TMV and P. syringae were completely abolished in plants in which the SA signalling pathway nonexpressor of pathogenesis-related genes 1 (NPR1) had been silenced or in transgenic plants defective in SA biosynthesis. In contrast, under both ambient and elevated [CO2], the susceptibility to B. cinerea highly increased in plants in which the JA signalling pathway proteinase inhibitors (PI) gene had been silenced or in a mutant affected in JA biosynthesis. However, plants affected in SA signalling remained less susceptible to this disease. These findings highlight the modulated antagonistic relationship between SA and JA that contributes to the variation in disease susceptibility under elevated [CO2]. This information will be critical for investigating how elevated CO2 may affect plant defence and the dynamics between plants and pathogens in both agricultural and natural ecosystems. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Antagonism between phytohormone signalling underlies the variation in disease susceptibility of tomato plants under elevated CO2

PubMed Central

Zhang, Shuai; Li, Xin; Sun, Zenghui; Shao, Shujun; Hu, Lingfei; Ye, Meng; Zhou, Yanhong; Xia, Xiaojian; Yu, Jingquan; Shi, Kai

2015-01-01

Increasing CO2 concentrations ([CO2]) have the potential to disrupt plant–pathogen interactions in natural and agricultural ecosystems, but the research in this area has often produced conflicting results. Variations in phytohormone salicylic acid (SA) and jasmonic acid (JA) signalling could be associated with variations in the responses of pathogens to plants grown under elevated [CO2]. In this study, interactions between tomato plants and three pathogens with different infection strategies were compared. Elevated [CO2] generally favoured SA biosynthesis and signalling but repressed the JA pathway. The exposure of plants to elevated [CO2] revealed a lower incidence and severity of disease caused by tobacco mosaic virus (TMV) and by Pseudomonas syringae, whereas plant susceptibility to necrotrophic Botrytis cinerea increased. The elevated [CO2]-induced and basal resistance to TMV and P. syringae were completely abolished in plants in which the SA signalling pathway nonexpressor of pathogenesis-related genes 1 (NPR1) had been silenced or in transgenic plants defective in SA biosynthesis. In contrast, under both ambient and elevated [CO2], the susceptibility to B. cinerea highly increased in plants in which the JA signalling pathway proteinase inhibitors (PI) gene had been silenced or in a mutant affected in JA biosynthesis. However, plants affected in SA signalling remained less susceptible to this disease. These findings highlight the modulated antagonistic relationship between SA and JA that contributes to the variation in disease susceptibility under elevated [CO2]. This information will be critical for investigating how elevated CO2 may affect plant defence and the dynamics between plants and pathogens in both agricultural and natural ecosystems. PMID:25657213

Heat-shock protein 70 (Hsp70) as a biochemical stress indicator: an experimental field test in two congeneric intertidal gastropods (genus: Tegula).

PubMed

Tomanek, Lars; Sanford, Eric

2003-12-01

Although previous studies have demonstrated that heat-shock protein 70 (Hsp70) can be induced by environmental stress, little is known about natural variation in this response over short time scales. We examined how Hsp70 levels varied over days to weeks in two intertidal snail species of the genus Tegula: Sampling was conducted both under naturally changing environmental conditions and in different vertical zones on a rocky shore. The subtidal to low-intertidal T. brunnea was transplanted into shaded and unshaded mid-intertidal cages to assess temporal variation in Hsps under conditions of increased stress. For comparison, the low to mid-intertidal T. funebralis was transplanted into mid-intertidal cages, within this species' natural zone of occurrence. Snails were sampled every 3 to 4 days for one month, and endogenous levels of two Hsp70-kDa family members (Hsp72 and Hsp74) were quantified using solid-phase immunochemistry. Following periods of midday low tides, levels of Hsps increased greatly in transplanted T. brunnea but not in T. funebralis. Levels of Hsps increased less in T. brunnea transplanted to shaded cages than to unshaded cages, suggesting that prolonged emersion and reduction in feeding time per se are factors that are only mildly stressful. Upregulated levels of Hsps returned to base levels within days. In unmanipulated snails collected from their natural zones, Hsp levels showed little change with thermal variation, indicating that these species did not experience thermally stressful conditions during this study. However, under common conditions in the mid-intertidal zone, Hsp70 levels reflected the different thermal sensitivities of the physiological systems of these two species.

Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans.

PubMed

Green, J W M; Snoek, L B; Kammenga, J E; Harvey, S C

2013-10-01

In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly investigated. Here, we report extensive natural genetic variation in dauer larvae development within growing populations across multiple wild isolates. Moreover, bin mapping of introgression lines (ILs) derived from the genetically divergent isolates N2 and CB4856 reveals 10 quantitative trait loci (QTLs) affecting dauer formation. Comparison of individual ILs to N2 identifies an additional eight QTLs, and sequential IL analysis reveals six more QTLs. Our results also show that a behavioural, laboratory-derived, mutation controlled by the neuropeptide Y receptor homolog npr-1 can affect dauer larvae development in growing populations. These findings illustrate the complex genetic architecture of variation in dauer larvae formation in C. elegans and may help to understand how the control of variation in dauer larvae development has evolved.

Analysis of cracked RC beams under vibration

NASA Astrophysics Data System (ADS)

Capozucca, R.; Magagnini, E.

2017-05-01

Among the methods of monitoring of integrity, vibration analysis is more convenient as non-destructive testing (NDT) method. Many aspects regarding the vibration monitoring of the structural integrity of damaged RC elements have not been completely analysed in literature. The correlation between the development of the crack pattern on concrete surface under bending loadings, as well as the width and depth of cracks, and the variation of dynamic parameters on a structural element is an important aspects that has to be more investigated. This paper deals with cracked RC beams controlled by NDT based on natural vibration, which may be correlated to damage degree due to cracking of concrete under severe state of loading. An experimental investigation on the assessment of RC beams in different scale under loading has been done through dynamic tests in different constraint conditions of edges measuring frequency values and frequency variation. Envelope of Frequency Response Functions (FRFs) are shown and the changes of natural frequency values are related to the damage degree of RC beams subjected to static tests. Finally, a comparison between data obtained by finite element analysis and experimental results is shown.

How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota.

PubMed

Bost, Alyssa; Franzenburg, Soeren; Adair, Karen L; Martinson, Vincent G; Loeb, Greg; Douglas, Angela E

2018-04-01

Despite evidence from laboratory experiments that perturbation of the gut microbiota affects many traits of the animal host, our understanding of the effect of variation in microbiota composition on animals in natural populations is very limited. The core purpose of this study on the fruit fly Drosophila melanogaster was to identify the impact of natural variation in the taxonomic composition of gut bacterial communities on host traits, with the gut transcriptome as a molecular index of microbiota-responsive host traits. Use of the gut transcriptome was validated by demonstrating significant transcriptional differences between the guts of laboratory flies colonized with bacteria and maintained under axenic conditions. Wild Drosophila from six field collections made over two years had gut bacterial communities of diverse composition, dominated to varying extents by Acetobacteraceae and Enterobacteriaceae. The gut transcriptomes also varied among collections and differed markedly from those of laboratory flies. However, no overall relationship between variation in the wild fly transcriptome and taxonomic composition of the gut microbiota was evident at all taxonomic scales of bacteria tested for both individual fly genes and functional categories in Gene Ontology. We conclude that the interaction between microbiota composition and host functional traits may be confounded by uncontrolled variation in both ecological circumstance and host traits (e.g., genotype, age physiological condition) under natural conditions, and that microbiota effects on host traits identified in the laboratory should, therefore, be extrapolated to field population with great caution. © 2017 John Wiley & Sons Ltd.

Body size and allometric shape variation in the molly Poecilia vivipara along a gradient of salinity and predation.

PubMed

Araújo, Márcio S; Perez, S Ivan; Magazoni, Maria Julia C; Petry, Ana C

2014-12-04

Phenotypic diversity among populations may result from divergent natural selection acting directly on traits or via correlated responses to changes in other traits. One of the most frequent patterns of correlated response is the proportional change in the dimensions of anatomical traits associated with changes in growth or absolute size, known as allometry. Livebearing fishes subject to predation gradients have been shown to repeatedly evolve larger caudal peduncles and smaller cranial regions under high predation regimes. Poecilia vivipara is a livebearing fish commonly found in coastal lagoons in the north of the state of Rio de Janeiro, Brazil. Similar to what is observed in other predation gradients, lagoons inhabited by P. vivipara vary in the presence of piscivorous fishes; contrary to other poeciliid systems, populations of P. vivipara vary greatly in body size, which opens the possibility of strong allometric effects on shape variation. Here we investigated body shape diversification among six populations of P. vivipara along a predation gradient and its relationship with allometric trajectories within and among populations. We found substantial body size variation and correlated shape changes among populations. Multivariate regression analysis showed that size variation among populations accounted for 66% of shape variation in females and 38% in males, suggesting that size is the most important dimension underlying shape variation among populations of P. vivipara in this system. Changes in the relative sizes of the caudal peduncle and cranial regions were only partly in line with predictions from divergent natural selection associated with predation regime. Our results suggest the possibility that adaptive shape variation among populations has been partly constrained by allometry in P. vivipara. Processes governing body size changes are therefore important in the diversification of this species. We conclude that in species characterized by substantial among-population differences in body size, ignoring allometric effects when investigating divergent natural selection's role in phenotypic diversification might not be warranted.

Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader

PubMed Central

Li, Shou-Li; Vasemägi, Anti; Ramula, Satu

2016-01-01

Background and Aims Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. Methods Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. Key Results It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (QST) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F′ST), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. Conclusions The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity. PMID:26420202

Plasticity of Lateralization: Schooling Predicts Hand Preference but not Hand Skill Asymmetry in a Non-Industrial Society

ERIC Educational Resources Information Center

Geuze, Reint H.; Schaafsma, Sara M.; Lust, Jessica M.; Bouma, Anke; Schiefenhovel, Wulf; Groothuis, Ton G. G.

2012-01-01

Considerable variation in the frequency of left-handedness between cultures has been reported, ranging from 0.5 to 24%. This variation in hand preference may have evolved under natural or cultural selection. It has been suggested that schooling affects handedness but as in most human societies only a selected and minor part of the population does…

Ecological interactions and the fitness effect of water-use efficiency: Competition and drought alter the impact of natural MPK12 alleles in Arabidopsis.

PubMed

Campitelli, Brandon E; Des Marais, David L; Juenger, Thomas E

2016-04-01

The presence of substantial genetic variation for water-use efficiency (WUE) suggests that natural selection plays a role in maintaining alleles that affect WUE. Soil water deficit can reduce plant survival, and is likely to impose selection to increase WUE, whereas competition for resources may select for decreased WUE to ensure water acquisition. We tested the fitness consequences of natural allelic variation in a single gene (MPK12) that influences WUE in Arabidopsis, using transgenic lines contrasting in MPK12 alleles, under four treatments; drought/competition, drought/no competition, well-watered/competition, well-watered/no competition. Results revealed an allele × environment interaction: Low WUE plants performed better in competition, resulting from increased resource consumption. Contrastingly, high WUE individuals performed better in no competition, irrespective of water availability, presumably from enhanced water conservation and nitrogen acquisition. Our findings suggest that selection can influence MPK12 evolution, and represents the first assessment of plant fitness resulting from natural allelic variation at a single locus affecting WUE. © 2016 John Wiley & Sons Ltd/CNRS.

Natural emissions under future climate condition and their effects on surface ozone in the Yangtze River Delta region, China

NASA Astrophysics Data System (ADS)

Xie, Min; Shu, Lei; Wang, Ti-jian; Liu, Qian; Gao, Da; Li, Shu; Zhuang, Bing-liang; Han, Yong; Li, Meng-meng; Chen, Pu-long

2017-02-01

The natural emissions of ozone precursors (NOx and VOCs) are sensitive to climate. Future climate change can impact O3 concentrations by perturbing these emissions. To better estimate the variation of natural emissions under different climate conditions and understand its effect on surface O3, we model the present and the future air quality over the Yangtze River Delta (YRD) region by running different simulations with the aid of the WRF-CALGRID model system that contains a natural emission module. Firstly, we estimate the natural emissions at present and in IPCC A1B scenario. The results show that biogenic VOC emission and soil NOx emission over YRD in 2008 is 657 Gg C and 19.1 Gg N, respectively. According to climate change, these emissions in 2050 will increase by 25.5% and 11.5%, respectively. Secondly, the effects of future natural emissions and meteorology on surface O3 are investigated and compared. It is found that the variations in meteorological fields can significantly alter the spatial distribution of O3 over YRD, with the increases of 5-15 ppb in the north and the decreases of -5 to -15 ppb in the south. However, only approximately 20% of the surface O3 increases caused by climate change can be attributed to the natural emissions, with the highest increment up to 2.4 ppb. Finally, Ra (the ratio of impacts from NOx and VOCs on O3 formation) and H2O2/HNO3 (the ratio between the concentrations of H2O2 and HNO3) are applied to study the O3 sensitivity in YRD. The results show that the transition value of H2O2/HNO3 will turn from 0.3 to 0.5 in 2008 to 0.4-0.8 in 2050. O3 formation in the YRD region will be insensitive to VOCs under future climate condition, implying more NOx need to be cut down. Our findings can help us understand O3 variation trend and put forward the reasonable and effective pollution control policies in these famous polluted areas.

In vitro fertilization experiments using sockeye salmon reveal that bigger eggs are more fertilizable under sperm limitation

PubMed Central

Macfarlane, Christopher P.; Hoysak, Drew J.; Liley, N. Robin; Gage, Matthew J.G.

2009-01-01

Although theory and widespread evidence show that the evolution of egg size is driven primarily by offspring and maternal fitness demands, an additional explanation invokes sperm limitation as a selective force that could also influence egg size optima. Levitan proposed that constraints from gamete encounter in external fertilization environments could select for enlargement of ova to increase the physical size of the fertilization target. We test this theory using in vitro fertilization experiments in an externally fertilizing fish. Sockeye salmon (Onchorhyncus nerka) females show considerable between-individual variation in ovum size, and we explored the consequences of this natural variation for the fertilization success of individual eggs under conditions of sperm limitation. By engineering consistent conditions where in vitro fertilization rate was always intermediate, we were able to compare the sizes of fertilized and unfertilized eggs across 20 fertilization replicates. After controlling for any changes in volume through incubation, results showed that successfully fertilized eggs were significantly larger than the eggs that failed to achieve fertilization. Under conditions without sperm limitation, fertility was unaffected by egg size. Our findings therefore support Levitan's theory, demonstrating empirically that some element of egg size variation could be selected by fertilization demands under sperm limitation. However, further research on sperm limitation in natural spawnings is required to assess the selective importance of these results. PMID:19364734

In vitro fertilization experiments using sockeye salmon reveal that bigger eggs are more fertilizable under sperm limitation.

PubMed

Macfarlane, Christopher P; Hoysak, Drew J; Liley, N Robin; Gage, Matthew J G

2009-07-07

Although theory and widespread evidence show that the evolution of egg size is driven primarily by offspring and maternal fitness demands, an additional explanation invokes sperm limitation as a selective force that could also influence egg size optima. Levitan proposed that constraints from gamete encounter in external fertilization environments could select for enlargement of ova to increase the physical size of the fertilization target. We test this theory using in vitro fertilization experiments in an externally fertilizing fish. Sockeye salmon (Onchorhyncus nerka) females show considerable between-individual variation in ovum size, and we explored the consequences of this natural variation for the fertilization success of individual eggs under conditions of sperm limitation. By engineering consistent conditions where in vitro fertilization rate was always intermediate, we were able to compare the sizes of fertilized and unfertilized eggs across 20 fertilization replicates. After controlling for any changes in volume through incubation, results showed that successfully fertilized eggs were significantly larger than the eggs that failed to achieve fertilization. Under conditions without sperm limitation, fertility was unaffected by egg size. Our findings therefore support Levitan's theory, demonstrating empirically that some element of egg size variation could be selected by fertilization demands under sperm limitation. However, further research on sperm limitation in natural spawnings is required to assess the selective importance of these results.

CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit.

PubMed

Brand, Arnon; Borovsky, Yelena; Hill, Theresa; Rahman, Khalis Afnan Abdul; Bellalou, Aharon; Van Deynze, Allen; Paran, Ilan

2014-10-01

We provide multiple evidences that CaGLK2 underlies a quantitative trait locus controlling natural variation in chlorophyll content and immature fruit color of pepper via modulating chloroplast compartment size. Pepper fruit quality is attributed to a variety of traits, affecting visual appearance, flavor, chemical composition and nutritional value. Among the quality traits, fruit color is of primary importance because the pigments that confer color are associated with nutrition, health and flavor. Although gene models have been proposed for qualitative aspects of fruit color, large natural variation in quantitative pigment content and fruit color exists in pepper. However, its genetic basis is largely unknown which hampers its utilization for plant improvement. We studied the role of GLK2, a GOLDEN2-like transcription factor that regulates chloroplast development in controlling natural variation for chlorophyll content and immature fruit color of pepper. The role of GLK2 in regulating fruit development has been studied previously in tomato using ectopic expression and the uniform ripening mutant analyses. However, pepper provides a unique opportunity to further study the function of this gene because of the wide natural variation of fruit colors in this species. Segregation, sequencing and expression analyses indicated that pepper GLK2 (CaGLK2) corresponds to the recently reported pc10 QTL that controls chloroplast development and chlorophyll content in pepper. CaGLK2 exerts its effect on chloroplast compartment size predominantly during immature fruit development. We show that the genetic background, sequence variation and expression pattern confer a complex and multi-level regulation of CaGLK2 and fruit color in Capsicum. The positive effect on fruit quality predominantly at the green stage conferred by CaGLK2 can be utilized to breed green pepper varieties with improved nutritional values and taste.

Day-to-day variations in the amplitude of the soil temperature cycle and impact on adult eclosion timing of the onion fly.

PubMed

Tanaka, Kazuhiro; Watari, Yasuhiko

2017-06-01

The onion fly Delia antiqua advances its eclosion timing with decreasing temperature amplitude to compensate for a depth-dependent phase delay of the zeitgeber. To elucidate whether or not naturally occurring day-to-day variations in the amplitude of soil temperature cycle disturb this compensatory response, we monitored daily variations in the temperature amplitude in natural soils and evaluated the impact on adult eclosion timing. Our results indicated that both median and variance of the soil temperature amplitude become smaller as depth increases. Insertion of a larger temperature fluctuation into the thermoperiod with smaller temperature amplitude induced a stronger phase delay, while insertion of a smaller temperature fluctuation into the thermoperiod with larger temperature amplitude had a weaker phase-advancing effect. It is therefore expected that larger diurnal temperature fluctuations disturb the compensatory response, particularly if they occur at deeper locations, while smaller temperature fluctuations do so only at shallower locations. Under natural conditions, however, the probability of occurrence of smaller or larger temperature fluctuations in shallower or deeper soils, respectively, is relatively small. Thus, naturally occurring day-to-day variations in the temperature amplitude rarely disturb the compensatory response, thereby having a subtle or negligible impact on adult eclosion timing.

Intraspecific Variation among Social Insect Colonies: Persistent Regional and Colony-Level Differences in Fire Ant Foraging Behavior

PubMed Central

Bockoven, Alison A.; Wilder, Shawn M.; Eubanks, Micky D.

2015-01-01

Individuals vary within a species in many ecologically important ways, but the causes and consequences of such variation are often poorly understood. Foraging behavior is among the most profitable and risky activities in which organisms engage and is expected to be under strong selection. Among social insects there is evidence that within-colony variation in traits such as foraging behavior can increase colony fitness, but variation between colonies and the potential consequences of such variation are poorly documented. In this study, we tested natural populations of the red imported fire ant, Solenopsis invicta, for the existence of colony and regional variation in foraging behavior and tested the persistence of this variation over time and across foraging habitats. We also reared single-lineage colonies in standardized environments to explore the contribution of colony lineage. Fire ants from natural populations exhibited significant and persistent colony and regional-level variation in foraging behaviors such as extra-nest activity, exploration, and discovery of and recruitment to resources. Moreover, colony-level variation in extra-nest activity was significantly correlated with colony growth, suggesting that this variation has fitness consequences. Lineage of the colony had a significant effect on extra-nest activity and exploratory activity and explained approximately half of the variation observed in foraging behaviors, suggesting a heritable component to colony-level variation in behavior. PMID:26197456

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

PubMed Central

Mao, Hude; Wang, Hongwei; Liu, Shengxue; Li, Zhigang; Yang, Xiaohong; Yan, Jianbing; Li, Jiansheng; Tran, Lam-Son Phan; Qin, Feng

2015-01-01

Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance. PMID:26387805

Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice

PubMed Central

Matsubara, Kazuki; Hori, Kiyosumi; Ogiso-Tanaka, Eri; Yano, Masahiro

2014-01-01

Flowering time in rice (Oryza sativa L.) is determined primarily by daylength (photoperiod), and natural variation in flowering time is due to quantitative trait loci involved in photoperiodic flowering. To date, genetic analysis of natural variants in rice flowering time has resulted in the positional cloning of at least 12 quantitative trait genes (QTGs), including our recently cloned QTGs, Hd17, and Hd16. The QTGs have been assigned to specific photoperiodic flowering pathways. Among them, 9 have homologs in the Arabidopsis genome, whereas it was evident that there are differences in the pathways between rice and Arabidopsis, such that the rice Ghd7–Ehd1–Hd3a/RFT1 pathway modulated by Hd16 is not present in Arabidopsis. In this review, we describe QTGs underlying natural variation in rice flowering time. Additionally, we discuss the implications of the variation in adaptive divergence and its importance in rice breeding. PMID:24860584

Natural selection on immune defense: A field experiment.

PubMed

Langeloh, Laura; Behrmann-Godel, Jasminca; Seppälä, Otto

2017-02-01

Predicting the evolution of phenotypic traits requires an understanding of natural selection on them. Despite its indispensability in the fight against parasites, selection on host immune defense has remained understudied. Theory predicts immune traits to be under stabilizing selection due to associated trade-offs with other fitness-related traits. Empirical studies, however, report mainly positive directional selection. This discrepancy could be caused by low phenotypic variation in the examined individuals and/or variation in host resource level that confounds trade-offs in empirical studies. In a field experiment where we maintained Lymnaea stagnalis snails individually in cages in a lake, we investigated phenotypic selection on two immune defense traits, phenoloxidase (PO)-like activity and antibacterial activity, in hemolymph. We used a diverse laboratory population and manipulated snail resource level by limiting their food supply. For six weeks, we followed immune activity, growth, and two fitness components, survival and fecundity of snails. We found that PO-like activity and growth were under stabilizing selection, while antibacterial activity was under positive directional selection. Selection on immune traits was mainly driven by variation in survival. The form of selection on immune defense apparently depends on the particular trait, possibly due to its importance for countering the present parasite community. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Calcification responses to diurnal variation in seawater carbonate chemistry by the coral Acropora formosa

NASA Astrophysics Data System (ADS)

Chan, W. Y.; Eggins, S. M.

2017-09-01

Significant diurnal variation in seawater carbonate chemistry occurs naturally in many coral reef environments, yet little is known of its effect on coral calcification. Laboratory studies on the response of corals to ocean acidification have manipulated the carbonate chemistry of experimental seawater to compare calcification rate changes under present-day and predicted future mean pH/Ωarag conditions. These experiments, however, have focused exclusively on differences in mean chemistry and have not considered diurnal variation. The aim of this study was to compare calcification responses of branching coral Acropora formosa under conditions with and without diurnal variation in seawater carbonate chemistry. To achieve this aim, we explored (1) a method to recreate natural diurnal variation in a laboratory experiment using the biological activities of a coral-reef mesocosm, and (2) a multi-laser 3D scanning method to accurately measure coral surface areas, essential to normalize their calcification rates. We present a cost- and time-efficient method of coral surface area estimation that is reproducible within 2% of the mean of triplicate measurements. Calcification rates were compared among corals subjected to a diurnal range in pH (total scale) from 7.8 to 8.2, relative to those at constant pH values of 7.8, 8.0 or 8.2. Mean calcification rates of the corals at the pH 7.8-8.2 (diurnal variation) treatment were not statistically different from the pH 8.2 treatment and were 34% higher than the pH 8.0 treatment despite similar mean seawater pH and Ωarag. Our results suggest that calcification of adult coral colonies may benefit from diurnal variation in seawater carbonate chemistry. Experiments that compare calcification rates at different constant pH without considering diurnal variation may have limitations.

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification.

PubMed

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D; Bodrossy, Levente; Hobday, Alistair J

2017-02-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO 2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. © 2017 The Author(s).

Coupling experimental and field-based approaches to decipher carbon sources in the shell of the great scallop, Pecten maximus (L.)

NASA Astrophysics Data System (ADS)

Marchais, V.; Richard, J.; Jolivet, A.; Flye-Sainte-Marie, J.; Thébault, J.; Jean, F.; Richard, P.; Paulet, Y.-M.; Clavier, J.; Chauvaud, L.

2015-11-01

This research investigated how the carbon isotopic composition of food source (δ13Cfood) and dissolved inorganic carbon (δ13CDIC) influences the carbon isotopic composition of Pecten maximus shells (δ13Cshell) under both experimental and natural conditions. The objectives are to better understand the relationship between P. maximus and its environment, and to specifically distinguish conditions under which calcification is influenced by respired CO2 derived from food sources versus conditions in which calcification uses inorganic carbon from seawater. Laboratory experiment investigated carbon incorporation into shell carbonates by maintaining scallops under conditions where the stable carbon isotopic composition of food sources was considerably depleted (-54‰), relative to values observed in the natural environment (-21‰). Laboratory experiment ran for 78 days under three temperature conditions, 15 °C, 21 °C and 25 °C. A survey of the environmental parameters and stable carbon isotopic composition into shell carbonate of natural population of P. maximus was also realized during the same year in the Bay of Brest, France. Data collected from both laboratory experiment and the natural environment confirmed that both δ13CDIC and δ13Cfood influence δ13Cshell values and that organic carbon incorporation (CM) averages about 10% (4.3-6.8% under experimental conditions and 1.9-16.6% in the natural environment). The shift in stable carbon isotopic composition from the uptake of depleted food sources under experimental conditions realized a marked divergence in the predicted equilibrium between calcium carbonate and ambient bicarbonate, relative to the natural environment. This offset was 1.7 ± 0.6‰ for scallops in their natural environment and 2.5 ± 0.5 and 3.2 ± 0.9‰ for scallops under experimental conditions at water temperatures of 15 °C and 21 °C, respectively. The offset of 3‰ for scallops subjected to laboratory experiment could not be explained in light of growth rate but may be related to food supply and/or temperature. Food source and temperature effects may also explain the annual variation observed in CM values measured from scallops in their natural environment. CM estimation from the natural population of P. maximus varied seasonally from around 2% at the end of winter, to 12% in summer. The seasonal variation resembles variability in the carbon isotopic composition of the food sources throughout the year with an exception at the end of winter.

Natural Variation in "Drosophila" Larval Reward Learning and Memory Due to a cGMP-Dependent Protein Kinase

ERIC Educational Resources Information Center

Kaun, Karla R.; Hendel, Thomas; Gerber, Bertram; Sokolowski, Marla B.

2007-01-01

Animals must be able to find and evaluate food to ensure survival. The ability to associate a cue with the presence of food is advantageous because it allows an animal to quickly identify a situation associated with a good, bad, or even harmful food. Identifying genes underlying these natural learned responses is essential to understanding this…

Borromean Windows for Three-Particle Systems under Screened Coulomb Interactions

NASA Astrophysics Data System (ADS)

Jiang, Zi-Shi; Song, Xiu-Dan; Zhou, Lin; Kar, Sabyasachi

2017-05-01

We have carried out calculations to search Borromean windows (BWs) for 11 different three-body systems interacting with screened Coulomb (Yukawa-type) potentials using Hylleraas-type wave functions within the framework of a variational approach. The critical values of the screening parameters for the ground states of the systems under consideration are reported for which the three-body systems are stable, while all the possible fragments are unbound; that is, it shows windows for Borromean binding. Supported by the National Natural Science Foundation of China under Grant No. 11304086, the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province of China under Grant No. UNPYSCT-2015019, and the Natural Science Foundation for Distinguished Young Scholars in Heilongjiang University under Grant No. JCL201503

Making quantitative morphological variation from basic developmental processes: where are we? The case of the Drosophila wing

PubMed Central

Alexis, Matamoro-Vidal; Isaac, Salazar-Ciudad; David, Houle

2015-01-01

One of the aims of evolutionary developmental biology is to discover the developmental origins of morphological variation. The discipline has mainly focused on qualitative morphological differences (e.g., presence or absence of a structure) between species. Studies addressing subtle, quantitative variation are less common. The Drosophila wing is a model for the study of development and evolution, making it suitable to investigate the developmental mechanisms underlying the subtle quantitative morphological variation observed in nature. Previous reviews have focused on the processes involved in wing differentiation, patterning and growth. Here, we investigate what is known about how the wing achieves its final shape, and what variation in development is capable of generating the variation in wing shape observed in nature. Three major developmental stages need to be considered: larval development, pupariation, and pupal development. The major cellular processes involved in the determination of tissue size and shape are cell proliferation, cell death, oriented cell division and oriented cell intercalation. We review how variation in temporal and spatial distribution of growth and transcription factors affects these cellular mechanisms, which in turn affects wing shape. We then discuss which aspects of the wing morphological variation are predictable on the basis of these mechanisms. PMID:25619644

High temperature and temperature variation undermine future disease susceptibility in a population of the invasive garden ant Lasius neglectus.

PubMed

Pamminger, Tobias; Steier, Thomas; Tragust, Simon

2016-06-01

Environmental temperature and temperature variation can have strong effects on the outcome of host-parasite interactions. Whilst such effects have been reported for different host systems, long-term consequences of pre-infection temperatures on host susceptibility and immunity remain understudied. Here, we show that experiencing both a biologically relevant increase in temperature and temperature variation undermines future disease susceptibility of the invasive garden ant Lasius neglectus when challenged with a pathogen under a constant temperature regime. In light of the economic and ecological importance of many social insects, our results emphasise the necessity to take the hosts' temperature history into account when studying host-parasite interactions under both natural and laboratory conditions, especially in the face of global change.

High temperature and temperature variation undermine future disease susceptibility in a population of the invasive garden ant Lasius neglectus

NASA Astrophysics Data System (ADS)

Pamminger, Tobias; Steier, Thomas; Tragust, Simon

2016-06-01

Environmental temperature and temperature variation can have strong effects on the outcome of host-parasite interactions. Whilst such effects have been reported for different host systems, long-term consequences of pre-infection temperatures on host susceptibility and immunity remain understudied. Here, we show that experiencing both a biologically relevant increase in temperature and temperature variation undermines future disease susceptibility of the invasive garden ant Lasius neglectus when challenged with a pathogen under a constant temperature regime. In light of the economic and ecological importance of many social insects, our results emphasise the necessity to take the hosts' temperature history into account when studying host-parasite interactions under both natural and laboratory conditions, especially in the face of global change.

Natural variation in learning rate and memory dynamics in parasitoid wasps: opportunities for converging ecology and neuroscience

PubMed Central

Hoedjes, Katja M.; Kruidhof, H. Marjolein; Huigens, Martinus E.; Dicke, Marcel; Vet, Louise E. M.; Smid, Hans M.

2011-01-01

Although the neural and genetic pathways underlying learning and memory formation seem strikingly similar among species of distant animal phyla, several more subtle inter- and intraspecific differences become evident from studies on model organisms. The true significance of such variation can only be understood when integrating this with information on the ecological relevance. Here, we argue that parasitoid wasps provide an excellent opportunity for multi-disciplinary studies that integrate ultimate and proximate approaches. These insects display interspecific variation in learning rate and memory dynamics that reflects natural variation in a daunting foraging task that largely determines their fitness: finding the inconspicuous hosts to which they will assign their offspring to develop. We review bioassays used for oviposition learning, the ecological factors that are considered to underlie the observed differences in learning rate and memory dynamics, and the opportunities for convergence of ecology and neuroscience that are offered by using parasitoid wasps as model species. We advocate that variation in learning and memory traits has evolved to suit an insect's lifestyle within its ecological niche. PMID:21106587

Parabolic Systems with p, q-Growth: A Variational Approach

NASA Astrophysics Data System (ADS)

Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo

2013-10-01

We consider the evolution problem associated with a convex integrand {f : {R}^{Nn}to [0,infty)} satisfying a non-standard p, q-growth assumption. To establish the existence of solutions we introduce the concept of variational solutions. In contrast to weak solutions, that is, mappings {u\\colon Ω_T to {R}^n} which solve partial_tu-div Df(Du)=0 weakly in {Ω_T}, variational solutions exist under a much weaker assumption on the gap q - p. Here, we prove the existence of variational solutions provided the integrand f is strictly convex and 2n/n+2 < p le q < p+1. These variational solutions turn out to be unique under certain mild additional assumptions on the data. Moreover, if the gap satisfies the natural stronger assumption 2le p le q < p+ minbig \\{1,4/n big \\}, we show that variational solutions are actually weak solutions. This means that solutions u admit the necessary higher integrability of the spatial derivative Du to satisfy the parabolic system in the weak sense, that is, we prove that uin L^q_locbig(0,T; W^{1,q}_loc(Ω,{R}^N)big).

Atmospheric hydrocarbon emissions and concentrations in the barnett shale natural gas production region.

PubMed

Zavala-Araiza, Daniel; Sullivan, David W; Allen, David T

2014-05-06

Hourly ambient hydrocarbon concentration data were collected, in the Barnett Shale Natural Gas Production Region, using automated gas chromatography (auto-GC), for the period from April 2010 to December 2011. Data for three sites were compared: a site in the geographical center of the natural gas production region (Eagle Mountain Lake (EML)); a rural/suburban site at the periphery of the production region (Flower Mound Shiloh), and an urban site (Hinton). The dominant hydrocarbon species observed in the Barnett Shale region were light alkanes. Analyses of daily, monthly, and hourly patterns showed little variation in relative composition. Observed concentrations were compared to concentrations predicted using a dispersion model (AERMOD) and a spatially resolved inventory of volatile organic compounds (VOC) emissions from natural gas production (Barnett Shale Special Emissions Inventory) prepared by the Texas Commission on Environmental Quality (TCEQ), and other emissions information. The predicted concentrations of VOC due to natural gas production were 0-40% lower than background corrected measurements, after accounting for potential under-estimation of certain emission categories. Hourly and daily variations in observed, background corrected concentrations were primarily explained by variability in meteorology, suggesting that episodic emission events had little impact on hourly averaged concentrations. Total emissions for VOC from natural gas production sources are estimated to be approximately 25,300 tons/yr, when accounting for potential under-estimation of certain emission categories. This region produced, in 2011, approximately 5 bcf/d of natural gas (100 Gg/d) for a VOC to natural gas production ratio (mass basis) of 0.0006.

X-autosome incompatibilities in Drosophila melanogaster: tests of Haldane’s rule and geographic patterns within species

PubMed Central

Lachance, Joseph; True, John R.

2010-01-01

Substantial genetic variation exists in natural populations of Drosophila melanogaster. This segregating variation includes alleles at different loci that interact to cause lethality or sterility (synthetic incompatibilities). Fitness epistasis in natural populations has important implications for speciation and the rate of adaptive evolution. To assess the prevalence of epistatic fitness interactions, we placed naturally occurring X chromosomes into genetic backgrounds derived from different geographic locations. Considerable amounts of synthetic incompatibilities were observed between X chromosomes and autosomes: greater than 44% of all combinations were either lethal or sterile. Sex-specific lethality and sterility were also tested to determine whether Haldane's rule holds for within-species variation. Surprisingly, we observed an excess of female sterility in genotypes that were homozygous, but not heterozygous, for the X chromosome. The recessive nature of these incompatibilities is similar to that predicted for incompatibilities underlying Haldane’s rule. Our study also found higher levels of sterility and lethality for genomes that contain chromosomes from different geographical regions. These findings are consistent with the view that genomes are co-adapted gene complexes and that geography affects the likelihood of epistatic fitness interactions. PMID:20455929

Genotype × Herbivore Effect on Leaf Litter Decomposition in Betula Pendula Saplings: Ecological and Evolutionary Consequences and the Role of Secondary Metabolites

PubMed Central

Silfver, Tarja; Paaso, Ulla; Rasehorn, Mira; Rousi, Matti; Mikola, Juha

2015-01-01

Plant genetic variation and herbivores can both influence ecosystem functioning by affecting the quantity and quality of leaf litter. Few studies have, however, investigated the effects of herbivore load on litter decomposition at plant genotype level. We reduced insect herbivory using an insecticide on one half of field-grown Betula Pendula saplings of 17 genotypes, representing random intrapopulation genetic variation, and allowed insects to naturally colonize the other half. We hypothesized that due to induced herbivore defence, saplings under natural herbivory produce litter of higher concentrations of secondary metabolites (terpenes and soluble phenolics) and have slower litter decomposition rate than saplings under reduced herbivory. We found that leaf damage was 89 and 53% lower in the insecticide treated saplings in the summer and autumn surveys, respectively, which led to 73% higher litter production. Litter decomposition rate was also affected by herbivore load, but the effect varied from positive to negative among genotypes and added up to an insignificant net effect at the population level. In contrast to our hypothesis, concentrations of terpenes and soluble phenolics were higher under reduced than natural herbivory. Those genotypes, whose leaves were most injured by herbivores, produced litter of lowest mass loss, but unlike we expected, the concentrations of terpenes and soluble phenolics were not linked to either leaf damage or litter decomposition. Our results show that (1) the genetic and herbivore effects on B. pendula litter decomposition are not mediated through variation in terpene or soluble phenolic concentrations and suggest that (2) the presumably higher insect herbivore pressure in the future warmer climate will not, at the ecological time scale, affect the mean decomposition rate in genetically diverse B. pendula populations. However, (3) due to the significant genetic variation in the response of decomposition to herbivory, evolutionary changes in mean decomposition rate are possible. PMID:25622034

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity.

PubMed

Granados-Cifuentes, Camila; Bellantuono, Anthony J; Ridgway, Tyrone; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

2013-04-08

Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader.

PubMed

Li, Shou-Li; Vasemägi, Anti; Ramula, Satu

2016-01-01

Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Natural variation and genetic make-up of leaf blade area in spring barley.

PubMed

Alqudah, Ahmad M; Youssef, Helmy M; Graner, Andreas; Schnurbusch, Thorsten

2018-04-01

GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes. Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals. To better understand the natural genetic variation of LA at four developmental stages, main culm LA was measured from 215 worldwide spring barleys including 92 photoperiod-sensitive accessions [PHOTOPERIOD RESPONSE LOCUS 1 (Ppd-H1)] and 123 accessions with reduced photoperiod sensitivity (ppd-H1) locus under controlled greenhouse conditions (long-day; 16/8 h; ~ 20/~ 16 °C day/night). The LA of Ppd-H1-carrying accessions was always smaller than in ppd-H1-carrying accessions. We found that nine SNPs from the Ppd-H1 gene were present in the collection of which marker 9 (M9; G/T in the CCT-domain) showed the most significant and consistent effect on LA at all studied developmental stages. Genome-wide association scans (GWAS) showed that the accessions carrying the ppd-H1 allele T/M9 (late heading) possessed more genetic variation in LA than the Ppd-H1 group carrying G/M9 (early heading). Several QTL with major effects on LA variation were found close to plant stature-related heading time, phytohormone- and sugar-related genes. The results provide evidence that natural variation of LA is an important source for improving grain yield, adaptation and canopy architecture of temperate cereals.

Optical investigation of effective permeability of dilute magnetic dielectrics with magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banerjee, Ananya, E-mail: banerjee.ananya2008@gmail.com; Sarkar, A.

The prime objective of this paper is to investigate the magnetic nature of dilute magnetic dielectrics (DMD) under variation of external magnetic field. The said variation is studied over developed nano-sized Gadolinium Oxide as a DMD system. The observed experimental field variation of the effective magnetic permeability is analyzed results of optical experiment. The experiment records the variation of Brewster angle of incident polarized LASER beam from the surface of developed DMD specimen with applied out of plane external magnetic field. The effective refractive index and hence relative magnetic permeability were estimated following electro-magnetic theory. The overall results obtained andmore » agreement between theory and experiment are good.« less

Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

PubMed Central

Chao, Dai-Yin; Silva, Adriano; Baxter, Ivan; Huang, Yu S.; Nordborg, Magnus; Danku, John; Lahner, Brett; Yakubova, Elena; Salt, David E.

2012-01-01

Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. PMID:22969436

Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes

PubMed Central

Karan, Ratna; DeLeon, Teresa; Biradar, Hanamareddy; Subudhi, Prasanta K.

2012-01-01

Background Salinity is a major environmental factor limiting productivity of crop plants including rice in which wide range of natural variability exists. Although recent evidences implicate epigenetic mechanisms for modulating the gene expression in plants under environmental stresses, epigenetic changes and their functional consequences under salinity stress in rice are underexplored. DNA methylation is one of the epigenetic mechanisms regulating gene expression in plant’s responses to environmental stresses. Better understanding of epigenetic regulation of plant growth and response to environmental stresses may create novel heritable variation for crop improvement. Methodology/Principal Findings Methylation sensitive amplification polymorphism (MSAP) technique was used to assess the effect of salt stress on extent and patterns of DNA methylation in four genotypes of rice differing in the degree of salinity tolerance. Overall, the amount of DNA methylation was more in shoot compared to root and the contribution of fully methylated loci was always more than hemi-methylated loci. Sequencing of ten randomly selected MSAP fragments indicated gene-body specific DNA methylation of retrotransposons, stress responsive genes, and chromatin modification genes, distributed on different rice chromosomes. Bisulphite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied with genotypes and tissue types irrespective of the level of salinity tolerance of rice genotypes. Conclusions/Significance The gene body methylation may have an important role in regulating gene expression in organ and genotype specific manner under salinity stress. Association between salt tolerance and methylation changes observed in some cases suggested that many methylation changes are not “directed”. The natural genetic variation for salt tolerance observed in rice germplasm may be independent of the extent and pattern of DNA methylation which may have been induced by abiotic stress followed by accumulation through the natural selection process. PMID:22761959

Immunity in a variable world

PubMed Central

Lazzaro, Brian P.; Little, Tom J.

2008-01-01

Immune function is likely to be a critical determinant of an organism's fitness, yet most natural animal and plant populations exhibit tremendous genetic variation for immune traits. Accumulating evidence suggests that environmental heterogeneity may retard the long-term efficiency of natural selection and even maintain polymorphism, provided alternative host genotypes are favoured under different environmental conditions. ‘Environment’ in this context refers to abiotic factors such as ambient temperature or availability of nutrient resources, genetic diversity of pathogens or competing physiological demands on the host. These factors are generally controlled in laboratory experiments measuring immune performance, but variation in them is likely to be very important in the evolution of resistance to infection. Here, we review some of the literature emphasizing the complexity of natural selection on immunity. Our aim is to describe how environmental and genetic heterogeneities, often excluded from experimentation as ‘noise’, may determine the evolutionary potential of populations or the potential for interacting species to coevolve. PMID:18926975

Aphid-encoded variability in susceptibility to a parasitoid

PubMed Central

2014-01-01

Background Many animals exhibit variation in resistance to specific natural enemies. Such variation may be encoded in their genomes or derived from infection with protective symbionts. The pea aphid, Acyrthosiphon pisum, for example, exhibits tremendous variation in susceptibility to a common natural enemy, the parasitic wasp Aphidius ervi. Pea aphids are often infected with the heritable bacterial symbiont, Hamiltonella defensa, which confers partial to complete resistance against this parasitoid depending on bacterial strain and associated bacteriophages. That previous studies found that pea aphids without H. defensa (or other symbionts) were generally susceptible to parasitism, together with observations of a limited encapsulation response, suggested that pea aphids largely rely on infection with H. defensa for protection against parasitoids. However, the limited number of uninfected clones previously examined, and our recent report of two symbiont-free resistant clones, led us to explicitly examine aphid-encoded variability in resistance to parasitoids. Results After rigorous screening for known and unknown symbionts, and microsatellite genotyping to confirm clonal identity, we conducted parasitism assays using fifteen clonal pea aphid lines. We recovered significant variability in aphid-encoded resistance, with variation levels comparable to that contributed by H. defensa. Because resistance can be costly, we also measured aphid longevity and cumulative fecundity of the most and least resistant aphid lines under permissive conditions, but found no trade-offs between higher resistance and these fitness parameters. Conclusions These results indicate that pea aphid resistance to A. ervi is more complex than previously appreciated, and that aphids employ multiple tactics to aid in their defense. While we did not detect a tradeoff, these may become apparent under stressful conditions or when resistant and susceptible aphids are in direct competition. Understanding sources and amounts of variation in resistance to natural enemies is necessary to understand the ecological and evolutionary dynamics of antagonistic interactions, such as the potential for coevolution, but also for the successful management of pest populations through biological control. PMID:24916045

Rate variation and estimation of divergence times using strict and relaxed clocks.

PubMed

Brown, Richard P; Yang, Ziheng

2011-09-26

Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models. Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, σ, was low (≤ 0.1), but were inappropriate when σ>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0. Posterior means of σ2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher σ2 for one or more partitions, supporting the simulation results. The strict clock can be superior for trees with shallow roots because of low levels of rate variation between branches. The LRT allows robust assessment of suitability of the clock model as does examination of posteriors on σ2.

Heritable Variation for Sex Ratio under Environmental Sex Determination in the Common Snapping Turtle (Chelydra Serpentina)

PubMed Central

Janzen, F. J.

1992-01-01

The magnitude of quantitative genetic variation for primary sex ratio was measured in families extracted from a natural population of the common snapping turtle (Chelydra serpentina), which possesses temperature-dependent sex determination (TSD). Eggs were incubated at three temperatures that produced mixed sex ratios. This experimental design provided estimates of the heritability of sex ratio in multiple environments and a test of the hypothesis that genotype X environment (G X E) interactions may be maintaining genetic variation for sex ratio in this population of C. serpentina. Substantial quantitative genetic variation for primary sex ratio was detected in all experimental treatments. These results in conjunction with the occurrence of TSD in this species provide support for three critical assumptions of Fisher's theory for the microevolution of sex ratio. There were statistically significant effects of family and incubation temperature on sex ratio, but no significant interaction was observed. Estimates of the genetic correlations of sex ratio across environments were highly positive and essentially indistinguishable from +1. These latter two findings suggest that G X E interaction is not the mechanism maintaining genetic variation for sex ratio in this system. Finally, although substantial heritable variation exists for primary sex ratio of C. serpentina under constant temperatures, estimates of the effective heritability of primary sex ratio in nature are approximately an order of magnitude smaller. Small effective heritability and a long generation time in C. serpentina imply that evolution of sex ratios would be slow even in response to strong selection by, among other potential agents, any rapid and/or substantial shifts in local temperatures, including those produced by changes in the global climate. PMID:1592234

SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae.

PubMed

Guo, Zhenhua; Adomas, Aleksandra B; Jackson, Erin D; Qin, Hong; Townsend, Jeffrey P

2011-06-01

We investigated the mechanism underlying the natural variation in longevity within natural populations using the model budding yeast, Saccharomyces cerevisiae. We analyzed whole-genome gene expression in four progeny of a natural S. cerevisiae strain that display differential replicative aging. Genes with different expression levels in short- and long-lived strains were classified disproportionately into metabolism, transport, development, transcription or cell cycle, and organelle organization (mitochondrial, chromosomal, and cytoskeletal). With several independent validating experiments, we detected 15 genes with consistent differential expression levels between the long- and the short-lived progeny. Among those 15, SIR2, HSP30, and TIM17 were upregulated in long-lived strains, which is consistent with the known effects of gene silencing, stress response, and mitochondrial function on aging. The link between SIR2 and yeast natural life span variation offers some intriguing ties to the allelic association of the human homolog SIRT1 to visceral obesity and metabolic response to lifestyle intervention. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Natural Variation of Molecular and Morphological Gibberellin Responses.

PubMed

Nam, Youn-Jeong; Herman, Dorota; Blomme, Jonas; Chae, Eunyoung; Kojima, Mikiko; Coppens, Frederik; Storme, Veronique; Van Daele, Twiggy; Dhondt, Stijn; Sakakibara, Hitoshi; Weigel, Detlef; Inzé, Dirk; Gonzalez, Nathalie

2017-01-01

Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis (Arabidopsis thaliana). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signaling. © 2017 American Society of Plant Biologists. All Rights Reserved.

Spin-Polarization in Quasi-Magnetic Tunnel Junctions

NASA Astrophysics Data System (ADS)

Xie, Zheng-Wei; Li, Ling

2017-05-01

Spin polarization in ferromagnetic metal/insulator/spin-filter barrier/nonmagnetic metal, referred to as quasi-magnetic tunnel junctions, is studied within the free-electron model. Our results show that large positive or negative spin-polarization can be obtained at high bias in quasi-magnetic tunnel junctions, and within large bias variation regions, the degree of spin-polarization can be linearly tuned by bias. These linear variation regions of spin-polarization with bias are influenced by the barrier thicknesses, barrier heights and molecular fields in the spin-filter (SF) layer. Among them, the variations of thickness and heights of the insulating and SF barrier layers have influence on the value of spin-polarization and the linear variation regions of spin-polarization with bias. However, the variations of molecular field in the SF layer only have influence on the values of the spin-polarization and the influences on the linear variation regions of spin-polarization with bias are slight. Supported by the Key Natural Science Fund of Sichuan Province Education Department under Grant Nos 13ZA0149 and 16ZA0047, and the Construction Plan for Scientific Research Innovation Team of Universities in Sichuan Province under Grant No 12TD008.

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

PubMed Central

Raman, Harsh; Raman, Rosy; Kilian, Andrzej; Detering, Frank; Carling, Jason; Coombes, Neil; Diffey, Simon; Kadkol, Gururaj; Edwards, David; McCully, Margaret; Ruperao, Pradeep; Parkin, Isobel A. P.; Batley, Jacqueline; Luckett, David J.; Wratten, Neil

2014-01-01

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. PMID:25006804

Temporal Variation of VOCs in Soils from Groundwater to the Surface/Subslab

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) is charged by Congress with protecting the nation’s natural resources. Under the mandate of national environmental laws, the EPA strives to formulate and implement actions leading to a compatible balance between human activities and ...

Multimodality Prediction of Chaotic Time Series with Sparse Hard-Cut EM Learning of the Gaussian Process Mixture Model

NASA Astrophysics Data System (ADS)

Zhou, Ya-Tong; Fan, Yu; Chen, Zi-Yi; Sun, Jian-Cheng

2017-05-01

The contribution of this work is twofold: (1) a multimodality prediction method of chaotic time series with the Gaussian process mixture (GPM) model is proposed, which employs a divide and conquer strategy. It automatically divides the chaotic time series into multiple modalities with different extrinsic patterns and intrinsic characteristics, and thus can more precisely fit the chaotic time series. (2) An effective sparse hard-cut expectation maximization (SHC-EM) learning algorithm for the GPM model is proposed to improve the prediction performance. SHC-EM replaces a large learning sample set with fewer pseudo inputs, accelerating model learning based on these pseudo inputs. Experiments on Lorenz and Chua time series demonstrate that the proposed method yields not only accurate multimodality prediction, but also the prediction confidence interval. SHC-EM outperforms the traditional variational learning in terms of both prediction accuracy and speed. In addition, SHC-EM is more robust and insusceptible to noise than variational learning. Supported by the National Natural Science Foundation of China under Grant No 60972106, the China Postdoctoral Science Foundation under Grant No 2014M561053, the Humanity and Social Science Foundation of Ministry of Education of China under Grant No 15YJA630108, and the Hebei Province Natural Science Foundation under Grant No E2016202341.

Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans.

PubMed

Harvey, Simon C; Barker, Gary L A; Shorto, Alison; Viney, Mark E

2009-07-18

The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is natural variation among C. elegans lines in the sensitivity of this decision to environmental conditions; that is, there is variation in the phenotypic plasticity of dauer larva development. We hypothesised that these differences may be transcriptionally controlled in early stage larvae. We investigated this by microarray analysis of different C. elegans lines under different environmental conditions, specifically the presence and absence of dauer larva-inducing pheromone. There were substantial transcriptional differences between four C. elegans lines under the same environmental conditions. The expression of approximately 2,000 genes differed between genetically different lines, with each line showing a largely line-specific transcriptional profile. The expression of genes that are markers of larval moulting suggested that the lines may be developing at different rates. The expression of a total of 89 genes was putatively affected by dauer larva or non-dauer larva-inducing conditions. Among the upstream regions of these genes there was an over-representation of DAF-16-binding motifs. Under the same environmental conditions genetically different lines of C. elegans had substantial transcriptional differences. This variation may be due to differences in the developmental rates of the lines. Different environmental conditions had a rather smaller effect on transcription. The preponderance of DAF-16-binding motifs upstream of these genes was consistent with these genes playing a key role in the decision between development into dauer or into non-dauer larvae. There was little overlap between the genes whose expression was affected by environmental conditions and previously identified loci involved in the plasticity of dauer larva development.

Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing tolerance in the southern range of Arabidopsis thaliana.

PubMed

Zhen, Ying; Ungerer, Mark C

2008-12-01

Elucidating the molecular basis of adaptive phenotypic variation represents a central aim in evolutionary biology. Traits exhibiting patterns of clinal variation represent excellent models for studies of molecular adaptation, especially when variation in phenotype can be linked to organismal fitness in different environments. Natural accessions of the model plant species Arabidopsis thaliana exhibit clinal variation in freezing tolerance that follows a gradient of temperature variability across the species' native range (Zhen Y, Ungerer MC. 2008. Clinal variation in freezing tolerance among natural accessions of A. thaliana. New Phytol. 177:419-427). Here, we report that this pattern of variation is attributable, at least in part, to relaxed purifying selection on members of a small family of transcriptional activators (the CBF/DREB1s) in the species' southern range. These regulatory genes play a critical role in the ability of A. thaliana plants to undergo cold acclimation and thereby achieve maximum freezing tolerance. Relative to accessions from northern regions, accessions of A. thaliana from the southern part of their geographic range exhibit levels of nonsynonymous nucleotide polymorphism that are approximately 2.8-fold higher across this small gene subfamily. Relaxed selection on the CBF/DREB1s in southern accessions also has resulted in multiple mutations in regulatory regions resulting in abrogated expression of particular subfamily members in particular accessions. These coding-region and regulatory mutations compromise the ability of these genes to act as efficient transcriptional activators during the cold acclimation process, as determined by reductions in rates of induction and maximum levels of expression in the downstream genes they regulate. This study highlights the potential role of regulatory genes in underlying adaptive phenotypic variation in nature.

Egg discrimination along a gradient of natural variation in eggshell coloration.

PubMed

Hanley, Daniel; Grim, Tomáš; Igic, Branislav; Samaš, Peter; López, Analía V; Shawkey, Matthew D; Hauber, Mark E

2017-02-08

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs' colours. We tested hosts' responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of egg colours. Hosts rejected brown eggs and accepted blue-green eggs along the natural egg colour gradient, irrespective of the total perceived dissimilarity from their own egg's colour. By contrast, their responses did not vary along the artificial colour gradient. Our results demonstrate that egg recognition is specifically tuned to the natural gradient of avian eggshell colour and suggest a novel decision rule. These results highlight the importance of considering sensory reception and decision rules when studying perception, and illustrate that our understanding of recognition processes benefits from examining natural variation in phenotypes. © 2017 The Authors.

Egg discrimination along a gradient of natural variation in eggshell coloration

PubMed Central

Grim, Tomáš; Igic, Branislav; Samaš, Peter; López, Analía V.; Shawkey, Matthew D.; Hauber, Mark E.

2017-01-01

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs' colours. We tested hosts' responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of egg colours. Hosts rejected brown eggs and accepted blue-green eggs along the natural egg colour gradient, irrespective of the total perceived dissimilarity from their own egg's colour. By contrast, their responses did not vary along the artificial colour gradient. Our results demonstrate that egg recognition is specifically tuned to the natural gradient of avian eggshell colour and suggest a novel decision rule. These results highlight the importance of considering sensory reception and decision rules when studying perception, and illustrate that our understanding of recognition processes benefits from examining natural variation in phenotypes. PMID:28179521

In situ monitoring of tracer tests: how to distinguish tracer recovery from natural background

NASA Astrophysics Data System (ADS)

Bailly-Comte, V.; Durepaire, X.; Batiot-Guilhe, C.; Schnegg, P.-A.

2018-03-01

Hydrogeological tracer tests are primarily conducted with fluorescent tracers. Field fluorometers make it possible to monitor tracers at very low concentrations (<1 ppb) and at high frequency. However, changes in natural fluorescence at a site resulting from variations of dissolved and suspended inorganic and organic material may compromise the measurement of useful signals, thereby limiting the chances of identifying or quantifying the real tracer recovery. An elevated natural signal can mask small concentrations of the tracer while its variability can give the impression of a false recovery. This article shows how the use of a combination of several continuous measurements at different wavelengths allows a better extraction of the natural signal. Field multispectral fluorometers were installed at two Mediterranean karst outlets; both drain carbonate systems but have different environmental conditions. The fluorometers functioned over several hydrologic cycles, in periods affected or not by artificial tracers, making it possible to observe natural signal variations at these sites. The optical properties of this type of field fluorometer were used to calculate the spectral response of the different optics of the measuring probe. These responses, superimposed on three-dimensional excitation/emission matrices produced from laboratory fluorescence measurements, allowed an understanding of what the fluorometer sees under natural flow conditions. The result is an innovative method for correcting artificial tracer results. This type of correction makes it possible to fine-tune the effect of natural background variation on tracer recovery curves for a clear identification of the tracer presence and a more precise quantification of its recovery.

Pick Your Poisson: An Educational Primer for Luria and Delbrück's Classic Paper.

PubMed

Meneely, Philip M

2016-02-01

The origin of beneficial mutations is fundamentally important in understanding the processes by which natural selection works. Using phage-resistant mutants in Escherichia coli as their model for identifying the origin of beneficial mutations, Luria and Delbrück distinguished between two different hypotheses. Under the first hypothesis, which they termed "acquired immunity," the phages induced bacteria to mutate to immunity; this predicts that none of the resistant mutants were present before infection by the phages. Under the second hypothesis, termed "mutation to immunity," resistant bacteria arose from random mutations independent of the presence of the phages; this predicts that resistant bacteria were present in the population before infection by the phages. These two hypotheses could be distinguished by calculating the frequencies at which resistant mutants arose in separate cultures infected at the same time and comparing these frequencies to the theoretical results under each model. The data clearly show that mutations arise at a frequency that is independent of the presence of the phages. By inference, natural selection reveals the genetic variation that is present in a population rather than inducing or causing this variation. Copyright © 2016 by the Genetics Society of America.

Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana).

PubMed

Nigenda-Morales, Sergio F; Hu, Yibo; Beasley, James C; Ruiz-Piña, Hugo A; Valenzuela-Galván, David; Wayne, Robert K

2018-06-01

Skin pigmentation and coat pigmentation are two of the best-studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g., camouflage) and signalling with other organisms (e.g., warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with skin pigmentation variation, we used RNA-Seq and quantified gene expression of wild opossums from tropical and temperate populations. Using differential expression analysis and a co-expression network approach, we found that expression variation in genes with melanocytic and immune functions is significantly associated with the degree of skin pigmentation variation and may be underlying this phenotypic difference. We also found evidence suggesting that the Wnt/β-catenin signalling pathway might be regulating the depigmentation observed in temperate populations. Based on our study results, we present several alternative hypotheses that may explain Gloger's rule pattern of skin pigmentation variation in opossum, including changes in pathogen diversity supporting a pathogen-resistant hypothesis, thermal stress associated with temperate environments, and pleiotropic and epistatic interactions between melanocytic and immune genes. © 2018 John Wiley & Sons Ltd.

Natural variation in germination responses of Arabidopsis to seasonal cues and their associated physiological mechanisms

PubMed Central

Barua, Deepak; Butler, Colleen; Tisdale, Tracy E.; Donohue, Kathleen

2012-01-01

Background and Aims Despite the intense interest in phenological adaptation to environmental change, the fundamental character of natural variation in germination is almost entirely unknown. Specifically, it is not known whether different genotypes within a species are germination specialists to particular conditions, nor is it known what physiological mechanisms of germination regulation vary in natural populations and how they are associated with responses to particular environmental factors. Methods We used a set of recombinant inbred genotypes of Arabidopsis thaliana, in which linkage disequilibrium has been disrupted over seven generations, to test for genetic variation and covariation in germination responses to distinct environmental factors. We then examined physiological mechanisms associated with those responses, including seed-coat permeability and sensitivity to the phytohormones gibberellic acid (GA) and abscisic acid (ABA). Key Results Genetic variation for germination was environment-dependent, but no evidence for specialization of germination to different conditions was found. Hormonal sensitivities also exhibited significant genetic variation, but seed-coat properties did not. GA sensitivity was associated with germination responses to multiple environmental factors, but seed-coat permeability and ABA sensitivity were associated with specific germination responses, suggesting that an evolutionary change in GA sensitivity could affect germination in multiple environments, but that of ABA sensitivity may affect germination under more restricted conditions. Conclusions The physiological mechanisms of germination responses to specific environmental factors therefore can influence the ability to adapt to diverse seasonal environments encountered during colonization of new habitats or with future predicted climate change. PMID:22012958

Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

PubMed

Chen, Bor-Sen; Yeh, Chin-Hsun

2017-12-01

We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

Vertical variations in the turbulent structure of the surface boundary layer over vineyards under unstable atmospheric conditions

USDA-ARS?s Scientific Manuscript database

Due to their highly-structured canopy, turbulent characteristics within and above vineyards, may not conform to those typically exhibited by other agricultural and natural ecosystems. Using data collected as a part of the Grape Remote sensing and Atmospheric Profiling and Evapotranspiration Experime...

Advanced in-situ measurement of soil carbon content using inelastic neutron scattering

USDA-ARS?s Scientific Manuscript database

Measurement and mapping of natural and anthropogenic variations in soil carbon stores is a critical component of any soil resource evaluation process. Emerging modalities for soil carbon analysis in the field is the registration of gamma rays from soil under neutron irradiation. The inelastic neutro...

Technological Change in Regulated Industries.

ERIC Educational Resources Information Center

Capron, William M., Ed.

The articles in this volume discuss how well industries operating under government regulation respond to technical innovation: do the effects of regulations vary among industries, and if so, does this result from variations in the regulatory approach, the organization of the firms, or the nature of the technology? Industries considered include…

Advances in Genetical Genomics of Plants

PubMed Central

Joosen, R.V.L.; Ligterink, W.; Hilhorst, H.W.M.; Keurentjes, J.J.B.

2009-01-01

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research. PMID:20514216

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

PubMed Central

2013-01-01

Background Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown. PMID:23565725

The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

PubMed

Roux, F; Bergelson, J

2016-01-01

In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. © 2016 Elsevier Inc. All rights reserved.

Natural mode of horizontal transmission of bovine leukemia virus (BLV): the potential role of tabanids (Tabanus spp.).

PubMed

Manet, G; Guilbert, X; Roux, A; Vuillaume, A; Parodi, A L

1989-10-01

In order to evaluate the potential role of hematophagous insects in the natural spreading of bovine leukemia virus (BLV) infection in cattle, a 2-year survey was carried out involving sequential serological tests on 3328 cattle in three different areas. A parallel entomological study was run over the same period, using continuous trapping, in order to determine both the density and variations of horsefly (Tabanus spp.) populations in the close vicinity of the herds. After statistical analysis, this space-time study showed that: (1) There is a significant positive geographical correlation between the rate of incidence of BLV infection and the density of the horsefly population. (2) Seasonal variations in the incidence rate exist; the highest rates are generally observed during summer (from July of September), and the lowest during winter, spring and early summer (from November to mid-July). (3) There is a time link between the rate of sero-conversion and the variations in activity of the horsefly population. All these data combined would appear to indicate that tabanids play a considerable role in the spread of BLV under natural conditions.

Identification of the fitness determinants of budding yeast on a natural substrate.

PubMed

Filteau, Marie; Charron, Guillaume; Landry, Christian R

2017-04-01

The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway.

Quality variations in black musli (curculigo orchioides gaertn.).

PubMed

Mathew, P P Joy Samuel; Savithri, K E; Skaria, Baby P; Kurien, Kochurani

2004-07-01

Black musli (Curculigo orchioides Gaertn.) one of the ayurvedic dasapushpa and a rejuvenating and aphrodisiac drug. Is on the verge of extinction and needs to be conserved and cultivated. Large variations are also observed in the quality of the crude drug available in the market. Study on the quality of C. orchioides in natural habitat, under cultivation and in trade in south India showed that there was considerable variation with biotypes and habitats. Drugs collected form the natural habitat was superior in quality to that produced by cultivation. Among the market samples collected from the various Zones of kerala, those from the High Ranges were superior in most of the quality parameters, which indicated its superiority for high quality drug formulation. Among the southern states, Tamil Nadu samples ranked next to High Range samples in this respect. There exists large variability in the market samples and there is felt-need for proper standardization of the crude drug for ensuring quality in the drug formulations.

Natural Changes in Brain Temperature Underlie Variations in Song Tempo during a Mating Behavior

PubMed Central

Aronov, Dmitriy; Fee, Michale S.

2012-01-01

The song of a male zebra finch is a stereotyped motor sequence whose tempo varies with social context – whether or not the song is directed at a female bird – as well as with the time of day. The neural mechanisms underlying these changes in tempo are unknown. Here we show that brain temperature recorded in freely behaving male finches exhibits a global increase in response to the presentation of a female bird. This increase strongly correlates with, and largely explains, the faster tempo of songs directed at a female compared to songs produced in social isolation. Furthermore, we find that the observed diurnal variations in song tempo are also explained by natural variations in brain temperature. Our findings suggest that brain temperature is an important variable that can influence the dynamics of activity in neural circuits, as well as the temporal features of behaviors that some of these circuits generate. PMID:23112858

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

PubMed Central

Mayer, Melanie G.; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J.

2015-01-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains´ pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition. PMID:26087034

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

PubMed

Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

2015-06-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for dauer regulation. We discuss the consequences of the novel vs. fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition.

Within and between Population Variation in Epidermal Club Cell Investment in a Freshwater Prey Fish: A Cautionary Tale for Evolutionary Ecologists

PubMed Central

Manek, Aditya K.; Ferrari, Maud C. O.; Pollock, Robyn J.; Vicente, Daniel; Weber, Lynn P.; Chivers, Douglas P.

2013-01-01

Many prey fishes possess large club cells in their epidermis. The role of these cells has garnered considerable attention from evolutionary ecologists. These cells likely form part of the innate immune system of fishes, however, they also have an alarm function, releasing chemical cues that serve to warn nearby conspecifics of danger. Experiments aimed at understanding the selection pressures leading to the evolution of these cells have been hampered by a surprisingly large intraspecific variation in epidermal club cell (ECC) investment. The goal of our current work was to explore the magnitude and nature of this variation in ECC investment. In a field survey, we documented large differences in ECC investment both within and between several populations of minnows. We then tested whether we could experimentally reduce variation in mean ECC number by raising fish under standard laboratory conditions for 4 weeks. Fish from different populations responded very differently to being held under standard laboratory conditions; some populations showed an increase in ECC investment while others remained unchanged. More importantly, we found some evidence that we could reduce within population variation in ECC investment through time, but could not reduce among-population variation in mean ECC investment. Given the large variation we observed in wild fish and our limited ability to converge mean cell number by holding the fish under standard conditions, we caution that future studies may be hard pressed to find subtle effects of various experimental manipulations; this will make elucidating the selection pressures leading to the evolution of the cells challenging. PMID:23469175

Microstructural changes in a cementitious membrane due to the application of a DC electric field.

PubMed

Covelo, Alba; Diaz, Belen; Freire, Lorena; Novoa, X Ramon; Perez, M Consuelo

2008-07-01

The use of electromigration techniques to accelerate chloride ions motion is commonly employed to characterise the permeability of cementitious samples to chlorides, a relevant parameter in reinforced concrete corrosion. This paper is devoted to the study of microstructure's changes occurring in mortar samples when submitted to natural diffusion and migration experiments. The application of an electric field reduces testing time in about one order of magnitude with respect to natural diffusion experiments. Nevertheless, the final sample's microstructure differs in both tests. Impedance Spectroscopy is employed for real time monitoring of microstructural changes. During migration experiments the global impedance undergoes important increase in shorter period of time compared to natural diffusion tests. So, the forced motion of ions through the concrete membrane induces significant variations in the porous structure, as confirmed by Mercury Intrusion Porosimetry. After migration experiments, an important increase in the capillary pore size (10-100 nm) was detected. Conversely, no relevant variations are found after natural diffusion tests. Results presented in this work cast doubt on the significance of diffusion coefficient values obtained under accelerated conditions.

Sexual selection and physical attractiveness : Implications for mating dynamics.

PubMed

Gangestad, S W

1993-09-01

Sexual selection processes have received much attention in recent years, attention reflected in interest in human mate preferences. Among these mate preferences are preferences for physical attractiveness. Preferences in and of themselves, however, do not fully explain the nature of the relationships that individuals attain. A tacit negotiation process underlies relationship formation and maintenance. The notion that preferences for physical attractiveness evolved under parasite-driven "good genes" sexual selection leads to predictions about the nature of trade-offs that individuals make between mates' physical attractiveness and investment potential. These predictions and relevant data are explored, with a primary emphasis on women's preferences for men's qualities. In addition, further implications of trade-offs are examined, most notably (a) the impact of environmental variations on the nature of mating and (b) some effects of trade-offs on infidelity and male attempts to control women.

Genetic variation and plasticity of Plantago coronopus under saline conditions

NASA Astrophysics Data System (ADS)

Smekens, Marret J.; van Tienderen, Peter H.

2001-08-01

Phenotypic plasticity may allow organisms to cope with variation in the environmental conditions they encounter in their natural habitats. Salt adaptation appears to be an excellent example of such a plastic response. Many plant species accumulate organic solutes in response to saline conditions. Comparative and molecular studies suggest that this is an adaptation to osmotic stress. However, evidence relating the physiological responses to fitness parameters is rare and requires assessing the potential costs and benefits of plasticity. We studied the response of thirty families derived from plants collected in three populations of Plantago coronopus in a greenhouse experiment under saline and non-saline conditions. We indeed found a positive selection gradient for the sorbitol percentage under saline conditions: plant families with a higher proportion of sorbitol produced more spikes. No effects of sorbitol on fitness parameters were found under non-saline conditions. Populations also differed genetically in leaf number, spike number, sorbitol concentration and percentages of different soluble sugars. Salt treatment led to a reduction of vegetative biomass and spike production but increased leaf dry matter percentage and leaf thickness. Both under saline and non-saline conditions there was a negative trade-off between vegetative growth and reproduction. Families with a high plasticity in leaf thickness had a lower total spike length under non-saline conditions. This would imply that natural selection under predominantly non-saline conditions would lead to a decrease in the ability to change leaf morphology in response to exposure to salt. All other tests revealed no indication for any costs of plasticity to saline conditions.

Adaptive Value of Phenological Traits in Stressful Environments: Predictions Based on Seed Production and Laboratory Natural Selection

PubMed Central

Glorieux, Cédric; Cuguen, Joel; Roux, Fabrice

2012-01-01

Phenological traits often show variation within and among natural populations of annual plants. Nevertheless, the adaptive value of post-anthesis traits is seldom tested. In this study, we estimated the adaptive values of pre- and post-anthesis traits in two stressful environments (water stress and interspecific competition), using the selfing annual species Arabidopsis thaliana. By estimating seed production and by performing laboratory natural selection (LNS), we assessed the strength and nature (directional, disruptive and stabilizing) of selection acting on phenological traits in A. thaliana under the two tested stress conditions, each with four intensities. Both the type of stress and its intensity affected the strength and nature of selection, as did genetic constraints among phenological traits. Under water stress, both experimental approaches demonstrated directional selection for a shorter life cycle, although bolting time imposes a genetic constraint on the length of the interval between bolting and anthesis. Under interspecific competition, results from the two experimental approaches showed discrepancies. Estimation of seed production predicted directional selection toward early pre-anthesis traits and long post-anthesis periods. In contrast, the LNS approach suggested neutrality for all phenological traits. This study opens questions on adaptation in complex natural environment where many selective pressures act simultaneously. PMID:22403624

Measuring the Sensitivity of Single-locus “Neutrality Tests” Using a Direct Perturbation Approach

PubMed Central

Garrigan, Daniel; Lewontin, Richard; Wakeley, John

2010-01-01

A large number of statistical tests have been proposed to detect natural selection based on a sample of variation at a single genetic locus. These tests measure the deviation of the allelic frequency distribution observed within populations from the distribution expected under a set of assumptions that includes both neutral evolution and equilibrium population demography. The present study considers a new way to assess the statistical properties of these tests of selection, by their behavior in response to direct perturbations of the steady-state allelic frequency distribution, unconstrained by any particular nonequilibrium demographic scenario. Results from Monte Carlo computer simulations indicate that most tests of selection are more sensitive to perturbations of the allele frequency distribution that increase the variance in allele frequencies than to perturbations that decrease the variance. Simulations also demonstrate that it requires, on average, 4N generations (N is the diploid effective population size) for tests of selection to relax to their theoretical, steady-state distributions following different perturbations of the allele frequency distribution to its extremes. This relatively long relaxation time highlights the fact that these tests are not robust to violations of the other assumptions of the null model besides neutrality. Lastly, genetic variation arising under an example of a regularly cycling demographic scenario is simulated. Tests of selection performed on this last set of simulated data confirm the confounding nature of these tests for the inference of natural selection, under a demographic scenario that likely holds for many species. The utility of using empirical, genomic distributions of test statistics, instead of the theoretical steady-state distribution, is discussed as an alternative for improving the statistical inference of natural selection. PMID:19744997

Total variation-based neutron computed tomography

NASA Astrophysics Data System (ADS)

Barnard, Richard C.; Bilheux, Hassina; Toops, Todd; Nafziger, Eric; Finney, Charles; Splitter, Derek; Archibald, Rick

2018-05-01

We perform the neutron computed tomography reconstruction problem via an inverse problem formulation with a total variation penalty. In the case of highly under-resolved angular measurements, the total variation penalty suppresses high-frequency artifacts which appear in filtered back projections. In order to efficiently compute solutions for this problem, we implement a variation of the split Bregman algorithm; due to the error-forgetting nature of the algorithm, the computational cost of updating can be significantly reduced via very inexact approximate linear solvers. We present the effectiveness of the algorithm in the significantly low-angular sampling case using synthetic test problems as well as data obtained from a high flux neutron source. The algorithm removes artifacts and can even roughly capture small features when an extremely low number of angles are used.

Virulence variations of Puccinia striiformis f. sp. tritici isolates sexually produced on Berberis spp. under natural conditions in China

USDA-ARS?s Scientific Manuscript database

The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), frequently causes significant yield losses in China, due to rapid development of new races that overcome resistance in wheat cultivars. Indirect evidence suggests that sexual reproduction occurs in the Pst population in China, but...

Remote sensing in Virginia agriculture

NASA Technical Reports Server (NTRS)

Pettry, D. E.; Newhouse, M. E.; Dunton, E. M., Jr.; Scott, J. H., Jr.

1972-01-01

An experimental investigation, designed to develop and evaluate multispectral sensing techniques used in sensing agricultural crops, is described. Initial studies were designed to detect plant species and associated diseases, soil variations, and cultural practices under natural environment conditions. In addition, crop varieties, age, spacing, plant height, percentage of ground cover, and plant vigor are determined.

A chance constraint estimation approach to optimizing resource management under uncertainty

Treesearch

Michael Bevers

2007-01-01

Chance-constrained optimization is an important method for managing risk arising from random variations in natural resource systems, but the probabilistic formulations often pose mathematical programming problems that cannot be solved with exact methods. A heuristic estimation method for these problems is presented that combines a formulation for order statistic...

Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas.

PubMed

Irwin, Judith A; Soumpourou, Eleni; Lister, Clare; Ligthart, Jan-Dick; Kennedy, Sue; Dean, Caroline

2016-09-01

Variation in flowering time and response to overwintering has been exploited to breed brassica vegetables that can be harvested year-round. Our knowledge of flowering time control now enables the investigation of the molecular basis of this important variation. Here, we show that a major determinant of heading date variation in Brassica oleracea is from variation in vernalization response through allelic variation at FLOWERING LOCUS C.C2 (BoFLC4). We characterize two alleles of BoFLC.C2 that are both functional and confer a requirement for vernalization, but they show distinct expression dynamics in response to cold. Complementation experiments in Arabidopsis thaliana revealed that the allelic variation results from cis polymorphism at BoFLC.C2, which quantitatively influences the degree of cold-induced epigenetic silencing. This results in one allelic variant conferring consistently later heading under both glasshouse and field conditions through reduced environmental sensitivity. Our results suggest that breeding of brassica varieties for commercially valuable variation in heading date has been achieved through the selection of cis polymorphism at FLC, similar to that underpinning natural variation in A. thaliana. This understanding will allow for the selection of alleles with distinct sensitivities to cold and robust heading dates under variable climatic conditions, and will facilitate the breeding of varieties more resistant to climate change. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

A new metric of inclusive fitness predicts the human mortality profile.

PubMed

Newman, Saul J; Easteal, Simon

2015-01-01

Biological species have evolved characteristic patterns of age-specific mortality across their life spans. If these mortality profiles are shaped by natural selection they should reflect underlying variation in the fitness effect of mortality with age. Direct fitness models, however, do not accurately predict the mortality profiles of many species. For several species, including humans, mortality rates vary considerably before and after reproductive ages, during life-stages when no variation in direct fitness is possible. Variation in mortality rates at these ages may reflect indirect effects of natural selection acting through kin. To test this possibility we developed a new two-variable measure of inclusive fitness, which we term the extended genomic output or EGO. Using EGO, we estimate the inclusive fitness effect of mortality at different ages in a small hunter-gatherer population with a typical human mortality profile. EGO in this population predicts 90% of the variation in age-specific mortality. This result represents the first empirical measurement of inclusive fitness of a trait in any species. It shows that the pattern of human survival can largely be explained by variation in the inclusive fitness cost of mortality at different ages. More generally, our approach can be used to estimate the inclusive fitness of any trait or genotype from population data on birth dates and relatedness.

Effects of Genetic Drift and Gene Flow on the Selective Maintenance of Genetic Variation

PubMed Central

Star, Bastiaan; Spencer, Hamish G.

2013-01-01

Explanations for the genetic variation ubiquitous in natural populations are often classified by the population–genetic processes they emphasize: natural selection or mutation and genetic drift. Here we investigate models that incorporate all three processes in a spatially structured population, using what we call a construction approach, simulating finite populations under selection that are bombarded with a steady stream of novel mutations. As expected, the amount of genetic variation compared to previous models that ignored the stochastic effects of drift was reduced, especially for smaller populations and when spatial structure was most profound. By contrast, however, for higher levels of gene flow and larger population sizes, the amount of genetic variation found after many generations was greater than that in simulations without drift. This increased amount of genetic variation is due to the introduction of slightly deleterious alleles by genetic drift and this process is more efficient when migration load is higher. The incorporation of genetic drift also selects for fitness sets that exhibit allele-frequency equilibria with larger domains of attraction: they are “more stable.” Moreover, the finiteness of populations strongly influences levels of local adaptation, selection strength, and the proportion of allele-frequency vectors that can be distinguished from the neutral expectation. PMID:23457235

Snail phenotypic variation and stress proteins: do different heat response strategies contribute to Waddington's widget in field populations?

PubMed

Köhler, Heinz-R; Lazzara, Raimondo; Dittbrenner, Nils; Capowiez, Yvan; Mazzia, Christophe; Triebskorn, Rita

2009-03-15

On the basis of studies with laboratory strains of Drosophila and Arabidopsis, it has been hypothesized that potential buffers to the expression of phenotypic morphological variation, such as Hsp90 and possibly Hsp70, represent important components of Waddington's widget, which may confer capacitive evolution. As studies on field populations of living organisms to test this hypothesis are lacking, we tested whether a heat response strategy involving high stress protein levels is associated with low morphological variation and vice versa, using four natural populations of Mediterranean pulmonate snails. In response to 8 hr of elevated temperatures, a population of Xeropicta derbentina with uniform shell pigmentation pattern showed remarkably high Hsp70 but low Hsp90 levels. In contrast, a highly variable population of Cernuella virgata kept both Hsp90 and Hsp70 levels low when held at diverse though environmentally relevant temperatures. Two other populations (Theba pisana and another X. derbentina population) with intermediate variation in shell pigmentation pattern were also intermediate in inducing Hsp70, though Hsp90 was maintained at a low level. The observed correlation of stress protein levels and coloration pattern variation provide the first indirect evidence for an association of stress proteins with Waddington's widget under natural conditions.

Impacts of ENSO events on cloud radiative effects in preindustrial conditions: Changes in cloud fraction and their dependence on interactive aerosol emissions and concentrations: IMPACT OF ENSO ON CLOUD RADIATIVE EFFECT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yang; Russell, Lynn M.; Xu, Li

The impacts of the El Niño–Southern Oscillation (ENSO) events on shortwave and longwave cloud radiative effects (CRESW and CRELW) and the underlying changes in cloud fraction as well as aerosol emissions, wet scavenging and transport are quantified using three 150-year simulations in preindustrial conditions by the CESM model. Compared to recent observations from Clouds and the Earth’s Radiant Energy System (CERES), the model simulation successfully reproduced larger variations of CRESW over the tropical western and central Pacific, Indonesian regions, and the eastern Pacific Ocean, as well as large variations of CRELW located mainly within the tropics. The ENSO cycle ismore » found to dominate interannual variations of cloud radiative effects, especially over the tropics. Relative to those during La Niña events, simulated cooling (warming) effects from CRESW (CRELW) during El Niño events are stronger over the tropical western and central Pacific Ocean, with the largest difference exceeding 40 Wm–2 (30 Wm–2), with weaker effects of 10–30 Wm–2 over Indonesian regions and the subtropical Pacific Ocean. Sensitivity tests show that variations of cloud radiative effects are mainly driven by ENSO-related changes in cloud fraction. The variations in medium and high cloud fractions each account for about 20–50% of the interannual variations of CRESW over the tropics and almost all of the variations of CRELW between 60°S and 60°N. The variation of low cloud fraction contributes most interannual variations of CRESW over the mid-latitude oceans. Variations in natural aerosol concentrations considering emissions, wet scavenging and transport explained 10–30% of the interannual variations of both CRESW and CRELW over the tropical Pacific, Indonesian regions and the tropical Indian Ocean. Changes in wet scavenging of natural aerosol modulate the variations of cloud radiative effects. Because of increased (decreased) precipitation over the tropical western Pacific Ocean in El Niño (La Niña) events, increased (decreased) wet scavenging of natural aerosols dampens more than 4–6% of variations of cloud radiative effects averaged over the tropics. In contrast, increased surface winds cause feedbacks that increase sea spray emissions that enhance the variations by 3–4% averaged over the tropics.« less

Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization

PubMed Central

Sofer, Imri; Crouzet, Sébastien M.; Serre, Thomas

2015-01-01

Observers can rapidly perform a variety of visual tasks such as categorizing a scene as open, as outdoor, or as a beach. Although we know that different tasks are typically associated with systematic differences in behavioral responses, to date, little is known about the underlying mechanisms. Here, we implemented a single integrated paradigm that links perceptual processes with categorization processes. Using a large image database of natural scenes, we trained machine-learning classifiers to derive quantitative measures of task-specific perceptual discriminability based on the distance between individual images and different categorization boundaries. We showed that the resulting discriminability measure accurately predicts variations in behavioral responses across categorization tasks and stimulus sets. We further used the model to design an experiment, which challenged previous interpretations of the so-called “superordinate advantage.” Overall, our study suggests that observed differences in behavioral responses across rapid categorization tasks reflect natural variations in perceptual discriminability. PMID:26335683

RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions

PubMed Central

2013-01-01

Background The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. We used RNA sequencing of Eutrema salsugineum, an extremophile relative of Arabidopsis thaliana, to investigate the extent to which genetic variation and controlled versus natural environments contribute to differences between transcript profiles. Results Using 10 million cDNA reads, we compared transcriptomes from two natural Eutrema accessions (originating from Yukon Territory, Canada and Shandong Province, China) grown under controlled conditions in cabinets and those from Yukon plants collected at a Yukon field site. We assessed the genetic heterogeneity between individuals using single-nucleotide polymorphisms (SNPs) and the expression patterns of 27,016 genes. Over 39,000 SNPs distinguish the Yukon from the Shandong accessions but only 4,475 SNPs differentiated transcriptomes of Yukon field plants from an inbred Yukon line. We found 2,989 genes that were differentially expressed between the three sample groups and multivariate statistical analyses showed that transcriptomes of individual plants from a Yukon field site were as reproducible as those from inbred plants grown under controlled conditions. Predicted functions based upon gene ontology classifications show that the transcriptomes of field plants were enriched by the differential expression of light- and stress-related genes, an observation consistent with the habitat where the plants were found. Conclusion Our expectation that comparative RNA-Seq analysis of transcriptomes from plants originating in natural habitats would be confounded by uncontrolled genetic and environmental factors was not borne out. Moreover, the transcriptome data shows little genetic variation between laboratory Yukon Eutrema plants and those found at a field site. Transcriptomes were reproducible and biological associations meaningful whether plants were grown in cabinets or found in the field. Thus RNA-Seq is a valuable approach to study native plants in natural environments and this technology can be exploited to discover new gene targets for improved crop performance under adverse conditions. PMID:23984645

Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action.

PubMed

Griswold, Cortland K

2015-12-21

Epistatic gene action occurs when mutations or alleles interact to produce a phenotype. Theoretically and empirically it is of interest to know whether gene interactions can facilitate the evolution of diversity. In this paper, we explore how epistatic gene action affects the additive genetic component or heritable component of multivariate trait variation, as well as how epistatic gene action affects the evolvability of multivariate traits. The analysis involves a sexually reproducing and recombining population. Our results indicate that under stabilizing selection conditions a population with a mixed additive and epistatic genetic architecture can have greater multivariate additive genetic variation and evolvability than a population with a purely additive genetic architecture. That greater multivariate additive genetic variation can occur with epistasis is in contrast to previous theory that indicated univariate additive genetic variation is decreased with epistasis under stabilizing selection conditions. In a multivariate setting, epistasis leads to less relative covariance among individuals in their genotypic, as well as their breeding values, which facilitates the maintenance of additive genetic variation and increases a population׳s evolvability. Our analysis involves linking the combinatorial nature of epistatic genetic effects to the ancestral graph structure of a population to provide insight into the consequences of epistasis on multivariate trait variation and evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hydrolysis and photolysis of diacylhydrazines-type insect growth regulator JS-118 in aqueous solutions under abiotic conditions.

PubMed

Hu, J-Y; Liu, C; Zhang, Y-C; Zheng, Z-X

2009-05-01

JS-118 is a diacylhydrazines-type insect growth regulator which is now used extensively in China. The hydrolysis and photolysis of the pesticide JS-118 in aqueous solutions have been assessed under natural and controlled conditions in this project. Hydrolysis experimental results show that JS-118 is quite stable in aqueous solutions in dark, with no significant variations be observed in degradation under various conditions. Abiotic hydrolysis is relatively unimportant compared to photolysis. The rate of photodecomposition of JS-118 in aqueous solutions follows first-order kinetics both in UV radiation and natural sunlight. The degradation rates are faster under UV light than sunlight, with the half-lives (t (1/2) = ln2/k) of 6.00-10.85 min and 6.63-10.16 day, respectively. Under UV light, two major photoproducts are detected, and tentatively identified according to HPLC-MS spectral information as N-t-butyl-N-(3,5-dimethylbenzoyl) and 3,7-dimethyl-benzoatedihydrofuran. The corresponding photolysis pathways of JS-118 are also proposed. The results obtained indicate that direct photoreaction is an important dissipation pathway of JS-118 in natural water systems.

Seasonal variation in the free-running period in two Talitrus saltator populations from Italian beaches differing in morphodynamics and human disturbance

NASA Astrophysics Data System (ADS)

Nardi, M.; Morgan, E.; Scapini, F.

2003-10-01

The sandhopper Talitrus saltator Montagu (Amphipoda) is a widespread species adapted to different changing environmental conditions and which typically shows a clear circadian rhythm of locomotor activity. The populations from two beaches on the western Italian coast differing in coastline dynamics (eroded versus dynamically stable) and human disturbance (inside a natural park versus freely used and cleaned for leisure) were studied to highlight intrapopulation variation in the endogenous locomotor rhythm. The activity of adult sandhoppers was studied under constant laboratory conditions within individual recording chambers. Variation of the free-running period was analysed at individual level within each population. Greater variability was found than previously reported for the circadian rhythm period of T. saltator, and seasonal variation was shown for the first time. Differences in the level of variation were correlated with coastline dynamics.

Selection on spur shape in Impatiens capensis.

PubMed

Young, Helen J

2008-06-01

Rapid speciation within some plant families has been attributed to the evolution of floral spurs and to the effect of spur length on plant reproductive success. The flowers of Impatiens capensis (jewelweed) possess a long, curved spur in which nectar is produced and stored. Spur length and curvature varies among plants within one population. Here I document that spur shape is variable in natural populations, variation within plants is less than variation among plants, and spur shape is correlated with components of female and male reproductive success. The apparent natural selection is weakly directional in 1 of 2 years, with greatest seed production and pollen removal occurring in flowers with the greatest spur curvature. Bee pollinator visit length is longest at flowers with highly curved spurs, and they leave less nectar in these spurs than in flowers with straighter spurs. Spur angle evolution may be limited, at least in part, by opposing selection by nectar-robbers who prefer to visit flowers with greater spur curvature. Other factors that might contribute to the maintenance of spur angle variation are temporal variation in the strength of selection and potential genetic correlations of spur shape with other traits under selection.

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

PubMed Central

Routaboul, Jean-Marc; Dubos, Christian; Beck, Gilles; Marquis, Catherine; Bidzinski, Przemyslaw; Loudet, Olivier; Lepiniec, Loïc

2012-01-01

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11–64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation. PMID:22442426

Species conservation and natural variation among populations [Chapter 5

Treesearch

Leonard F. Ruggiero; Michael K. Schwartz; Keith B. Aubry; Charles J. Krebs; Amanda Stanley; Steven W. Buskirk

2000-01-01

In conservation planning, the importance of natural variation is often given inadequate consideration. However, ignoring the implications of variation within species may result in conservation strategies that jeopardize, rather than conserve, target species (see Grieg 1979; Turcek 1951; Storfer 1999). Natural variation in the traits of individuals and populations is...

Stress-Related Gene Expression Reflects Morphophysiological Responses to Water Deficit1[OPEN

PubMed Central

Vile, Denis; Bediee, Alexis; Dauzat, Myriam; Luchaire, Nathalie; Kamrowska, Dominika; Granier, Christine

2017-01-01

Acclimation to water deficit (WD) enables plants to maintain growth under unfavorable environmental conditions, although the mechanisms are not completely understood. In this study, the natural variation of long-term acclimation to moderate and severe soil WD was investigated in 18 Arabidopsis (Arabidopsis thaliana) accessions using PHENOPSIS, an automated phenotyping platform. Soil water content was adjusted at an early stage of plant development and maintained at a constant level until reproductive age was achieved. The accessions were selected based on the expression levels of ANNEXIN1, a drought-related marker. Severe WD conditions had a greater effect on most of the measured morphophysiological traits than moderate WD conditions. Multivariate analyses indicated that trait responses associated with plant size and water management drove most of the variation. Accessions with similar responses at these two levels were grouped in clusters that displayed different response strategies to WD. The expression levels of selected stress-response genes revealed large natural variation under WD conditions. Responses of morphophysiological traits, such as projected rosette area, transpiration rate, and rosette water content, were correlated with changes in the expression of stress-related genes, such as NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 and N-MYC DOWNREGULATED-LIKE1 (NDL1), in response to WD. Interestingly, the morphophysiological acclimation response to WD also was reflected in the gene expression levels (most notably those of NDL1, CHALCONE SYNTHASE, and MYB DOMAIN PROTEIN44) in plants cultivated under well-watered conditions. Our results may lead to the development of biomarkers and predictors of plant morphophysiological responses based on gene expression patterns. PMID:28522456

Asynchrony of senescence among phenotypic traits in a wild mammal population

PubMed Central

Hayward, Adam D.; Moorad, Jacob; Regan, Charlotte E.; Berenos, Camillo; Pilkington, Jill G.; Pemberton, Josephine M.; Nussey, Daniel H.

2015-01-01

The degree to which changes in lifespan are coupled to changes in senescence in different physiological systems and phenotypic traits is a central question in biogerontology. It is underpinned by deeper biological questions about whether or not senescence is a synchronised process, or whether levels of synchrony depend on species or environmental context. Understanding how natural selection shapes patterns of synchrony in senescence across physiological systems and phenotypic traits demands the longitudinal study of many phenotypes under natural conditions. Here, we examine the patterns of age-related variation in late adulthood in a wild population of Soay sheep (Ovis aries) that have been the subject of individual-based monitoring for thirty years. We examined twenty different phenotypic traits in both males and females, encompassing vital rates (survival and fecundity), maternal reproductive performance (offspring birth weight, birth date and survival), male rutting behaviour, home range measures, parasite burdens, and body mass. We initially quantified age-related variation in each trait having controlled for annual variation in the environment, among-individual variation and selective disappearance effects. We then standardised our age-specific trait means and tested whether age trajectories could be meaningfully grouped according to sex or the type of trait. Whilst most traits showed age-related declines in later life, we found striking levels of asynchrony both within and between the sexes. Of particular note, female fecundity and reproductive performance declined with age, but male annual reproductive success did not. We also discovered that whilst home range size and quality decline with age in females, home range size increases with age in males. Our findings highlight the complexity of phenotypic ageing under natural conditions and, along with emerging data from other wild populations and laboratory models, suggest that the long-standing hypothesis within evolutionary biology that fitness-related traits should senesce in a synchronous manner is seriously flawed. PMID:26277618

Tree-stem diameter fluctuates with the lunar tides and perhaps with geomagnetic activity.

PubMed

Barlow, Peter W; Mikulecký, Miroslav; Střeštík, Jaroslav

2010-11-01

Our initial objective has been to examine the suggestion of Zürcher et al. (Nature 392:665–666, 1998) that the naturally occurring variations in stem diameter of two experimental trees of Picea alba were related to near simultaneous variations in the lunisolar tidal acceleration. The relationship was positive: Lunar peaks were roughly synchronous with stem diameter peaks. To extend the investigation of this putative relationship, additional data on stem diameter variations from six other tree species were gathered from published literature. Sixteen sets of data were analysed retrospectively using graphical representations as well as cosinor analysis, statistical cross-correlation and cross-spectral analysis, together with estimated values of the lunisolar tidal acceleration corresponding to the sites, dates and times of collection of the biological data. Positive relationships were revealed between the daily variations of stem diameter and the variations of the lunisolar tidal acceleration. Although this relationship could be mediated by a 24.8-h lunar rhythm, the presence of a solar rhythm of 24.0 h could not be ruled out. Studies of transpiration in two of the observed trees indicated that although this variable was not linked to stem diameter variation, it might also be subject to lunisolar gravitational regulation. In three cases, the geomagnetic Thule index showed a weak but reciprocal relationship with stem diameter variation, as well as a positive relationship with the lunisolar tidal force. In conclusion, it seems that lunar gravity alone could influence stem diameter variation and that, under certain circumstances, additional regulation may come from the geomagnetic flux.

Which climate change path are we following? Bad news from Scots pine

PubMed Central

D’Andrea, Ettore; Rezaie, Negar; Cammarano, Mario; Matteucci, Giorgio

2017-01-01

Current expectations on future climate derive from coordinated experiments, which compile many climate models for sampling the entire uncertainty related to emission scenarios, initial conditions, and modelling process. Quantifying this uncertainty is important for taking decisions that are robust under a wide range of possible future conditions. Nevertheless, if uncertainty is too large, it can prevent from planning specific and effective measures. For this reason, reducing the spectrum of the possible scenarios to a small number of one or a few models that actually represent the climate pathway influencing natural ecosystems would substantially increase our planning capacity. Here we adopt a multidisciplinary approach based on the comparison of observed and expected spatial patterns of response to climate change in order to identify which specific models, among those included in the CMIP5, catch the real climate variation driving the response of natural ecosystems. We used dendrochronological analyses for determining the geographic pattern of recent growth trends for three European species of trees. At the same time, we modelled the climatic niche for the same species and forecasted the suitability variation expected across Europe under each different GCM. Finally, we estimated how well each GCM explains the real response of ecosystems, by comparing the expected variation with the observed growth trends. Doing this, we identified four climatic models that are coherent with the observed trends. These models are close to the highest range limit of the climatic variations expected by the ensemble of the CMIP5 models, suggesting that current predictions of climate change impacts on ecosystems could be underestimated. PMID:29252985

Which climate change path are we following? Bad news from Scots pine.

PubMed

Bombi, Pierluigi; D'Andrea, Ettore; Rezaie, Negar; Cammarano, Mario; Matteucci, Giorgio

2017-01-01

Current expectations on future climate derive from coordinated experiments, which compile many climate models for sampling the entire uncertainty related to emission scenarios, initial conditions, and modelling process. Quantifying this uncertainty is important for taking decisions that are robust under a wide range of possible future conditions. Nevertheless, if uncertainty is too large, it can prevent from planning specific and effective measures. For this reason, reducing the spectrum of the possible scenarios to a small number of one or a few models that actually represent the climate pathway influencing natural ecosystems would substantially increase our planning capacity. Here we adopt a multidisciplinary approach based on the comparison of observed and expected spatial patterns of response to climate change in order to identify which specific models, among those included in the CMIP5, catch the real climate variation driving the response of natural ecosystems. We used dendrochronological analyses for determining the geographic pattern of recent growth trends for three European species of trees. At the same time, we modelled the climatic niche for the same species and forecasted the suitability variation expected across Europe under each different GCM. Finally, we estimated how well each GCM explains the real response of ecosystems, by comparing the expected variation with the observed growth trends. Doing this, we identified four climatic models that are coherent with the observed trends. These models are close to the highest range limit of the climatic variations expected by the ensemble of the CMIP5 models, suggesting that current predictions of climate change impacts on ecosystems could be underestimated.

Abiotic versus biotic drivers of ocean pH variation under fast sea ice in McMurdo Sound, Antarctica.

PubMed

Matson, Paul G; Washburn, Libe; Martz, Todd R; Hofmann, Gretchen E

2014-01-01

Ocean acidification is expected to have a major effect on the marine carbonate system over the next century, particularly in high latitude seas. Less appreciated is natural environmental variation within these systems, particularly in terms of pH, and how this natural variation may inform laboratory experiments. In this study, we deployed sensor-equipped moorings at 20 m depths at three locations in McMurdo Sound, comprising deep (bottom depth>200 m: Hut Point Peninsula) and shallow environments (bottom depth ∼25 m: Cape Evans and New Harbor). Our sensors recorded high-frequency variation in pH (Hut Point and Cape Evans only), tide (Cape Evans and New Harbor), and water mass properties (temperature and salinity) during spring and early summer 2011. These collective observations showed that (1) pH differed spatially both in terms of mean pH (Cape Evans: 8.009±0.015; Hut Point: 8.020±0.007) and range of pH (Cape Evans: 0.090; Hut Point: 0.036), and (2) pH was not related to the mixing of two water masses, suggesting that the observed pH variation is likely not driven by this abiotic process. Given the large daily fluctuation in pH at Cape Evans, we developed a simple mechanistic model to explore the potential for biotic processes--in this case algal photosynthesis--to increase pH by fixing carbon from the water column. For this model, we incorporated published photosynthetic parameters for the three dominant algal functional groups found at Cape Evans (benthic fleshy red macroalgae, crustose coralline algae, and sea ice algal communities) to estimate oxygen produced/carbon fixed from the water column underneath fast sea ice and the resulting pH change. These results suggest that biotic processes may be a primary driver of pH variation observed under fast sea ice at Cape Evans and potentially at other shallow sites in McMurdo Sound.

Abiotic versus Biotic Drivers of Ocean pH Variation under Fast Sea Ice in McMurdo Sound, Antarctica

PubMed Central

Matson, Paul G.; Washburn, Libe; Martz, Todd R.; Hofmann, Gretchen E.

2014-01-01

Ocean acidification is expected to have a major effect on the marine carbonate system over the next century, particularly in high latitude seas. Less appreciated is natural environmental variation within these systems, particularly in terms of pH, and how this natural variation may inform laboratory experiments. In this study, we deployed sensor-equipped moorings at 20 m depths at three locations in McMurdo Sound, comprising deep (bottom depth>200 m: Hut Point Peninsula) and shallow environments (bottom depth ∼25 m: Cape Evans and New Harbor). Our sensors recorded high-frequency variation in pH (Hut Point and Cape Evans only), tide (Cape Evans and New Harbor), and water mass properties (temperature and salinity) during spring and early summer 2011. These collective observations showed that (1) pH differed spatially both in terms of mean pH (Cape Evans: 8.009±0.015; Hut Point: 8.020±0.007) and range of pH (Cape Evans: 0.090; Hut Point: 0.036), and (2) pH was not related to the mixing of two water masses, suggesting that the observed pH variation is likely not driven by this abiotic process. Given the large daily fluctuation in pH at Cape Evans, we developed a simple mechanistic model to explore the potential for biotic processes – in this case algal photosynthesis – to increase pH by fixing carbon from the water column. For this model, we incorporated published photosynthetic parameters for the three dominant algal functional groups found at Cape Evans (benthic fleshy red macroalgae, crustose coralline algae, and sea ice algal communities) to estimate oxygen produced/carbon fixed from the water column underneath fast sea ice and the resulting pH change. These results suggest that biotic processes may be a primary driver of pH variation observed under fast sea ice at Cape Evans and potentially at other shallow sites in McMurdo Sound. PMID:25221950

LPCAT1 controls phosphate homeostasis in a zinc-dependent manner

PubMed Central

Kisko, Mushtak; Bouain, Nadia; Safi, Alaeddine; Medici, Anna; Akkers, Robert C; Secco, David; Fouret, Gilles; Krouk, Gabriel; Aarts, Mark GM; Busch, Wolfgang

2018-01-01

All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation. PMID:29453864

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits.

PubMed

van Heerwaarden, Joost; van Zanten, Martijn; Kruijer, Willem

2015-10-01

Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables, under the implicit assumption that natural selection imposes correlations between phenotypes, environments and genotypes. In practice, observed trait and environmental data are manifestations of unknown selective forces and are only indirectly associated with adaptive genetic variation. In theory, improved estimation of these forces could enable more powerful detection of loci under selection. Here we present an approach in which we approximate adaptive variation by modeling phenotypes as a function of the environment and using the predicted trait in multivariate and univariate genome-wide association analysis (GWAS). Based on computer simulations and published flowering time data from the model plant Arabidopsis thaliana, we find that environmentally predicted traits lead to higher recovery of functional loci in multivariate GWAS and are more strongly correlated to allele frequencies at adaptive loci than individual environmental variables. Our results provide an example of the use of environmental data to obtain independent and meaningful information on adaptive genetic variation.

High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal

PubMed Central

Aguilar, Andres; Roemer, Gary; Debenham, Sally; Binns, Matthew; Garcelon, David; Wayne, Robert K.

2004-01-01

The San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers. Such low levels of variation imply lower resistance to pathogens, reduced fitness, and problems in distinguishing kin from non-kin. In vertebrates, the MHC contains genes that influence disease resistance and kin recognition and may be under intense balancing selection in some populations. Hence, genetic variation at the MHC might persist despite the extreme monomorphism shown by neutral markers. We examine variation of five loci within the MHC of San Nicolas Island foxes and find remarkably high levels of variation. Further, we show by simulation that genetic monomorphism at neutral loci and high MHC variation could arise only through an extreme population bottleneck of <10 individuals, ≈10–20 generations ago, accompanied by unprecedented selection coefficients of >0.5 on MHC loci. These results support the importance of balancing selection as a mechanism to maintain variation in natural populations and expose the difficulty of using neutral markers as surrogates for variation in fitness-related loci. PMID:14990802

The Music One-to-One Project: Developing Approaches to Music with Parents and Under-Two-Year-Olds

ERIC Educational Resources Information Center

Young, Susan; Street, Alison; Davies, Eleanor

2007-01-01

Detailed analyses of adult-infant interaction among some European and North American populations have revealed that it resides on characteristics such as synchronous timing, phrasing, pitch contours and variations of dynamic intensity that are essentially musical in nature. Moreover, this musicality of infancy is the medium which enables and…

Genetic variation of piperidine alkaloids in Pinus ponderosa from a common garden

Treesearch

Elizabeth A. Gerson; Rick G. Kelsey; Bradley J. St. Clair

2012-01-01

Most species of pine and spruce synthesize and accumulate variable quantities of alkaloids in their tissues. These compounds express numerous types of biological activities in bioassay and could potentially offer resistance against enemies, although this function has never been confirmed for any known enemies of pine or spruce under natural conditions. The...

Identification of the fitness determinants of budding yeast on a natural substrate

PubMed Central

Filteau, Marie; Charron, Guillaume; Landry, Christian R

2017-01-01

The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway. PMID:27935595

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

Identifying environmental correlates of intraspecific genetic variation.

PubMed

Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

2016-09-01

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.

PubMed

Ibstedt, Sebastian; Stenberg, Simon; Bagés, Sara; Gjuvsland, Arne B; Salinas, Francisco; Kourtchenko, Olga; Samy, Jeevan K A; Blomberg, Anders; Omholt, Stig W; Liti, Gianni; Beltran, Gemma; Warringer, Jonas

2015-01-01

Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ultra-low-power and robust digital-signal-processing hardware for implantable neural interface microsystems.

PubMed

Narasimhan, S; Chiel, H J; Bhunia, S

2011-04-01

Implantable microsystems for monitoring or manipulating brain activity typically require on-chip real-time processing of multichannel neural data using ultra low-power, miniaturized electronics. In this paper, we propose an integrated-circuit/architecture-level hardware design framework for neural signal processing that exploits the nature of the signal-processing algorithm. First, we consider different power reduction techniques and compare the energy efficiency between the ultra-low frequency subthreshold and conventional superthreshold design. We show that the superthreshold design operating at a much higher frequency can achieve comparable energy dissipation by taking advantage of extensive power gating. It also provides significantly higher robustness of operation and yield under large process variations. Next, we propose an architecture level preferential design approach for further energy reduction by isolating the critical computation blocks (with respect to the quality of the output signal) and assigning them higher delay margins compared to the noncritical ones. Possible delay failures under parameter variations are confined to the noncritical components, allowing graceful degradation in quality under voltage scaling. Simulation results using prerecorded neural data from the sea-slug (Aplysia californica) show that the application of the proposed design approach can lead to significant improvement in total energy, without compromising the output signal quality under process variations, compared to conventional design approaches.

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors.

PubMed

Kim, Hee Ryung; Duc, Nguyen Minh; Chung, Ka Young

2018-03-01

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Evolution in plant populations as a driver of ecological changes in arthropod communities

PubMed Central

Johnson, Marc T.J.; Vellend, Mark; Stinchcombe, John R.

2009-01-01

Heritable variation in traits can have wide-ranging impacts on species interactions, but the effects that ongoing evolution has on the temporal ecological dynamics of communities are not well understood. Here, we identify three conditions that, if experimentally satisfied, support the hypothesis that evolution by natural selection can drive ecological changes in communities. These conditions are: (i) a focal population exhibits genetic variation in a trait(s), (ii) there is measurable directional selection on the trait(s), and (iii) the trait(s) under selection affects variation in a community variable(s). When these conditions are met, we expect evolution by natural selection to cause ecological changes in the community. We tested these conditions in a field experiment examining the interactions between a native plant (Oenothera biennis) and its associated arthropod community (more than 90 spp.). Oenothera biennis exhibited genetic variation in several plant traits and there was directional selection on plant biomass, life-history strategy (annual versus biennial reproduction) and herbivore resistance. Genetically based variation in biomass and life-history strategy consistently affected the abundance of common arthropod species, total arthropod abundance and arthropod species richness. Using two modelling approaches, we show that evolution by natural selection in large O. biennis populations is predicted to cause changes in the abundance of individual arthropod species, increases in the total abundance of arthropods and a decline in the number of arthropod species. In small O. biennis populations, genetic drift is predicted to swamp out the effects of selection, making the evolution of plant populations unpredictable. In short, evolution by natural selection can play an important role in affecting the dynamics of communities, but these effects depend on several ecological factors. The framework presented here is general and can be applied to other systems to examine the community-level effects of ongoing evolution. PMID:19414473

Assessing intraspecific variation in effective dispersal along an altitudinal gradient: a test in two Mediterranean high-mountain plants.

PubMed

Lara-Romero, Carlos; Robledo-Arnuncio, Juan J; García-Fernández, Alfredo; Iriondo, Jose M

2014-01-01

Plant recruitment depends among other factors on environmental conditions and their variation at different spatial scales. Characterizing dispersal in contrasting environments may thus be necessary to understand natural intraspecific variation in the processes underlying recruitment. Silene ciliata and Armeria caespitosa are two representative species of cryophilic pastures above the tree line in Mediterranean high mountains. No explicit estimations of dispersal kernels have been made so far for these or other high-mountain plants. Such data could help to predict their dispersal and recruitment patterns in a context of changing environments under ongoing global warming. We used an inverse modelling approach to analyse effective seed dispersal patterns in five populations of both Silene ciliata and Armeria caespitosa along an altitudinal gradient in Sierra de Guadarrama (Madrid, Spain). We considered four commonly employed two-dimensional seedling dispersal kernels exponential-power, 2Dt, WALD and log-normal. No single kernel function provided the best fit across all populations, although estimated mean dispersal distances were short (<1 m) in all cases. S. ciliata did not exhibit significant among-population variation in mean dispersal distance, whereas significant differences in mean dispersal distance were found in A. caespitosa. Both S. ciliata and A. caespitosa exhibited among-population variation in the fecundity parameter and lacked significant variation in kernel shape. This study illustrates the complexity of intraspecific variation in the processes underlying recruitment, showing that effective dispersal kernels can remain relatively invariant across populations within particular species, even if there are strong variations in demographic structure and/or physical environment among populations, while the invariant dispersal assumption may not hold for other species in the same environment. Our results call for a case-by-case analysis in a wider range of plant taxa and environments to assess the prevalence and magnitude of intraspecific dispersal variation.

Worldwide organic soil carbon and nitrogen data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zinke, P.J.; Stangenberger, A.G.; Post, W.M.

The objective of the research presented in this package was to identify data that could be used to estimate the size of the soil organic carbon pool under relatively undisturbed soil conditions. A subset of the data can be used to estimate amounts of soil carbon storage at equilibrium with natural soil-forming factors. The magnitude of soil properties so defined is a resulting nonequilibrium values for carbon storage. Variation in these values is due to differences in local and geographic soil-forming factors. Therefore, information is included on location, soil nitrogen content, climate, and vegetation along with carbon density and variation.

Cryptic genetic variation, evolution's hidden substrate

PubMed Central

Paaby, Annalise B.; Rockman, Matthew V.

2016-01-01

Cryptic genetic variation is invisible under normal conditions but fuel for evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles in need of constant suppression. CGV emerges from both neutral and selective processes and it may inform how human populations respond to change. In experimental settings, CGV facilitates adaptation, but does it play an important role in the real world? We review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution. PMID:24614309

Quantitative Variation in Responses to Root Spatial Constraint within Arabidopsis thaliana[OPEN

PubMed Central

Joseph, Bindu; Lau, Lillian; Kliebenstein, Daniel J.

2015-01-01

Among the myriad of environmental stimuli that plants utilize to regulate growth and development to optimize fitness are signals obtained from various sources in the rhizosphere that give an indication of the nutrient status and volume of media available. These signals include chemical signals from other plants, nutrient signals, and thigmotropic interactions that reveal the presence of obstacles to growth. Little is known about the genetics underlying the response of plants to physical constraints present within the rhizosphere. In this study, we show that there is natural variation among Arabidopsis thaliana accessions in their growth response to physical rhizosphere constraints and competition. We mapped growth quantitative trait loci that regulate a positive response of foliar growth to short physical constraints surrounding the root. This is a highly polygenic trait and, using quantitative validation studies, we showed that natural variation in EARLY FLOWERING3 (ELF3) controls the link between root constraint and altered shoot growth. This provides an entry point to study how root and shoot growth are integrated to respond to environmental stimuli. PMID:26243313

Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.

PubMed

Francisco, Marta; Joseph, Bindu; Caligagan, Hart; Li, Baohua; Corwin, Jason A; Lin, Catherine; Kerwin, Rachel E; Burow, Meike; Kliebenstein, Daniel J

2016-01-01

A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

EasyDelta: A spreadsheet for kinetic modeling of the stable carbon isotope composition of natural gases

NASA Astrophysics Data System (ADS)

Zou, Yan-Rong; Wang, Lianyuan; Shuai, Yanhua; Peng, Ping'an

2005-08-01

A new kinetic model and an Excel © spreadsheet program for modeling the stable carbon isotope composition of natural gases is provided in this paper. The model and spreadsheet could be used to describe and predict the variances in stable carbon isotope of natural gases under both experimental and geological conditions with heating temperature or geological time. It is a user-friendly convenient tool for the modeling of isotope variation with time under experimental and geological conditions. The spreadsheet, based on experimental data, requires the input of the kinetic parameters of gaseous hydrocarbons generation. Some assumptions are made in this model: the conventional (non-isotope species) kinetic parameters represent the light isotope species; the initial isotopic value is the same for all parallel chemical reaction of gaseous hydrocarbons generation for simplicity, the re-exponential factor ratio, 13A/ 12A, is a constant, and both heavy and light isotope species have similar activation energy distribution. These assumptions are common in modeling of isotope ratios. The spreadsheet is used for searching the best kinetic parameters of the heavy isotope species to reach the minimum errors compared with experimental data, and then extrapolating isotopic changes to the thermal history of sedimentary basins. A short calculation example on the variation in δ13C values of methane is provided in this paper to show application to geological conditions.

Pleiotropy in the wild: the dormancy gene DOG1 exerts cascading control on life cycles.

PubMed

Chiang, George C K; Barua, Deepak; Dittmar, Emily; Kramer, Elena M; de Casas, Rafael Rubio; Donohue, Kathleen

2013-03-01

In the wild, organismal life cycles occur within seasonal cycles, so shifts in the timing of developmental transitions can alter the seasonal environment experienced subsequently. Effects of genes that control the timing of prior developmental events can therefore be magnified in the wild because they determine seasonal conditions experienced by subsequent life stages, which can influence subsequent phenotypic expression. We examined such environmentally induced pleiotropy of developmental-timing genes in a field experiment with Arabidopsis thaliana. When studied in the field under natural seasonal variation, an A. thaliana seed-dormancy gene, Delay Of Germination 1 (DOG1), was found to influence not only germination, but also flowering time, overall life history, and fitness. Flowering time of the previous generation, in turn, imposed maternal effects that altered germination, the effects of DOG1 alleles, and the direction of natural selection on these alleles. Thus under natural conditions, germination genes act as flowering genes and potentially vice versa. These results illustrate how seasonal environmental variation can alter pleiotropic effects of developmental-timing genes, such that effects of genes that regulate prior life stages ramify to influence subsequent life stages. In this case, one gene acting at the seed stage impacted the entire life cycle. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Differences in the selection response of serially repeated color pattern characters: standing variation, development, and evolution.

PubMed

Allen, Cerisse E; Beldade, Patrícia; Zwaan, Bas J; Brakefield, Paul M

2008-03-26

There is spectacular morphological diversity in nature but lineages typically display a limited range of phenotypes. Because developmental processes generate the phenotypic variation that fuels natural selection, they are a likely source of evolutionary biases, facilitating some changes and limiting others. Although shifts in developmental regulation are associated with morphological differences between taxa, it is unclear how underlying mechanisms affect the rate and direction of evolutionary change within populations under selection. Here we focus on two ecologically relevant features of butterfly wing color patterns, eyespot size and color composition, which are similarly and strongly correlated across the serially repeated eyespots. Though these two characters show similar patterns of standing variation and covariation within a population, they differ in key features of their underlying development. We targeted pairs of eyespots with artificial selection for coordinated (concerted selection) versus independent (antagonistic selection) change in their color composition and size and compared evolutionary responses of the two color pattern characters. The two characters respond to selection in strikingly different ways despite initially similar patterns of variation in all directions present in the starting population. Size (determined by local properties of a diffusing inductive signal) evolves flexibly in all selected directions. However, color composition (determined by a tissue-level response to the signal concentration gradient) evolves only in the direction of coordinated change. There was no independent evolutionary change in the color composition of two eyespots in response to antagonistic selection. Moreover, these differences in the directions of short-term evolutionary change in eyespot size and color composition within a single species are consistent with the observed wing pattern diversity in the genus. Both characters respond rapidly to selection for coordinated change, but there are striking differences in their response to selection for antagonistic, independent change across eyespots. While many additional factors may contribute to both short- and long-term evolutionary response, we argue that the compartmentalization of developmental processes can influence the diversification of serial repeats such as butterfly eyespots, even under strong selection.

Assessing the complex architecture of polygenic traits in diverged yeast populations.

PubMed

Cubillos, Francisco A; Billi, Eleonora; Zörgö, Enikö; Parts, Leopold; Fargier, Patrick; Omholt, Stig; Blomberg, Anders; Warringer, Jonas; Louis, Edward J; Liti, Gianni

2011-04-01

Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is to identify the causative variants driving phenotypic variation. Recently, the baker's yeast, Saccharomyces cerevisiae has emerged as a powerful model for dissecting complex traits. However, past studies using a laboratory strain were unable to reveal the complete architecture of polygenic traits. Here, we present a linkage study using 576 recombinant strains obtained from crosses of isolates representative of the major lineages. The meiotic recombinational landscape appears largely conserved between populations; however, strain-specific hotspots were also detected. Quantitative measurements of growth in 23 distinct ecologically relevant environments show that our recombinant population recapitulates most of the standing phenotypic variation described in the species. Linkage analysis detected an average of 6.3 distinct QTLs for each condition tested in all crosses, explaining on average 39% of the phenotypic variation. The QTLs detected are not constrained to a small number of loci, and the majority are specific to a single cross-combination and to a specific environment. Moreover, crosses between strains of similar phenotypes generate greater variation in the offspring, suggesting the presence of many antagonistic alleles and epistatic interactions. We found that subtelomeric regions play a key role in defining individual quantitative variation, emphasizing the importance of the adaptive nature of these regions in natural populations. This set of recombinant strains is a powerful tool for investigating the complex architecture of polygenic traits. © 2011 Blackwell Publishing Ltd.

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

PubMed Central

Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.

2016-01-01

Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

Vectorial mask optimization methods for robust optical lithography

NASA Astrophysics Data System (ADS)

Ma, Xu; Li, Yanqiu; Guo, Xuejia; Dong, Lisong; Arce, Gonzalo R.

2012-10-01

Continuous shrinkage of critical dimension in an integrated circuit impels the development of resolution enhancement techniques for low k1 lithography. Recently, several pixelated optical proximity correction (OPC) and phase-shifting mask (PSM) approaches were developed under scalar imaging models to account for the process variations. However, the lithography systems with larger-NA (NA>0.6) are predominant for current technology nodes, rendering the scalar models inadequate to describe the vector nature of the electromagnetic field that propagates through the optical lithography system. In addition, OPC and PSM algorithms based on scalar models can compensate for wavefront aberrations, but are incapable of mitigating polarization aberrations in practical lithography systems, which can only be dealt with under the vector model. To this end, we focus on developing robust pixelated gradient-based OPC and PSM optimization algorithms aimed at canceling defocus, dose variation, wavefront and polarization aberrations under a vector model. First, an integrative and analytic vector imaging model is applied to formulate the optimization problem, where the effects of process variations are explicitly incorporated in the optimization framework. A steepest descent algorithm is then used to iteratively optimize the mask patterns. Simulations show that the proposed algorithms can effectively improve the process windows of the optical lithography systems.

A test of genetic models for the evolutionary maintenance of same-sex sexual behaviour.

PubMed

Hoskins, Jessica L; Ritchie, Michael G; Bailey, Nathan W

2015-06-22

The evolutionary maintenance of same-sex sexual behaviour (SSB) has received increasing attention because it is perceived to be an evolutionary paradox. The genetic basis of SSB is almost wholly unknown in non-human animals, though this is key to understanding its persistence. Recent theoretical work has yielded broadly applicable predictions centred on two genetic models for SSB: overdominance and sexual antagonism. Using Drosophila melanogaster, we assayed natural genetic variation for male SSB and empirically tested predictions about the mode of inheritance and fitness consequences of alleles influencing its expression. We screened 50 inbred lines derived from a wild population for male-male courtship and copulation behaviour, and examined crosses between the lines for evidence of overdominance and antagonistic fecundity selection. Consistent variation among lines revealed heritable genetic variation for SSB, but the nature of the genetic variation was complex. Phenotypic and fitness variation was consistent with expectations under overdominance, although predictions of the sexual antagonism model were also supported. We found an unexpected and strong paternal effect on the expression of SSB, suggesting possible Y-linkage of the trait. Our results inform evolutionary genetic mechanisms that might maintain low but persistently observed levels of male SSB in D. melanogaster, but highlight a need for broader taxonomic representation in studies of its evolutionary causes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Collisions and Trapping of Time Delayed Solitons in Optical Waveguides with Orthogonally Polarized Modes

NASA Astrophysics Data System (ADS)

Zhou, Huan; Li, Jin-Hua; Chow, Kwok-Wing; Xiao, Shao-Rong; Sun, Ting-Ting

2017-04-01

The interactions and collisions of time delayed solitons in optical waveguides with orthogonally polarized modes are studied. Direct numerical simulations of the coherently coupled nonlinear Schrödinger equations are performed, and neither the high birefringence nor the low birefringence approximations are invoked. Trapping of solitary pulses occurs when the birefringence parameter is small or the four-wave mixing parameter is large. The distance before the first collision depends strongly on the initial separation of the two solitary pulses. Variational techniques are employed to calculate this distance, and results agree with those from the full simulations very well. Supported by the National Natural Science Foundation of China under Grant Nos. 11605090 and 11447113, Natural Science Foundation of Jiangsu Provincial Universities under Grant No. 14KJB140009 and the startup Foundation for Introducing Talent of Nanjing University of Information Science and Technology under Grant No. 2241131301064

Express yourself: bold individuals induce enhanced morphological defences

PubMed Central

Hulthén, Kaj; Chapman, Ben B.; Nilsson, P. Anders; Hollander, Johan; Brönmark, Christer

2014-01-01

Organisms display an impressive array of defence strategies in nature. Inducible defences (changes in morphology and/or behaviour within a prey's lifetime) allow prey to decrease vulnerability to predators and avoid unnecessary costs of expression. Many studies report considerable interindividual variation in the degree to which inducible defences are expressed, yet what underlies this variation is poorly understood. Here, we show that individuals differing in a key personality trait also differ in the magnitude of morphological defence expression. Crucian carp showing risky behaviours (bold individuals) expressed a significantly greater morphological defence response when exposed to a natural enemy when compared with shy individuals. Furthermore, we show that fish of different personality types differ in their behavioural plasticity, with shy fish exhibiting greater absolute plasticity than bold fish. Our data suggest that individuals with bold personalities may be able to compensate for their risk-prone behavioural type by expressing enhanced morphological defences. PMID:24335987

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Seasonal and Lunar Month Periods Observed in Natural Neutron Flux at High Altitude

NASA Astrophysics Data System (ADS)

Stenkin, Yuri; Alekseenko, Victor; Cai, Zeyu; Cao, Zhen; Cattaneo, Claudio; Cui, Shuwang; Giroletti, Elio; Gromushkin, Dmitry; Guo, Cong; Guo, Xuewen; He, Huihai; Liu, Ye; Ma, Xinhua; Shchegolev, Oleg; Vallania, Piero; Vigorito, Carlo; Zhao, Jing

2017-07-01

Air radon concentration measurement is useful for research on geophysical effects, but it is strongly sensitive to site geology and many geophysical and microclimatic processes such as wind, ventilation, air humidity and so on inducing very big fluctuations on the concentration of radon in air. On the contrary, monitoring the radon concentration in soil by measuring the thermal neutron flux reduces environmental effects. In this paper, we report some experimental results on the natural thermal neutron flux as well as on the concentration of air radon and its variations at 4300 m asl. These results were obtained with unshielded thermal neutron scintillation detectors (en-detectors) and radon monitors located inside the ARGO-YBJ experimental hall. The correlation of these variations with the lunar month and 1-year period is undoubtedly confirmed. A method for earthquake prediction provided by a global net of en-detectors is currently under study.

Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis.

PubMed

Bentsink, Leónie; Jowett, Jemma; Hanhart, Corrie J; Koornneef, Maarten

2006-11-07

Genetic variation for seed dormancy in nature is a typical quantitative trait controlled by multiple loci on which environmental factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a major scientific challenge, which also has relevance for agriculture and ecology. In this study we describe the identification of the DELAY OF GERMINATION 1 (DOG1) gene previously identified as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated by a combination of positional cloning and mutant analysis and is absolutely required for the induction of seed dormancy. DOG1 is a member of a small gene family of unknown molecular function, with five members in Arabidopsis. The functional natural allelic variation present in Arabidopsis is caused by polymorphisms in the cis-regulatory region of the DOG1 gene and results in considerable expression differences between the DOG1 alleles of the accessions analyzed.

Evolutionary potential of upper thermal tolerance: biogeographic patterns and expectations under climate change.

PubMed

Diamond, Sarah E

2017-02-01

How will organisms respond to climate change? The rapid changes in global climate are expected to impose strong directional selection on fitness-related traits. A major open question then is the potential for adaptive evolutionary change under these shifting climates. At the most basic level, evolutionary change requires the presence of heritable variation and natural selection. Because organismal tolerances of high temperature place an upper bound on responding to temperature change, there has been a surge of research effort on the evolutionary potential of upper thermal tolerance traits. Here, I review the available evidence on heritable variation in upper thermal tolerance traits, adopting a biogeographic perspective to understand how heritability of tolerance varies across space. Specifically, I use meta-analytical models to explore the relationship between upper thermal tolerance heritability and environmental variability in temperature. I also explore how variation in the methods used to obtain these thermal tolerance heritabilities influences the estimation of heritable variation in tolerance. I conclude by discussing the implications of a positive relationship between thermal tolerance heritability and environmental variability in temperature and how this might influence responses to future changes in climate. © 2016 New York Academy of Sciences.

Genome-wide association study uncovers a novel QTL allele of AtS40-3 that affects the sex ratio of cyst nematodes in Arabidopsis.

PubMed

Anwer, Muhammad Arslan; Anjam, Muhammad Shahzad; Shah, Syed Jehangir; Hasan, M Shamim; Naz, Ali A; Grundler, Florian M W; Siddique, Shahid

2018-03-24

Plant-parasitic cyst nematodes are obligate sedentary parasites that infect the roots of a broad range of host plants. Cyst nematodes are sexually dimorphic, but differentiation into male or female is strongly influenced by interactions with the host environment. Female populations typically predominate under favorable conditions, whereas male populations predominate under adverse conditions. Here, we performed a genome-wide association study (GWAS) in an Arabidopsis diversity panel to identify host loci underlying variation in susceptibility to cyst nematode infection. Three different susceptibility parameters were examined, with the aim of providing insights into the infection process, the number of females and males present in the infected plant, and the female-to-male sex ratio. GWAS results suggested that variation in sex ratio is associated with a novel quantitative trait locus allele on chromosome 4. Subsequent candidate genes and functional analyses revealed that a senescence-associated transcription factor, AtS40-3, and PPR may act in combination to influence nematode sex ratio. A detailed molecular characterization revealed that variation in nematode sex ratio was due to the disturbed common promoter of AtS40-3 and PPR genes. Additionally, single nucleotide polymorphisms in the coding sequence of AtS40-3 might contribute to the natural variation in nematode sex ratio.

Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions.

PubMed

Chidawanyika, Frank; Mudavanhu, Pride; Nyamukondiwa, Casper

2012-11-09

The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such opportunities through predation or parasitism of pests and plant direct or indirect defense mechanisms that can all be important components of sustainable integrated pest management programs. Inevitably, the efficacy of biological control systems is highly dependent on natural enemy-prey interactions, which will likely be modified by changing climates. Therefore, knowledge of how insect pests and their natural enemies respond to climate variation is of fundamental importance in understanding biological insect pest management under global climate change. Here, we discuss biological control, its challenges under climate change scenarios and how increased global temperatures will require adaptive management strategies to cope with changing status of insects and their natural enemies.

Stress-Related Gene Expression Reflects Morphophysiological Responses to Water Deficit.

PubMed

Rymaszewski, Wojciech; Vile, Denis; Bediee, Alexis; Dauzat, Myriam; Luchaire, Nathalie; Kamrowska, Dominika; Granier, Christine; Hennig, Jacek

2017-07-01

Acclimation to water deficit (WD) enables plants to maintain growth under unfavorable environmental conditions, although the mechanisms are not completely understood. In this study, the natural variation of long-term acclimation to moderate and severe soil WD was investigated in 18 Arabidopsis ( Arabidopsis thaliana ) accessions using PHENOPSIS, an automated phenotyping platform. Soil water content was adjusted at an early stage of plant development and maintained at a constant level until reproductive age was achieved. The accessions were selected based on the expression levels of ANNEXIN1 , a drought-related marker. Severe WD conditions had a greater effect on most of the measured morphophysiological traits than moderate WD conditions. Multivariate analyses indicated that trait responses associated with plant size and water management drove most of the variation. Accessions with similar responses at these two levels were grouped in clusters that displayed different response strategies to WD The expression levels of selected stress-response genes revealed large natural variation under WD conditions. Responses of morphophysiological traits, such as projected rosette area, transpiration rate, and rosette water content, were correlated with changes in the expression of stress-related genes, such as NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 and N-MYC DOWNREGULATED-LIKE1 ( NDL1 ), in response to WD Interestingly, the morphophysiological acclimation response to WD also was reflected in the gene expression levels (most notably those of NDL1 , CHALCONE SYNTHASE , and MYB DOMAIN PROTEIN44 ) in plants cultivated under well-watered conditions. Our results may lead to the development of biomarkers and predictors of plant morphophysiological responses based on gene expression patterns. © 2017 American Society of Plant Biologists. All Rights Reserved.

Natural variation underlies alterations in NRAT1 expression and function that play a key role in rice aluminum tolerance

USDA-ARS?s Scientific Manuscript database

Aluminum (Al) toxicity is a major constraint for crop production on acid soils which comprise approximately 40% of arable land in the tropics and subtropics. Rice is the most Al tolerant cereal crop, and offers a good model for identifying Al tolerance genes and mechanisms. Here we investigated natu...

Anharmonic dynamics of a mass O-spring oscillator

NASA Astrophysics Data System (ADS)

Filipponi, A.; Cavicchia, D. R.

2011-07-01

We investigate the dynamics of a one-dimensional oscillator made of a mass connected to a circular spring under uniaxial extension. The functional dependence of the elastic energy on the strain is obtained by solving the differential equations resulting from a variational formalism common to Euler's elastica problem. The calculated nonlinear force agrees with the experiment, confirming the anharmonic nature of the oscillator.

Wheat cultivars selected for high Fv /Fm under heat stress maintain high photosynthesis, total chlorophyll, stomatal conductance, transpiration and dry matter.

PubMed

Sharma, Dew Kumari; Andersen, Sven Bode; Ottosen, Carl-Otto; Rosenqvist, Eva

2015-02-01

The chlorophyll fluorescence parameter Fv /Fm reflects the maximum quantum efficiency of photosystem II (PSII) photochemistry and has been widely used for early stress detection in plants. Previously, we have used a three-tiered approach of phenotyping by Fv /Fm to identify naturally existing genetic variation for tolerance to severe heat stress (3 days at 40°C in controlled conditions) in wheat (Triticum aestivum L.). Here we investigated the performance of the previously selected cultivars (high and low group based on Fv /Fm value) in terms of growth and photosynthetic traits under moderate heat stress (1 week at 36/30°C day/night temperature in greenhouse) closer to natural heat waves in North-Western Europe. Dry matter accumulation after 7 days of heat stress was positively correlated to Fv /Fm . The high Fv /Fm group maintained significantly higher total chlorophyll and net photosynthetic rate (PN ) than the low group, accompanied by higher stomatal conductance (gs ), transpiration rate (E) and evaporative cooling of the leaf (ΔT). The difference in PN between the groups was not caused by differences in PSII capacity or gs as the variation in Fv /Fm and intracellular CO2 (Ci ) was non-significant under the given heat stress. This study validated that our three-tiered approach of phenotyping by Fv /Fm performed under increasing severity of heat was successful in identifying wheat cultivars differing in photosynthesis under moderate and agronomically more relevant heat stress. The identified cultivars may serve as a valuable resource for further studies to understand the physiological mechanisms underlying the genetic variability in heat sensitivity of photosynthesis. © 2014 Scandinavian Plant Physiology Society.

Signal, noise, and variation in neural and sensory-motor latency

PubMed Central

Lee, Joonyeol; Joshua, Mati; Medina, Javier F.; Lisberger, Stephen G.

2016-01-01

Analysis of the neural code for sensory-motor latency in smooth pursuit eye movements reveals general principles of neural variation and the specific origin of motor latency. The trial-by-trial variation in neural latency in MT comprises: a shared component expressed as neuron-neuron latency correlations; and an independent component that is local to each neuron. The independent component arises heavily from fluctuations in the underlying probability of spiking with an unexpectedly small contribution from the stochastic nature of spiking itself. The shared component causes the latency of single neuron responses in MT to be weakly predictive of the behavioral latency of pursuit. Neural latency deeper in the motor system is more strongly predictive of behavioral latency. A model reproduces both the variance of behavioral latency and the neuron-behavior latency correlations in MT if it includes realistic neural latency variation, neuron-neuron latency correlations in MT, and noisy gain control downstream from MT. PMID:26971946

Highly polygenic variation in environmental perception determines dauer larvae formation in growing populations of Caenorhabditis elegans.

PubMed

Green, James W M; Stastna, Jana J; Orbidans, Helen E; Harvey, Simon C

2014-01-01

Determining how complex traits are genetically controlled is a requirement if we are to predict how they evolve and how they might respond to selection. This requires understanding how distinct, and often more simple, life history traits interact and change in response to environmental conditions. In order to begin addressing such issues, we have been analyzing the formation of the developmentally arrested dauer larvae of Caenorhabditis elegans under different conditions. We find that 18 of 22 previously identified quantitative trait loci (QTLs) affecting dauer larvae formation in growing populations, assayed by determining the number of dauer larvae present at food patch exhaustion, can be recovered under various environmental conditions. We also show that food patch size affects both the ability to detect QTLs and estimates of effect size, and demonstrate that an allele of nath-10 affects dauer larvae formation in growing populations. To investigate the component traits that affect dauer larvae formation in growing populations we map, using the same introgression lines, QTLs that affect dauer larvae formation in response to defined amounts of pheromone. This identifies 36 QTLs, again demonstrating the highly polygenic nature of the genetic variation underlying dauer larvae formation. These data indicate that QTLs affecting the number of dauer larvae at food exhaustion in growing populations of C. elegans are highly reproducible, and that nearly all can be explained by variation affecting dauer larvae formation in response to defined amounts of pheromone. This suggests that most variation in dauer larvae formation in growing populations is a consequence of variation in the perception of the food and pheromone environment (i.e. chemosensory variation) and in the integration of these cues.

Naturally occurring variation in tadpole morphology and performance linked to predator regime

Treesearch

James B. Johnson; Daniel Saenz; Cory K. Adams; Toby J. Hibbitts

2015-01-01

Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic...

Kinetics of ozone-initiated oxidation of textile dye, Amaranth in aqueous systems.

PubMed

Dachipally, Purnachandar; Jonnalagadda, Sreekanth B

2011-01-01

The ozone facilitated oxidation mechanism of water soluble azo anionic dye, amaranth (Am) was investigated monitoring the depletion kinetics of the dye spectrometrically at 521 nm. The oxidation kinetics of the dye by ozone was studied under semi-batch conditions, by bubbling ozone enriched oxygen through the aqueous reaction mixture of dye, as function of flow rate, ionic strength, [O(3)] and pH variations. With excess concentration of ozone and other reagents and low [amaranth], reaction followed pseudo-first-order kinetics with respect to the dye. Added neutral salts had marginal effect on the reaction rate and the variation of pH from 7 to 2 and 7 to 12 exerted only small increases in the reaction rate suggesting molecular ozone possibly is the principle reactive species in oxidation of dye. The reaction order with respect ozone was near unity and it varied slightly with pH and flow rate variations. The overall second-order rate constant for the reaction was (105 ± 4) M(-1) min(-1). The main oxidation products immediately after amaranth decolorization were identified. The reaction mechanism and overall rate law were proposed. After spiking the seawater, river water and wastewaters with Amaranth dye, the reaction rates and trends in BOD and COD under control and natural conditions were investigated. The rate of depletion of the dye in natural waters was relatively lower, but the ozonation process significantly decreased both the BOD and COD levels.

Ice-cover effects on competitive interactions between two fish species.

PubMed

Helland, Ingeborg P; Finstad, Anders G; Forseth, Torbjørn; Hesthagen, Trygve; Ugedal, Ola

2011-05-01

1. Variations in the strength of ecological interactions between seasons have received little attention, despite an increased focus on climate alterations on ecosystems. Particularly, the winter situation is often neglected when studying competitive interactions. In northern temperate freshwaters, winter implies low temperatures and reduced food availability, but also strong reduction in ambient light because of ice and snow cover. Here, we study how brown trout [Salmo trutta (L.)] respond to variations in ice-cover duration and competition with Arctic charr [Salvelinus alpinus (L.)], by linking laboratory-derived physiological performance and field data on variation in abundance among and within natural brown trout populations. 2. Both Arctic charr and brown trout reduced resting metabolic rate under simulated ice-cover (darkness) in the laboratory, compared to no ice (6-h daylight). However, in contrast to brown trout, Arctic charr was able to obtain positive growth rate in darkness and had higher food intake in tank experiments than brown trout. Arctic charr also performed better (lower energy loss) under simulated ice-cover in a semi-natural environment with natural food supply. 3. When comparing brown trout biomass across 190 Norwegian lakes along a climate gradient, longer ice-covered duration decreased the biomass only in lakes where brown trout lived together with Arctic charr. We were not able to detect any effect of ice-cover on brown trout biomass in lakes where brown trout was the only fish species. 4. Similarly, a 25-year time series from a lake with both brown trout and Arctic charr showed that brown trout population growth rate depended on the interaction between ice breakup date and Arctic charr abundance. High charr abundance was correlated with low trout population growth rate only in combination with long winters. 5. In conclusion, the two species differed in performance under ice, and the observed outcome of competition in natural populations was strongly dependent on duration of the ice-covered period. Our study shows that changes in ice phenology may alter species interactions in Northern aquatic systems. Increased knowledge of how adaptations to winter conditions differ among coexisting species is therefore vital for our understanding of ecological impacts of climate change. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Natural selection stops the evolution of male attractiveness

PubMed Central

Hine, Emma; McGuigan, Katrina; Blows, Mark W.

2011-01-01

Sexual selection in natural populations acts on highly heritable traits and tends to be relatively strong, implicating sexual selection as a causal agent in many phenotypic radiations. Sexual selection appears to be ineffectual in promoting phenotypic divergence among contemporary natural populations, however, and there is little evidence from artificial selection experiments that sexual fitness can evolve. Here, we demonstrate that a multivariate male trait preferred by Drosophila serrata females can respond to selection and results in the maintenance of male mating success. The response to selection was associated with a gene of major effect increasing in frequency from 12 to 35% in seven generations. No further response to selection, or increase in frequency of the major gene, was observed between generations 7 and 11, indicating an evolutionary limit had been reached. Genetic analyses excluded both depletion of genetic variation and overdominance as causes of the evolutionary limit. Relaxing artificial selection resulted in the loss of 52% of the selection response after a further five generations, demonstrating that the response under artificial sexual selection was opposed by antagonistic natural selection. We conclude that male D. serrata sexually selected traits, and attractiveness to D. serrata females conferred by these traits, were held at an evolutionary limit by the lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness. Our results suggest that sexual selection is unlikely to cause divergence among natural populations without a concomitant change in natural selection, a conclusion consistent with observational evidence from natural populations. PMID:21321197

Buoyancy Limitation of Filamentous Cyanobacteria under Prolonged Pressure due to the Gas Vesicles Collapse

NASA Astrophysics Data System (ADS)

Abeynayaka, Helayaye Damitha Lakmali; Asaeda, Takashi; Kaneko, Yasuko

2017-08-01

Freshwater cyanobacterium Pseudanabaena galeata were cultured in chambers under artificially generated pressures, which correspond to the hydrostatic pressures at deep water. Variations occurred in gas vesicles volume, and buoyancy state of cells under those conditions were analyzed at different time intervals (5 min, 1 day, and 5 days). Variations in gas vesicles morphology of cells were observed by transmission electron microscopy images. Settling velocity ( Vs) of cells which governs the buoyancy was observed with the aid of a modified optical microscope. Moreover, effects of the prolonged pressure on cell ballast composition (protein and polysaccharides) were examined. Elevated pressure conditions reduced the cell ballast and caused a complete disappearance of gas vesicles in Pseudanabaena galeata cells. Hence cyanobacteria cells were not able to float within the study period. Observations and findings of the study indicate the potential application of hydrostatic pressure, which naturally occurred in hypolimnion of lakes, to inhibit the re-suspension of cyanobacteria cells.

Buoyancy Limitation of Filamentous Cyanobacteria under Prolonged Pressure due to the Gas Vesicles Collapse.

PubMed

Abeynayaka, Helayaye Damitha Lakmali; Asaeda, Takashi; Kaneko, Yasuko

2017-08-01

Freshwater cyanobacterium Pseudanabaena galeata were cultured in chambers under artificially generated pressures, which correspond to the hydrostatic pressures at deep water. Variations occurred in gas vesicles volume, and buoyancy state of cells under those conditions were analyzed at different time intervals (5 min, 1 day, and 5 days). Variations in gas vesicles morphology of cells were observed by transmission electron microscopy images. Settling velocity (Vs) of cells which governs the buoyancy was observed with the aid of a modified optical microscope. Moreover, effects of the prolonged pressure on cell ballast composition (protein and polysaccharides) were examined. Elevated pressure conditions reduced the cell ballast and caused a complete disappearance of gas vesicles in Pseudanabaena galeata cells. Hence cyanobacteria cells were not able to float within the study period. Observations and findings of the study indicate the potential application of hydrostatic pressure, which naturally occurred in hypolimnion of lakes, to inhibit the re-suspension of cyanobacteria cells.

(In) Sensitivity to spatial distortion in natural scenes

PubMed Central

Bex, Peter J.

2010-01-01

The perception of object structure in the natural environment is remarkably stable under large variation in image size and projection, especially given our insensitivity to spatial position outside the fovea. Sensitivity to periodic spatial distortions that were introduced into one quadrant of gray-scale natural images was measured in a 4AFC task. Observers were able to detect the presence of distortions in unfamiliar images even though they did not significantly affect the amplitude spectrum. Sensitivity depended on the spatial period of the distortion and on the image structure at the location of the distortion. The results suggest that the detection of distortion involves decisions made in the late stages of image perception and is based on an expectation of the typical structure of natural scenes. PMID:20462324

Experimental evolution across different thermal regimes yields genetic divergence in recombination fraction but no divergence in temperature associated plastic recombination.

PubMed

Kohl, Kathryn P; Singh, Nadia D

2018-04-01

Phenotypic plasticity is pervasive in nature. One mechanism underlying the evolution and maintenance of such plasticity is environmental heterogeneity. Indeed, theory indicates that both spatial and temporal variation in the environment should favor the evolution of phenotypic plasticity under a variety of conditions. Cyclical environmental conditions have also been shown to yield evolved increases in recombination frequency. Here, we use a panel of replicated experimental evolution populations of D. melanogaster to test whether variable environments favor enhanced plasticity in recombination rate and/or increased recombination rate in response to temperature. In contrast to expectation, we find no evidence for either enhanced plasticity in recombination or increased rates of recombination in the variable environment lines. Our data confirm a role of temperature in mediating recombination fraction in D. melanogaster, and indicate that recombination is genetically and plastically depressed under lower temperatures. Our data further suggest that the genetic architectures underlying plastic recombination and population-level variation in recombination rate are likely to be distinct. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Can Evolution Supply What Ecology Demands?

PubMed

Kokko, Hanna; Chaturvedi, Anurag; Croll, Daniel; Fischer, Martin C; Guillaume, Frédéric; Karrenberg, Sophie; Kerr, Ben; Rolshausen, Gregor; Stapley, Jessica

2017-03-01

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

PubMed

Willing, Eva-Maria; Bentzen, Paul; van Oosterhout, Cock; Hoffmann, Margarete; Cable, Joanne; Breden, Felix; Weigel, Detlef; Dreyer, Christine

2010-03-01

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

Variation in Genomic Methylation in Natural Populations of Chinese White Poplar

PubMed Central

Ma, Kaifeng; Song, Yuepeng; Yang, Xiaohui; Zhang, Zhiyi; Zhang, Deqiang

2013-01-01

Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match. PMID:23704963

Variable sexually dimorphic gene expression in laboratory strains of Drosophila melanogaster.

PubMed

Baker, Dean A; Meadows, Lisa A; Wang, Jing; Dow, Julian At; Russell, Steven

2007-12-10

Wild-type laboratory strains of model organisms are typically kept in isolation for many years, with the action of genetic drift and selection on mutational variation causing lineages to diverge with time. Natural populations from which such strains are established, show that gender-specific interactions in particular drive many aspects of sequence level and transcriptional level variation. Here, our goal was to identify genes that display transcriptional variation between laboratory strains of Drosophila melanogaster, and to explore evidence of gender-biased interactions underlying that variability. Transcriptional variation among the laboratory genotypes studied occurs more frequently in males than in females. Qualitative differences are also apparent to suggest that genes within particular functional classes disproportionately display variation in gene expression. Our analysis indicates that genes with reproductive functions are most often divergent between genotypes in both sexes, however a large proportion of female variation can also be attributed to genes without expression in the ovaries. The present study clearly shows that transcriptional variation between common laboratory strains of Drosophila can differ dramatically due to sexual dimorphism. Much of this variation reflects sex-specific challenges associated with divergent physiological trade-offs, morphology and regulatory pathways operating within males and females.

Potential for adaptation to climate change: family-level variation in fitness-related traits and their responses to heat waves in a snail population.

PubMed

Leicht, Katja; Seppälä, Katri; Seppälä, Otto

2017-06-15

On-going global climate change poses a serious threat for natural populations unless they are able to evolutionarily adapt to changing environmental conditions (e.g. increasing average temperatures, occurrence of extreme weather events). A prerequisite for evolutionary change is within-population heritable genetic variation in traits subject to selection. In relation to climate change, mainly phenological traits as well as heat and desiccation resistance have been examined for such variation. Therefore, it is important to investigate adaptive potential under climate change conditions across a broader range of traits. This is especially true for life-history traits and defences against natural enemies (e.g. parasites) since they influence organisms' fitness both directly and through species interactions. We examined the adaptive potential of fitness-related traits and their responses to heat waves in a population of a freshwater snail, Lymnaea stagnalis. We estimated family-level variation and covariation in life history (size, reproduction) and constitutive immune defence traits [haemocyte concentration, phenoloxidase (PO)-like activity, antibacterial activity of haemolymph] in snails experimentally exposed to typical (15 °C) and heat wave (25 °C) temperatures. We also assessed variation in the reaction norms of these traits between the treatments. We found that at the heat wave temperature, snails were larger and reproduced more, while their immune defence was reduced. Snails showed high family-level variation in all examined traits within both temperature treatments. The only negative genetic correlation (between reproduction and antibacterial activity) appeared at the high temperature. However, we found no family-level variation in the responses of most examined traits to the experimental heat wave (i.e. largely parallel reaction norms between the treatments). Only the reduction of PO-like activity when exposed to the high temperature showed family-level variation, suggesting that the cost of heat waves may be lower for some families and could evolve under selection. Our results suggest that there is genetic potential for adaptation within both thermal environments and that trait evolution may not be strongly affected by trade-offs between them. However, rare differences in thermal reaction norms across families indicate limited evolutionary potential in the responses of snails to changing temperatures during extreme weather events.

Naturally Inspired Firefly Controller For Stabilization Of Double Inverted Pendulum

NASA Astrophysics Data System (ADS)

Srikanth, Kavirayani; Nagesh, Gundavarapu

2015-12-01

A double inverted pendulum plant as an established model that is analyzed as part of this work was tested under the influence of time delay, where the controller was fine tuned using a firefly algorithm taking into considering the fitness function of variation of the cart position and to minimize the cart position displacement and still stabilize it effectively. The naturally inspired algorithm which imitates the fireflies definitely is an energy efficient method owing to the inherent logic of the way the fireflies respond collectively and has shown that critical time delays makes the system healthy.

Cryptic genetic variation: evolution's hidden substrate.

PubMed

Paaby, Annalise B; Rockman, Matthew V

2014-04-01

Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.

To what extent is altitudinal variation of functional traits driven by genetic adaptation in European oak and beech?

PubMed

Bresson, Caroline C; Vitasse, Yann; Kremer, Antoine; Delzon, Sylvain

2011-11-01

The phenotypic responses of functional traits in natural populations are driven by genetic diversity and phenotypic plasticity. These two mechanisms enable trees to cope with rapid climate change. We studied two European temperate tree species (sessile oak and European beech), focusing on (i) in situ variations of leaf functional traits (morphological and physiological) along two altitudinal gradients and (ii) the extent to which these variations were under environmental and/or genetic control using a common garden experiment. For all traits, altitudinal trends tended to be highly consistent between species and transects. For both species, leaf mass per area displayed a positive linear correlation with altitude, whereas leaf size was negatively correlated with altitude. We also observed a significant increase in leaf physiological performance with increasing altitude: populations at high altitudes had higher maximum rates of assimilation, stomatal conductance and leaf nitrogen content than those at low altitudes. In the common garden experiment, genetic differentiation between populations accounted for 0-28% of total phenotypic variation. However, only two traits (leaf mass per area and nitrogen content) exhibited a significant cline. The combination of in situ and common garden experiments used here made it possible to demonstrate, for both species, a weaker effect of genetic variation than of variations in natural conditions, suggesting a strong effect of the environment on leaf functional traits. Finally, we demonstrated that intrapopulation variability was systematically higher than interpopulation variability, whatever the functional trait considered, indicating a high potential capacity to adapt to climate change.

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

PubMed Central

van Zanten, Martijn

2015-01-01

Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables, under the implicit assumption that natural selection imposes correlations between phenotypes, environments and genotypes. In practice, observed trait and environmental data are manifestations of unknown selective forces and are only indirectly associated with adaptive genetic variation. In theory, improved estimation of these forces could enable more powerful detection of loci under selection. Here we present an approach in which we approximate adaptive variation by modeling phenotypes as a function of the environment and using the predicted trait in multivariate and univariate genome-wide association analysis (GWAS). Based on computer simulations and published flowering time data from the model plant Arabidopsis thaliana, we find that environmentally predicted traits lead to higher recovery of functional loci in multivariate GWAS and are more strongly correlated to allele frequencies at adaptive loci than individual environmental variables. Our results provide an example of the use of environmental data to obtain independent and meaningful information on adaptive genetic variation. PMID:26496492

Sesquiterpene lactone stereochemistry influences herbivore resistance and plant fitness in the field

PubMed Central

Ahern, Jeffrey R.; Whitney, Kenneth D.

2014-01-01

Background and Aims Stereochemical variation is widely known to influence the bioactivity of compounds in the context of pharmacology and pesticide science, but our understanding of its importance in mediating plant–herbivore interactions is limited, particularly in field settings. Similarly, sesquiterpene lactones are a broadly distributed class of putative defensive compounds, but little is known about their activities in the field. Methods Natural variation in sesquiterpene lactones of the common cocklebur, Xanthium strumarium (Asteraceae), was used in conjunction with a series of common garden experiments to examine relationships between stereochemical variation, herbivore damage and plant fitness. Key Results The stereochemistry of sesquiterpene lactone ring junctions helped to explain variation in plant herbivore resistance. Plants producing cis-fused sesquiterpene lactones experienced significantly higher damage than plants producing trans-fused sesquiterpene lactones. Experiments manipulating herbivore damage above and below ambient levels found that herbivore damage was negatively correlated with plant fitness. This pattern translated into significant fitness differences between chemotypes under ambient levels of herbivore attack, but not when attack was experimentally reduced via pesticide. Conclusions To our knowledge, this work represents only the second study to examine sesquiterpene lactones as defensive compounds in the field, the first to document herbivore-mediated natural selection on sesquiterpene lactone variation and the first to investigate the ecological significance of the stereochemistry of the lactone ring junction. The results indicate that subtle differences in stereochemistry may be a major determinant of the protective role of secondary metabolites and thus of plant fitness. As stereochemical variation is widespread in many groups of secondary metabolites, these findings suggest the possibility of dynamic evolutionary histories within the Asteraceae and other plant families showing extensive stereochemical variation. PMID:24380844

Sesquiterpene lactone stereochemistry influences herbivore resistance and plant fitness in the field.

PubMed

Ahern, Jeffrey R; Whitney, Kenneth D

2014-03-01

Stereochemical variation is widely known to influence the bioactivity of compounds in the context of pharmacology and pesticide science, but our understanding of its importance in mediating plant-herbivore interactions is limited, particularly in field settings. Similarly, sesquiterpene lactones are a broadly distributed class of putative defensive compounds, but little is known about their activities in the field. Natural variation in sesquiterpene lactones of the common cocklebur, Xanthium strumarium (Asteraceae), was used in conjunction with a series of common garden experiments to examine relationships between stereochemical variation, herbivore damage and plant fitness. The stereochemistry of sesquiterpene lactone ring junctions helped to explain variation in plant herbivore resistance. Plants producing cis-fused sesquiterpene lactones experienced significantly higher damage than plants producing trans-fused sesquiterpene lactones. Experiments manipulating herbivore damage above and below ambient levels found that herbivore damage was negatively correlated with plant fitness. This pattern translated into significant fitness differences between chemotypes under ambient levels of herbivore attack, but not when attack was experimentally reduced via pesticide. To our knowledge, this work represents only the second study to examine sesquiterpene lactones as defensive compounds in the field, the first to document herbivore-mediated natural selection on sesquiterpene lactone variation and the first to investigate the ecological significance of the stereochemistry of the lactone ring junction. The results indicate that subtle differences in stereochemistry may be a major determinant of the protective role of secondary metabolites and thus of plant fitness. As stereochemical variation is widespread in many groups of secondary metabolites, these findings suggest the possibility of dynamic evolutionary histories within the Asteraceae and other plant families showing extensive stereochemical variation.

Colony-level behavioural variation correlates with differences in expression of the foraging gene in red imported fire ants.

PubMed

Bockoven, Alison A; Coates, Craig J; Eubanks, Micky D

2017-11-01

Among social insects, colony-level variation is likely to be widespread and has significant ecological consequences. Very few studies, however, have documented how genetic factors relate to behaviour at the colony level. Differences in expression of the foraging gene have been associated with differences in foraging and activity of a wide variety of organisms. We quantified expression of the red imported fire ant foraging gene (sifor) in workers from 21 colonies collected across the natural range of Texas fire ant populations, but maintained under standardized, environmentally controlled conditions. Colonies varied significantly in their behaviour. The most active colonies had up to 10 times more active foragers than the least active colony and more than 16 times as many workers outside the nest. Expression differences among colonies correlated with this colony-level behavioural variation. Colonies with higher sifor expression in foragers had, on average, significantly higher foraging activity, exploratory activity and recruitment to nectar than colonies with lower expression. Expression of sifor was also strongly correlated with worker task (foraging vs. working in the interior of the nest). These results provide insight into the genetic and physiological processes underlying collective differences in social behaviour. Quantifying variation in expression of the foraging gene may provide an important tool for understanding and predicting the ecological consequences of colony-level behavioural variation. © 2017 John Wiley & Sons Ltd.

Deep Learning for Population Genetic Inference.

PubMed

Sheehan, Sara; Song, Yun S

2016-03-01

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

Deep Learning for Population Genetic Inference

PubMed Central

Sheehan, Sara; Song, Yun S.

2016-01-01

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

Natural time analysis on the ultra-low frequency magnetic field variations prior to the 2016 Kumamoto (Japan) earthquakes

NASA Astrophysics Data System (ADS)

Potirakis, Stelios M.; Schekotov, Alexander; Asano, Tomokazu; Hayakawa, Masashi

2018-04-01

On 15 April 2016 a very strong and shallow earthquake (EQ) (MW = 7.0 , depth ∼ 10 km) occurred in Southwest Japan under the city of Kumamoto, while two very strong foreshocks (MW = 6.2 and MW = 6.0) preceded by about one day. The Kumamoto EQs being very catastrophic, have already attracted much attention among the scientific community in a quest for understanding the generation mechanism, as well as for reporting any preseismic anomalies in various observables and assessing the effectivity of the current early warning systems. In the present article we report precursory behavior of the ground-based observed ultra-low frequency (ULF) magnetic field variations before the Kumamoto EQs. By analyzing specific ULF magnetic field characteristics in terms of the recently introduced natural time (NT) analysis method, we identified that ULF magnetic field variations presented critical features from 2 weeks up to 1 month before the Kumamoto EQs. Specifically, the ULF magnetic field characteristics Fh , Fz , Dh and δDep were analyzed. The first two represent variations of the horizontal and vertical components of the geomagnetic field. The third and fourth characteristics correspond to the depression (decrease) and a relative depression of the horizontal magnetic field variations, respectively. The latter depends on the degree of ionospheric disturbance. All of them were found to reach criticality before the Kumamoto EQs; however, in different time periods for each characteristic.

Ecological and evolutionary consequences of tri-trophic interactions: Spatial variation and effects of plant density.

PubMed

Abdala-Roberts, Luis; Parra-Tabla, Víctor; Moreira, Xoaquín; Ramos-Zapata, José

2017-02-01

The factors driving variation in species interactions are often unknown, and few studies have made a link between changes in interactions and the strength of selection. We report on spatial variation in functional responses by a seed predator (SP) and its parasitic wasps associated with the herb Ruellia nudiflora . We assessed the influence of plant density on consumer responses and determined whether density effects and spatial variation in functional responses altered natural selection by these consumers on the plant. We established common gardens at two sites in Yucatan, Mexico, and planted R. nudiflora at two densities in each garden. We recorded fruit output and SP and parasitoid attack; calculated relative fitness (seed number) under scenarios of three trophic levels (accounting for SP and parasitoid effects), two trophic levels (accounting for SP but not parasitoid effects), and one trophic level (no consumer effects); and compared selection strength on fruit number under these scenarios across sites and densities. There was spatial variation in SP recruitment, whereby the SP functional response was negatively density-dependent at one site but density-independent at the other; parasitoid responses were density-independent and invariant across sites. Site variation in SP attack led, in turn, to differences in SP selection on fruit output, and parasitoids did not alter SP selection. There were no significant effects of density at either site. Our results provide a link between consumer functional responses and consumer selection on plants, which deepens our understanding of geographic variation in the evolutionary outcomes of multitrophic interactions. © 2017 Botanical Society of America.

Variation in Leaf Respiration Rates at Night Correlates with Carbohydrate and Amino Acid Supply1[OPEN

PubMed Central

Lee, Chun Pong; Cheng, Riyan

2017-01-01

Plant respiration can theoretically be fueled by and dependent upon an array of central metabolism components; however, which ones are responsible for the quantitative variation found in respiratory rates is unknown. Here, large-scale screens revealed 2-fold variation in nighttime leaf respiration rate (RN) among mature leaves from an Arabidopsis (Arabidopsis thaliana) natural accession collection grown under common favorable conditions. RN variation was mostly maintained in the absence of genetic variation, which emphasized the low heritability of RN and its plasticity toward relatively small environmental differences within the sampling regime. To pursue metabolic explanations for leaf RN variation, parallel metabolite level profiling and assays of total protein and starch were performed. Within an accession, RN correlated strongly with stored carbon substrates, including starch and dicarboxylic acids, as well as sucrose, major amino acids, shikimate, and salicylic acid. Among different accessions, metabolite-RN correlations were maintained with protein, sucrose, and major amino acids but not stored carbon substrates. A complementary screen of the effect of exogenous metabolites and effectors on leaf RN revealed that (1) RN is stimulated by the uncoupler FCCP and high levels of substrates, demonstrating that both adenylate turnover and substrate supply can limit leaf RN, and (2) inorganic nitrogen did not stimulate RN, consistent with limited nighttime nitrogen assimilation. Simultaneous measurements of RN and protein synthesis revealed that these processes were largely uncorrelated in mature leaves. These results indicate that differences in preceding daytime metabolic activities are the major source of variation in mature leaf RN under favorable controlled conditions. PMID:28615345

Genome-wide scans for loci under selection in humans

PubMed Central

2005-01-01

Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection. PMID:16004726

Revisiting diversity: cultural variation reveals the constructed nature of emotion perception.

PubMed

Gendron, Maria

2017-10-01

The extent of cultural variation in emotion perception has long been assumed to be bounded by underlying universality. A growing body of research reveals, however, that evidence of universality in emotion perception is method-bound. Without the assumption of underlying universality, new lines of inquiry become relevant. Accumulating evidence suggests that cultures vary in what cues are relevant to perceptions of emotion. Further, cultural groups vary in their spontaneous inferences; mental state inference does not appear to be the only, or even most routine, mode of perception across cultures. Finally, setting universality assumptions aside requires innovation in the theory and measurement of culture. Recent studies reveal the promise of refinements in psychological approaches to culture. Together, the available evidence is consistent with a view of emotion perceptions as actively constructed by perceivers to fit the social and physical constraints of their cultural worlds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic variation in aggregation behaviour and interacting phenotypes in Drosophila.

PubMed

Philippe, Anne-Sophie; Jeanson, Raphael; Pasquaretta, Cristian; Rebaudo, Francois; Sueur, Cedric; Mery, Frederic

2016-03-30

Aggregation behaviour is the tendency for animals to group together, which may have important consequences on individual fitness. We used a combination of experimental and simulation approaches to study how genetic variation and social environment interact to influence aggregation dynamics in Drosophila To do this, we used two different natural lines of Drosophila that arise from a polymorphism in the foraging gene (rovers and sitters). We placed groups of flies in a heated arena. Flies could freely move towards one of two small, cooler refuge areas. In groups of the same strain, sitters had a greater tendency to aggregate. The observed behavioural variation was based on only two parameters: the probability of entering a refuge and the likelihood of choosing a refuge based on the number of individuals present. We then directly addressed how different strains interact by mixing rovers and sitters within a group. Aggregation behaviour of each line was strongly affected by the presence of the other strain, without changing the decision rules used by each. Individuals obeying local rules shaped complex group dynamics via a constant feedback loop between the individual and the group. This study could help to identify the circumstances under which particular group compositions may improve individual fitness through underlying aggregation mechanisms under specific environmental conditions. © 2016 The Author(s).

Analysis of river health variation under the background of urbanization based on entropy weight and matter-element model: A case study in Huzhou City in the Yangtze River Delta, China.

PubMed

Pan, Guangbo; Xu, Youpeng; Yu, Zhihui; Song, Song; Zhang, Yuan

2015-05-01

Maintaining the health of the river ecosystem is an essential ecological and environmental guarantee for regional sustainable development and one of the basic objectives in water resource management. With the rapid development of urbanization, the river health situation is deteriorating, especially in urban areas. The river health evaluation is a complex process that involves various natural and social components; eight eco-hydrological indicators were selected to establish an evaluation system, and the variation of river health status under the background of urbanization was explored based on entropy weight and matter-element model. The comprehensive correlative degrees of urban river health of Huzhou City in 2001, 2006 and 2010 were then calculated. The results indicated that river health status of the study area was in the direction of pathological trend, and the impact of limiting factors (such as Shannon's diversity index and agroforestry output growth rate) played an important role in river health. The variation of maximum correlative degree could be classified into stationary status, deterioration status, deterioration-to-improvement status, and improvement-to-deterioration status. There was a severe deterioration situation of river health under the background of urbanization. Copyright © 2015 Elsevier Inc. All rights reserved.

Geographical variation in parasitism shapes larval immune function in a phytophagous insect

NASA Astrophysics Data System (ADS)

Vogelweith, Fanny; Dourneau, Morgane; Thiéry, Denis; Moret, Yannick; Moreau, Jérôme

2013-12-01

Two of the central goals of immunoecology are to understand natural variation in the immune system among populations and to identify those selection pressures that shape immune traits. Maintenance of the immune system can be costly, and both food quality and parasitism selection pressure are factors potentially driving immunocompetence. In tritrophic interactions involving phytophagous insects, host plants, and natural enemies, the immunocompetence of phytophagous insects is constrained by selective forces from both the host plants and the natural enemies. Here, we assessed the roles of host plants and natural enemies as selective pressures on immune variation among natural populations of Lobesia botrana. Our results showed marked geographical variation in immune defenses and parasitism among different natural populations. Larval immune functions were dependent of the host plant quality and were positively correlated to parasitism, suggesting that parasitoids select for greater investment into immunity in moth. Furthermore, investment in immune defense was negatively correlated with body size, suggesting that it is metabolically expensive. The findings emphasize the roles of host plants and parasitoids as selective forces shaping host immune functions in natural conditions. We argue that kinds of study are central to understanding natural variations in immune functions, and the selective forces beyond.

Cell growth and lipid accumulation of a microalgal mutant Scenedesmus sp. Z-4 by combining light/dark cycle with temperature variation.

PubMed

Ma, Chao; Zhang, Yan-Bo; Ho, Shih-Hsin; Xing, De-Feng; Ren, Nan-Qi; Liu, Bing-Feng

2017-01-01

The light/dark cycle is one of the most important factors affecting the microalgal growth and lipid accumulation. Biomass concentration and lipid productivity could be enhanced by optimization of light/dark cycles, and this is considered an effective control strategy for microalgal cultivation. Currently, most research on effects of light/dark cycles on algae is carried out under autotrophic conditions and little information is about the effects under mixotrophic cultivation. At the same time, many studies related to mixotrophic cultivation of microalgal strains, even at large scale, have been performed to obtain satisfactory biomass and lipid production. Therefore, it is necessary to investigate cellular metabolism under autotrophic and mixotrophic conditions at different light/dark cycles. Even though microalgal lipid production under optimal environmental factors has been reported by some researchers, the light/dark cycle and temperature are regarded as separate parameters in their studies. In practical cases, light/dark cycling and temperature variation during the day occur simultaneously. Therefore, studies about the combined effects of light/dark cycles and temperature variation on microalgal lipid production are of practical value, potentially providing significant guidelines for large-scale microalgal cultivation under natural conditions. In this work, cell growth and lipid accumulation of an oleaginous microalgal mutant, Scenedesmus sp. Z-4, were investigated at five light/dark cycles (0 h/24 h, 8 h/16 h, 12 h/12 h, 16 h/8 h, and 24 h/0 h) in batch culture. The results showed that the optimal light/dark cycle was 12 h/12 h, when maximum lipid productivity rates of 56.8 and 182.6 mg L -1  day -1 were obtained under autotrophic and mixotrophic cultivation, respectively. Poor microalgal growth and lipid accumulation appeared in the light/dark cycles of 0 h/24 h and 24 h/0 h under autotrophic condition. Prolonging the light duration was unfavorable to the production of chlorophyll a and b, which was mainly due to photooxidation effect. Polysaccharide was converted into lipid and protein when the light irradiation time increased from 0 to 12 h; however, further increasing irradiation time had a negative effect on lipid accumulation. Due to the dependence of autotrophically cultured cells on light energy, the light/dark cycle has a more remarkable influence on cellular metabolism under autotrophic conditions. Furthermore, the combined effects of temperature variation and light/dark cycle of 12 h/12 h on cell growth and lipid accumulation of microalgal mutant Z-4 were investigated under mixotrophic cultivation, and the results showed that biomass was mainly produced at higher temperatures during the day, and a portion of biomass was converted into lipid under dark condition. The extension of irradiation time was beneficial to biomass accumulation, but not in favor of lipid production. Even though effects of light/dark cycles on autotrophic and mixotrophic cells were not exactly the same, the optimal lipid productivities of Scenedesmus sp. Z-4 under both cultivation conditions were achieved at the light/dark of 12 h/12 h. This may be attributed to its long-term acclimation in natural environment. By combining temperature variation with optimal light/dark cycle of 12 h/12 h, this study will be of great significance for practical microalgae-biodiesel production in the outdoor conditions.

Size variation, growth strategies, and the evolution of modularity in the mammalian skull.

PubMed

Porto, Arthur; Shirai, Leila Teruko; de Oliveira, Felipe Bandoni; Marroig, Gabriel

2013-11-01

Allometry is a major determinant of within-population patterns of association among traits and, therefore, a major component of morphological integration studies. Even so, the influence of size variation over evolutionary change has been largely unappreciated. Here, we explore the interplay between allometric size variation, modularity, and life-history strategies in the skull from representatives of 35 mammalian families. We start by removing size variation from within-species data and analyzing its influence on integration magnitudes, modularity patterns, and responses to selection. We also carry out a simulation in which we artificially alter the influence of size variation in within-taxa matrices. Finally, we explore the relationship between size variation and different growth strategies. We demonstrate that a large portion of the evolution of modularity in the mammalian skull is associated to the evolution of growth strategies. Lineages with highly altricial neonates have adult variation patterns dominated by size variation, leading to high correlations among traits regardless of any underlying modular process and impacting directly their potential to respond to selection. Greater influence of size variation is associated to larger intermodule correlations, less individualized modules, and less flexible responses to natural selection. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Intra-plant Variation in Nectar Sugar Composition in Two Aquilegia Species (Ranunculaceae): Contrasting Patterns under Field and Glasshouse Conditions

PubMed Central

Canto, Azucena; Pérez, Ricardo; Medrano, Mónica; Castellanos, María Clara; Herrera, Carlos M.

2007-01-01

Background and Aims Intra-specific variation in nectar chemistry under natural conditions has been only rarely explored, yet it is an essential aspect of our understanding of how pollinator-mediated selection might act on nectar traits. This paper examines intra-specific variation in nectar sugar composition in field and glasshouse plants of the bumblebee-pollinated perennial herbs Aquilegia vulgaris subsp. vulgaris and Aquilegia pyrenaica subsp. cazorlensis (Ranunculaceae). The aims of the study are to assess the generality of extreme intra-plant variation in nectar sugar composition recently reported for other species in the field, and gaining insight on the possible mechanisms involved. Methods The proportions of glucose, fructose and sucrose in single-nectary nectar samples collected from field and glasshouse plants were determined using high performance liquid chromatography. A hierarchical variance partition was used to dissect total variance into components due to variation among plants, flowers within plants, and nectaries within flowers. Key Results Nectar of the two species was mostly sucrose-dominated, but composition varied widely in the field, ranging from sucrose-only to fructose-dominated. Most intra-specific variance was due to differences among nectaries of the same flower, and flowers of the same plant. The high intra-plant variation in sugar composition exhibited by field plants vanished in the glasshouse, where nectar composition emerged as a remarkably constant feature across plants, flowers and nectaries. Conclusions In addition to corroborating the results of previous studies documenting extreme intra-plant variation in nectar sugar composition in the field, this study suggests that such variation may ultimately be caused by biotic factors operating on the nectar in the field but not in the glasshouse. Pollinator visitation and pollinator-borne yeasts are suggested as likely causal agents. PMID:17259227

Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants.

PubMed

Branham, Sandra E; Wright, Sara J; Reba, Aaron; Morrison, Ginnie D; Linder, C Randal

2016-05-01

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation.

PubMed

Kouvaris, Kostas; Clune, Jeff; Kounios, Loizos; Brede, Markus; Watson, Richard A

2017-04-01

One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments. Such variability is crucial for evolvability, but poorly understood. In particular, how can natural selection favour developmental organisations that facilitate adaptive evolution in previously unseen environments? Such a capacity suggests foresight that is incompatible with the short-sighted concept of natural selection. A potential resolution is provided by the idea that evolution may discover and exploit information not only about the particular phenotypes selected in the past, but their underlying structural regularities: new phenotypes, with the same underlying regularities, but novel particulars, may then be useful in new environments. If true, we still need to understand the conditions in which natural selection will discover such deep regularities rather than exploiting 'quick fixes' (i.e., fixes that provide adaptive phenotypes in the short term, but limit future evolvability). Here we argue that the ability of evolution to discover such regularities is formally analogous to learning principles, familiar in humans and machines, that enable generalisation from past experience. Conversely, natural selection that fails to enhance evolvability is directly analogous to the learning problem of over-fitting and the subsequent failure to generalise. We support the conclusion that evolving systems and learning systems are different instantiations of the same algorithmic principles by showing that existing results from the learning domain can be transferred to the evolution domain. Specifically, we show that conditions that alleviate over-fitting in learning systems successfully predict which biological conditions (e.g., environmental variation, regularity, noise or a pressure for developmental simplicity) enhance evolvability. This equivalence provides access to a well-developed theoretical framework from learning theory that enables a characterisation of the general conditions for the evolution of evolvability.

Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird

PubMed Central

Bonneaud, Camille; Balenger, Susan L.; Russell, Andrew F.; Zhang, Jiangwen; Hill, Geoffrey E.; Edwards, Scott V.

2011-01-01

Wild organisms are under increasing pressure to adapt rapidly to environmental changes. Predicting the impact of these changes on natural populations requires an understanding of the speed with which adaptive phenotypes can arise and spread, as well as of the underlying mechanisms. However, our understanding of these parameters is poor in natural populations. Here we use experimental and molecular approaches to investigate the recent emergence of resistance in eastern populations of North American house finches (Carpodacus mexicanus) to Mycoplasma galliseptum (MG), a severe conjunctivitis-causing bacterium. Two weeks following an experimental infection that took place in 2007, finches from eastern US populations with a 12-y history of exposure to MG harbored 33% lower MG loads in their conjunctivae than finches from western US populations with no prior exposure to MG. Using a cDNA microarray, we show that this phenotypic difference in resistance was associated with differences in splenic gene expression, with finches from the exposed populations up-regulating immune genes postinfection and those from the unexposed populations generally down-regulating them. The expression response of western US birds to experimental infection in 2007 was more similar to that of the eastern US birds studied in 2000, 7 y earlier in the epizootic, than to that of eastern birds in 2007. These results support the hypothesis that resistance has evolved by natural selection in the exposed populations over the 12 y of the epizootic. We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation. PMID:21525409

Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension

PubMed Central

2012-01-01

Background While studying long-lived mutants has advanced our understanding of the processes involved in ageing, the mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. Here, we characterise genome-wide expression patterns of a long-lived, natural variant of Drosophila melanogaster resulting from selection for starvation resistance (SR) and compare it with normal-lived control flies (C). We do this at two time points representing middle age (90% survival) and old age (10% survival) respectively, in three adult diets (malnutrition, optimal food, and overfeeding). Results We found profound differences between Drosophila lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived Drosophila. The stress-related genes, including those involved in proteolysis and cytochrome P450, were generally higher expressed in SR flies and showed a smaller increase in expression with age compared to C flies. The genes involved in reproduction showed a lower expression in middle-aged SR than in C flies and, unlike C flies, a lack of their downregulation with age. Further, we found that malnutrition strongly affected age-associated transcript patterns overriding the differences between the lines. However, under less stressful dietary conditions, line and diet affected age-dependent expression similarly. Finally, we present lists of candidate markers of ageing and lifespan extension. Conclusions Our study unveils transcriptional changes associated with lifespan extension in SR Drosophila. The results suggest that natural genetic variation for SR and lifespan can operate through similar transcriptional mechanisms as those of dietary restriction and life-extending mutations. PMID:22559237

Colony-specific calcification and mortality under ocean acidification in the branching coral Montipora digitata.

PubMed

Kavousi, Javid; Tanaka, Yasuaki; Nishida, Kozue; Suzuki, Atsushi; Nojiri, Yukihiro; Nakamura, Takashi

2016-08-01

Ocean acidification (OA) threatens calcifying marine organisms including reef-building corals. In this study, we examined the OA responses of individual colonies of the branching scleractinian coral Montipora digitata. We exposed nubbins of unique colonies (n = 15) to ambient or elevated pCO2 under natural light and temperature regimes for 110 days. Although elevated pCO2 exposure on average reduced calcification, individual colonies showed unique responses ranging from declines in positive calcification to negative calcification (decalcification) to no change. Similarly, mortality was greater on average in elevated pCO2, but also showed colony-specific patterns. High variation in colony responses suggests the possibility that ongoing OA may lead to natural selection of OA-tolerant colonies within a coral population. Copyright © 2016 Elsevier Ltd. All rights reserved.

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

PubMed Central

Veltsos, P; Gregson, E; Morrissey, B; Slate, J; Hoikkala, A; Butlin, R K; Ritchie, M G

2015-01-01

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power. PMID:26198076

Modeling, Modal Properties, and Mesh Stiffness Variation Instabilities of Planetary Gears

NASA Technical Reports Server (NTRS)

Parker, Robert G.; Lin, Jian; Krantz, Timothy L. (Technical Monitor)

2001-01-01

Planetary gear noise and vibration are primary concerns in their applications in helicopters, automobiles, aircraft engines, heavy machinery and marine vehicles. Dynamic analysis is essential to the noise and vibration reduction. This work analytically investigates some critical issues and advances the understanding of planetary gear dynamics. A lumped-parameter model is built for the dynamic analysis of general planetary gears. The unique properties of the natural frequency spectra and vibration modes are rigorously characterized. These special structures apply for general planetary gears with cyclic symmetry and, in practically important case, systems with diametrically opposed planets. The special vibration properties are useful for subsequent research. Taking advantage of the derived modal properties, the natural frequency and vibration mode sensitivities to design parameters are investigated. The key parameters include mesh stiffnesses, support/bearing stiffnesses, component masses, moments of inertia, and operating speed. The eigen-sensitivities are expressed in simple, closed-form formulae associated with modal strain and kinetic energies. As disorders (e.g., mesh stiffness variation. manufacturing and assembling errors) disturb the cyclic symmetry of planetary gears, their effects on the free vibration properties are quantitatively examined. Well-defined veering rules are derived to identify dramatic changes of natural frequencies and vibration modes under parameter variations. The knowledge of free vibration properties, eigen-sensitivities, and veering rules provide important information to effectively tune the natural frequencies and optimize structural design to minimize noise and vibration. Parametric instabilities excited by mesh stiffness variations are analytically studied for multi-mesh gear systems. The discrepancies of previous studies on parametric instability of two-stage gear chains are clarified using perturbation and numerical methods. The operating conditions causing parametric instabilities are expressed in closed-form suitable for design guidance. Using the well-defined modal properties of planetary gears, the effects of mesh parameters on parametric instability are analytically identified. Simple formulae are obtained to suppress particular instabilities by adjusting contact ratios and mesh phasing.

The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis.

PubMed

Dilkes, Brian P; Spielman, Melissa; Weizbauer, Renate; Watson, Brian; Burkart-Waco, Diana; Scott, Rod J; Comai, Luca

2008-12-09

The molecular mechanisms underlying lethality of F1 hybrids between diverged parents are one target of speciation research. Crosses between diploid and tetraploid individuals of the same genotype can result in F1 lethality, and this dosage-sensitive incompatibility plays a role in polyploid speciation. We have identified variation in F1 lethality in interploidy crosses of Arabidopsis thaliana and determined the genetic architecture of the maternally expressed variation via QTL mapping. A single large-effect QTL, DR. STRANGELOVE 1 (DSL1), was identified as well as two QTL with epistatic relationships to DSL1. DSL1 affects the rate of postzygotic lethality via expression in the maternal sporophyte. Fine mapping placed DSL1 in an interval encoding the maternal effect transcription factor TTG2. Maternal parents carrying loss-of-function mutations in TTG2 suppressed the F1 lethality caused by paternal excess interploidy crosses. The frequency of cellularization in the endosperm was similarly affected by both natural variation and ttg2 loss-of-function mutants. The simple genetic basis of the natural variation and effects of single-gene mutations suggests that F1 lethality in polyploids could evolve rapidly. Furthermore, the role of the sporophytically active TTG2 gene in interploidy crosses indicates that the developmental programming of the mother regulates the viability of interploidy hybrid offspring.

Detectability of landscape effects on recolonization increases with regional population density

PubMed Central

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-01-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level. PMID:26257881

Leaf Photosynthetic Parameters Related to Biomass Accumulation in a Global Rice Diversity Survey1[OPEN

PubMed Central

Zheng, Guangyong; Hamdani, Saber; Essemine, Jemaa; Song, Qingfeng; Wang, Hongru

2017-01-01

Mining natural variations is a major approach to identify new options to improve crop light use efficiency. So far, successes in identifying photosynthetic parameters positively related to crop biomass accumulation through this approach are scarce, possibly due to the earlier emphasis on properties related to leaf instead of canopy photosynthetic efficiency. This study aims to uncover rice (Oryza sativa) natural variations to identify leaf physiological parameters that are highly correlated with biomass accumulation, a surrogate of canopy photosynthesis. To do this, we systematically investigated 14 photosynthetic parameters and four morphological traits in a rice population, which consists of 204 U.S. Department of Agriculture-curated minicore accessions collected globally and 11 elite Chinese rice cultivars in both Beijing and Shanghai. To identify key components responsible for the variance of biomass accumulation, we applied a stepwise feature-selection approach based on linear regression models. Although there are large variations in photosynthetic parameters measured in different environments, we observed that photosynthetic rate under low light (Alow) was highly related to biomass accumulation and also exhibited high genomic inheritability in both environments, suggesting its great potential to be used as a target for future rice breeding programs. Large variations in Alow among modern rice cultivars further suggest the great potential of using this parameter in contemporary rice breeding for the improvement of biomass and, hence, yield potential. PMID:28739819

Detectability of landscape effects on recolonization increases with regional population density.

PubMed

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-07-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level.

Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme

PubMed Central

Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

2015-01-01

Molecular biologists have long recognized carcinogenesis as an evolutionary process that involves natural selection. Cancer is driven by the somatic evolution of cell lineages. In this study, the evolution of somatic cancer cell lineages during carcinogenesis was modeled as an equilibrium point (ie, phenotype of attractor) shifting, the process of a nonlinear stochastic evolutionary biological network. This process is subject to intrinsic random fluctuations because of somatic genetic and epigenetic variations, as well as extrinsic disturbances because of carcinogens and stressors. In order to maintain the normal function (ie, phenotype) of an evolutionary biological network subjected to random intrinsic fluctuations and extrinsic disturbances, a network robustness scheme that incorporates natural selection needs to be developed. This can be accomplished by selecting certain genetic and epigenetic variations to modify the network structure to attenuate intrinsic fluctuations efficiently and to resist extrinsic disturbances in order to maintain the phenotype of the evolutionary biological network at an equilibrium point (attractor). However, during carcinogenesis, the remaining (or neutral) genetic and epigenetic variations accumulate, and the extrinsic disturbances become too large to maintain the normal phenotype at the desired equilibrium point for the nonlinear evolutionary biological network. Thus, the network is shifted to a cancer phenotype at a new equilibrium point that begins a new evolutionary process. In this study, the natural selection scheme of an evolutionary biological network of carcinogenesis was derived from a robust negative feedback scheme based on the nonlinear stochastic Nash game strategy. The evolvability and phenotypic robustness criteria of the evolutionary cancer network were also estimated by solving a Hamilton–Jacobi inequality – constrained optimization problem. The simulation revealed that the phenotypic shift of the lung cancer-associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme. PMID:26244004

Comparative proteomic responses of two bermudagrass (Cynodon dactylon (L). Pers.) varieties contrasting in drought stress resistance.

PubMed

Shi, Haitao; Ye, Tiantian; Chan, Zhulong

2014-09-01

Drought (water-deficit) stress is a serious environmental problem in plant growth and cultivation. As one of widely cultivated warm-season turfgrass, bermudagrass (Cynodon dactylon (L). Pers.) exhibits drastic natural variation in the drought stress resistance in leaves and stems of different varieties. In this study, proteomic analysis was performed to identify drought-responsive proteins in both leaves and stems of two bermudagrass varieties contrasting in drought stress resistance, including drought sensitive variety (Yukon) and drought tolerant variety (Tifgreen). Through comparative proteomic analysis, 39 proteins with significantly changed abundance were identified, including 3 commonly increased and 2 decreased proteins by drought stress in leaves and stems of Yukon and Tifgreen varieties, 2 differentially regulated proteins in leaves and stems of two varieties after drought treatment, 23 proteins increased by drought stress in Yukon variety and constitutively expressed in Tifgreen variety, and other 3 differentially expressed proteins under control and drought stress conditions. Among them, proteins involved in photosynthesis (PS), glycolysis, N-metabolism, tricarboxylicacid (TCA) and redox pathways were largely enriched, which might be contributed to the natural variation of drought resistance between Yukon and Tifgreen varieties. These studies provide new insights to understand the molecular mechanism underlying bermudagrass response to drought stress. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

PubMed

Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

2016-01-01

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

PubMed Central

Kesari, Ravi; Lasky, Jesse R.; Villamor, Joji Grace; Des Marais, David L.; Chen, Ying-Jiun C.; Liu, Tzu-Wen; Juenger, Thomas E.; Verslues, Paul E.

2012-01-01

Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the Arabidopsis accession Shakdara (Sha) was threefold less than that of Landsberg erecta (Ler) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme Δ1-pyrroline-5-carboxylate synthetase1 (P5CS1) as a basis for the lower proline of Sha. Sha P5CS1 had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip P5CS1). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip P5CS1 splice variant constituted as much as half of the total P5CS1 transcript. In a larger panel of Arabidopsis accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip P5CS1 among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that P5CS1 may have evolved under positive selection, and more extensive correlation of exon 3-skip P5CS1 production than proline abundance with climate conditions of natural accessions also suggest a role of P5CS1 in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip P5CS1 in natural variation of proline metabolism, and suggest an association of P5CS1 and its alternative splicing with environmental adaptation. PMID:22615385

Natural Selection on Individual Variation in Tolerance of Gastrointestinal Nematode Infection

PubMed Central

Hayward, Adam D.; Nussey, Daniel H.; Wilson, Alastair J.; Berenos, Camillo; Pilkington, Jill G.; Watt, Kathryn A.; Pemberton, Josephine M.; Graham, Andrea L.

2014-01-01

Hosts may mitigate the impact of parasites by two broad strategies: resistance, which limits parasite burden, and tolerance, which limits the fitness or health cost of increasing parasite burden. The degree and causes of variation in both resistance and tolerance are expected to influence host–parasite evolutionary and epidemiological dynamics and inform disease management, yet very little empirical work has addressed tolerance in wild vertebrates. Here, we applied random regression models to longitudinal data from an unmanaged population of Soay sheep to estimate individual tolerance, defined as the rate of decline in body weight with increasing burden of highly prevalent gastrointestinal nematode parasites. On average, individuals lost weight as parasite burden increased, but whereas some lost weight slowly as burden increased (exhibiting high tolerance), other individuals lost weight significantly more rapidly (exhibiting low tolerance). We then investigated associations between tolerance and fitness using selection gradients that accounted for selection on correlated traits, including body weight. We found evidence for positive phenotypic selection on tolerance: on average, individuals who lost weight more slowly with increasing parasite burden had higher lifetime breeding success. This variation did not have an additive genetic basis. These results reveal that selection on tolerance operates under natural conditions. They also support theoretical predictions for the erosion of additive genetic variance of traits under strong directional selection and fixation of genes conferring tolerance. Our findings provide the first evidence of selection on individual tolerance of infection in animals and suggest practical applications in animal and human disease management in the face of highly prevalent parasites. PMID:25072883

Epigenetic Differentiation of Natural Populations of Lilium bosniacum Associated with Contrasting Habitat Conditions.

PubMed

Zoldoš, Vlatka; Biruš, Ivan; Muratovic, Edina; Šatovic, Zlatko; Vojta, Aleksandar; Robin, Odile; Pustahija, Fatima; Bogunic, Faruk; Vicic Bockor, Vedrana; Siljak-Yakovlev, Sonja

2018-01-01

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Among-species differences in pollen quality and quantity limitation: implications for endemics in biodiverse hotspots.

PubMed

Alonso, Conchita; Navarro-Fernández, Carmen M; Arceo-Gómez, Gerardo; Meindl, George A; Parra-Tabla, Víctor; Ashman, Tia-Lynn

2013-11-01

Insufficient pollination is a function of quantity and quality of pollen receipt, and the relative contribution of each to pollen limitation may vary with intrinsic plant traits and extrinsic ecological properties. Community-level studies are essential to evaluate variation across species in quality limitation under common ecological conditions. This study examined whether endemic species are more limited by pollen quantity or quality than non-endemic co-flowering species in three endemic-rich plant communities located in biodiversity hotspots of different continents (Andalusia, California and Yucatan). Natural variations in pollen receipt and pollen tube formation were analysed for 20 insect-pollinated plants. Endemic and non-endemic species that co-flowered were paired in order to estimate and compare the quantity and quality components of pre-zygotic pollination success, obtained through piecewise regression analysis of the relationship between pollen grains and pollen tubes of naturally pollinated wilted flowers. Pollen tubes did not frequently exceed the number of ovules per flower. Only the combination of abundant and good quality pollen and a low number of ovules per flower conferred relief from pre-zygotic pollen limitation in the three stochastic pollination environments studied. Quality of pollen receipt was found to be as variable as quantity among study species. The relative pollination success of endemic and non-endemic species, and its quantity and quality components, was community dependent. Assessing both quality and quantity of pollen receipt is key to determining the ovule fertilization potential of both endemic and widespread plants in biodiverse hotspot regions. Large natural variation among flowers of the same species in the two components and pollen tube formation deserves further analysis in order to estimate the environmental, phenotypic and intraindividual sources of variation that may affect how plants evolve to overcome this limitation in different communities worldwide.

Bold colors in a cryptic lineage: do Eastern Indigo Snakes exhibit color dimorphism?

PubMed

Deitloff, Jennifer; Johnson, Valerie M; Guyer, Craig

2013-01-01

Many species exhibit variation in the color of their scales, feathers, or fur. Various forms of natural selection, such as mimicry, crypsis, and species recognition, as well as sexual selection, can influence the evolution of color. Eastern Indigo Snakes (Drymarchon couperi), a federally threatened species, have coloration on the sides of the head and the chin that can vary from black to red or cream. Despite significant conservations efforts for this species, little is known about its biology in the field. Past researchers have proposed that the color variation on the head and chin is associated with the sex of the individual. Alternatively, color might vary among individuals because it is controlled by genes that are under natural selection or neutral evolution. We tested these alternative hypotheses by examining whether coloration of the sublabial, submaxillary, and ventral scales of this species differed by sex or among clutches. We used color spectrometry to characterize important aspects of color in two ways: by examining overall color differences across the entire color spectrum and by comparing differences within the ultraviolet, yellow, and red colorbands. We found that Eastern Indigo Snakes do not exhibit sexual dichromatism, but their coloration does vary among clutches; therefore, the pattern of sexual selection leading to sexual dichromatism observed in many squamates does not appear to play a role in the evolution and maintenance of color variation in Eastern Indigo Snakes. We suggest that future studies should focus on determining whether color variation in these snakes is determined by maternal effects or genetic components and if color is influenced by natural selection or neutral evolutionary processes. Studying species that exhibit bright colors within lineages that are not known for such coloration will contribute greatly to our understanding of the evolutionary and ecological factors that drive these differences.

Bioavailability of fluoride in drinking water: a human experimental study.

PubMed

Maguire, A; Zohouri, F V; Mathers, J C; Steen, I N; Hindmarch, P N; Moynihan, P J

2005-11-01

It has been suggested that systemic fluoride absorption from drinking water may be influenced by the type of fluoride compound in the water and by water hardness. Using a human double-blind cross-over trial, we conducted this study to measure c(max), T(max), and Area Under the Curve (AUC) for plasma F concentration against time, following the ingestion of naturally fluoridated hard and soft waters, artificially fluoridated hard and soft waters, and a reference water. Mean AUC over 0 to 8 hours was 1330, 1440, 1679, 1566, and 1328 ng F.min.mL(-1) for naturally fluoridated soft, naturally fluoridated hard, artificially fluoridated soft, artificially fluoridated hard, and reference waters, respectively, with no statistically significant differences among waters for AUC, c(max), or T(max). Any differences in fluoride bioavailability between drinking waters in which fluoride is present naturally or added artificially, or the waters are hard or soft, were small compared with large within- and between-subject variations in F absorption. Abbreviations used: F, fluoride; AUC, Area under the Curve for plasma F concentration against time; AUC(0-3), Area under the Curve for plasma F concentration against time for 0 to 3 hours following water ingestion; AUC(0-8), Area under the Curve for plasma F concentration against time for 0 to 8 hours following water ingestion; c(max), maximum plasma F concentration corrected for baseline plasma F and dose (i.e., F concentration of individual waters); T(max), time of c(max).

Variation in floral morphology and plant reproductive success in four Ipomoea species (Convolvulaceae) with contrasting breeding systems.

PubMed

Delgado-Dávila, R; Martén-Rodríguez, S; Huerta-Ramos, G

2016-11-01

This study tested the hypothesis that self-compatibility would be associated with floral traits that facilitate autonomous self-pollination to ensure reproduction under low pollinator visitation. In a comparison of two pairs of Ipomoea species with contrasting breeding systems, we predicted that self-compatible (SC) species would have smaller, less variable flowers, reduced herkogamy, lower pollinator visitation and higher reproductive success than their self-incompatible (SI) congeners. We studied sympatric species pairs, I. hederacea (SC)- I. mitchellae (SI) and I. purpurea (SC)-I. indica (SI), in Mexico, over two years. We quantified variation in floral traits and nectar production, documented pollinator visitation, and determined natural fruit and seed set. Hand-pollination and bagging experiments were conducted to determine potential for autonomous self-pollination and apomixis. Self-compatible Ipomoea species had smaller flowers and lower nectar production than SI species; however, floral variation and integration did not vary according to breeding system. Bees were primary pollinators of all species, but visitation rates were seven times lower in SC than SI species. SC species had a high capacity for autonomous self-pollination due to reduced herkogamy at the highest anther levels. Self-compatible species had two to six times higher fruit set than SI species. Results generally support the hypothesis that self-compatibility and autonomous self-pollination ensure reproduction under low pollinator visitation. However, high variation in morphological traits of SC Ipomoea species suggests they maintain variation through outcrossing. Furthermore, reduced herkogamy was associated with high potential for autonomous self-pollination, providing a reproductive advantage that possibly underlies transitions to self-compatibility in Ipomoea. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

Uncovering Spatial Variation in Acoustic Environments Using Sound Mapping.

PubMed

Job, Jacob R; Myers, Kyle; Naghshineh, Koorosh; Gill, Sharon A

2016-01-01

Animals select and use habitats based on environmental features relevant to their ecology and behavior. For animals that use acoustic communication, the sound environment itself may be a critical feature, yet acoustic characteristics are not commonly measured when describing habitats and as a result, how habitats vary acoustically over space and time is poorly known. Such considerations are timely, given worldwide increases in anthropogenic noise combined with rapidly accumulating evidence that noise hampers the ability of animals to detect and interpret natural sounds. Here, we used microphone arrays to record the sound environment in three terrestrial habitats (forest, prairie, and urban) under ambient conditions and during experimental noise introductions. We mapped sound pressure levels (SPLs) over spatial scales relevant to diverse taxa to explore spatial variation in acoustic habitats and to evaluate the number of microphones needed within arrays to capture this variation under both ambient and noisy conditions. Even at small spatial scales and over relatively short time spans, SPLs varied considerably, especially in forest and urban habitats, suggesting that quantifying and mapping acoustic features could improve habitat descriptions. Subset maps based on input from 4, 8, 12 and 16 microphones differed slightly (< 2 dBA/pixel) from those based on full arrays of 24 microphones under ambient conditions across habitats. Map differences were more pronounced with noise introductions, particularly in forests; maps made from only 4-microphones differed more (> 4 dBA/pixel) from full maps than the remaining subset maps, but maps with input from eight microphones resulted in smaller differences. Thus, acoustic environments varied over small spatial scales and variation could be mapped with input from 4-8 microphones. Mapping sound in different environments will improve understanding of acoustic environments and allow us to explore the influence of spatial variation in sound on animal ecology and behavior.

Curvature-induced stiffness and the spatial variation of wavelength in wrinkled sheets

PubMed Central

Hohlfeld, Evan; King, Hunter; Huang, Jiangshui; Qiu, Zhanlong; Russell, Thomas P.; Menon, Narayanan; Vella, Dominic; Davidovitch, Benny

2016-01-01

Wrinkle patterns in compressed thin sheets are ubiquitous in nature and technology, from the furrows on our foreheads to crinkly plant leaves, from ripples on plastic-wrapped objects to the protein film on milk. The current understanding of an elementary descriptor of wrinkles—their wavelength—is restricted to deformations that are parallel, spatially uniform, and nearly planar. However, most naturally occurring wrinkles do not satisfy these stipulations. Here we present a scheme that quantitatively explains the wrinkle wavelength beyond such idealized situations. We propose a local law that incorporates both mechanical and geometrical effects on the spatial variation of wrinkle wavelength. Our experiments on thin polymer films provide strong evidence for its validity. Understanding how wavelength depends on the properties of the sheet and the underlying liquid or elastic subphase is crucial for applications where wrinkles are used to sculpt surface topography, to measure properties of the sheet, or to infer forces applied to a film. PMID:26787902

Effects of Convective Transport on the Budget of Amazonian Aerosol under Background Conditions

NASA Astrophysics Data System (ADS)

Wang, J.; Krejci, R.; Giangrande, S. E.; Kuang, C.; Barbosa, H. M.; Brito, J.; Carbone, S.; Chi, X.; Comstock, J. M.; Ditas, F.; Lavric, J. V.; Manninen, H. E.; Mei, F.; Moran, D.; Pöhlker, C.; Pöhlker, M. L.; Saturno, J.; Schmid, B.; Souza, R. A. F. D.; Springston, S. R.; Tomlinson, J. M.; Toto, T.; Walter, D.; Wimmer, D.; Smith, J. N.; Machado, L.; Artaxo, P.; Andreae, M. O.; Martin, S. T.

2016-12-01

Aerosol particles can strongly influence the radiative properties of clouds, and they represent one of the largest uncertainties in computer simulations of climate change. The large uncertainty is in large part due to a poor understanding of processes under natural conditions, which serves as the baseline to measure change against. Understanding the processes under natural conditions is critical for a reliable assessment and quantification of ongoing and future climate change. The Amazon rainforest is one of the few continental regions where aerosol particles and their precursors can be studied under near-natural conditions. Here we examine the aerosol number and CCN budget under background conditions in the Amazon basin using data collected during the Observations and Modeling of the Green Ocean Amazon (GoAmazon 2014/5) campaign, which took place from January 2014 to December 2015 near Manaus, Brazil. The aerosol size spectrum was observed at the Amazon Tall Tower Observatory (ATTO), 150 km upwind of Manaus, and its variation with convection and precipitation during the wet season is presented. Air masses arriving at the ATTO during the wet season are typically brought by the northeasterly trade winds and travel across at least 1000 km of undeveloped tropical rainforest, therefore are generally clean. Also shown are vertical profiles of aerosol observed onboard the DOE Gulfstream-1 research aircraft. The impact of convective transport on the budget of boundary layer aerosol and CCN under the background conditions is discussed.

Fractal model of polarization switching kinetics in ferroelectrics under nonequilibrium conditions of electron irradiation

NASA Astrophysics Data System (ADS)

Maslovskaya, A. G.; Barabash, T. K.

2018-03-01

The paper presents the results of the fractal and multifractal analysis of polarization switching current in ferroelectrics under electron irradiation, which allows statistical memory effects to be estimated at dynamics of domain structure. The mathematical model of formation of electron beam-induced polarization current in ferroelectrics was suggested taking into account the fractal nature of domain structure dynamics. In order to realize the model the computational scheme was constructed using the numerical solution approximation of fractional differential equation. Evidences of electron beam-induced polarization switching process in ferroelectrics were specified at a variation of control model parameters.

Synchronization and Cardio-pulmonary feedback in Sleep Apnea

NASA Astrophysics Data System (ADS)

Xu, Limei; Ivanov, Plamen Ch.; Chen, Zhi; Hu, Kun; Paydarfar, David; Stanley, H. Eugene

2004-03-01

Findings indicate a dynamical coupling between respiratory and cardiac function. However, the nature of this nonlinear interaction remains not well understood. We investigate transient patterns in the cardio-pulmonary interaction under healthy conditions by means of cross-correlation and nonlinear synchronization techniques, and we compare how these patterns change under pathologic conditions such as obstructive sleep apnea --- a periodic cessation of breathing during sleep. We find that during apnea episodes the nonlinear features of cardio-pulmonary interaction change intermittently, and can exhibit variations characterized by different time delays in the phase synchronization between breathing and heartbeat dynamics.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Timelapse ultrasonic tomography for measuring damage localization in geomechanics laboratory tests.

PubMed

Tudisco, Erika; Roux, Philippe; Hall, Stephen A; Viggiani, Giulia M B; Viggiani, Gioacchino

2015-03-01

Variation of mechanical properties in materials can be detected non-destructively using ultrasonic measurements. In particular, changes in elastic wave velocity can occur due to damage, i.e., micro-cracking and particles debonding. Here the challenge of characterizing damage in geomaterials, i.e., rocks and soils, is addressed. Geomaterials are naturally heterogeneous media in which the deformation can localize, so that few measurements of acoustic velocity across the sample are not sufficient to capture the heterogeneities. Therefore, an ultrasonic tomography procedure has been implemented to map the spatial and temporal variations in propagation velocity, which provides information on the damage process. Moreover, double beamforming has been successfully applied to identify and isolate multiple arrivals that are caused by strong heterogeneities (natural or induced by the deformation process). The applicability of the developed experimental technique to laboratory geomechanics testing is illustrated using data acquired on a sample of natural rock before and after being deformed under triaxial compression. The approach is then validated and extended to time-lapse monitoring using data acquired during plane strain compression of a sample including a well defined layer with different mechanical properties than the matrix.

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

CaAP2 transcription factor is a candidate gene for a flowering repressor and a candidate for controlling natural variation of flowering time in Capsicum annuum.

PubMed

Borovsky, Yelena; Sharma, Vinod K; Verbakel, Henk; Paran, Ilan

2015-06-01

The APETALA2 transcription factor homolog CaAP2 is a candidate gene for a flowering repressor in pepper, as revealed by induced-mutation phenotype, and a candidate underlying a major QTL controlling natural variation in flowering time. To decipher the genetic control of transition to flowering in pepper (Capsicum spp.) and determine the extent of gene function conservation compared to model species, we isolated and characterized several ethyl methanesulfonate (EMS)-induced mutants that vary in their flowering time compared to the wild type. In the present study, we report on the isolation of an early-flowering mutant that flowers after four leaves on the primary stem compared to nine leaves in the wild-type 'Maor'. By genetic mapping and sequencing of putative candidate genes linked to the mutant phenotype, we identified a member of the APETALA2 (AP2) transcription factor family, CaAP2, which was disrupted in the early-flowering mutant. CaAP2 is a likely ortholog of AP2 that functions as a repressor of flowering in Arabidopsis. To test whether CaAP2 has an effect on controlling natural variation in the transition to flowering in pepper, we performed QTL mapping for flowering time in a cross between early and late-flowering C. annuum accessions. We identified a major QTL in a region of chromosome 2 in which CaAP2 was the most significant marker, explaining 52 % of the phenotypic variation of the trait. Sequence comparison of the CaAP2 open reading frames in the two parents used for QTL mapping did not reveal significant variation. In contrast, significant differences in expression level of CaAP2 were detected between near-isogenic lines that differ for the flowering time QTL, supporting the putative function of CaAP2 as a major repressor of flowering in pepper.

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

PubMed Central

Phung, Tanya N.; Lohmueller, Kirk E.

2016-01-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation. PMID:27508305

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

PubMed

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only if more of the genome is under purifying selection than currently believed. Our work has implications for understanding the evolution of genomes and interpreting patterns of genetic variation.

Carbon and energy fluxes from China's largest freshwater lake

NASA Astrophysics Data System (ADS)

Gan, G.; LIU, Y.

2017-12-01

Carbon and energy fluxes between lakes and the atmosphere are important aspects of hydrology, limnology, and ecology studies. China's largest freshwater lake, the Poyang lake experiences tremendous water-land transitions periodically throughout the year, which provides natural experimental settings for the study of carbon and energy fluxes. In this study, we use the eddy covariance technique to explore the seasonal and diurnal variation patterns of sensible and latent heat fluxes of Poyang lake during its high-water and low-water periods, when the lake is covered by water and mudflat, respectively. We also determine the annual NEE of Poyang lake and the variations of NEE's components: Gross Primary Productivity (GPP) and Ecosystem Respiration (Re). Controlling factors of seasonal and diurnal variations of carbon and energy fluxes are analyzed, and land cover impacts on the variation patterns are also studied. Finally, the coupling between the carbon and energy fluxes are analyzed under different atmospheric, boundary stability and land cover conditions.

Heterochrony underpins natural variation in Cardamine hirsuta leaf form

PubMed Central

Cartolano, Maria; Pieper, Bjorn; Lempe, Janne; Tattersall, Alex; Huijser, Peter; Tresch, Achim; Darrah, Peter R.; Hay, Angela; Tsiantis, Miltos

2015-01-01

A key problem in biology is whether the same processes underlie morphological variation between and within species. Here, by using plant leaves as an example, we show that the causes of diversity at these two evolutionary scales can be divergent. Some species like the model plant Arabidopsis thaliana have simple leaves, whereas others like the A. thaliana relative Cardamine hirsuta bear complex leaves comprising leaflets. Previous work has shown that these interspecific differences result mostly from variation in local tissue growth and patterning. Now, by cloning and characterizing a quantitative trait locus (QTL) for C. hirsuta leaf shape, we find that a different process, age-dependent progression of leaf form, underlies variation in this trait within species. This QTL effect is caused by cis-regulatory variation in the floral repressor ChFLC, such that genotypes with low-expressing ChFLC alleles show both early flowering and accelerated age-dependent changes in leaf form, including faster leaflet production. We provide evidence that this mechanism coordinates leaf development with reproductive timing and may help to optimize resource allocation to the next generation. PMID:26243877

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

PubMed

Herrera, C M; Bazaga, P

2011-04-01

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions. © 2011 Blackwell Publishing Ltd.

Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness.

PubMed

Kerwin, Rachel; Feusier, Julie; Corwin, Jason; Rubin, Matthew; Lin, Catherine; Muok, Alise; Larson, Brandon; Li, Baohua; Joseph, Bindu; Francisco, Marta; Copeland, Daniel; Weinig, Cynthia; Kliebenstein, Daniel J

2015-04-13

Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana.

Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

PubMed Central

Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

2016-01-01

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact epistatically with mutant alleles. PMID:27459710

First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction

NASA Astrophysics Data System (ADS)

Zhao, Xiu-Qin; Liu, Ni; Liang, Jiu-Qing

2017-05-01

In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. Supported by the National Natural Science Foundation of China under Grant Nos. 11275118, 11404198, 91430109, 61505100, 51502189, and the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi Province (STIP) under Grant No. 2014102, and the Launch of the Scientific Research of Shanxi University under Grant No. 011151801004, and the National Fundamental Fund of Personnel Training under Grant No. J1103210. The Natural Science Foundation of Shanxi Province under Grant No. 2015011008

On the Overdispersed Molecular Clock

PubMed Central

Takahata, Naoyuki

1987-01-01

Rates of molecular evolution at some loci are more irregular than described by simple Poisson processes. Three situations under which molecular evolution would not follow simple Poisson processes are reevaluated from the viewpoint of the neutrality hypothesis: (i) concomitant or multiple substitutions in a gene, (ii) fluctuating substitution rates in time caused by coupled effects of deleterious mutations and bottlenecks, and (iii) changes in the degree of selective constraints against a gene (neutral space) caused by successive substitutions. The common underlying assumption that these causes are lineage nonspecific excludes the case where mutation rates themselves change systematically among lineages or taxonomic groups, and severely limits the extent of variation in the number of substitutions among lineages. Even under this stringent condition, however, the third hypothesis, the fluctuating neutral space model, can generate fairly large variation. This is described by a time-dependent renewal process, which does not exhibit any episodic nature of molecular evolution. It is argued that the observed elevated variances in the number of nucleotide or amino acid substitutions do not immediately call for positive Darwinian selection in molecular evolution. PMID:3596230

Inner Core Tomography Under Africa

NASA Astrophysics Data System (ADS)

Irving, J. C. E.

2014-12-01

Hemispherical structure in the inner core has been observed using both normal mode and body wave data, but the more regional scale properties of the inner core are still the subject of ongoing debate. The nature of the vertical boundary regions between the eastern and western hemispheres will be an important constraint on dynamical processes at work in the inner core. With limited data available, earlier inner core studies defined each boundary using one line of longitude, but this may not be a sufficient description for what could be one of the inner core's most heterogeneous regions. Here, I present a large, hand-picked dataset of PKPbc-PKPdf differential travel times which sample the inner core under Africa, where the proposed position of one hemisphere boundary is located. The dataset contains polar, intermediate and equatorial rays through the inner core, and the presence of crossing raypaths makes regional-scale tomography of the inner core feasible. I invert the data to find regional variations in inner core anisotropy under different parts of Africa, and present both anisotropy and voigt isotropic velocity variations of this important portion of the inner core.

Body Morphology, Energy Stores, and Muscle Enzyme Activity Explain Cricket Acoustic Mate Attraction Signaling Variation

PubMed Central

Thomson, Ian R.; Darveau, Charles-A.; Bertram, Susan M.

2014-01-01

High mating success in animals is often dependent on males signalling attractively with high effort. Since males should be selected to maximize their reproductive success, female preferences for these traits should result in minimal signal variation persisting in the population. However, extensive signal variation persists. The genic capture hypothesis proposes genetic variation persists because fitness-conferring traits depend on an individual's basic processes, including underlying physiological, morphological, and biochemical traits, which are themselves genetically variable. To explore the traits underlying signal variation, we quantified among-male differences in signalling, morphology, energy stores, and the activities of key enzymes associated with signalling muscle metabolism in two species of crickets, Gryllus assimilis (chirper: <20 pulses/chirp) and G. texensis (triller: >20 pulses/chirp). Chirping G. assimilis primarily fuelled signalling with carbohydrate metabolism: smaller individuals and individuals with increased thoracic glycogen stores signalled for mates with greater effort; individuals with greater glycogen phosphorylase activity produced more attractive mating signals. Conversely, the more energetic trilling G. texensis fuelled signalling with both lipid and carbohydrate metabolism: individuals with increased β-hydroxyacyl-CoA dehydrogenase activity and increased thoracic free carbohydrate content signalled for mates with greater effort; individuals with higher thoracic and abdominal carbohydrate content and higher abdominal lipid stores produced more attractive signals. Our findings suggest variation in male reproductive success may be driven by hidden physiological trade-offs that affect the ability to uptake, retain, and use essential nutrients, although the results remain correlational in nature. Our findings indicate that a physiological perspective may help us to understand some of the causes of variation in behaviour. PMID:24608102

Natural Variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gordon, Sean

2013-03-01

Sean Gordon of the USDA on Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network

PubMed Central

Kozlov, Konstantin N.; Kulakovskiy, Ivan V.; Zubair, Asif; Marjoram, Paul; Lawrie, David S.; Nuzhdin, Sergey V.; Samsonova, Maria G.

2017-01-01

Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression. The analysis reveals that the sequence variants increase (decrease) gene expression if located within binding sites of repressors (activators). We show that the sign of SNP influence (activation or repression) may change in time and space and elucidate the origin of this change in specific examples. The thermodynamic modeling approach predicts non-local and non-linear effects arising from SNPs, and combinations of SNPs, in individual fly genotypes. Simulation of individual fly genotypes using our model reveals that this non-linearity reduces to almost additive inputs from multiple SNPs. Further, we see signatures of the action of purifying selection in the gap gene regulatory regions. To infer the specific targets of purifying selection, we analyze the patterns of polymorphism in the data at two phenotypic levels: the strengths of binding and expression. We find that combinations of SNPs show evidence of being under selective pressure, while individual SNPs do not. The model predicts that SNPs appear to accumulate in the genotypes of the natural population in a way biased towards small increases in activating action on the expression pattern. Taken together, these results provide a systems-level view of how genetic variation translates to the level of gene regulatory networks via combinatorial SNP effects. PMID:28898266

Electrical and Electrorheological Properties of Alumina/Natural Rubber (STR XL) Composites

PubMed Central

Tangboriboon, Nuchnapa; Uttanawanit, Nuttapot; Longtong, Mean; Wongpinthong, Piraya; Sirivat, Anuvat; Kunanuruksapong, Ruksapong

2010-01-01

The electrorheological properties (ER) of natural rubber (XL)/alumina (Al2O3) composites were investigated in oscillatory shear mode under DC electrical field strengths between 0 to 2 kV/mm. SEM micrographs indicate a mean particle size of 9.873 ± 0.034 µm and particles that are moderately dispersed in the matrix. The XRD patterns indicate Al2O3 is of the β-phase polytype which possesses high ionic conductivity. The storage modulus (G′) of the composites, or the rigidity, increases by nearly two orders of magnitude, with variations in particle volume fraction and electrical field strength. The increase in the storage modulus is caused the ionic polarization of the alumina particles and the induced dipole moments set up in the natural rubber matrix.

Collisionless Dynamics and the Cosmic Web

NASA Astrophysics Data System (ADS)

Hahn, Oliver

2016-10-01

I review the nature of three-dimensional collapse in the Zeldovich approximation, how it relates to the underlying nature of the three-dimensional Lagrangian manifold and naturally gives rise to a hierarchical structure formation scenario that progresses through collapse from voids to pancakes, filaments and then halos. I then discuss how variations of the Zeldovich approximation (based on the gravitational or the velocity potential) have been used to define classifications of the cosmic large-scale structure into dynamically distinct parts. Finally, I turn to recent efforts to devise new approaches relying on tessellations of the Lagrangian manifold to follow the fine-grained dynamics of the dark matter fluid into the highly non-linear regime and both extract the maximum amount of information from existing simulations as well as devise new simulation techniques for cold collisionless dynamics.

The genomic basis of adaptive evolution in threespine sticklebacks

PubMed Central

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Lander, Eric S; Di Palma, Federica

2012-01-01

Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature. PMID:22481358

Single Crystals Grown Under Unconstrained Conditions

NASA Astrophysics Data System (ADS)

Sunagawa, Ichiro

Based on detailed investigations on morphology (evolution and variation in external forms), surface microtopography of crystal faces (spirals and etch figures), internal morphology (growth sectors, growth banding and associated impurity partitioning) and perfection (dislocations and other lattice defects) in single crystals, we can deduce how and by what mechanism the crystal grew and experienced fluctuation in growth parameters through its growth and post-growth history under unconstrained condition. The information is useful not only in finding appropriate way to growing highly perfect and homogeneous single crystals, but also in deciphering letters sent from the depth of the Earth and the Space. It is also useful in discriminating synthetic from natural gemstones. In this chapter, available methods to obtain molecular information are briefly summarized, and actual examples to demonstrate the importance of this type of investigations are selected from both natural minerals (diamond, quartz, hematite, corundum, beryl, phlogopite) and synthetic crystals (SiC, diamond, corundum, beryl).

The genomic basis of adaptive evolution in threespine sticklebacks.

PubMed

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Baldwin, Jen; Bloom, Toby; Jaffe, David B; Nicol, Robert; Wilkinson, Jane; Lander, Eric S; Di Palma, Federica; Lindblad-Toh, Kerstin; Kingsley, David M

2012-04-04

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

Effects of ambient and preceding temperatures and metabolic genes on flight metabolism in the Glanville fritillary butterfly.

PubMed

Wong, Swee Chong; Oksanen, Alma; Mattila, Anniina L K; Lehtonen, Rainer; Niitepõld, Kristjan; Hanski, Ilkka

2016-02-01

Flight is essential for foraging, mate searching and dispersal in many insects, but flight metabolism in ectotherms is strongly constrained by temperature. Thermal conditions vary greatly in natural populations and may hence restrict fitness-related activities. Working on the Glanville fritillary butterfly (Melitaea cinxia), we studied the effects of temperature experienced during the first 2 days of adult life on flight metabolism, genetic associations between flight metabolic rate and variation in candidate metabolic genes, and genotype-temperature interactions. The maximal flight performance was reduced by 17% by 2 days of low ambient temperature (15 °C) prior to the flight trial, mimicking conditions that butterflies commonly encounter in nature. A SNP in phosphoglucose isomerase (Pgi) had a significant association on flight metabolic rate in males and a SNP in triosephosphate isomerase (Tpi) was significantly associated with flight metabolic rate in females. In the Pgi SNP, AC heterozygotes had higher flight metabolic rate than AA homozygotes following low preceding temperature, but the trend was reversed following high preceding temperature, consistent with previous results on genotype-temperature interaction for this SNP. We suggest that these results on 2-day old butterflies reflect thermal effect on the maturation of flight muscles. These results highlight the consequences of variation in thermal conditions on the time scale of days, and they contribute to a better understanding of the complex dynamics of flight metabolism and flight-related activities under conditions that are relevant for natural populations living under variable thermal conditions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Europium anomaly in plagioclase feldspar - Experimental results and semiquantitative model.

NASA Technical Reports Server (NTRS)

Weill, D. F.; Drake, M. J.

1973-01-01

The partition of europium between plagioclase feldspar and magmatic liquid is considered in terms of the distribution coefficients for divalent and trivalent europium. A model equation is derived giving the europium anomaly in plagioclase as a function of temperature and oxygen fugacity. The model explains europium anomalies in plagioclase synthesized under controlled laboratory conditions as well as the variations of the anomaly observed in natural terrestrial and extraterrestrial igneous rocks.

Europium anomaly in plagioclase feldspar: experimental results and semiquantitative model.

PubMed

Weill, D F; Drake, M J

1973-06-08

The partition of europium between plagioclase feldspar and magmatic liquid is considered in terms of the distribution coefficients for divalent and trivalent europium. A model equation is derived giving the europium anomaly in plagioclase as a function of temperature and oxygen fugacity. The model explains europium anomalies in plagioclase synthesized under controlled laboratory conditions as well as the variations of the anomaly observed in natural terrestrial and extraterrestrial igneous rocks.

Free Vibrations of Nonthin Elliptic Cylindrical Shells of Variable Thickness

NASA Astrophysics Data System (ADS)

Grigorenko, A. Ya.; Efimova, T. L.; Korotkikh, Yu. A.

2017-11-01

The problem of the free vibrations of nonthin elliptic cylindrical shells of variable thickness under various boundary conditions is solved using the refined Timoshenko-Mindlin theory. To solve the problem, an effective numerical approach based on the spline-approximation and discrete-orthogonalization methods is used. The effect of the cross-sectional shape, thickness variation law, material properties, and boundary conditions on the natural frequency spectrum of the shells is analyzed.

Understanding litter decomposition in semiarid ecosystems: linking leaf traits, UV exposure and rainfall variability

PubMed Central

Gaxiola, Aurora; Armesto, Juan J.

2015-01-01

Differences in litter quality, microbial activity or abiotic conditions cannot fully account for the variability in decomposition rates observed in semiarid ecosystems. Here we tested the role of variation in litter quality, water supply, and UV radiation as drivers of litter decomposition in arid lands. And show that carry-over effects of litter photodegradation during dry periods can regulate decomposition during subsequent wet periods. We present data from a two-phase experiment, where we first exposed litter from a drought-deciduous and an evergreen shrub to natural UV levels during five, rainless summer months and, subsequently, in the laboratory, we assessed the carry-over effects of photodegradation on biomass loss under different irrigation treatments representing the observed range of local rainfall variation among years (15–240 mm). Photodegradation of litter in the field produced average carbon losses of 12%, but deciduous Proustia pungens lost >25%, while evergreen Porlieria chilensis less than 5%. Natural exposure to UV significantly reduced carbon-to-nitrogen and lignin:N ratios in Proustia litter but not in Porlieria. During the subsequent wet phase, remaining litter biomass was lower in Proustia than in Porlieria. Indeed UV exposure increased litter decomposition of Proustia under low and medium rainfall treatments, whereas no carry-over effects were detected under high rainfall treatment. Consequently, for deciduous Proustia carry-over effects of UV exposure were negligible under high irrigation. Litter decomposition of the evergreen Porlieria depended solely on levels of rainfall that promote microbial decomposers. Our two-phase experiment revealed that both the carry-over effects of photodegradation and litter quality, modulated by inter-annual variability in rainfall, can explain the marked differences in decomposition rates and the frequent decoupling between rainfall and litter decomposition observed in semiarid ecosystems. PMID:25852705

Genetic Dissection of Photoperiod Response Based on GWAS of Pre-Anthesis Phase Duration in Spring Barley

PubMed Central

Alqudah, Ahmad M.; Sharma, Rajiv; Pasam, Raj K.; Graner, Andreas; Kilian, Benjamin; Schnurbusch, Thorsten

2014-01-01

Heading time is a complex trait, and natural variation in photoperiod responses is a major factor controlling time to heading, adaptation and grain yield. In barley, previous heading time studies have been mainly conducted under field conditions to measure total days to heading. We followed a novel approach and studied the natural variation of time to heading in a world-wide spring barley collection (218 accessions), comprising of 95 photoperiod-sensitive (Ppd-H1) and 123 accessions with reduced photoperiod sensitivity (ppd-H1) to long-day (LD) through dissecting pre-anthesis development into four major stages and sub-phases. The study was conducted under greenhouse (GH) conditions (LD; 16/8 h; ∼20/∼16°C day/night). Genotyping was performed using a genome-wide high density 9K single nucleotide polymorphisms (SNPs) chip which assayed 7842 SNPs. We used the barley physical map to identify candidate genes underlying genome-wide association scans (GWAS). GWAS for pre-anthesis stages/sub-phases in each photoperiod group provided great power for partitioning genetic effects on floral initiation and heading time. In addition to major genes known to regulate heading time under field conditions, several novel QTL with medium to high effects, including new QTL having major effects on developmental stages/sub-phases were found to be associated in this study. For example, highly associated SNPs tagged the physical regions around HvCO1 (barley CONSTANS1) and BFL (BARLEY FLORICAULA/LEAFY) genes. Based upon our GWAS analysis, we propose a new genetic network model for each photoperiod group, which includes several newly identified genes, such as several HvCO-like genes, belonging to different heading time pathways in barley. PMID:25420105

Testing phenotypic trade-offs in the chemical defence strategy of Scots pine under growth-limiting field conditions.

PubMed

Villari, Caterina; Faccoli, Massimo; Battisti, Andrea; Bonello, Pierluigi; Marini, Lorenzo

2014-09-01

Plants protect themselves from pathogens and herbivores through fine-tuned resource allocation, including trade-offs among resource investments to support constitutive and inducible defences. However, empirical research, especially concerning conifers growing under natural conditions, is still scarce. We investigated the complexity of constitutive and induced defences in a natural Scots pine (Pinus sylvestris L.) stand under growth-limiting conditions typical of alpine environments. Phenotypic trade-offs at three hierarchical levels were tested by investigating the behaviour of phenolic compounds and terpenoids of outer bark and phloem. We tested resource-derived phenotypic correlations between (i) constitutive and inducible defences vs tree ring growth, (ii) different constitutive defence metabolites and (iii) constitutive concentration and inducible variation of individual metabolites. Tree ring growth was positively correlated only with constitutive concentration of total terpenoids, and no overall phenotypic trade-offs between different constitutive defensive metabolites were found. At the lowest hierarchical level tested, i.e., at the level of relationship between constitutive and inducible variation of individual metabolites, we found that different compounds displayed different behaviours; we identified five different defensive metabolite response types, based on direction and strength of the response, regardless of tree age and growth rate. Therefore, under growth-limiting field conditions, Scots pine appears to utilize varied and complex outer bark and phloem defence chemistry, in which only part of the constitutive specialized metabolism is influenced by tree growth, and individual components do not appear to be expressed in a mutually exclusive manner in either constitutive or inducible metabolism. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Understanding litter decomposition in semiarid ecosystems: linking leaf traits, UV exposure and rainfall variability.

PubMed

Gaxiola, Aurora; Armesto, Juan J

2015-01-01

Differences in litter quality, microbial activity or abiotic conditions cannot fully account for the variability in decomposition rates observed in semiarid ecosystems. Here we tested the role of variation in litter quality, water supply, and UV radiation as drivers of litter decomposition in arid lands. And show that carry-over effects of litter photodegradation during dry periods can regulate decomposition during subsequent wet periods. We present data from a two-phase experiment, where we first exposed litter from a drought-deciduous and an evergreen shrub to natural UV levels during five, rainless summer months and, subsequently, in the laboratory, we assessed the carry-over effects of photodegradation on biomass loss under different irrigation treatments representing the observed range of local rainfall variation among years (15-240 mm). Photodegradation of litter in the field produced average carbon losses of 12%, but deciduous Proustia pungens lost >25%, while evergreen Porlieria chilensis less than 5%. Natural exposure to UV significantly reduced carbon-to-nitrogen and lignin:N ratios in Proustia litter but not in Porlieria. During the subsequent wet phase, remaining litter biomass was lower in Proustia than in Porlieria. Indeed UV exposure increased litter decomposition of Proustia under low and medium rainfall treatments, whereas no carry-over effects were detected under high rainfall treatment. Consequently, for deciduous Proustia carry-over effects of UV exposure were negligible under high irrigation. Litter decomposition of the evergreen Porlieria depended solely on levels of rainfall that promote microbial decomposers. Our two-phase experiment revealed that both the carry-over effects of photodegradation and litter quality, modulated by inter-annual variability in rainfall, can explain the marked differences in decomposition rates and the frequent decoupling between rainfall and litter decomposition observed in semiarid ecosystems.

Rhodnius prolixus and Rhodnius robustus-like (Hemiptera, Reduviidae) wing asymmetry under controlled conditions of population density and feeding frequency.

PubMed

Márquez, E J; Saldamando-Benjumea, C I

2013-09-01

Habitat change in Rhodnius spp may represent an environmental challenge for the development of the species, particularly when feeding frequency and population density vary in nature. To estimate the effect of these variables in stability on development, the degree of directional asymmetry (DA) and fluctuating asymmetry (FA) in the wing size and shape of R. prolixus and R. robustus-like were measured under laboratory controlled conditions. DA and FA in wing size and shape were significant in both species, but their variation patterns showed both inter-specific and sexual dimorphic differences in FA of wing size and shape induced by nutrition stress. These results suggest different abilities of the genotypes and sexes of two sylvatic and domestic genotypes of Rhodnius to buffer these stress conditions. However, both species showed non-significant differences in the levels of FA between treatments that simulated sylvan vs domestic conditions, indicating that the developmental noise did not explain the variation in wing size and shape found in previous studies. Thus, this result confirm that the variation in wing size and shape in response to treatments constitute a plastic response of these genotypes to population density and feeding frequency.

Defining the consequences of genetic variation on a proteome–wide scale

PubMed Central

Chick, Joel M.; Munger, Steven C.; Simecek, Petr; Huttlin, Edward L.; Choi, Kwangbom; Gatti, Daniel M.; Raghupathy, Narayanan; Svenson, Karen L.; Churchill, Gary A.; Gygi, Steven P.

2016-01-01

Genetic variation modulates protein expression through both transcriptional and post-transcriptional mechanisms. To characterize the consequences of natural genetic diversity on the proteome, here we combine a multiplexed, mass spectrometry-based method for protein quantification with an emerging outbred mouse model containing extensive genetic variation from eight inbred founder strains. By measuring genome-wide transcript and protein expression in livers from 192 Diversity outbred mice, we identify 2,866 protein quantitative trait loci (pQTL) with twice as many local as distant genetic variants. These data support distinct transcriptional and post-transcriptional models underlying the observed pQTL effects. Using a sensitive approach to mediation analysis, we often identified a second protein or transcript as the causal mediator of distant pQTL. Our analysis reveals an extensive network of direct protein–protein interactions. Finally, we show that local genotype can provide accurate predictions of protein abundance in an independent cohort of collaborative cross mice. PMID:27309819

Variation in founder groups promotes establishment success in the wild

PubMed Central

Forsman, Anders; Wennersten, Lena; Karlsson, Magnus; Caesar, Sofia

2012-01-01

Environmental changes currently pose severe threats to biodiversity, and reintroductions and translocations are increasingly used to protect declining populations and species from extinction. Theory predicts that establishment success should be higher for more variable groups of dissimilar individuals. To test this ‘diversity promotes establishment’ hypothesis, we introduced colour polymorphic pygmy grasshoppers (Tetrix subulata) to different sites in the wild. The number of descendants found at the release sites the subsequent year increased with increasing number of colour morphs in the founder group, and variation in founder groups also positively affected colour morph diversity in the established populations. Since colour morphs differ in morphology, physiology, behaviour, reproductive life history and types of niche used, these findings demonstrate that variation among individuals in functionally important traits promotes establishment success under natural conditions, and further indicate that founder diversity may contribute to evolutionary rescue and increased population persistence. PMID:22456885

Wetland Feature Extraction in Poyang Lake from Muti-Sensor and Multi-Temporal Images

NASA Astrophysics Data System (ADS)

Zhang, Li; Desnos, Yves-Louis; Wang, Yeqiao; Chen, Xiaoling; Zmuda, Andy; Yesou, Herve

2016-08-01

Under the high dynamic hydrological variations and impacts from human activities, the nature wetlands of Poyang Lake face major challenges in biodiversity decline and wetland degradation. Variations of Poyang Lake wetlands are difficult to map by a single source or one time remote sensing imagery because the landscape is dominated by herbaceous vegetation and aquatic macrophytes which are altered and controlled by the water level. This study selected and combined time series NDVI, Green Ratio Vegetation Index (GRVI) and Modified Normalized Different Water Index (MNDWI), Backscattering coefficients(σ0) (VV&VH mode), Shannon Entropy (SE) and H/α wishart classification value derived from Sentinel 1A and Sentinel 2A to investigate the spatial-temporal variation of wetlands in autumn and spring growing season with discussions about the possibility of monitoring the wetland vegetation by C-band dual-pol datasets.

Conversion of tropical lowland forest reduces nutrient return through litterfall, and alters nutrient use efficiency and seasonality of net primary production.

PubMed

Kotowska, Martyna M; Leuschner, Christoph; Triadiati, Triadiati; Hertel, Dietrich

2016-02-01

Tropical landscapes are not only rapidly transformed by ongoing land-use change, but are additionally confronted by increasing seasonal climate variation. There is an increasing demand for studies analyzing the effects and feedbacks on ecosystem functioning of large-scale conversions of tropical natural forest into intensively managed cash crop agriculture. We analyzed the seasonality of aboveground litterfall, fine root litter production, and aboveground woody biomass production (ANPP(woody)) in natural lowland forests, rubber agroforests under natural tree cover ("jungle rubber"), rubber and oil palm monocultures along a forest-to-agriculture transformation gradient in Sumatra. We hypothesized that the temporal fluctuation of litter production increases with increasing land-use intensity, while the associated nutrient fluxes and nutrient use efficiency (NUE) decrease. Indeed, the seasonal variation of aboveground litter production and ANPP(woody) increased from the natural forest to the plantations, while aboveground litterfall generally decreased. Nutrient return through aboveground litter was mostly highest in the natural forest; however, it was significantly lower only in rubber plantations. NUE of N, P and K was lowest in the oil palm plantations, with natural forest and the rubber systems showing comparably high values. Root litter production was generally lower than leaf litter production in all systems, while the root-to-leaf ratio of litter C flux increased along the land-use intensity gradient. Our results suggest that nutrient and C cycles are more directly affected by climate seasonality in species-poor agricultural systems than in species-rich forests, and therefore might be more susceptible to inter-annual climate fluctuation and climate change.

Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: implications for grassland restoration with climate change

PubMed Central

Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

2015-01-01

Identifying suitable genetic stock for restoration often employs a ‘best guess’ approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations. PMID:26240607

Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains' precipitation gradient: implications for grassland restoration with climate change.

PubMed

Johnson, Loretta C; Olsen, Jacob T; Tetreault, Hannah; DeLaCruz, Angel; Bryant, Johnny; Morgan, Theodore J; Knapp, Mary; Bello, Nora M; Baer, Sara G; Maricle, Brian R

2015-08-01

Identifying suitable genetic stock for restoration often employs a 'best guess' approach. Without adaptive variation studies, restoration may be misguided. We test the extent to which climate in central US grasslands exerts selection pressure on a foundation grass big bluestem (Andropogon gerardii), widely used in restorations, and resulting in local adaptation. We seeded three regional ecotypes of A. gerardii in reciprocal transplant garden communities across 1150 km precipitation gradient. We measured ecological responses over several timescales (instantaneous gas exchange, medium-term chlorophyll absorbance, and long-term responses of establishment and cover) in response to climate and biotic factors and tested if ecotypes could expand range. The ecotype from the driest region exhibited greatest cover under low rainfall, suggesting local adaptation under abiotic stress. Unexpectedly, no evidence for cover differences between ecotypes exists at mesic sites where establishment and cover of all ecotypes were low, perhaps due to strong biotic pressures. Expression of adaptive differences is strongly environment specific. Given observed adaptive variation, the most conservative restoration strategy would be to plant the local ecotype, especially in drier locations. With superior performance of the most xeric ecotype under dry conditions and predicted drought, this ecotype may migrate eastward, naturally or with assistance in restorations.

Mini-review: Strategies for Variation and Evolution of Bacterial Antigens

PubMed Central

Foley, Janet

2015-01-01

Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evolution and numerous commonalities reflecting considerations of natural selection and biochemical restraints. Unlike in viruses, mechanisms of antigenic variation in most bacteria involve larger DNA movement such as gene conversion or DNA rearrangement, although some antigens vary due to point mutations or modified transcriptional regulation. The convergent evolution that promotes antigenic variation integrates various evolutionary forces: these include mutations underlying variant production; drift which could remove alleles especially early in infection or during life history phases in arthropod vectors (when the bacterial population size goes through a bottleneck); selection not only for any particular variant but also for the mechanism for the production of variants (i.e., selection for mutability); and overcoming negative selection against variant production. This review highlights the complexities of drivers of antigenic variation, in particular extending evaluation beyond the commonly cited theory of immune evasion. A deeper understanding of the diversity of purpose and mechanisms of antigenic variation in bacteria will contribute to greater insight into bacterial pathogenesis, ecology and coevolution with hosts. PMID:26288700

Identification of natural high-oleate mutants from the USDA Peanut Germplasm Collection

USDA-ARS?s Scientific Manuscript database

Natural genetic variation may exist in plant germplasm collections. Identifying genetic variation may provide useful materials for breeders to develop new cultivars. After screening 8,846 cultivated peanut germplasm accessions by gas chromatography analysis, we identified three natural mutant lines ...

Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchin Strongylocentrotus purpuratus.

PubMed

Kelly, Morgan W; Padilla-Gamiño, Jacqueline L; Hofmann, Gretchen E

2013-08-01

A rapidly growing body of literature documents the potential negative effects of CO2 -driven ocean acidification (OA) on marine organisms. However, nearly all this work has focused on the effects of future conditions on modern populations, neglecting the role of adaptation. Rapid evolution can alter demographic responses to environmental change, ultimately affecting the likelihood of population persistence, but the capacity for adaptation will differ among populations and species. Here, we measure the capacity of the ecologically important purple sea urchin Strongylocentrotus purpuratus to adapt to OA, using a breeding experiment to estimate additive genetic variance for larval size (an important component of fitness) under future high-pCO2 /low-pH conditions. Although larvae reared under future conditions were smaller than those reared under present-day conditions, we show that there is also abundant genetic variation for body size under elevated pCO2 , indicating that this trait can evolve. The observed heritability of size was 0.40 ± 0.32 (95% CI) under low pCO2 , and 0.50 ± 0.30 under high-pCO2 conditions. Accounting for the observed genetic variation in models of future larval size and demographic rates substantially alters projections of performance for this species in the future ocean. Importantly, our model shows that after incorporating the effects of adaptation, the OA-driven decrease in population growth rate is up to 50% smaller, than that predicted by the 'no-adaptation' scenario. Adults used in the experiment were collected from two sites on the coast of the Northeast Pacific that are characterized by different pH regimes, as measured by autonomous sensors. Comparing results between sites, we also found subtle differences in larval size under high-pCO2 rearing conditions, consistent with local adaptation to carbonate chemistry in the field. These results suggest that spatially varying selection may help to maintain genetic variation necessary for adaptation to future OA. © 2013 John Wiley & Sons Ltd.

The timing of GIGANTEA expression during day/night cycles varies with the geographical origin of Arabidopsis accessions.

PubMed

de Montaigu, Amaury; Coupland, George

2017-07-03

Latitudinal clines in circadian rhythms have consistently been described in various plant species, with the most recent examples appearing in soybean cultivars and in monkey flower natural populations. These latitudinal clines provide evidence that natural variation in circadian rhythms is adaptive, but it is still unclear what adaptive benefits this variation confers, particularly because circadian rhythms are not usually measured in day/night conditions that reflect those experienced by organisms in nature. Here, we report that daily rhythms of GIGANTEA expression respond to day length in a way that depends on the latitude of origin of Arabidopsis accessions. We additionally extend previous findings by confirming that natural variation in GI expression affects growth related traits, and alters the expression of different target genes. The results support the idea that natural variation in daily rhythms of expression have broad effects on plant development and are of potential adaptive value.

Daily variation in natural disaster casualties: information flows, safety, and opportunity costs in tornado versus hurricane strikes.

PubMed

Zahran, Sammy; Tavani, Daniele; Weiler, Stephan

2013-07-01

Casualties from natural disasters may depend on the day of the week they strike. With data from the Spatial Hazard Events and Losses Database for the United States (SHELDUS), daily variation in hurricane and tornado casualties from 5,043 tornado and 2,455 hurricane time/place events is analyzed. Hurricane forecasts provide at-risk populations with considerable lead time. Such lead time allows strategic behavior in choosing protective measures under hurricane threat; opportunity costs in terms of lost income are higher during weekdays than during weekends. On the other hand, the lead time provided by tornadoes is near zero; hence tornados generate no opportunity costs. Tornado casualties are related to risk information flows, which are higher during workdays than during leisure periods, and are related to sheltering-in-place opportunities, which are better in permanent buildings like businesses and schools. Consistent with theoretical expectations, random effects negative binomial regression results indicate that tornado events occurring on the workdays of Monday through Thursday are significantly less lethal than tornados that occur on weekends. In direct contrast, and also consistent with theory, the expected count of hurricane casualties increases significantly with weekday occurrences. The policy implications of observed daily variation in tornado and hurricane events are considered. © 2012 Society for Risk Analysis.

Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity

PubMed Central

Walter, Katharine S.; Carpi, Giovanna; Evans, Benjamin R.; Caccone, Adalgisa; Diuk-Wasser, Maria A.

2016-01-01

Hosts including humans, other vertebrates, and arthropods, are frequently infected with heterogeneous populations of pathogens. Within-host pathogen diversity has major implications for human health, epidemiology, and pathogen evolution. However, pathogen diversity within-hosts is difficult to characterize and little is known about the levels and sources of within-host diversity maintained in natural populations of disease vectors. Here, we examine genomic variation of the Lyme disease bacteria, Borrelia burgdorferi (Bb), in 98 individual field-collected tick vectors as a model for study of within-host processes. Deep population sequencing reveals extensive and previously undocumented levels of Bb variation: the majority (~70%) of ticks harbor mixed strain infections, which we define as levels Bb diversity pre-existing in a diverse inoculum. Within-tick diversity is thus a sample of the variation present within vertebrate hosts. Within individual ticks, we detect signatures of positive selection. Genes most commonly under positive selection across ticks include those involved in dissemination in vertebrate hosts and evasion of the vertebrate immune complement. By focusing on tick-borne Bb, we show that vectors can serve as epidemiological and evolutionary sentinels: within-vector pathogen diversity can be a useful and unbiased way to survey circulating pathogen diversity and identify evolutionary processes occurring in natural transmission cycles. PMID:27414806

Condition dependence and the nature of genetic variation for male sex comb bristle number in Drosophila melanogaster.

PubMed

Ahuja, Abha; De Vito, Scott; Singh, Rama S

2011-04-01

Genetic architecture of variation underlying male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila, was examined. First, in order to test for condition dependence, diet was manipulated in a set of ten Drosophila melanogaster full-sib families. We confirmed heightened condition dependent expression of sex comb bristle number and its female homologue (distal transverse row bristles) as compared to non-sex sternopleural bristles. Significant genotype by environment effects were detected for the sex traits indicating a genetic basis for condition dependence. Next we measured sex comb bristle number and sternopleural bristle number, as well as residual mass, a commonly used condition index, in a set of thirty half-sib families. Sire effect was not significant for sex comb and sternopleural bristle number, and we detected a strong dominance and/or maternal effect or X chromosome effect for both traits. A strong sire effect was detected for condition and its heritability was the highest as compared to sex comb and sternopleural bristles. We discuss our results in light of the rapid response to divergent artificial selection for sex comb bristle number reported previously. The nature of genetic variation for male sex traits continues to be an important unresolved issue in evolutionary biology.

A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation, population viability and genetic variation.

PubMed

Gomez-Mestre, Ivan; Jovani, Roger

2013-11-22

An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.

Reproducibility and consistency of proteomic experiments on natural populations of a non-model aquatic insect.

PubMed

Hidalgo-Galiana, Amparo; Monge, Marta; Biron, David G; Canals, Francesc; Ribera, Ignacio; Cieslak, Alexandra

2014-01-01

Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2-3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.

Measurements of wind-waves under transient wind conditions.

NASA Astrophysics Data System (ADS)

Shemer, Lev; Zavadsky, Andrey

2015-11-01

Wind forcing in nature is always unsteady, resulting in a complicated evolution pattern that involves numerous time and space scales. In the present work, wind waves in a laboratory wind-wave flume are studied under unsteady forcing`. The variation of the surface elevation is measured by capacitance wave gauges, while the components of the instantaneous surface slope in across-wind and along-wind directions are determined by a regular or scanning laser slope gauge. The locations of the wave gauge and of the laser slope gauge are separated by few centimeters in across-wind direction. Instantaneous wind velocity was recorded simultaneously using Pitot tube. Measurements are performed at a number of fetches and for different patterns of wind velocity variation. For each case, at least 100 independent realizations were recorded for a given wind velocity variation pattern. The accumulated data sets allow calculating ensemble-averaged values of the measured parameters. Significant differences between the evolution patterns of the surface elevation and of the slope components were found. Wavelet analysis was applied to determine dominant wave frequency of the surface elevation and of the slope variation at each instant. Corresponding ensemble-averaged values acquired by different sensors were computed and compared. Analysis of the measured ensemble-averaged quantities at different fetches makes it possible to identify different stages in the wind-wave evolution and to estimate the appropriate time and length scales.

Reproducibility and Consistency of Proteomic Experiments on Natural Populations of a Non-Model Aquatic Insect

PubMed Central

Hidalgo-Galiana, Amparo; Monge, Marta; Biron, David G.; Canals, Francesc; Ribera, Ignacio; Cieslak, Alexandra

2014-01-01

Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2–3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments. PMID:25133588

Extensive Natural Intraspecific Variation in Stoichiometric (C:N:P) Composition in Two Terrestrial Insect Species

PubMed Central

Bertram, S. M.; Bowen, M.; Kyle, M.; Schade, J. D.

2008-01-01

Heterotrophic organisms must obtain essential elements in sufficient quantities from their food. Because plants naturally exhibit extensive variation in their elemental content, it is important to quantify the within-species stoichiometric variation of consumers. If extensive stoichiometric variation exists, it may help explain consumer variation in life-history strategy and fitness. To date, however, research on stoichiometric variation has focused on interspecific differences and assumed minimal intraspecific differences. Here this assumption is tested. Natural variation is quantified in body stoichiometry of two terrestrial insects: the generalist field cricket, Gryllus texensis Cade and Otte (Orthoptera: Gryllidae) and a specialist curculionid weevil, Sabinia setosa (Le Conte) (Coleoptera: Curculionidae). Both species exhibited extensive intraspecific stoichiometric variation. Cricket body nitrogen content ranged from 8–12% and there was a four-fold difference in body phosphorus content, ranging from 0.32–1.27%. Body size explained half this stoichiometric variation, with larger individuals containing less nitrogen and phosphorus. Weevils exhibited an almost three-fold difference in body phosphorus content, ranging from 0.38–0.97%. Overall, the variation observed within each of these species is comparable to the variation previously observed across almost all terrestrial insect species. PMID:20298114

The effects of UV radiation A and B on diurnal variation in photosynthesis in three taxonomically and ecologically diverse microbial mats

NASA Technical Reports Server (NTRS)

Cockell, C. S.; Rothschild, L. J.

1999-01-01

Photosynthetic primary production, the basis of most global food chains, is inhibited by UV radiation. Evaluating UV inhibition is therefore important for assessing the role of natural levels of UV radiation in regulating ecosystem behavior as well as the potential impact of stratospheric ozone depletion on global ecosystems. As both photosynthesis and UV fluxes are subject to diurnal variations, we examined the diurnal variability of the effect of UV radiation on photosynthesis in three diverse algal mats. In one of the mats (Cyanidium caldarium) a small mean decrease in primary productivity over the whole day occurred when both UVA and UVB were screened out. In two of the mats (Lyngbya aestuarii and Zygogonium sp.) we found a mean increase in the total primary productivity over the day when UVB alone was screened and a further increase when UVA and UVB were both screened out. Variations in the effects of UV radiation were found at different times of the day. This diurnal variability may be because even under the same solar radiation flux, there are different factors that may control photosynthetic rate, including nutritional status and other physiological processes in the cell. The results show the importance of assessing the complete diurnal productivity. For some of the time points the increase in the mean was still within the standard deviations in primary productivity, illustrating the difficulty in dissecting UV effects from other natural variations.

ANIMAL BEHAVIOR AND WELL-BEING SYMPOSIUM: Interaction between coping style/personality, stress, and welfare: Relevance for domestic farm animals.

PubMed

Koolhaas, J M; Van Reenen, C G

2016-06-01

This paper will argue that understanding animal welfare and the individual vulnerability to stress-related disease requires a fundamental understanding of functional individual variation as it occurs in nature as well as the underlying neurobiology and neuroendocrinology. Ecological studies in feral populations of mice, fish, and birds start to recognize the functional significance of phenotypes that individually differ in their behavioral and neuroendocrine response to environmental challenge. Recent studies indicate that the individual variation within a species may buffer the species for strong fluctuations in the natural habitat. Similarly, evolutionary ancient behavioral trait characteristics have now been identified in a range of domestic farm animals including cattle, pigs, and horses. Individual variation in behavior can be summarized in a 3-dimensional model with coping style, emotionality, and sociality as independent dimensions. These dimensions can be considered trait characteristics that are stable over time and across situations within the individual. This conceptual model has several consequences. First, the coping style dimension is strongly associated with differential stress vulnerability. Social stress studies show that proactive individuals are resilient under stable environmental conditions but vulnerable when outcome expectancies are violated. Reactive individuals are, in fact, rather flexible and seem to adapt more easily to a changing environment. A second consequence relates to genetics and breeding. Genetic selection for one trait usually implies selection for other traits as well. It is discussed that a more balanced breeding program that takes into account biologically functional temperamental traits will lead to more robust domestic farm animals. Finally, the relationship between temperamental traits, animal production, fitness, and welfare is discussed.

Polymorphism at the avpr1a locus in male prairie voles correlated with genetic but not social monogamy in field populations.

PubMed

Solomon, N G; Richmond, A R; Harding, P A; Fries, A; Jacquemin, S; Schaefer, R L; Lucia, K E; Keane, B

2009-11-01

Integrative studies of genetics, neurobiology and behaviour indicate that polymorphism in specific genes contributes to variation observed in some complex social behaviours. The neuropeptide arginine vasopressin plays an important role in the regulation of a variety of social behaviours, including social attachment of males to females, through its action on the vasopressin 1a receptor (V1aR). In socially monogamous prairie voles (Microtus ochrogaster), polymorphism in the length of microsatellite DNA within the regulatory region of the gene (avpr1a) encoding the V1aR predicts differences among males in neural expression of V1aRs and partner preference under laboratory conditions. However, understanding the extent to which V1aR mediates variation in prairie vole social and reproductive behaviour observed in nature requires investigating the consequences of avpr1a polymorphism and environmental influences under ecologically relevant conditions. We examined the relationship between avpr1a length polymorphism and monogamy among male prairie voles living in 0.1 ha enclosures during a time similar to their natural lifespan. We found no evidence that avpr1a genotype of males predicts variation in social monogamy measured in the field but some indices of social monogamy were affected by population density. Parentage data indicated that a male's avpr1a genotype significantly influenced the number of females with which he sired offspring and the total number of offspring sired. Total brain concentrations of V1aR mRNA were not associated with either male behaviour or avpr1a genotype. These data show that melding ecological field studies with neurogenetics can substantially augment our understanding of the effects of genes and environment on social behaviours.

The acousto-ultrasonic approach

NASA Technical Reports Server (NTRS)

Vary, Alex

1987-01-01

The nature and underlying rationale of the acousto-ultrasonic approach is reviewed, needed advanced signal analysis and evaluation methods suggested, and application potentials discussed. Acousto-ultrasonics is an NDE technique combining aspects of acoustic emission methodology with ultrasonic simulation of stress waves. This approach uses analysis of simulated stress waves for detecting and mapping variations of mechanical properties. Unlike most NDE, acousto-ultrasonics is less concerned with flaw detection than with the assessment of the collective effects of various flaws and material anomalies. Acousto-ultrasonics has been applied chiefly to laminated and filament-wound fiber reinforced composites. It has been used to assess the significant strength and toughness reducing effects that can be wrought by combinations of essentially minor flaws and diffuse flaw populations. Acousto-ultrasonics assesses integrated defect states and the resultant variations in properties such as tensile, shear, and flexural strengths and fracture resistance. Matrix cure state, porosity, fiber orientation, fiber volume fraction, fiber-matrix bonding, and interlaminar bond quality are underlying factors.

Bare TiO2 and graphene oxide TiO2 photocatalysts on the degradation of selected pesticides and influence of the water matrix

NASA Astrophysics Data System (ADS)

Cruz, Marta; Gomez, Cristina; Duran-Valle, Carlos J.; Pastrana-Martínez, Luisa M.; Faria, Joaquim L.; Silva, Adrián M. T.; Faraldos, Marisol; Bahamonde, Ana

2017-09-01

The photocatalytic activity of a home-made titanium dioxide (TiO2) and its corresponding composite based on graphene oxide (GO), the GO-TiO2 catalyst, has been investigated under UV-vis in the photodegradation of a mixture of four pesticides classified by the European Union as priority pollutants: diuron, alachlor, isoproturon and atrazine. The influence of two water matrices (ultrapure or natural water) was also studied. Natural water led to a decrease on the degradation of the studied pollutants when the bare TiO2 photocatalyst was employed, since this water contains both inorganic and organic species that are dissolved and commonly restrain the photocatalytic process. On the contrary, the photo-efficiency of the GO-TiO2 composite seems to be less affected by water matrix variation, with very good initial pesticide photodegradation rates under both natural and ultrapure water matrices. A comparative study between GO-TiO2 and the commercial Evonik TiO2 P25 catalyst was also carried out to analyze the photocatalytic degradation of these pesticides under visible light illumination conditions. Once again, a higher photocatalytic activity was found for the GO-TiO2 composite.

Do acid volatile sulfides (AVS) influence the accumulation of sediment-bound metals to benthic invertebrates under natural field conditions?

PubMed

De Jonge, Maarten; Dreesen, Freja; De Paepe, Josefina; Blust, Ronny; Bervoets, Lieven

2009-06-15

The present study evaluates the influence of acid volatile sulfides (AVS) on accumulation of sediment-bound metals in benthic invertebrates under natural field conditions. Natural sediments, pore water, surface water, and two species of widespread benthic invertebrates (Chironomus gr. thummi and Tubifex tubifex) were collected from 17 historical polluted Flemish lowland rivers and measured for metal concentrations. Different sediment characteristics were determined (AVS, organic matter, clay content) and multiple regression was used to study their relationship with accumulated metals in the invertebrates. Physical and chemical analysis of the field samples indicated low metal concentrations in the water and pore water, but very high metal concentrations in the sediment and the invertebrates, especially for Pb (5.99 micromol/ g). In general, metal accumulation in chironomids and tubificid worms was most strongly correlated with total metal concentrations in the sediment and sediment metal concentrations normalized for organic matter and clay content. Following the results of the linear regression model, AVS did not turn out to be a significant variable in describing variation in metal accumulation. Our study clearly demonstrates that, in addition to the results gained from experiments under lab conditions, benthic invertebrates can accumulate metals from unspiked field sediments even when there's an excess of AVS.

The Advanced Part of a Treatise on the Dynamics of a System of Rigid Bodies

NASA Astrophysics Data System (ADS)

Routh, Edward John

2013-03-01

Preface; 1. Moving axes and relative motion; 2. Oscillations about equilibrium; 3. Oscillations about a state of motion; 4. Motion of a body under no forces; 5. Motion of a body under any forces; 6. Nature of the motion given by linear equations and the conditions of stability; 7. Free and forced oscillations; 8. Determination of the constants of integration in terms of the initial conditions; 9. Calculus of finite differences; 10. Calculus of variations; 11. Precession and nutation; 12. Motion of the moon about its centre; 13. Motion of a string or chain; 14. Motion of a membrane; Notes.

The role of discharge variation in scaling of drainage area and food chain length in rivers

USGS Publications Warehouse

Sabo, John L.; Finlay, Jacques C.; Kennedy, Theodore A.; Post, David M.

2010-01-01

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

Electromagnetic finite elements based on a four-potential variational principle

NASA Technical Reports Server (NTRS)

Schuler, James J.; Felippa, Carlos A.

1991-01-01

Electromagnetic finite elements based on a variational principle that uses the electromagnetic four-potential as a primary variable are derived. This choice is used to construct elements suitable for downstream coupling with mechanical and thermal finite elements for the analysis of electromagnetic/mechanical systems that involve superconductors. The main advantages of the four-potential as a basis for finite element formulation are that the number of degrees of freedom per node remains modest as the problem dimensionally increases, that jump discontinuities on interfaces are naturally accommodated, and that statics as well as dynamics may be treated without any a priori approximations. The new elements are tested on an axisymmetric problem under steady state forcing conditions. The results are in excellent agreement with analytical solutions.

Disentangling the benefits of sex.

PubMed

Roze, Denis

2012-01-01

Understanding the evolutionary advantage of sexual reproduction remains one of the most fundamental questions in evolutionary biology. Most of the current hypotheses rely on the fact that sex increases genetic variation, thereby enhancing the efficiency of natural selection; an important body of theoretical work has defined the conditions under which sex can be favoured through this effect. Over the last decade, experimental evolution in model organisms has provided evidence that sex indeed allows faster rates of adaptation. A new study on facultatively sexual rotifers shows that increased rates of sex can be favoured during adaptation to new environmental conditions and explores the cause of this effect. The results provide support for the idea that the benefits of increasing genetic variation may compensate for the short-term costs of sexual reproduction.

The role of discharge variation in scaling of drainage area and food chain length in rivers.

PubMed

Sabo, John L; Finlay, Jacques C; Kennedy, Theodore; Post, David M

2010-11-12

Food chain length (FCL) is a fundamental component of food web structure. Studies in a variety of ecosystems suggest that FCL is determined by energy supply, environmental stability, and/or ecosystem size, but the nature of the relationship between environmental stability and FCL, and the mechanism linking ecosystem size to FCL, remain unclear. Here we show that FCL increases with drainage area and decreases with hydrologic variability and intermittency across 36 North American rivers. Our analysis further suggests that hydrologic variability is the mechanism underlying the correlation between ecosystem size and FCL in rivers. Ecosystem size lengthens river food chains by integrating and attenuating discharge variation through stream networks, thereby enhancing environmental stability in larger river systems.

In-plane stability analysis of non-uniform cross-sectioned curved beams

NASA Astrophysics Data System (ADS)

Öztürk, Hasan; Yeşilyurt, İsa; Sabuncu, Mustafa

2006-09-01

In this study, in-plane stability analysis of non-uniform cross-sectioned thin curved beams under uniformly distributed dynamic loads is investigated by using the Finite Element Method. The first and second unstable regions are examined for dynamic stability. In-plane vibration and in-plane buckling are also studied. Two different finite element models, representing variations of cross-section, are developed by using simple strain functions in the analysis. The results obtained from this study are compared with the results of other investigators in existing literature for the fundamental natural frequency and critical buckling load. The effects of opening angle, variations of cross-section, static and dynamic load parameters on the stability regions are shown in graphics.

Effects of river geomorphology on the spatial importance of aquatic energy flows into terrestrial food webs

NASA Astrophysics Data System (ADS)

Muehlbauer, J. D.; Doyle, M. W.; Tockner, K.

2011-12-01

This presentation will present the results of a meta-analysis on river-floodplain carbon/energy subsidies. This analysis combines data from the existing body of literature (ca. 100 studies) to determine a "stream signature:" a regression equation that fits the decline in aquatic-derived energy in terrestrial predator food webs as a function of distance from the river. The nature of this decay curve and its implications for river/riparian ecological dynamics will be desrcibed. Variation in this metric due to the influence of stream order, river bank characteristics, and channel geomorphology will be assessed. In addition, the implications of variation in the stream signature for terrestrial aquatic food webs under different geomorphic and anthropogenic scenarios will be discussed.

Ancient homology underlies adaptive mimetic diversity across butterflies

PubMed Central

Gallant, Jason R.; Imhoff, Vance E.; Martin, Arnaud; Savage, Wesley K.; Chamberlain, Nicola L.; Pote, Ben L.; Peterson, Chelsea; Smith, Gabriella E.; Evans, Benjamin; Reed, Robert D.; Kronforst, Marcus R.; Mullen, Sean P.

2014-01-01

Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged >65 million years ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time. PMID:25198507

Fractal nature of aluminum alloys substructures under creep and its implications

NASA Astrophysics Data System (ADS)

Fernández, R.; Bruno, G.; González-Doncel, G.

2018-04-01

The present work offers an explanation for the variation of the power-law stress exponent, n, with the stress σ normalized to the shear modulus G in aluminum alloys. The approach is based on the assumption that the dislocation structure generated with deformation has a fractal nature. It fully explains the evolution of n with σ/G even beyond the so-called power law breakdown region. Creep data from commercially pure Al99.8%, Al-3.85%Mg, and ingot AA6061 alloy tested at different temperatures and stresses are used to validate the proposed ideas. Finally, it is also shown that the fractal description of the dislocation structure agrees well with current knowledge.

Effects of source and seasonal variations of natural organic matters on the fate and transport of CeO2 nanoparticles in the environment

EPA Science Inventory

Natural organic matter (NOM) affects the stability and transport of nanoparticles (NPs) in natural waters by modifying their physiochemical properties. Source location, and seasonal variations, influence their molecular, physical and electrical charge properties. To understand th...

Characterization of newly identified natural high-oleate mutant from the USDA cultivated peanut germplasm collection

USDA-ARS?s Scientific Manuscript database

In plants and animals, natural genetic variation may exist in germplasm collection. Mining and utilizing this variation may provide benefits for new breed/cultivar development. From screening over 4,000 cultivated peanut germplasm accessions, we identified two natural mutant lines with 80% oleic aci...

Natural habitats matter: Determinants of spatial pattern in the composition of animal assemblages of the Czech Republic

NASA Astrophysics Data System (ADS)

Divíšek, Jan; Zelený, David; Culek, Martin; Št'astný, Karel

2014-08-01

Studies that explore species-environment relationships at a broad scale are usually limited by the availability of sufficient habitat description, which is often too coarse to differentiate natural habitat patches. Therefore, it is not well understood how the distribution of natural habitats affects broad-scale patterns in the distribution of animal species. In this study, we evaluate the role of field-mapped natural habitats, land-cover types derived from remote sensing and climate on the composition of assemblages of five distinct animal groups, namely non-volant mammals, birds, reptiles, amphibians and butterflies native to the Czech Republic. First, we used variation partitioning based on redundancy analysis to evaluate the extent to which the environmental variables and their spatial structure might underlie the observed spatial patterns in the composition of animal assemblages. Second, we partitioned variations explained by climate, natural habitats and land-cover to compare their relative importance. Finally, we tested the independent effects of each variable in order to evaluate the significance of their contributions to the environmental model. Our results showed that spatial patterns in the composition of assemblages of almost all the considered animal groups may be ascribed mostly to variations in the environment. Although the shared effects of climatic variables, natural habitats and land-cover types explained the largest proportion of variation in each animal group, the variation explained purely by natural habitats was always higher than the variation explained purely by climate or land-cover. We conclude that most spatial variation in the composition of assemblages of almost all animal groups probably arises from biological processes operating within a spatially structured environment and suggest that natural habitats are important to explain observed patterns because they often perform better than habitat descriptions based on remote sensing. This underlines the value of using appropriate habitat data, for which high-resolution and large-area field-mapping projects are necessary.

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama

PubMed Central

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M. T.; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range. PMID:26863538

Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait specificity in Drosophila melanogaster.

PubMed

Takahashi, Kazuo H

2015-11-01

Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster and then investigated the trait specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist. © 2015 John Wiley & Sons Ltd.

Low Predictability of Colour Polymorphism in Introduced Guppy (Poecilia reticulata) Populations in Panama.

PubMed

Martínez, Celestino; Chavarría, Carmen; Sharpe, Diana M T; De León, Luis Fernando

2016-01-01

Colour polymorphism is a recurrent feature of natural populations, and its maintenance has been studied in a range of taxa in their native ranges. However, less is known about whether (and how) colour polymorphism is maintained when populations are removed from their native environments, as in the case of introduced species. We here address this issue by analyzing variation in colour patterns in recently-discovered introduced populations of the guppy (Poecilia reticulata) in Panama. Specifically, we use classic colour analysis to estimate variation in the number and the relative area of different colour spots across low predation sites in the introduced Panamanian range of the species. We then compare this variation to that found in the native range of the species under low- and high predation regimes. We found aspects of the colour pattern that were both consistent and inconsistent with the classical paradigm of colour evolution in guppies. On one hand, the same colours that dominated in native populations (orange, iridescent and black) were also the most dominant in the introduced populations in Panama. On the other, there were no clear differences between either introduced-low and native low- and high predation populations. Our results are therefore only partially consistent with the traditional role of female preference in the absence of predators, and suggest that additional factors could influence colour patterns when populations are removed from their native environments. Future research on the interaction between female preference and environmental variability (e.g. multifarious selection), could help understand adaptive variation in this widely-introduced species, and the contexts under which variation in adaptive traits parallels (or not) variation in the native range.

Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean.

PubMed

Syed, Naeem H; Prince, Silvas J; Mutava, Raymond N; Patil, Gunvant; Li, Song; Chen, Wei; Babu, Valliyodan; Joshi, Trupti; Khan, Saad; Nguyen, Henry T

2015-12-01

Circadian clocks are a great evolutionary innovation and provide competitive advantage during the day/night cycle and under changing environmental conditions. The circadian clock mediates expression of a large proportion of genes in plants, achieving a harmonious relationship between energy metabolism, photosynthesis, and biotic and abiotic stress responses. Here it is shown that multiple paralogues of clock genes are present in soybean (Glycine max) and mediate flooding and drought responses. Differential expression of many clock and SUB1 genes was found under flooding and drought conditions. Furthermore, natural variation in the amplitude and phase shifts in PRR7 and TOC1 genes was also discovered under drought and flooding conditions, respectively. PRR3 exhibited flooding- and drought-specific splicing patterns and may work in concert with PRR7 and TOC1 to achieve energy homeostasis under flooding and drought conditions. Higher expression of TOC1 also coincides with elevated levels of abscisic acid (ABA) and variation in glucose levels in the morning and afternoon, indicating that this response to abiotic stress is mediated by ABA, endogenous sugar levels, and the circadian clock to fine-tune photosynthesis and energy utilization under stress conditions. It is proposed that the presence of multiple clock gene paralogues with variation in DNA sequence, phase, and period could be used to screen exotic germplasm to find sources for drought and flooding tolerance. Furthermore, fine tuning of multiple clock gene paralogues (via a genetic engineering approach) should also facilitate the development of flooding- and drought-tolerant soybean varieties. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Interactive Effects of Nutrient and Mechanical Stresses on Plant Morphology

PubMed Central

Puijalon, Sara; Lena, Jean-Paul; Bornette, Gudrun

2007-01-01

Background and Aims Plant species frequently encounter multiple stresses under natural conditions, and the way they cope with these stresses is a major determinant of their ecological breadth. The way mechanical (e.g. wind, current) and resource stresses act simultaneously on plant morphological traits has been poorly addressed, even if both stresses often interact. This paper aims to assess whether hydraulic stress affects plant morphology in the same way at different nutrient levels. Methods An examination was made of morphological variations of an aquatic plant species growing under four hydraulic stress (flow velocity) gradients located in four habitats distributed along a nutrient gradient. Morphological traits covering plant size, dry mass allocation, organ water content and foliage architecture were measured. Key Results Significant interactive effects of flow velocity and nutrient level were observed for all morphological traits. In particular, increased flow velocity resulted in size reductions under low nutrient conditions, suggesting an adaptive response to flow stress (escape strategy). On the other hand, moderate increases in flow velocity resulted in increased size under high nutrient conditions, possibly related to an inevitable growth response to a higher nutrient supply induced by water renewal at the plant surface. For some traits (e.g. dry mass allocation), a consistent sense of variation as a result of increasing flow velocity was observed, but the amount of variation was either reduced or amplified under nutrient-rich compared with nutrient-poor conditions, depending on the traits considered. Conclusions These results suggest that, for a given species, a stress factor may result, in contrasting patterns and hence strategies, depending on a second stress factor. Such results emphasize the relevance of studies on plant responses to multiple stresses for understanding the actual ecological breadth of species. PMID:17913725

avpr1a length polymorphism is not associated with either social or genetic monogamy in free-living prairie voles.

PubMed

Mabry, Karen E; Streatfeild, Craig A; Keane, Brian; Solomon, Nancy G

2011-01-01

Recent discoveries of single-gene influences on social behaviour have generated a great deal of interest in the proximate mechanisms underlying the expression of complex behaviours. Length polymorphism in a microsatellite in the regulatory region of the gene encoding the vasopressin 1a receptor (avpr1a) has been associated with both inter- and intra-specific variation in socially monogamous behaviour in voles (genus Microtus) under laboratory conditions. Here, we evaluate the relationship between avpr1a length polymorphism and social associations, genetic monogamy, and reproductive success in free-living prairie vole (M. ochrogaster) populations. We found no evidence of a relationship between avpr1a microsatellite length and any of our correlates of either social or genetic monogamy in the field. Our results, especially when taken in conjunction with those of recent experimental studies in semi-natural enclosures, suggest that avpr1a polymorphism is unlikely to have been a major influence in the evolution or maintenance of social monogamy in prairie voles under natural conditions.

avpr1a length polymorphism is not associated with either social or genetic monogamy in free-living prairie voles

PubMed Central

Mabry, Karen E.; Streatfeild, Craig A.; Keane, Brian; Solomon, Nancy G.

2010-01-01

Recent discoveries of single-gene influences on social behaviour have generated a great deal of interest in the proximate mechanisms underlying the expression of complex behaviours. Length polymorphism in a microsatellite in the regulatory region of the gene encoding the vasopressin 1a receptor (avpr1a) has been associated with both inter- and intra-specific variation in socially monogamous behaviour in voles (genus Microtus) under laboratory conditions. Here, we evaluate the relationship between avpr1a length polymorphism and social associations, genetic monogamy, and reproductive success in free-living prairie vole (M. ochrogaster) populations. We found no evidence of a relationship between avpr1a microsatellite length and any of our correlates of either social or genetic monogamy in the field. Our results, especially when taken in conjunction with those of recent experimental studies in semi-natural enclosures, suggest that avpr1a polymorphism is unlikely to have been a major influence in the evolution or maintenance of social monogamy in prairie voles under natural conditions. PMID:21442019

Strain rate dependent calcite microfabric evolution - An experiment carried out by nature

NASA Astrophysics Data System (ADS)

Rogowitz, Anna; Grasemann, Bernhard; Huet, Benjamin; Habler, Gerlinde

2014-12-01

A flanking structure developed along a secondary shear zone in calcite marbles, on Syros (Cyclades, Greece), provides a natural laboratory for directly studying the effects of strain rate variations on calcite deformation at identical pressure and temperature conditions. The presence and rotation of a fracture during progressive deformation caused extreme variations in finite strain and strain rate, forming a localized ductile shear zone that shows different microstructures and textures. Textures and the degree of intracrystalline deformation were measured by electron backscattered diffraction. Marbles from the host rocks and the shear zone, which deformed at various strain rates, display crystal-preferred orientation, suggesting that the calcite preferentially deformed by intracrystalline-plastic deformation. Increasing strain rate results in a switch from subgrain rotation to bulging recrystallization in the dislocation-creep regime. With increasing strain rate, we observe in fine-grained (3 μm) ultramylonitic zones a change in deformation regime from grain-size insensitive to grain-size sensitive. Paleowattmeter and the paleopiezometer suggest strain rates for the localized shear zone around 10-10 s-1 and for the marble host rock around 10-12 s-1. We conclude that varying natural strain rates can have a first-order effect on the microstructures and textures that developed under the same metamorphic conditions.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches.

PubMed

Hassenrück, Christiane; Fink, Artur; Lichtschlag, Anna; Tegetmeyer, Halina E; de Beer, Dirk; Ramette, Alban

2016-05-01

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. © FEMS 2016.

Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS.

PubMed

Campoli, Chiara; Drosse, Benedikt; Searle, Iain; Coupland, George; von Korff, Maria

2012-03-01

Variation in photoperiod response is a major factor determining plant development and the agronomic performance of crops. The genetic control of photoperiodic flowering has been elucidated in the model plant Arabidopsis, and many of the identified genes are structurally conserved in the grasses. In this study, HvCO1, the closest barley ortholog of the key photoperiod response gene CONSTANS in Arabidopsis, was over-expressed in the spring barley Golden Promise. Over-expression of HvCO1 accelerated time to flowering in long- and short-day conditions and caused up-regulation of HvFT1 mRNA under long-day conditions. However, the transgenic plants retained a response to photoperiod, suggesting the presence of photoperiod response factors acting downstream of HvCO1 transcription. Analysis of a population segregating for HvCO1 over-expression and natural genetic variation at Ppd-H1 demonstrated that Ppd-H1 acts downstream of HvCO1 transcription on HvFT1 expression and flowering. Furthermore, variation at Ppd-H1 did not affect diurnal expression of HvCO1 or HvCO2. Over-expression of HvCO1 increased transcription of the spring allele of Vrn-H1 in long- and short-day conditions, while genetic variation at Ppd-H1 did not affect Vrn-H1 expression. Over-expression of HvCO1 and natural genetic variation at Ppd-H1 accelerated inflorescence development and stem elongation. Thus, HvCO1 probably induces flowering by activating HvFT1 whilst Ppd-H1 regulates HvFT1 independently of HvCO1 mRNA, and all three genes also appear to have a strong effect in promoting inflorescence development. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Controlling Factors of Soil CO2 Efflux in Pinus yunnanensis across Different Stand Ages

PubMed Central

Wang, Shaojun; Zhao, Jixia; Chen, Qibo

2015-01-01

The characteristics of soil respiration (Rs) across different stand ages have not been well investigated. In this study, we identified temporal variation of Rs and its driving factors under three nature forest stands (e.g. 15-yr-old, 30-yr-old, and 45-yr-old) of Pinus yunnanensis in the Plateau of Mid-Yunnan, China. No consistent tendency was found on the change of Rs with the stand ages. Rs was ranked in the order of 30-yr-old > 45-yr-old >15-yr-old. Rs in 15-yr-old stand was the most sensitive to soil temperature (Ts) among the three sites. However, Ts only explained 30-40% of the seasonal dynamics of Rs at the site. Soil water content (Sw) was the major controlling factor of temporal variation at the three sites. Sw explained 88-93% of seasonal variations of Rs in the 30-yr-old stand, and 63.7-72.7% in the 15-yr-old and 79.1-79.6% in the 45-yr-old stands. In addition, we found that pH, available nitrogen (AN), C/N and total phosphorus (TP) contributed significantly to the seasonal variation of Rs. Sw was significantly related with pH, total nitrogen (TN), AN and TP, suggesting that Sw can affect Rs through improving soil acid-base property and soil texture, and increasing availability of soil nutrient. The results indicated that besides soil water, soil properties (e. g. pH, AN, C/N and TP) were also the important in controlling the temporal variations of Rs across different stand ages in the nature forestry. PMID:25996943

Heavy Metals in the Atmosphere over the Northern Coast of Eurasia: Interannual Variations in Winter and Summer

NASA Astrophysics Data System (ADS)

Vinogradova, A. A.; Ivanova, Yu. A.

2017-12-01

Interannual variations in the level of anthropogenic contamination of the surface air in the northern areas of Russia are studied, which are related to a change in the direction of air mass transport. The transport of air and heavy metals to four sites located on territories of nature reserves on the coast of the Arctic Ocean (from the Kola Peninsula to a delta of the Lena River) in winter (January) and summer (July) is analyzed for 2000-2013. Indices of atmospheric circulation and data on the emission of pollutants into the atmosphere in cities and regions of Russia are involved in the analysis. Concentrations of seven heavy metals in the surface air are evaluated in the Arctic regions under study and their interannual, spatial, and seasonal variations are discussed. A strong interannual variability of atmospheric circulation differently influences the variations in the atmosphere contamination with different anthropogenic heavy metals in various areas of the north of Russia. The concentration ratios of heavy metals under study are different for each site in different years. The interannual and seasonal variations in the contamination level have maximum values for heavy metals arriving from most distant sources. Thus, the results of measuring the content of anthropogenic contaminants in the air of reference areas during one season or even one year should not serve a basis for longterm conclusions and forecasts. It would be also unjustified to make general conclusions on the contamination level of the environment from observation results for only one contaminant and/or only at a single site.

Purifying synthetic high-strength wastewater by microalgae chlorella vulgaris under various light emitting diode wavelengths and intensities

PubMed Central

2013-01-01

The high-strength wastewater is now well known as a threat to the natural water since it is highly possible to arouse water eutrophication or algal blooms. The effects of various light emitting diode wavelengths and intensities on the microalgae biological wastewater treatment system was studied in this research. The various nutrient removals and economic efficiencies represented similar variation trends, and these variations under both high C and N loading treatments were similar too. The order for microalgae C. vulgaris reproduction in terms of dry weight and nutrient removal efficiency both were red > white > yellow > blue, under high carbon and nitrogen loading treatments, indicating that the red light was the optimum light wavelength. Furthermore, considering the optimal light intensity in terms of nutrient removal efficiency was 2500 and 2000 μmol/m2•s, while in terms of economic efficiency was 1000, 1500 and 2000 μmol/m2•s. Therefore, the optimum light intensity was found to be 2000 μmol/m2•s. In addition, the optimal experimental illumination time was determined as 120 h. The Chlorella vulgaris microalgae biological wastewater treatment system utilized in this research was able to purify the high-strength carbon and nitrogen wastewater effectively under optimum light wavelength and intensity. PMID:24499586

GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

PubMed Central

Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

2015-01-01

Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

Multigenic Natural Variation Underlies Caenorhabditis elegans Olfactory Preference for the Bacterial Pathogen Serratia marcescens

PubMed Central

Glater, Elizabeth E.; Rockman, Matthew V.; Bargmann, Cornelia I.

2013-01-01

The nematode Caenorhabditis elegans can use olfaction to discriminate among different kinds of bacteria, its major food source. We asked how natural genetic variation contributes to choice behavior, focusing on differences in olfactory preference behavior between two wild-type C. elegans strains. The laboratory strain N2 strongly prefers the odor of Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to the odor of Escherichia coli, a commonly used laboratory food source. The divergent Hawaiian strain CB4856 has a weaker attraction to Serratia than the N2 strain, and this behavioral difference has a complex genetic basis. At least three quantitative trait loci (QTLs) from the CB4856 Hawaii strain (HW) with large effect sizes lead to reduced Serratia preference when introgressed into an N2 genetic background. These loci interact and have epistatic interactions with at least two antagonistic QTLs from HW that increase Serratia preference. The complex genetic architecture of this C. elegans trait is reminiscent of the architecture of mammalian metabolic and behavioral traits. PMID:24347628

Variation and evolution of male sex combs in Drosophila: nature of selection response and theories of genetic variation for sexual traits.

PubMed

Ahuja, Abha; Singh, Rama S

2008-05-01

We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.

Spatial and temporal demographic variation drives within-season fluctuations in sexual selection.

PubMed

Kasumovic, Michael M; Bruce, Matthew J; Andrade, Maydianne C B; Herberstein, Marie E

2008-09-01

Our understanding of selection in nature stems mainly from whole-season and cross-sectional estimates of selection gradients. These estimates suggest that selection is relatively constant within, but fluctuates between seasons. However, the strength of selection depends on demographics, and because demographics can vary within seasons, there is a gap in our understanding regarding the extent to which seasonal fluctuations in demographics may cause variation in selection. Here we use two populations of the golden orb-web spider (Nephila plumipes) that differ in density to examine how demographics change within a season and whether there are correlated shifts in selection. We demonstrate that there is within-season variation in sex ratio and density at multiple spatial and temporal scales. This variation led to changes in the competitive challenges that males encountered at different times of the season and was correlated with significant variation in selection gradients on male size and weight between sampling periods. We highlight the importance of understanding the biology of the organism under study to correctly determine the relevant scale in which to examine selection. We also argue that studies may underestimate the true variation in selection by averaging values, leading to misinterpretation of the effect of selection on phenotypic evolution.

Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?

PubMed

Dodd, Richard S; Hüberli, Daniel; Douhovnikoff, Vlad; Harnik, Tamar Y; Afzal-Rafii, Zara; Garbelotto, Matteo

2005-01-01

California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high.

Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector

PubMed Central

Dickson, Laura B.; Jiolle, Davy; Minard, Guillaume; Moltini-Conclois, Isabelle; Volant, Stevenn; Ghozlane, Amine; Bouchier, Christiane; Ayala, Diego; Paupy, Christophe; Moro, Claire Valiente; Lambrechts, Louis

2017-01-01

Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector. PMID:28835919

FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions

PubMed Central

Iwayama, Koji; Aisaka, Yuri; Kutsuna, Natsumaro

2017-01-01

Abstract Motivation: Considerable attention has been given to the quantification of environmental effects on organisms. In natural conditions, environmental factors are continuously changing in a complex manner. To reveal the effects of such environmental variations on organisms, transcriptome data in field environments have been collected and analyzed. Nagano et al. proposed a model that describes the relationship between transcriptomic variation and environmental conditions and demonstrated the capability to predict transcriptome variation in rice plants. However, the computational cost of parameter optimization has prevented its wide application. Results: We propose a new statistical model and efficient parameter optimization based on the previous study. We developed and released FIT, an R package that offers functions for parameter optimization and transcriptome prediction. The proposed method achieves comparable or better prediction performance within a shorter computational time than the previous method. The package will facilitate the study of the environmental effects on transcriptomic variation in field conditions. Availability and Implementation: Freely available from CRAN (https://cran.r-project.org/web/packages/FIT/). Contact: anagano@agr.ryukoku.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online PMID:28158396

The effects of oil spills on marine fish: Implications of spatial variation in natural mortality.

PubMed

Langangen, Ø; Olsen, E; Stige, L C; Ohlberger, J; Yaragina, N A; Vikebø, F B; Bogstad, B; Stenseth, N C; Hjermann, D Ø

2017-06-15

The effects of oil spills on marine biological systems are of great concern, especially in regions with high biological production of harvested resources such as in the Northeastern Atlantic. The scientific studies of the impact of oil spills on fish stocks tend to ignore that spatial patterns of natural mortality may influence the magnitude of the impact over time. Here, we first illustrate how spatial variation in natural mortality may affect the population impact by considering a thought experiment. Second, we consider an empirically based example of Northeast Arctic cod to extend the concept to a realistic setting. Finally, we present a scenario-based investigation of how the degree of spatial variation in natural mortality affects the impact over a gradient of oil spill sizes. Including the effects of spatial variations in natural mortality tends to widen the impact distribution, hence increasing the probability of both high and low impact events. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Characterizing Sub-Daily Flow Regimes: Implications of Hydrologic Resolution on Ecohydrology Studies

DOE PAGES

Bevelhimer, Mark S.; McManamay, Ryan A.; O'Connor, B.

2014-05-26

Natural variability in flow is a primary factor controlling geomorphic and ecological processes in riverine ecosystems. Within the hydropower industry, there is growing pressure from environmental groups and natural resource managers to change reservoir releases from daily peaking to run-of-river operations on the basis of the assumption that downstream biological communities will improve under a more natural flow regime. In this paper, we discuss the importance of assessing sub-daily flows for understanding the physical and ecological dynamics within river systems. We present a variety of metrics for characterizing sub-daily flow variation and use these metrics to evaluate general trends amongmore » streams affected by peaking hydroelectric projects, run-of-river projects and streams that are largely unaffected by flow altering activities. Univariate and multivariate techniques were used to assess similarity among different stream types on the basis of these sub-daily metrics. For comparison, similar analyses were performed using analogous metrics calculated with mean daily flow values. Our results confirm that sub-daily flow metrics reveal variation among and within streams that are not captured by daily flow statistics. Using sub-daily flow statistics, we were able to quantify the degree of difference between unaltered and peaking streams and the amount of similarity between unaltered and run-of-river streams. The sub-daily statistics were largely uncorrelated with daily statistics of similar scope. Furthermore, on short temporal scales, sub-daily statistics reveal the relatively constant nature of unaltered streamreaches and the highly variable nature of hydropower-affected streams, whereas daily statistics show just the opposite over longer temporal scales.« less

Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae

PubMed Central

Hope, Elyse A.; Dunham, Maitreya J.

2014-01-01

The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and “flocs” (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. PMID:25060625

Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae.

PubMed

Hope, Elyse A; Dunham, Maitreya J

2014-07-24

The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and "flocs" (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. Copyright © 2014 Hope and Dunham.

Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals.

PubMed

Suzuki, Taichi A

2017-10-01

Recent studies in model organisms have shown that compositional variation in the microbiome can affect a variety of host phenotypes including those related to digestion, development, immunity, and behavior. Natural variation in the microbiome within and between natural populations and species may also affect host phenotypes and thus fitness in the wild. Here, I review recent evidence that compositional variation in the microbiome may affect host phenotypes and fitness in wild mammals. Studies over the last decade indicate that natural variation in the mammalian microbiome may be important in the assistance of energy uptake from different diet types, detoxification of plant secondary compounds, protection from pathogens, chemical communication, and behavior. I discuss the importance of combining both field observations and manipulative experiments in a single system to fully characterize the functions and fitness effects of the microbiome. Finally, I discuss the evolutionary consequences of mammal-microbiome associations by proposing a framework to test how natural selection on hosts is mediated by the microbiome. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Segmental intelligibility of synthetic speech produced by rule.

PubMed

Logan, J S; Greene, B G; Pisoni, D B

1989-08-01

This paper reports the results of an investigation that employed the modified rhyme test (MRT) to measure the segmental intelligibility of synthetic speech generated automatically by rule. Synthetic speech produced by ten text-to-speech systems was studied and compared to natural speech. A variation of the standard MRT was also used to study the effects of response set size on perceptual confusions. Results indicated that the segmental intelligibility scores formed a continuum. Several systems displayed very high levels of performance that were close to or equal to scores obtained with natural speech; other systems displayed substantially worse performance compared to natural speech. The overall performance of the best system, DECtalk--Paul, was equivalent to the data obtained with natural speech for consonants in syllable-initial position. The findings from this study are discussed in terms of the use of a set of standardized procedures for measuring intelligibility of synthetic speech under controlled laboratory conditions. Recent work investigating the perception of synthetic speech under more severe conditions in which greater demands are made on the listener's processing resources is also considered. The wide range of intelligibility scores obtained in the present study demonstrates important differences in perception and suggests that not all synthetic speech is perceptually equivalent to the listener.

Segmental intelligibility of synthetic speech produced by rule

PubMed Central

Logan, John S.; Greene, Beth G.; Pisoni, David B.

2012-01-01

This paper reports the results of an investigation that employed the modified rhyme test (MRT) to measure the segmental intelligibility of synthetic speech generated automatically by rule. Synthetic speech produced by ten text-to-speech systems was studied and compared to natural speech. A variation of the standard MRT was also used to study the effects of response set size on perceptual confusions. Results indicated that the segmental intelligibility scores formed a continuum. Several systems displayed very high levels of performance that were close to or equal to scores obtained with natural speech; other systems displayed substantially worse performance compared to natural speech. The overall performance of the best system, DECtalk—Paul, was equivalent to the data obtained with natural speech for consonants in syllable-initial position. The findings from this study are discussed in terms of the use of a set of standardized procedures for measuring intelligibility of synthetic speech under controlled laboratory conditions. Recent work investigating the perception of synthetic speech under more severe conditions in which greater demands are made on the listener’s processing resources is also considered. The wide range of intelligibility scores obtained in the present study demonstrates important differences in perception and suggests that not all synthetic speech is perceptually equivalent to the listener. PMID:2527884

Natural frequencies of thin rectangular plates clamped on contour using the Finite Element Method

NASA Astrophysics Data System (ADS)

(Barboni Haţiegan, L.; Haţiegan, C.; Gillich, G. R.; Hamat, C. O.; Vasile, O.; Stroia, M. D.

2018-01-01

This paper presents the determining of natural frequencies of plates without and with damages using the finite element method of SolidWorks program. The first thirty natural frequencies obtained for thin rectangular rectangular plates clamped on contour without and with central damages a for different dimensions. The relative variation of natural frequency was determined and the obtained results by the finite element method (FEM) respectively relative variation of natural frequency, were graphically represented according to their vibration natural modes. Finally, the obtained results were compared.

A nanometallic nickel-coated, glass-fibre-based structural health monitoring system for polymer composites

NASA Astrophysics Data System (ADS)

Balaji, R.; Sasikumar, M.

2017-09-01

Glass-fibre-reinforced polymer matrix composites are widely used in various industries because of their unique high strength to weight ratio. Unlike metals, strain-induced and damage states of composites are complicated to predict under real-time loading due to their anisotropic nature. With that focus, a piezoresistive nanomaterial-based structural health monitoring system for laminated polymer composites is proposed to measure the strain induced in the composite under real-time loading. Nanometallic nickel-coated glass fibres are embedded into the polymer composites to monitor the strain and damage induced in them. The nanometallic nickel is coated over the glass fibre by a dip coating technique using epoxy as the binding agent. A microcontroller-based electrical resistance measurement system is used to measure the piezoresistive variation in the coated glass fibre under real-time loading. Using the piezoresistance variation of the embedded nanometallic nickel-coated glass fibre, the real-time strain and damage induced in the composite can be correlated. The piezoresistive response of the coated glass fibre is descibed in two phases, the deformation phase and the failure phase, which clearly show the various states of strain and damage induced in the composites.

Deuterium: Natural variations used as a biological tracer

USGS Publications Warehouse

Gleason, J.D.; Friedman, I.

1970-01-01

The suggestion is made that isotope tracing be carried out by monitoring the natural variations in deuterium concentrations. As an example, the natural variations in deuterium concentrations between food and water collected in Illinois and food and water collected in Colorado were used to determine the residence time of water in the blood and urine of rats. We observed not only a 51/2-day turnover time of water in the blood and urine, but also evidence for the influx of water vapor from the atmosphere through the lungs into the blood.

An analytical variational method for the biased quantum Rabi model in the ultra-strong coupling regime

NASA Astrophysics Data System (ADS)

Mao, Bin-Bin; Liu, Maoxin; Wu, Wei; Li, Liangsheng; Ying, Zu-Jian; Luo, Hong-Gang

2018-05-01

Not Available Project supported by the National Natural Science Foundation of China (Grant Nos. 11674139, 11604009, and 11704025), the Program for Changjiang Scholars and Innovative Research Team in University, China (Grant No. IRT-16R35), and the Fundamental Research Funds for the Central Universities, China. ZJY also acknowledges the financial support of the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open Grant No. 618083 (CNTQC).

Characterization of aluminum selenide bi-layer thin film

NASA Astrophysics Data System (ADS)

Boolchandani, Sarita; Soni, Gyanesh; Srivastava, Subodh; Vijay, Y. K.

2018-05-01

The Aluminum Selenide (AlSe) bi-layer thin films were grown on glass substrate using thermal evaporation method under high vacuum condition. The morphological characterization was done using SEM. Electrical measurement with temperature variation shows that thin films exhibit the semiconductor nature. The optical properties of prepared thin films have also been characterized by UV-VIS spectroscopy measurements. The band gap of composite thin films has been calculated by Tauc's relation at different temperature ranging 35°C-100°C.

The relative nature of fertilization success: Implications for the study of post-copulatory sexual selection

PubMed Central

2008-01-01

Background The determination of genetic variation in sperm competitive ability is fundamental to distinguish between post-copulatory sexual selection models based on good-genes vs compatible genes. The sexy-sperm and the good-sperm hypotheses for the evolution of polyandry require additive (intrinsic) effects of genes influencing sperm competitiveness, whereas the genetic incompatibility hypothesis invokes non-additive genetic effects. A male's sperm competitive ability is typically estimated from his fertilization success, a measure that is dependent on the ability of rival sperm competitors to fertilize the ova. It is well known that fertilization success may be conditional to genotypic interactions among males as well as between males and females. However, the consequences of effects arising from the random sampling of sperm competitors upon the estimation of genetic variance in sperm competitiveness have been overlooked. Here I perform simulations of mating trials performed in the context of sibling analysis to investigate whether the ability to detect additive genetic variance underlying the sperm competitiveness phenotype is hindered by the relative nature of fertilization success measurements. Results Fertilization success values render biased sperm competitive ability values. Furthermore, asymmetries among males in the errors committed when estimating sperm competitive abilities are likely to exist as long as males exhibit variation in sperm competitiveness. Critically, random effects arising from the relative nature of fertilization success lead to an underestimation of underlying additive genetic variance in sperm competitive ability. Conclusion The results show that, regardless of the existence of genotypic interactions affecting the output of sperm competition, fertilization success is not a perfect predictor of sperm competitive ability because of the stochasticity of the background used to obtain fertilization success measures. Random effects need to be considered in the debate over the maintenance of genetic variation in sperm competitiveness, and when testing good-genes and compatible-genes processes as explanations of polyandrous behaviour using repeatability/heritability data in sperm competitive ability. These findings support the notion that the genetic incompatibility hypothesis needs to be treated as an alternative hypothesis, rather than a null hypothesis, in studies that fail to detect intrinsic sire effects on the sperm competitiveness phenotype. PMID:18474087

Vibration-based structural health monitoring using adaptive statistical method under varying environmental condition

NASA Astrophysics Data System (ADS)

Jin, Seung-Seop; Jung, Hyung-Jo

2014-03-01

It is well known that the dynamic properties of a structure such as natural frequencies depend not only on damage but also on environmental condition (e.g., temperature). The variation in dynamic characteristics of a structure due to environmental condition may mask damage of the structure. Without taking the change of environmental condition into account, false-positive or false-negative damage diagnosis may occur so that structural health monitoring becomes unreliable. In order to address this problem, an approach to construct a regression model based on structural responses considering environmental factors has been usually used by many researchers. The key to success of this approach is the formulation between the input and output variables of the regression model to take into account the environmental variations. However, it is quite challenging to determine proper environmental variables and measurement locations in advance for fully representing the relationship between the structural responses and the environmental variations. One alternative (i.e., novelty detection) is to remove the variations caused by environmental factors from the structural responses by using multivariate statistical analysis (e.g., principal component analysis (PCA), factor analysis, etc.). The success of this method is deeply depending on the accuracy of the description of normal condition. Generally, there is no prior information on normal condition during data acquisition, so that the normal condition is determined by subjective perspective with human-intervention. The proposed method is a novel adaptive multivariate statistical analysis for monitoring of structural damage detection under environmental change. One advantage of this method is the ability of a generative learning to capture the intrinsic characteristics of the normal condition. The proposed method is tested on numerically simulated data for a range of noise in measurement under environmental variation. A comparative study with conventional methods (i.e., fixed reference scheme) demonstrates the superior performance of the proposed method for structural damage detection.

Understanding the effect of carbon status on stem diameter variations

PubMed Central

De Swaef, Tom; Driever, Steven M.; Van Meulebroek, Lieven; Vanhaecke, Lynn; Marcelis, Leo F. M.; Steppe, Kathy

2013-01-01

Background Carbon assimilation and leaf-to-fruit sugar transport are, along with plant water status, the driving mechanisms for fruit growth. An integrated comprehension of the plant water and carbon relationships is therefore essential to better understand water and dry matter accumulation. Variations in stem diameter result from an integrated response to plant water and carbon status and are as such a valuable source of information. Methods A mechanistic water flow and storage model was used to relate variations in stem diameter to phloem sugar loading and sugar concentration dynamics in tomato. The simulation results were compared with an independent model, simulating phloem sucrose loading at the leaf level based on photosynthesis and sugar metabolism kinetics and enabled a mechanistic interpretation of the ‘one common assimilate pool’ concept for tomato. Key Results Combining stem diameter variation measurements and mechanistic modelling allowed us to distinguish instantaneous dynamics in the plant water relations and gradual variations in plant carbon status. Additionally, the model combined with stem diameter measurements enabled prediction of dynamic variables which are difficult to measure in a continuous and non-destructive way, such as xylem water potential and phloem hydrostatic potential. Finally, dynamics in phloem sugar loading and sugar concentration were distilled from stem diameter variations. Conclusions Stem diameter variations, when used in mechanistic models, have great potential to continuously monitor and interpret plant water and carbon relations under natural growing conditions. PMID:23186836

Natural Variation in the Thermotolerance of Neural Function and Behavior due to a cGMP-Dependent Protein Kinase

PubMed Central

Dawson-Scully, Ken; Armstrong, Gary A.B.; Kent, Clement; Robertson, R. Meldrum; Sokolowski, Marla B.

2007-01-01

Although it is acknowledged that genetic variation contributes to individual differences in thermotolerance, the specific genes and pathways involved and how they are modulated by the environment remain poorly understood. We link natural variation in the thermotolerance of neural function and behavior in Drosophila melanogaster to the foraging gene (for, which encodes a cGMP-dependent protein kinase (PKG)) as well as to its downstream target, protein phosphatase 2A (PP2A). Genetic and pharmacological manipulations revealed that reduced PKG (or PP2A) activity caused increased thermotolerance of synaptic transmission at the larval neuromuscular junction. Like synaptic transmission, feeding movements were preserved at higher temperatures in larvae with lower PKG levels. In a comparative assay, pharmacological manipulations altering thermotolerance in a central circuit of Locusta migratoria demonstrated conservation of this neuroprotective pathway. In this circuit, either the inhibition of PKG or PP2A induced robust thermotolerance of neural function. We suggest that PKG and therefore the polymorphism associated with the allelic variation in for may provide populations with natural variation in heat stress tolerance. for's function in behavior is conserved across most organisms, including ants, bees, nematodes, and mammals. PKG's role in thermotolerance may also apply to these and other species. Natural variation in thermotolerance arising from genes involved in the PKG pathway could impact the evolution of thermotolerance in natural populations. PMID:17712421

Hard and Soft Selection Revisited: How Evolution by Natural Selection Works in the Real World.

PubMed

Reznick, David

2016-01-01

The modern synthesis of evolutionary biology unified Darwin's natural selection with Mendelian genetics, but at the same time it created the dilemma of genetic load. Lewontin and Hubby's (1966) and Harris's (1966) characterization of genetic variation in natural populations increased the apparent burden of this load. Neutrality or near neutrality of genetic variation was one mechanism proposed for the revealed excessive genetic variation. Bruce Wallace coined the term "soft selection" to describe an alternative way for natural selection to operate that was consistent with observed variation. He envisioned nature as presenting ecological vacancies that could be filled by diverse genotypes. Survival and successful reproduction was a combined function of population density, genotype, and genotype frequencies, rather than a fixed value of the relative fitness of each genotype. My goal in this review is to explore the importance of soft selection in the real world. My motive and that of my colleagues as described here is not to explain what maintains genetic variation in natural populations, but rather to understand the factors that shape how organisms adapt to natural environments. We characterize how feedbacks between ecology and evolution shape both evolution and ecology. These feedbacks are mediated by density- and frequency-dependent selection, the mechanisms that underlie soft selection. Here, I report on our progress in characterizing these types of selection with a combination of a consideration of the published literature and the results from my collaborators' and my research on natural populations of guppies. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies

PubMed Central

Acland, Gregory M.

2014-01-01

Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision. PMID:22065099

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

PubMed Central

Quintela, María; Johansson, Magnus P.; Kristjánsson, Bjarni K.; Barreiro, Rodolfo; Laurila, Anssi

2014-01-01

The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence. PMID:25007329

Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies.

PubMed

Miyadera, Keiko; Acland, Gregory M; Aguirre, Gustavo D

2012-02-01

Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision.

Loci under selection during multiple range expansions of an invasive plant are mostly population specific, but patterns are associated with climate.

PubMed

Zenni, Rafael D; Hoban, Sean M

2015-07-01

Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate-related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene-level patterns of evolution may be population specific. © 2015 John Wiley & Sons Ltd.

Bold Colors in a Cryptic Lineage: Do Eastern Indigo Snakes Exhibit Color Dimorphism?

PubMed Central

Deitloff, Jennifer; Johnson, Valerie M.; Guyer, Craig

2013-01-01

Many species exhibit variation in the color of their scales, feathers, or fur. Various forms of natural selection, such as mimicry, crypsis, and species recognition, as well as sexual selection, can influence the evolution of color. Eastern Indigo Snakes (Drymarchon couperi), a federally threatened species, have coloration on the sides of the head and the chin that can vary from black to red or cream. Despite significant conservations efforts for this species, little is known about its biology in the field. Past researchers have proposed that the color variation on the head and chin is associated with the sex of the individual. Alternatively, color might vary among individuals because it is controlled by genes that are under natural selection or neutral evolution. We tested these alternative hypotheses by examining whether coloration of the sublabial, submaxillary, and ventral scales of this species differed by sex or among clutches. We used color spectrometry to characterize important aspects of color in two ways: by examining overall color differences across the entire color spectrum and by comparing differences within the ultraviolet, yellow, and red colorbands. We found that Eastern Indigo Snakes do not exhibit sexual dichromatism, but their coloration does vary among clutches; therefore, the pattern of sexual selection leading to sexual dichromatism observed in many squamates does not appear to play a role in the evolution and maintenance of color variation in Eastern Indigo Snakes. We suggest that future studies should focus on determining whether color variation in these snakes is determined by maternal effects or genetic components and if color is influenced by natural selection or neutral evolutionary processes. Studying species that exhibit bright colors within lineages that are not known for such coloration will contribute greatly to our understanding of the evolutionary and ecological factors that drive these differences. PMID:23691245

Low-level contrast statistics are diagnostic of invariance of natural textures

PubMed Central

Groen, Iris I. A.; Ghebreab, Sennay; Lamme, Victor A. F.; Scholte, H. Steven

2012-01-01

Texture may provide important clues for real world object and scene perception. To be reliable, these clues should ideally be invariant to common viewing variations such as changes in illumination and orientation. In a large image database of natural materials, we found textures with low-level contrast statistics that varied substantially under viewing variations, as well as textures that remained relatively constant. This led us to ask whether textures with constant contrast statistics give rise to more invariant representations compared to other textures. To test this, we selected natural texture images with either high (HV) or low (LV) variance in contrast statistics and presented these to human observers. In two distinct behavioral categorization paradigms, participants more often judged HV textures as “different” compared to LV textures, showing that textures with constant contrast statistics are perceived as being more invariant. In a separate electroencephalogram (EEG) experiment, evoked responses to single texture images (single-image ERPs) were collected. The results show that differences in contrast statistics correlated with both early and late differences in occipital ERP amplitude between individual images. Importantly, ERP differences between images of HV textures were mainly driven by illumination angle, which was not the case for LV images: there, differences were completely driven by texture membership. These converging neural and behavioral results imply that some natural textures are surprisingly invariant to illumination changes and that low-level contrast statistics are diagnostic of the extent of this invariance. PMID:22701419

Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abraham, Paul E.; Wang, Xiaojing; Ranjan, Priya

The availability of next-generation sequencing technologies has rapidly transformed our ability to link genotypes to phenotypes, and as such, promises to facilitate the dissection of genetic contribution to complex traits. Although discoveries of genetic associations will further our understanding of biology, once candidate variants have been identified, investigators are faced with the challenge of characterizing the functional effects on proteins encoded by such genes. Here we show how next-generation RNA sequencing data can be exploited to construct genotype-specific protein sequence databases, which provide a clearer picture of the molecular toolbox underlying cellular and organismal processes and their variation in amore » natural population. For this study, we used two individual genotypes (DENA-17-3 and VNDL-27-4) from a recent genome wide association (GWA) study of Populus trichocarpa, an obligate outcrosser that exhibits tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs) and insertions and deletions (INDELS). Based on large-scale identification of SAAPs, we profiled the frequency of 128 types of naturally occurring amino acid substitutions, with a subset of SAAPs occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. In addition, we were able to explore the diploid landscape of Populus at the proteome-level, allowing the characterization of heterozygous variants.« less

Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa

DOE PAGES

Abraham, Paul E.; Wang, Xiaojing; Ranjan, Priya; ...

2015-10-20

The availability of next-generation sequencing technologies has rapidly transformed our ability to link genotypes to phenotypes, and as such, promises to facilitate the dissection of genetic contribution to complex traits. Although discoveries of genetic associations will further our understanding of biology, once candidate variants have been identified, investigators are faced with the challenge of characterizing the functional effects on proteins encoded by such genes. Here we show how next-generation RNA sequencing data can be exploited to construct genotype-specific protein sequence databases, which provide a clearer picture of the molecular toolbox underlying cellular and organismal processes and their variation in amore » natural population. For this study, we used two individual genotypes (DENA-17-3 and VNDL-27-4) from a recent genome wide association (GWA) study of Populus trichocarpa, an obligate outcrosser that exhibits tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs) and insertions and deletions (INDELS). Based on large-scale identification of SAAPs, we profiled the frequency of 128 types of naturally occurring amino acid substitutions, with a subset of SAAPs occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. In addition, we were able to explore the diploid landscape of Populus at the proteome-level, allowing the characterization of heterozygous variants.« less

Effect of temperature on the permeability of gas adsorbed coal under triaxial stress conditions

NASA Astrophysics Data System (ADS)

Li, Xiangchen; Yan, Xiaopeng; Kang, Yili

2018-04-01

The combined effects of gas sorption, stress and temperature play a significant role in the changing behavior of gas permeability in coal seams. The effect of temperature on nitrogen and methane permeability of naturally fractured coal is investigated. Coal permeability, P-wave velocity and axial strain were simultaneously measured under two effective stresses and six different temperatures. The results showed that the behavior of nitrogen and methane permeability presented nonmonotonic changes with increasing temperature. The variation in the P-wave velocity and axial strain showed a good correspondence with coal permeability. A higher effective stress limited the bigger deformation and caused the small change in permeability. Methane adsorption and desorption significantly influence the mechanical properties of coal and play an important role in the variations in coal permeability. The result of coal permeability during a complete stress-strain process showed that the variation in permeability is determined by the evolution of the internal structure. The increase in the temperature of the gas saturated coal causes the complex interaction between matrix swelling, matrix shrinkage and micro-fracture generation, which leads to the complex changes in coal structure and permeability. These results are helpful to understand the gas transport mechanism for exploiting coal methane by heat injection.

Genotypic variation influences reproductive success and thermal stress tolerance in the reef building coral, Acropora palmata

NASA Astrophysics Data System (ADS)

Baums, I. B.; Devlin-Durante, M. K.; Polato, N. R.; Xu, D.; Giri, S.; Altman, N. S.; Ruiz, D.; Parkinson, J. E.; Boulay, J. N.

2013-09-01

The branching coral Acropora palmata is a foundation species of Caribbean reefs that has been decimated in recent decades by anthropogenic and natural stressors. Declines in population density and genotypic diversity likely reduce successful sexual reproduction in this self-incompatible hermaphrodite and might impede recovery. We investigated variation among genotypes in larval development under thermally stressful conditions. Six two-parent crosses and three four-parent batches were reared under three temperatures and sampled over time. Fertilization rates differed widely with two-parent crosses having lower fertilization rates (5-56 %, mean 22 % ± 22 SD) than batches (from 31 to 87 %, mean 59 % ± 28 SD). Parentage analysis of larvae in batch cultures showed differences in gamete compatibility among parents, coinciding with significant variation in both sperm morphology and egg size. While all larval batches developed more rapidly at increased water temperatures, rate of progression through developmental stages varied among batches, as did swimming speed. Together, these results indicate that loss of genotypic diversity exacerbates already severe limitations in sexual reproductive success of A. palmata. Nevertheless, surviving parental genotypes produce larvae that do vary in their phenotypic response to thermal stress, with implications for adaptation, larval dispersal and population connectivity in the face of warming sea surface temperatures.

Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

PubMed

Ren, Jing; Chen, Liang; Jin, Xiaoli; Zhang, Miaomiao; You, Frank M; Wang, Jirui; Frenkel, Vladimir; Yin, Xuegui; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2017-01-01

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ F ST ≤ 0.15) or high genetic differentiation ( F ST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different F ST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

[Distribution characteristics of soil organic carbon of burned area under different restorations.

PubMed

Li, Hong Yun; Xin, Ying; Zhao, Yu Sen

2016-09-01

The distribution characteristics of soil organic carbon (SOC), soil dissolved organic carbon (DOC) and soil microbial biomass carbon (MBC) under different restorations were studied in Larix gmelinii plantation, Pinus sylvestris var. mongolica plantation, artificial promotion poplar-birch forest and the natural secondary poplar-birch forest restored from burned area after the severe fire of Greater Xing' an Mountains in 1987. The results showed that the variations in SOC, DOC and MBC ranged from 9.63 to 79.72 g·kg -1 , from 33.21 to 186.30 mg·kg -1 and from 200.85 to 1755.63 mg·kg -1 , respectively, which decreased with soil depth increasing. There was significant diffe-rence in SOC, DOC and MBC among different restorations, with the maximum carbon contents for artificial promotion poplar-birch forest, followed by L. gmelinii plantation, natural secondary poplar-birch forest and P. sylvestris var. mongolica plantation successively. The soil microbial quotient va-ried from 1.1% under P. sylvestris var. mongolica plantation to 2.3% under artificial promotion poplar-birch forest, and its vertical distributions were different in the four restoration forests. Correlation analysis indicated that MBC had a significant positive correlation with SOC and DOC, respectively. The activity of soil organic carbon in artificial promotion poplar-birch forest was higher than in other forest stands, suggesting a stronger capacity of the soil carbon cycle through natural regeneration with artificial promotion on burned area in Greater Xing'an Mountains.

Transport of oxaliplatin species in water-saturated natural soil.

PubMed

Goykhman, Natalia; Dror, Ishai; Berkowitz, Brian

2018-06-05

This study reports the transport characteristics of the organometallic anticancer compound oxaliplatin and its derivatives in natural soil-water environments. Although pharmaceuticals and their derivatives have for many years been detected in water resources, and linked to toxicological impacts on ecological systems, their transport in soil and groundwater is not fully understood. Specifically, studies that describe transport of organometallic pharmaceuticals in porous media are rare, and the transport characteristics of platinum complexes have received little attention. Oxaliplatin transport was studied in sand, as a function of two added natural chelators (citrate and humic acid), and in soil, under four continuously monitored, environmentally-relevant redox conditions: oxic, nitrate reducing, iron reducing and methanogenic. In sand, oxaliplatin species retention was about 7%, and affected only mildly by added citrate, and by humic acid under buffered pH. Transport with unbuffered humic acid was affected significantly by pH variations, and exhibited strong retention at pH < 8. In soil, unexpectedly similar breakthrough patterns of oxaliplatin species were found for all redox conditions, exhibiting linear, reversible retention of 79-87%. The strongest retention was observed under iron reducing conditions, whereas the weakest retention was under oxic conditions. Increased cation activity appears to promote weaker sorption. The results indicate that soil composition is the leading factor affecting oxaliplatin species mobility and fate in the soil-water environment, followed by the weaker factors of redox conditions and cation activities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sedimentation and response to sea-level rise of a restored marsh with reduced tidal exchange: Comparison with a natural tidal marsh

USGS Publications Warehouse

Vandenbruwaene, W.; Maris, T.; Cahoon, D.R.; Meire, P.; Temmerman, S.

2011-01-01

Along coasts and estuaries, formerly embanked land is increasingly restored into tidal marshes in order to re-establish valuable ecosystem services, such as buffering against flooding. Along the Scheldt estuary (Belgium), tidal marshes are restored on embanked land by allowing a controlled reduced tide (CRT) into a constructed basin, through a culvert in the embankment. In this way tidal water levels are significantly lowered (ca. 3 m) so that a CRT marsh can develop on formerly embanked land with a ca. 3 m lower elevation than the natural tidal marshes. In this study we compared the long-term change in elevation (ΔE) within a CRT marsh and adjacent natural tidal marsh. Over a period of 4 years, the observed spatio-temporal variations in ΔE rate were related to variations in inundation depth, and this relationship was not significantly different for the CRT marsh and natural tidal marsh. A model was developed to simulate the ΔE over the next century. (1) Under a scenario without mean high water level (MHWL) rise in the estuary, the model shows that the marsh elevation-ΔE feedback that is typical for a natural tidal marsh (i.e. rising marsh elevation results in decreasing inundation depth and therefore a decreasing increase in elevation) is absent in the basin of the CRT marsh. This is because tidal exchange of water volumes between the estuary and CRT marsh are independent from the CRT marsh elevation but dependent on the culvert dimensions. Thus the volume of water entering the CRT remains constant regardless of the marsh elevation. Consequently the CRT MHWL follows the increase in CRT surface elevation, resulting after 75 years in a 2–2.5 times larger elevation gain in the CRT marsh, and a faster reduction of spatial elevation differences. (2) Under a scenario of constant MHWL rise (historical rate of 1.5 cm a-1), the equilibrium elevation (relative to MHWL) is 0.13 m lower in the CRT marsh and is reached almost 2 times faster. (3) Under a scenario of accelerated MHWL rise (acceleration of 0.02 cm a-1), the CRT marsh is much less able to keep up with the MHWL rise; after 75 years the CRT elevation is already 0.21 m lower than for the natural marsh. In conclusion, this study demonstrates that although short-term (4 years) ΔE rates are similar in a restored CRT marsh and natural tidal marsh, these ecosystems may evolve differently in response to sea-level rise in the longer term (10–100 years).

Molecular mechanisms of epigenetic variation in plants.

PubMed

Fujimoto, Ryo; Sasaki, Taku; Ishikawa, Ryo; Osabe, Kenji; Kawanabe, Takahiro; Dennis, Elizabeth S

2012-01-01

Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.

The natural selection of altruistic traits.

PubMed

Boehm, C

1999-09-01

Proponents of the standard evolutionary biology paradigm explain human "altruism" in terms of either nepotism or strict reciprocity. On that basis our underlying nature is reduced to a function of inclusive fitness: human nature has to be totally selfish or nepotistic. Proposed here are three possible paths to giving costly aid to nonrelatives, paths that are controversial because they involve assumed pleiotropic effects or group selection. One path is pleiotropic subsidies that help to extend nepotistic helping behavior from close family to nonrelatives. Another is "warfare"-if and only if warfare recurred in the Paleolithic. The third and most plausible hypothesis is based on the morally based egalitarian syndrome of prehistoric hunter-gatherers, which reduced phenotypic variation at the within-group level, increased it at the between-group level, and drastically curtailed the advantages of free riders. In an analysis consistent with the fundamental tenets of evolutionary biology, these three paths are evaluated as explanations for the evolutionary development of a rather complicated human social nature.

Developmental constraints shape the evolution of the nematode mid-developmental transition.

PubMed

Zalts, Harel; Yanai, Itai

2017-03-27

Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same 'hourglass' pattern of variation may result from increased positive selection at the earlier and later stages of development. To distinguish between these scenarios, we examined gene expression variation in a population of the nematode Caenorhabditis elegans using an experimental design that eliminated the influence of positive selection. By measuring gene expression for all genes throughout development in 20 strains, we found that variations were highly uneven throughout development, with a significant depletion during mid-embryogenesis. In particular, the family of homeodomain transcription factors, whose expression generally coincides with mid-embryogenesis, evolved under high constraint. Our data further show that genes responsible for the integration of germ layers during morphogenesis are the most constrained class of genes. Together, these results provide strong evidence for developmental constraints as the mechanism underlying the hourglass model of animal evolution. Understanding the pattern and mechanism of developmental constraints provides a framework to understand how evolutionary processes have interacted with embryogenesis and led to the diversity of animal life on Earth.

Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

PubMed Central

2013-01-01

Background Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. Results To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70–15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. Conclusions We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization. PMID:24341723

Flutter Analysis of a Transonic Fan

NASA Technical Reports Server (NTRS)

Srivastava, R.; Bakhle, M. A.; Keith, T. G., Jr.; Stefko, G. L.

2002-01-01

This paper describes the calculation of flutter stability characteristics for a transonic forward swept fan configuration using a viscous aeroelastic analysis program. Unsteady Navier-Stokes equations are solved on a dynamically deforming, body fitted, grid to obtain the aeroelastic characteristics using the energy exchange method. The non-zero inter-blade phase angle is modeled using phase-lagged boundary conditions. Results obtained show good correlation with measurements. It is found that the location of shock and variation of shock strength strongly influenced stability. Also, outboard stations primarily contributed to stability characteristics. Results demonstrate that changes in blade shape impact the calculated aerodynamic damping, indicating importance of using accurate blade operating shape under centrifugal and steady aerodynamic loading for flutter prediction. It was found that the calculated aerodynamic damping was relatively insensitive to variation in natural frequency.

The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes.

PubMed

Hayden, Eric J; Bratulic, Sinisa; Koenig, Iwo; Ferrada, Evandro; Wagner, Andreas

2014-02-01

The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population's response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.

Spatial variation in abiotic and biotic factors in a floodplain determine anuran body size and growth rate at metamorphosis.

PubMed

Indermaur, Lukas; Schmidt, Benedikt R; Tockner, Klement; Schaub, Michael

2010-07-01

Body size at metamorphosis is a critical trait in the life history of amphibians. Despite the wide-spread use of amphibians as experimental model organisms, there is a limited understanding of how multiple abiotic and biotic factors affect the variation in metamorphic traits under natural conditions. The aim of our study was to quantify the effects of abiotic and biotic factors on spatial variation in the body size of tadpoles and size at metamorphosis of the European common toad (Bufo b. spinosus). Our study population was distributed over the riverbed (active tract) and the fringing riparian forest of a natural floodplain. The riverbed had warm ponds with variable hydroperiod and few predators, whereas the forest had ponds with the opposite characteristics. Spatial variation in body size at metamorphosis was governed by the interactive effects of abiotic and biotic factors. The particular form of the interaction between water temperature and intraspecific tadpole density suggests that abiotic factors laid the foundation for biotic factors: intraspecific density decreased growth only at high temperature. Predation and intraspecific density jointly reduced metamorphic size. Interspecific density had a negligible affect on body size at metamorphosis, suggesting weak inter-anuran interactions in the larval stage. Population density at metamorphosis was about one to two orders of magnitudes higher in the riverbed ponds than in the forest ponds, mainly because of lower tadpole mortality. Based on our results, we conclude that ponds in the riverbed appear to play a pivotal role for the population because tadpole growth and survival is best in this habitat.

Centennial to millennial variations of atmospheric methane during the early Holocene

NASA Astrophysics Data System (ADS)

Yang, Ji-Woong; Ahn, Jinho; Brook, Edward

2015-04-01

Atmospheric CH4 is one of the most important greenhouse gases. Ice core studies revealed strong correlations between millennial CH4 variations and Greenland climate during the last glacial period. However, millennial to sub-millennial CH4 variations during interglacial periods are not well studied. Recently, several high-resolution data sets have been produced for the late Holocene, but it is difficult to distinguish natural- from anthropogenic changes. In contrast, the methane budget of the early Holocene is not affected by anthropogenic disturbances, thus may help us better understand natural CH4 control mechanisms under interglacial climate boundary conditions. Here we present our new high-precision and high-resolution atmospheric CH4 record from Siple Dome ice core, Antarctica that covers the early Holocene. We used our new wet extraction system at Seoul National University that shows a good precision of ~1 ppb. Our data show several tens of ppb of centennial- to millennial CH4 variations and an anti-correlative evolution with Greenland climate on the millennial time scale. The CH4 record could have been affected by many different types of forcing, including temperature, precipitation (monsoon intensity), biomass burning, sea surface temperature, and solar activity. According to our data, early Holocene CH4 is well correlated with records of hematite stained grains (HSG) in North Atlantic sediment records, within age uncertainties. A red-noise spectral analysis yields peaks at frequencies of ~1270 and ~80 years, which are similar to solar frequencies, but further investigations are needed to determine major controlling factor of atmospheric CH4during the early Holocene.

Is biotic resistance enhanced by natural variation in diversity?

USGS Publications Warehouse

Grace, James B.; Harrison, Susan P.; Cornell, Howard

2017-01-01

Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the underlying processes by dissecting how biotic resistance to new invaders may be shaped by the same environmental influences that determine diversity and other community properties.In grasslands with heterogeneous soils, we added invaders and removed competitors to analyze the causes of invasion resistance. Abiotic resistance was measured using invader success in the absence of the resident community. Biotic resistance was measured as the reduction in invader success in the presence of the resident community.Invaders were most successful where biotic resistance was lowest and abiotic resistance was highest, confirming the dominant role of biotic resistance. Contrary to theory, though, biotic resistance was highest where both species richness and functional diversity were lowest. In the multivariate framework of a structural equation model, biotic resistance was independent of community diversity, and was highest where fertile soils led to high community biomass.Seed predation slightly augmented biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results.We conclude that in natural systems, diversity may be correlated with invasibility and yet have little effect on biotic resistance to invasion. More generally, the environmental causes of variation in diversity should be considered when examining the potential functional consequences of diversity.

Genetic architecture of the circadian clock and flowering time in Brassica rapa.

PubMed

Lou, P; Xie, Q; Xu, X; Edwards, C E; Brock, M T; Weinig, C; McClung, C R

2011-08-01

The circadian clock serves to coordinate physiology and behavior with the diurnal cycles derived from the daily rotation of the earth. In plants, circadian rhythms contribute to growth and yield and, hence, to both agricultural productivity and evolutionary fitness. Arabidopsis thaliana has served as a tractable model species in which to dissect clock mechanism and function, but it now becomes important to define the extent to which the Arabidopsis model can be extrapolated to other species, including crops. Accordingly, we have extended our studies to the close Arabidopsis relative and crop species, Brassica rapa. We have investigated natural variation in circadian function and flowering time among multiple B. rapa collections. There is wide variation in clock function, based on a robust rhythm in cotyledon movement, within a collection of B. rapa accessions, wild populations and recombinant inbred lines (RILs) derived from a cross between parents from two distinct subspecies, a rapid cycling Chinese cabbage (ssp. pekinensis) and a Yellow Sarson oilseed (ssp. trilocularis). We further analyzed the RILs to identify the quantitative trait loci (QTL) responsible for this natural variation in clock period and temperature compensation, as well as for flowering time under different temperature and day length settings. Most clock and flowering-time QTL mapped to overlapping chromosomal loci. We have exploited micro-synteny between the Arabidopsis and B. rapa genomes to identify candidate genes for these QTL.

Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens.

PubMed

Schulenburg, Hinrich; Ewbank, Jonathan J

2004-11-22

Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts.

Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens

PubMed Central

Schulenburg, Hinrich; Ewbank, Jonathan J

2004-01-01

Background Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. Results Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. Conclusions The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts. PMID:15555070

Motives underlying healthy eating: using the Food Choice Questionnaire to explain variation in dietary intake.

PubMed

Pollard, T M; Steptoe, A; Wardle, J

1998-04-01

The Food Choice Questionnaire (FCQ), which measures the reported importance to a given individual of nine factors underlying food choice, and a food frequency questionnaire, were administered to 241 participants, who were also required to classify their diet as either 'standard', 'low in red meat' or 'vegetarian'. Respondents describing their diet as low in red meat attributed greater importance to health, natural content, weight control and ethical concern in their food choice than did those who described their diets as standard, whereas vegetarians differed significantly from those with a standard diet only on the score for ethical concern. Differences between men and women and between students and non-students in the frequency of consumption of a number of foods were shown to be mediated by differences in the importance attached to FCQ factors. Thus the generally healthier diets of women compared to men appeared to be accounted for by the greater importance attributed by women to weight control, natural content and ethical concerns.

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

PubMed Central

Shen, Xia; De Jonge, Jennifer; Forsberg, Simon K. G.; Pettersson, Mats E.; Sheng, Zheya; Hennig, Lars; Carlborg, Örjan

2014-01-01

As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress. PMID:25503602

Effect of Chemical Treatments on Flax Fibre Reinforced Polypropylene Composites on Tensile and Dome Forming Behaviour

PubMed Central

Wang, Wentian; Lowe, Adrian; Kalyanasundaram, Shankar

2015-01-01

Tensile tests were performed on two different natural fibre composites (same constituent material, similar fibre fraction and thickness but different weave structure) to determine changes in mechanical properties caused by various aqueous chemical treatments and whether any permanent changes remain on drying. Scanning electronic microscopic examinations suggested that flax fibres and the flax/polypropylene interface were affected by the treatments resulting in tensile property variations. The ductility of natural fibre composites was improved significantly under wet condition and mechanical properties (elongation-to-failure, stiffness and strength) can almost retain back to pre-treated levels when dried from wet condition. Preheating is usually required to improve the formability of material in rapid forming, and the chemical treatments performed in this study were far more effective than preheating. The major breakthrough in improving the formability of natural fibre composites can aid in rapid forming of this class of material system. PMID:25789505

How could fully scaled carps appear in natural waters in Madagascar?

PubMed Central

Hervet, Caroline

2016-01-01

The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the ‘mirror’ reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms. PMID:27559059

Global Curvature Buckling and Snapping of Spherical Shells.

NASA Astrophysics Data System (ADS)

Pezzulla, Matteo; Stoop, Norbert; Steranka, Mark; Bade, Abdikhalaq; Trejo, Miguel; Holmes, Douglas

A spherical shell under external pressure will eventually buckle locally through the development of a dimple. However, when a free spherical shell is subject to variations in natural curvature, it will either buckle globally or snap towards a buckled configuration. We study the similarities and differences between pressure and curvature instabilities in spherical shells. We show how the critical buckling natural curvature is largely independent of the thinness and half-angle of the shell, while the critical snapping natural curvature grows linearly with the half-angle. As a result, we demonstrate how a critical half-angle, depending only on the thinness of the shell, sets the threshold between two different kinds of snapping: as a rule of thumb, shallow shells snap into everted shells, while deep shells snap into buckled shells. As the developed models are purely geometrical, the results are applicable to a large variety of stimuli and scales. NSF CAREER CMMI-1454153.

OMA analysis of a launcher under operational conditions with time-varying properties

NASA Astrophysics Data System (ADS)

Eugeni, M.; Coppotelli, G.; Mastroddi, F.; Gaudenzi, P.; Muller, S.; Troclet, B.

2018-05-01

The objective of this paper is the investigation of the capability of operational modal analysis approaches to deal with time-varying system in the low-frequency domain. Specifically, the problem of the identification of the dynamic properties of a launch vehicle, working under actual operative conditions, is studied. Two OMA methods are considered: the frequency-domain decomposition and the Hilbert transform method. It is demonstrated that both OMA approaches allow the time-tracking of modal parameters, namely, natural frequencies, damping ratios, and mode shapes, from the response accelerations only recorded during actual flight tests of a launcher characterized by a large mass variation due to fuel burning typical of the first phase of the flight.

Environmental Variation Generates Environmental Opportunist Pathogen Outbreaks.

PubMed

Anttila, Jani; Kaitala, Veijo; Laakso, Jouni; Ruokolainen, Lasse

2015-01-01

Many socio-economically important pathogens persist and grow in the outside host environment and opportunistically invade host individuals. The environmental growth and opportunistic nature of these pathogens has received only little attention in epidemiology. Environmental reservoirs are, however, an important source of novel diseases. Thus, attempts to control these diseases require different approaches than in traditional epidemiology focusing on obligatory parasites. Conditions in the outside-host environment are prone to fluctuate over time. This variation is a potentially important driver of epidemiological dynamics and affect the evolution of novel diseases. Using a modelling approach combining the traditional SIRS models to environmental opportunist pathogens and environmental variability, we show that epidemiological dynamics of opportunist diseases are profoundly driven by the quality of environmental variability, such as the long-term predictability and magnitude of fluctuations. When comparing periodic and stochastic environmental factors, for a given variance, stochastic variation is more likely to cause outbreaks than periodic variation. This is due to the extreme values being further away from the mean. Moreover, the effects of variability depend on the underlying biology of the epidemiological system, and which part of the system is being affected. Variation in host susceptibility leads to more severe pathogen outbreaks than variation in pathogen growth rate in the environment. Positive correlation in variation on both targets can cancel the effect of variation altogether. Moreover, the severity of outbreaks is significantly reduced by increase in the duration of immunity. Uncovering these issues helps in understanding and controlling diseases caused by environmental pathogens.

Genetic dissection of the maize (Zea mays L.) MAMP response.

PubMed

Zhang, Xinye; Valdés-López, Oswaldo; Arellano, Consuelo; Stacey, Gary; Balint-Kurti, Peter

2017-06-01

Loci associated with variation in maize responses to two microbe-associated molecular patterns (MAMPs) were identified. MAMP responses were correlated. No relationship between MAMP responses and quantitative disease resistance was identified. Microbe-associated molecular patterns (MAMPs) are highly conserved molecules commonly found in microbes which can be recognized by plant pattern recognition receptors. Recognition triggers a suite of responses including production of reactive oxygen species (ROS) and nitric oxide (NO) and expression changes of defense-related genes. In this study, we used two well-studied MAMPs (flg22 and chitooctaose) to challenge different maize lines to determine whether there was variation in the level of responses to these MAMPs, to dissect the genetic basis underlying that variation and to understand the relationship between MAMP response and quantitative disease resistance (QDR). Naturally occurring quantitative variation in ROS, NO production, and defense genes expression levels triggered by MAMPs was observed. A major quantitative traits locus (QTL) associated with variation in the ROS production response to both flg22 and chitooctaose was identified on chromosome 2 in a recombinant inbred line (RIL) population derived from the maize inbred lines B73 and CML228. Minor QTL associated with variation in the flg22 ROS response was identified on chromosomes 1 and 4. Comparison of these results with data previously obtained for variation in QDR and the defense response in the same RIL population did not provide any evidence for a common genetic basis controlling variation in these traits.

Why mutual helping in most natural systems is neither conflict-free nor based on maximal conflict.

PubMed

Bshary, Redouan; Zuberbühler, Klaus; van Schaik, Carel P

2016-02-05

Mutual helping for direct benefits can be explained by various game theoretical models, which differ mainly in terms of the underlying conflict of interest between two partners. Conflict is minimal if helping is self-serving and the partner benefits as a by-product. In contrast, conflict is maximal if partners are in a prisoner's dilemma with both having the pay-off-dominant option of not returning the other's investment. Here, we provide evolutionary and ecological arguments for why these two extremes are often unstable under natural conditions and propose that interactions with intermediate levels of conflict are frequent evolutionary endpoints. We argue that by-product helping is prone to becoming an asymmetric investment game since even small variation in by-product benefits will lead to the evolution of partner choice, leading to investments by the chosen class. Second, iterated prisoner's dilemmas tend to take place in stable social groups where the fitness of partners is interdependent, with the effect that a certain level of helping is self-serving. In sum, intermediate levels of mutual helping are expected in nature, while efficient partner monitoring may allow reaching higher levels. © 2016 The Author(s).

Why mutual helping in most natural systems is neither conflict-free nor based on maximal conflict

PubMed Central

Bshary, Redouan; Zuberbühler, Klaus; van Schaik, Carel P.

2016-01-01

Mutual helping for direct benefits can be explained by various game theoretical models, which differ mainly in terms of the underlying conflict of interest between two partners. Conflict is minimal if helping is self-serving and the partner benefits as a by-product. In contrast, conflict is maximal if partners are in a prisoner's dilemma with both having the pay-off-dominant option of not returning the other's investment. Here, we provide evolutionary and ecological arguments for why these two extremes are often unstable under natural conditions and propose that interactions with intermediate levels of conflict are frequent evolutionary endpoints. We argue that by-product helping is prone to becoming an asymmetric investment game since even small variation in by-product benefits will lead to the evolution of partner choice, leading to investments by the chosen class. Second, iterated prisoner's dilemmas tend to take place in stable social groups where the fitness of partners is interdependent, with the effect that a certain level of helping is self-serving. In sum, intermediate levels of mutual helping are expected in nature, while efficient partner monitoring may allow reaching higher levels. PMID:26729931

Complex multifractal nature in Mycobacterium tuberculosis genome

PubMed Central

Mandal, Saurav; Roychowdhury, Tanmoy; Chirom, Keilash; Bhattacharya, Alok; Brojen Singh, R. K.

2017-01-01

The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates). C(r) follows significantly different scaling rules in different subgroups of isolates, but all the isolates follow one parameter scaling law. The richness in complexity of each subgroup can be quantified by the measures of multifractal parameters displaying a pattern in which XDR isolates have highest value and lowest for drug sensitive isolates. Therefore C(r) and multifractal functions can be useful parameters for analysis of genomic sequences. PMID:28440326

Identification of related gene/protein names based on an HMM of name variations.

PubMed

Yeganova, L; Smith, L; Wilbur, W J

2004-04-01

Gene and protein names follow few, if any, true naming conventions and are subject to great variation in different occurrences of the same name. This gives rise to two important problems in natural language processing. First, can one locate the names of genes or proteins in free text, and second, can one determine when two names denote the same gene or protein? The first of these problems is a special case of the problem of named entity recognition, while the second is a special case of the problem of automatic term recognition (ATR). We study the second problem, that of gene or protein name variation. Here we describe a system which, given a query gene or protein name, identifies related gene or protein names in a large list. The system is based on a dynamic programming algorithm for sequence alignment in which the mutation matrix is allowed to vary under the control of a fully trainable hidden Markov model.

Complex multifractal nature in Mycobacterium tuberculosis genome

NASA Astrophysics Data System (ADS)

Mandal, Saurav; Roychowdhury, Tanmoy; Chirom, Keilash; Bhattacharya, Alok; Brojen Singh, R. K.

2017-04-01

The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates). C(r) follows significantly different scaling rules in different subgroups of isolates, but all the isolates follow one parameter scaling law. The richness in complexity of each subgroup can be quantified by the measures of multifractal parameters displaying a pattern in which XDR isolates have highest value and lowest for drug sensitive isolates. Therefore C(r) and multifractal functions can be useful parameters for analysis of genomic sequences.

Local Populations of Arabidopsis thaliana Show Clear Relationship between Photoperiodic Sensitivity of Flowering Time and Altitude

PubMed Central

Lewandowska-Sabat, Anna M.; Fjellheim, Siri; Olsen, Jorunn E.; Rognli, Odd A.

2017-01-01

Adaptation of plants to local conditions that vary substantially within their geographic range is essential for seasonal timing of flowering, a major determinant of plant reproductive success. This study investigates photoperiodic responses in natural populations of Arabidopsis thaliana from high northern latitudes and their significance for local adaptation. Thirty lineages from ten local A. thaliana populations, representing different locations across an altitudinal gradient (2–850 m a.s.l.) in Norway, were grown under uniform controlled conditions, and used to screen for responses to five different photoperiods. We studied relationships between variation in photoperiodic sensitivity of flowering time, altitude, and climatic factors associated with the sites of origin. We found that variation in response to photoperiod is significantly correlated with altitude and climatic variables associated with the sites of origin of the populations. Populations originating from lower altitudes showed stronger photoperiodic sensitivity than populations from higher altitudes. Our results indicate that the altitudinal climatic gradient generates clinal variation in adaptive traits in A. thaliana. PMID:28659966

Constraining DALECv2 using multiple data streams and ecological constraints: analysis and application

DOE PAGES

Delahaies, Sylvain; Roulstone, Ian; Nichols, Nancy

2017-07-10

We use a variational method to assimilate multiple data streams into the terrestrial ecosystem carbon cycle model DALECv2 (Data Assimilation Linked Ecosystem Carbon). Ecological and dynamical constraints have recently been introduced to constrain unresolved components of this otherwise ill-posed problem. We recast these constraints as a multivariate Gaussian distribution to incorporate them into the variational framework and we demonstrate their advantage through a linear analysis. By using an adjoint method we study a linear approximation of the inverse problem: firstly we perform a sensitivity analysis of the different outputs under consideration, and secondly we use the concept of resolution matricesmore » to diagnose the nature of the ill-posedness and evaluate regularisation strategies. We then study the non-linear problem with an application to real data. Finally, we propose a modification to the model: introducing a spin-up period provides us with a built-in formulation of some ecological constraints which facilitates the variational approach.« less

Constraining DALECv2 using multiple data streams and ecological constraints: analysis and application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delahaies, Sylvain; Roulstone, Ian; Nichols, Nancy

We use a variational method to assimilate multiple data streams into the terrestrial ecosystem carbon cycle model DALECv2 (Data Assimilation Linked Ecosystem Carbon). Ecological and dynamical constraints have recently been introduced to constrain unresolved components of this otherwise ill-posed problem. We recast these constraints as a multivariate Gaussian distribution to incorporate them into the variational framework and we demonstrate their advantage through a linear analysis. By using an adjoint method we study a linear approximation of the inverse problem: firstly we perform a sensitivity analysis of the different outputs under consideration, and secondly we use the concept of resolution matricesmore » to diagnose the nature of the ill-posedness and evaluate regularisation strategies. We then study the non-linear problem with an application to real data. Finally, we propose a modification to the model: introducing a spin-up period provides us with a built-in formulation of some ecological constraints which facilitates the variational approach.« less

Reliability Analysis of Retaining Walls Subjected to Blast Loading by Finite Element Approach

NASA Astrophysics Data System (ADS)

GuhaRay, Anasua; Mondal, Stuti; Mohiuddin, Hisham Hasan

2018-02-01

Conventional design methods adopt factor of safety as per practice and experience, which are deterministic in nature. The limit state method, though not completely deterministic, does not take into account effect of design parameters, which are inherently variable such as cohesion, angle of internal friction, etc. for soil. Reliability analysis provides a measure to consider these variations into analysis and hence results in a more realistic design. Several studies have been carried out on reliability of reinforced concrete walls and masonry walls under explosions. Also, reliability analysis of retaining structures against various kinds of failure has been done. However, very few research works are available on reliability analysis of retaining walls subjected to blast loading. Thus, the present paper considers the effect of variation of geotechnical parameters when a retaining wall is subjected to blast loading. However, it is found that the variation of geotechnical random variables does not have a significant effect on the stability of retaining walls subjected to blast loading.

Neuroendocrinology of Sexual Plasticity in Teleost Fishes

PubMed Central

Godwin, John

2010-01-01

The study of sex differences has produced major insights into the organization of animal phenotypes and the regulatory mechanisms generating phenotypic variation from similar genetic templates. Teleost fishes display the greatest diversity of sexual expression among vertebrate animals. This diversity appears to arise from diversity in the timing of sex determination and less functional interdependence among the components of sexuality relative to tetrapod vertebrates. Teleost model systems therefore provide powerful models for understanding gonadal and non-gonadal influences on behavioral and physiological variation. This review addresses socially controlled sex change and alternate male phenotypes in fishes. These sexual patterns are informative natural experiments that illustrate how variation in conserved neuroendocrine pathways can give rise to a wide range of reproductive adaptations. Key regulatory factors underlying sex change and alternative male phenotypes that have been identified to date include steroid hormones and the neuropeptides GnRH and arginine vasotocin, but genomic approaches are now implicating a diversity of other influences as well. PMID:20176046

Genetic variation affecting host-parasite interactions: different genes affect different aspects of sigma virus replication and transmission in Drosophila melanogaster.

PubMed

Bangham, Jenny; Kim, Kang-Wook; Webster, Claire L; Jiggins, Francis M

2008-04-01

In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.

Introduction to natural disturbances and historic range of variation: type, frequency, severity, and post-disturbance structure in central hardwood forests

Treesearch

Katie Greenberg; Beverly S. Collins; Henry McNab; Douglas K. Miller; Gary R. Wein

2015-01-01

EXCERPT FROM: Natural Disturbances and Historic Range Variation 2015. Throughout the history of upland hardwood forests of the Central Hardwood Region, natural disturbances have been integral to shaping forest structure and composition, and essential in maintaining diverse biotic...

Effects of simulated warming on soil respiration to XiaoPo lake

NASA Astrophysics Data System (ADS)

Zhao, Shuangkai; Chen, Kelong; Wu, Chengyong; Mao, Yahui

2018-02-01

The main flux of carbon cycling in terrestrial and atmospheric ecosystems is soil respiration, and soil respiration is one of the main ways of soil carbon output. This is of great significance to explore the dynamic changes of soil respiration rate and its effect on temperature rise, and the correlation between environmental factors and soil respiration. In this study, we used the open soil carbon flux measurement system (LI-8100, LI-COR, NE) in the experimental area of the XiaoPo Lake wetland in the Qinghai Lake Basin, and the Kobresia (Rs) were measured, and the soil respiration was simulated by simulated temperature (OTC) and natural state. The results showed that the temperature of 5 cm soil was 1.37 °C higher than that of the control during the experiment, and the effect of warming was obvious. The respiration rate of soil under warming and natural conditions showed obvious diurnal variation and monthly variation. The effect of warming on soil respiration rate was promoted and the effect of precipitation on soil respiration rate was inhibited. Further studies have shown that the relationship between soil respiration and 5 cm soil temperature under the control and warming treatments can be described by the exponential equation, and the correlation analysis between the two plots shows a very significant exponential relationship (p < 0.001). The warming treatment not only increased the Q10 value of soil respiration rate, but also increased the sensitivity of soil respiration rate. The relationship between soil respiration and soil moisture can be explained by the quadratic linear equation (p < 0.05). It can be concluded that under the condition of sufficient rainfall, the soil temperature is the main influencing factor of soil respiration in this region.

Male-killing endosymbionts: influence of environmental conditions on persistence of host metapopulation

PubMed Central

2008-01-01

Background Male killing endosymbionts manipulate their arthropod host reproduction by only allowing female embryos to develop into infected females and killing all male offspring. Because of the reproductive manipulation, we expect them to have an effect on the evolution of host dispersal rates. In addition, male killing endosymbionts are expected to approach fixation when fitness of infected individuals is larger than that of uninfected ones and when transmission from mother to offspring is nearly perfect. They then vanish as the host population crashes. High observed infection rates and among-population variation in natural systems can consequently not be explained if defense mechanisms are absent and when transmission efficiency is perfect. Results By simulating the host-endosymbiont dynamics in an individual-based metapopulation model we show that male killing endosymbionts increase host dispersal rates. No fitness compensations were built into the model for male killing endosymbionts, but they spread as a group beneficial trait. Host and parasite populations face extinction under panmictic conditions, i.e. conditions that favor the evolution of high dispersal in hosts. On the other hand, deterministic 'curing' (only parasite goes extinct) can occur under conditions of low dispersal, e.g. under low environmental stochasticity and high dispersal mortality. However, high and stable infection rates can be maintained in metapopulations over a considerable spectrum of conditions favoring intermediate levels of dispersal in the host. Conclusion Male killing endosymbionts without explicit fitness compensation spread as a group selected trait into a metapopulation. Emergent feedbacks through increased evolutionary stable dispersal rates provide an alternative explanation for both, the high male-killing endosymbiont infection rates and the high among-population variation in local infection rates reported for some natural systems. PMID:18764948

Genetic differentiation in life history traits and thermal stress performance across a heterogeneous dune landscape in Arabidopsis lyrata.

PubMed

Wos, Guillaume; Willi, Yvonne

2018-05-26

Over very short spatial scales, the habitat of a species can differ in multiple abiotic and biotic factors. These factors may impose natural selection on several traits and can cause genetic differentiation within a population. We studied multivariate genetic differentiation in a plant species of a sand dune landscape by linking environmental variation with differences in genotypic trait values and gene expression levels to find traits and candidate genes of microgeographical adaptation. Maternal seed families of Arabidopsis lyrata were collected in Saugatuck Dunes State Park, Michigan, USA, and environmental parameters were recorded at each collection site. Offspring plants were raised in climate chambers and exposed to one of three temperature treatments: regular occurrence of frost, heat, or constant control conditions. Several traits were assessed: plant growth, time to flowering, and frost and heat resistance. The strongest trait-environment association was between a fast switch to sexual reproduction and weaker growth under frost, and growing in the open, away from trees. The second strongest association was between the trait combination of small plant size and early flowering under control conditions combined with large size under frost, and the combination of environmental conditions of growing close to trees, at low vegetation cover, on dune bottoms. Gene expression analysis by RNA-seq revealed candidate genes involved in multivariate trait differentiation. The results support the hypothesis that in natural populations, many environmental factors impose selection, and that they affect multiple traits, with the relative direction of trait change being complex. The results highlight that heterogeneity in the selection environment over small spatial scales is a main driver of the maintenance of adaptive genetic variation within populations.

Natural variations in the geomagnetically trapped electron population

NASA Technical Reports Server (NTRS)

Vampola, A. L.

1972-01-01

Temporal variations in the trapped natural electron flux intensities and energy spectra are discussed and demonstrated using recent satellite data. These data are intended to acquaint the space systems engineer with the types of natural variations that may be encountered during a mission and to augment the models of the electron environment currently being used in space system design and orbit selection. An understanding of the temporal variations which may be encountered should prove helpful. Some of the variations demonstrated here which are not widely known include: (1) addition of very energetic electrons to the outer zone during moderate magnetic storms: (2) addition of energetic electrons to the inner zone during major magnetic storms; (3) inversions in the outer zone electron energy spectrum during the decay phase of a storm injection event and (4) occasional formation of multiple maxima in the flux vs altitude profile of moderately energetic electrons.

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

PubMed Central

Cook, Daniel E.; Zdraljevic, Stefan; Tanny, Robyn E.; Seo, Beomseok; Riccardi, David D.; Noble, Luke M.; Rockman, Matthew V.; Alkema, Mark J.; Braendle, Christian; Kammenga, Jan E.; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C.

2016-01-01

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. PMID:27449056

Generalist dispersers promote germination of an alien fleshy-fruited tree invading natural grasslands

PubMed Central

Vázquez, María Belén; Zalba, Sergio Martín

2017-01-01

Plants with animal-dispersed fruits seem to overcome the barriers that limit their spread into new habitats more easily than other invasive plants and, at the same time, they pose special difficulties for containment, control or eradication. The effects of animals on plant propagules can be very diverse, with positive, neutral or negative consequences for germination and recruitment. Moreover, the environmental conditions where the seeds are deposited and where the post-dispersal processes take place can be crucial for their fate. Prunus mahaleb is a fleshy-fruited tree invading natural grasslands in the Argentine Pampas. In this study, we analyzed the importance of pulp removal, endocarp scarification and the effects of vectors on its germination response, by means of germination experiments both in the laboratory and under semi-natural conditions. Our laboratory results demonstrated that endocarp scarification enhances germination and suggests that vestiges of pulp on the stones have inhibitory effects. Frugivores exert a variety of effects on germination responses and this variation can be explained by their differing influence on pulp removal and endocarp scarification. Most frugivores produced a positive effect on germination under laboratory conditions, in comparison to intact fruits and hand-peeled stones. We observed different degrees of pulp removal from the surface of the stones by the dispersers which was directly correlated to the germination response. On the other hand, all the treatments showed high germination responses under semi-natural conditions suggesting that post-dispersal processes, like seed burial, and the exposure to natural conditions might exert a positive effect on germination response, attenuating the plant's dependence on the dispersers’ gut treatment. Our results highlight the need to consider the whole seed dispersal process and the value of combining laboratory and field tests. PMID:28207815

Natural genetic variation in social environment choice: context-dependent gene-environment correlation in Drosophila melanogaster.

PubMed

Saltz, Julia B

2011-08-01

Gene-environment correlation (rGE) occurs when an individual's genotype determines its choice of environment, generating a correlation between environment and genotype frequency. In particular, social rGE, caused by genetic variation in social environment choice, can critically determine both individual development and the course of social selection. Despite its foundational role in social evolution and developmental psychology theory, natural genetic variation in social environment choice has scarcely been examined empirically. Drosophila melanogaster provides an ideal system for investigating social rGE. Flies live socially in nature and have many opportunities to make social decisions; and natural, heterozygous genotypes may be replicated, enabling comparisons between genotypes across environments. Using this approach, I show that all aspects of social environment choice vary among natural genotypes, demonstrating pervasive social rGE. Surprisingly, genetic variation in group-size preference was density dependent, indicating that the behavioral and evolutionary consequences of rGE may depend on the context in which social decisions are made. These results provide the first detailed investigation of social rGE, and illustrate that that genetic variation may influence organismal performance by specifying the environment in which traits are expressed. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

A Secular Variation Model for Igrf-12 Based on Swarm Data and Inverse Geodynamo Modelling

NASA Astrophysics Data System (ADS)

Fournier, A.; Aubert, J.; Erwan, T.

2014-12-01

We are proposing a secular variation candidate model for the 12th generation of the international geomagnetic reference field, spanning the years 2015-2020. The novelty of our approach stands in the initialization of a 5-yr long integration of a numerical model of Earth's dynamo by means of inverse geodynamo modelling, as introduced by Aubert (GJI, 2014). This inverse technique combines the information coming from the observations (in the form of an instantaneous estimate of the Gauss coefficients for the magnetic field and its secular variation) with that coming from the multivariate statistics of a free run of a numerical model of the geodynamo. The Gauss coefficients and their error covariance properties are determined from Swarm data along the lines detailed by Thébault et al. (EPS, 2010). The numerical model of the geodynamo is the so-called Coupled Earth Dynamo model (Aubert et al., Nature, 2013), whose variability possesses a strong level of similarity with that of the geomagnetic field. We illustrate and assess the potential of this methodology by applying it to recent time intervals, with an initialization based on CHAMP data, and conclude by presenting our SV candidate, whose initialization is based on the 1st year of Swarm data This work is supported by the French "Agence Nationale de la Recherche" under the grant ANR-11-BS56-011 (http://avsgeomag.ipgp.fr) and by the CNES. References: Aubert, J., Geophys. J. Int. 197, 1321-1334, 2014, doi: 10.1093/gji/ggu064 Aubert, J., Finlay, C., Fournier, F. Nature 502, 219-223, 2013, doi: 10.1038/nature12574 Thébault E. , A. Chulliat, S. Maus, G. Hulot, B. Langais, A. Chambodut and M. Menvielle, Earth Planets Space, Vol. 62 (No. 10), pp. 753-763, 2010.

Plasticity in functional traits in the context of climate change: a case study of the subalpine forb Boechera stricta (Brassicaceae).

PubMed

Anderson, Jill T; Gezon, Zachariah J

2015-04-01

Environmental variation often induces shifts in functional traits, yet we know little about whether plasticity will reduce extinction risks under climate change. As climate change proceeds, phenotypic plasticity could enable species with limited dispersal capacity to persist in situ, and migrating populations of other species to establish in new sites at higher elevations or latitudes. Alternatively, climate change could induce maladaptive plasticity, reducing fitness, and potentially stalling adaptation and migration. Here, we quantified plasticity in life history, foliar morphology, and ecophysiology in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In this region, warming winters are reducing snowpack and warming springs are advancing the timing of snow melt. We hypothesized that traits that were historically advantageous in hot and dry, low-elevation locations will be favored at higher elevation sites due to climate change. To test this hypothesis, we quantified trait variation in natural populations across an elevational gradient. We then estimated plasticity and genetic variation in common gardens at two elevations. Finally, we tested whether climatic manipulations induce plasticity, with the prediction that plants exposed to early snow removal would resemble individuals from lower elevation populations. In natural populations, foliar morphology and ecophysiology varied with elevation in the predicted directions. In the common gardens, trait plasticity was generally concordant with phenotypic clines from the natural populations. Experimental snow removal advanced flowering phenology by 7 days, which is similar in magnitude to flowering time shifts over 2-3 decades of climate change. Therefore, snow manipulations in this system can be used to predict eco-evolutionary responses to global change. Snow removal also altered foliar morphology, but in unexpected ways. Extensive plasticity could buffer against immediate fitness declines due to changing climates. © 2014 John Wiley & Sons Ltd.

Scanning electron microscopy analysis of hair index on Karachi's population for social and professional appearance enhancement.

PubMed

Ali, N; Zohra, R R; Qader, S A U; Mumtaz, M

2015-06-01

Hair texture, appearance and pigment play an important role in social and professional communication and maintaining an overall appearance. This study was especially designed for morphological assessment of hair damage caused to Karachi's population due to natural factors and cosmetic treatments using scanning electron microscopy (SEM) technique. Hair samples under the study of synthetic factor's effect were given several cosmetic treatments (hot straightened, bleached, synthetic dyed and henna dyed) whereas samples under natural factor's effect (variation in gender, age and pigmentation) were left untreated. Morphological assessment was performed using SEM technique. Results obtained were statistically analysed using minitab 16 and spss 18 softwares. Scanning electron microscopy images revealed less number of cuticular scales in males than females of same age although size of cuticular scales was found to be larger in males than in females. Mean hair index of white hair was greater than black hair of the same head as it is comparatively newly originated. Tukey's method revealed that among cosmetic treatments, bleaching and synthetic henna caused most of the damage to the hair. Statistical evaluation of results obtained from SEM analysis revealed that human scalp hair index show morphological variation with respect to age, gender, hair pigmentation, chemical and physical treatments. Individuals opting for cosmetic treatments could clearly visualize the extent of hair damage these may cause in long run. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

The genetic basis of natural variation for iron homeostasis in the maize IBM population

PubMed Central

2014-01-01

Background Iron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis. Results In hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively. Conclusions From the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2’-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK). PMID:24400634

Ability of Bumblebees to Discriminate Differences in the Shape of Artificial Flowers of Primula sieboldii (Primulaceae)

PubMed Central

Yoshioka, Yosuke; Ohashi, Kazuharu; Konuma, Akihiro; Iwata, Hiroyoshi; Ohsawa, Ryo; Ninomiya, Seishi

2007-01-01

Background and Aims Flower shapes are important visual cues for pollinators. However, the ability of pollinators to discriminate between flower shapes under natural conditions is poorly understood. This study focused on the diversity of flower shape in Primula sieboldii and investigated the ability of bumblebees to discriminate between flowers by combining computer graphics with a traditional behavioural experiment. Methods Elliptic Fourier descriptors described shapes by transforming coordinate information for the contours into coefficients, and principal components analysis summarized these coefficients. Using these methods, artificial flowers were created based on the natural diversity of petal shape in P. sieboldii. Dual-choice tests were then performed to investigate the ability of the bumblebees to detect differences in the aspect ratio of petals and the depth of their head notch. Key Results The insects showed no significant ability to detect differences in the aspect ratio of the petals under natural conditions unless the morphological distance increased to an unrealistic level. These results suggest the existence of a perception threshold for distances in this parameter. The bumblebees showed a significant preference for narrow petals even after training using flowers with wide petals. The bumblebees showed a significant ability to discriminate based on the depth of the petal head notch after training using artificial flowers with a deep head notch. However, they showed no discrimination in tests with training using extreme distances between flowers in this parameter. Conclusions A new type of behavioural experiment was demonstrated using real variation in flower corolla shape in P. sieboldii. If the range in aspect ratios of petals expands much further, bumblebees may learn to exhibit selective behaviour. However, because discrimination by bumblebees under natural conditions was low, there may be no strong selective behaviour based on innate or learned preferences under natural conditions. PMID:17553825

Projecting pest population dynamics under global warming: the combined effect of inter- and intra-annual variations.

PubMed

Zidon, Royi; Tsueda, Hirotsugu; Morin, Efrat; Morin, Shai

2016-06-01

The typical short generation length of insects makes their population dynamics highly sensitive not only to mean annual temperatures but also to their intra-annual variations. To consider the combined effect of both thermal factors under global warming, we propose a modeling framework that links general circulation models (GCMs) with a stochastic weather generator and population dynamics models to predict species population responses to inter- and intra-annual temperature changes. This framework was utilized to explore future changes in populations of Bemisia tabaci, an invasive insect pest-species that affects multiple agricultural systems in the Mediterranean region. We considered three locations representing different pest status and climatic conditions: Montpellier (France), Seville (Spain), and Beit-Jamal (Israel). We produced ensembles of local daily temperature realizations representing current and future (mid-21st century) climatic conditions under two emission scenarios for the three locations. Our simulations predicted a significant increase in the average number of annual generations and in population size, and a significant lengthening of the growing season in all three locations. A negative effect was found only in Seville for the summer season, where future temperatures lead to a reduction in population size. High variability in population size was observed between years with similar annual mean temperatures, suggesting a strong effect of intra-annual temperature variation. Critical periods were from late spring to late summer in Montpellier and from late winter to early summer in Seville and Beit-Jamal. Although our analysis suggested that earlier seasonal activity does not necessarily lead to increased populations load unless an additional generation is produced, it is highly likely that the insect will become a significant pest of open-fields at Mediterranean latitudes above 40° during the next 50 years. Our simulations also implied that current predictions based on mean temperature anomalies are relatively conservative and it is better to apply stochastic tools to resolve complex responses to climate change while taking natural variability into account. In summary, we propose a modeling framework capable of determining distinct intra-annual temperature patterns leading to large or small population sizes, for pest risk assessment and management planning of both natural and agricultural ecosystems.

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes

PubMed Central

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-01-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. PMID:29367403

Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes

PubMed Central

Deschamps, Matthieu; Laval, Guillaume; Fagny, Maud; Itan, Yuval; Abel, Laurent; Casanova, Jean-Laurent; Patin, Etienne; Quintana-Murci, Lluis

2016-01-01

Human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. A comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. Using full-genome sequence variation from the 1000 Genomes Project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. We identify a gene set under the strongest selective constraints, mutations in which are likely to predispose individuals to life-threatening disease, as illustrated by STAT1 and TRAF3. We then evaluate the occurrence of local adaptation and detect 57 high-scoring signals of positive selection at innate immunity genes, variation in which has been associated with susceptibility to common infectious or autoimmune diseases. Furthermore, we show that most adaptations targeting coding variation have occurred in the last 6,000–13,000 years, the period at which populations shifted from hunting and gathering to farming. Finally, we show that innate immunity genes present higher Neandertal introgression than the remainder of the coding genome. Notably, among the genes presenting the highest Neandertal ancestry, we find the TLR6-TLR1-TLR10 cluster, which also contains functional adaptive variation in Europeans. This study identifies highly constrained genes that fulfill essential, non-redundant functions in host survival and reveals others that are more permissive to change—containing variation acquired from archaic hominins or adaptive variants in specific populations—improving our understanding of the relative biological importance of innate immunity pathways in natural conditions. PMID:26748513

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

PubMed Central

Rudman, Seth M.; Rodriguez-Cabal, Mariano A.; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W.; Crutsinger, Gregory M.

2015-01-01

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

PubMed

Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

2015-08-07

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. © 2015 The Author(s).

A Mixed-Methods Trial of Broad Band Noise and Nature Sounds for Tinnitus Therapy: Group and Individual Responses Modeled under the Adaptation Level Theory of Tinnitus.

PubMed

Durai, Mithila; Searchfield, Grant D

2017-01-01

Objectives: A randomized cross-over trial in 18 participants tested the hypothesis that nature sounds, with unpredictable temporal characteristics and high valence would yield greater improvement in tinnitus than constant, emotionally neutral broadband noise. Study Design: The primary outcome measure was the Tinnitus Functional Index (TFI). Secondary measures were: loudness and annoyance ratings, loudness level matches, minimum masking levels, positive and negative emotionality, attention reaction and discrimination time, anxiety, depression and stress. Each sound was administered using MP3 players with earbuds for 8 continuous weeks, with a 3 week wash-out period before crossing over to the other treatment sound. Measurements were undertaken for each arm at sound fitting, 4 and 8 weeks after administration. Qualitative interviews were conducted at each of these appointments. Results: From a baseline TFI score of 41.3, sound therapy resulted in TFI scores at 8 weeks of 35.6; broadband noise resulted in significantly greater reduction (8.2 points) after 8 weeks of sound therapy use than nature sounds (3.2 points). The positive effect of sound on tinnitus was supported by secondary outcome measures of tinnitus, emotion, attention, and psychological state, but not interviews. Tinnitus loudness level match was higher for BBN at 8 weeks; while there was little change in loudness level matches for nature sounds. There was no change in minimum masking levels following sound therapy administration. Self-reported preference for one sound over another did not correlate with changes in tinnitus. Conclusions: Modeled under an adaptation level theory framework of tinnitus perception, the results indicate that the introduction of broadband noise shifts internal adaptation level weighting away from the tinnitus signal, reducing tinnitus magnitude. Nature sounds may modify the affective components of tinnitus via a secondary, residual pathway, but this appears to be less important for sound effectiveness. The different rates of adaptation to broadband noise and nature sound by the auditory system may explain the different tinnitus loudness level matches. In addition to group effects there also appears to be a great deal of individual variation. A sound therapy framework based on adaptation level theory is proposed that accounts for individual variation in preference and response to sound. Clinical Trial Registration: www.anzctr.org.au, identifier #12616000742471.

A Mixed-Methods Trial of Broad Band Noise and Nature Sounds for Tinnitus Therapy: Group and Individual Responses Modeled under the Adaptation Level Theory of Tinnitus

PubMed Central

Durai, Mithila; Searchfield, Grant D.

2017-01-01

Objectives: A randomized cross-over trial in 18 participants tested the hypothesis that nature sounds, with unpredictable temporal characteristics and high valence would yield greater improvement in tinnitus than constant, emotionally neutral broadband noise. Study Design: The primary outcome measure was the Tinnitus Functional Index (TFI). Secondary measures were: loudness and annoyance ratings, loudness level matches, minimum masking levels, positive and negative emotionality, attention reaction and discrimination time, anxiety, depression and stress. Each sound was administered using MP3 players with earbuds for 8 continuous weeks, with a 3 week wash-out period before crossing over to the other treatment sound. Measurements were undertaken for each arm at sound fitting, 4 and 8 weeks after administration. Qualitative interviews were conducted at each of these appointments. Results: From a baseline TFI score of 41.3, sound therapy resulted in TFI scores at 8 weeks of 35.6; broadband noise resulted in significantly greater reduction (8.2 points) after 8 weeks of sound therapy use than nature sounds (3.2 points). The positive effect of sound on tinnitus was supported by secondary outcome measures of tinnitus, emotion, attention, and psychological state, but not interviews. Tinnitus loudness level match was higher for BBN at 8 weeks; while there was little change in loudness level matches for nature sounds. There was no change in minimum masking levels following sound therapy administration. Self-reported preference for one sound over another did not correlate with changes in tinnitus. Conclusions: Modeled under an adaptation level theory framework of tinnitus perception, the results indicate that the introduction of broadband noise shifts internal adaptation level weighting away from the tinnitus signal, reducing tinnitus magnitude. Nature sounds may modify the affective components of tinnitus via a secondary, residual pathway, but this appears to be less important for sound effectiveness. The different rates of adaptation to broadband noise and nature sound by the auditory system may explain the different tinnitus loudness level matches. In addition to group effects there also appears to be a great deal of individual variation. A sound therapy framework based on adaptation level theory is proposed that accounts for individual variation in preference and response to sound. Clinical Trial Registration: www.anzctr.org.au, identifier #12616000742471. PMID:28337139

Parallel shifts in ecology and natural selection in an island lizard

PubMed Central

Calsbeek, Ryan; Buermann, Wolfgang; Smith, Thomas B

2009-01-01

Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered both habitat use and natural selection in the brown anole, Anolis sagrei. Results In natural populations, lizards increased their use of vegetation in wet years and this was correlated with selection on limb length but not body size. By contrast, a die-back of vegetation caused by drought was followed by reduced arboreality, selection on body size, and relaxed selection on limb length. With the return of the rains and recovery of vegetation, selection reverted back to pre-drought pattern of selection acting on limb length but not body size. To test for the impact of vegetation loss on natural selection during the drought, we experimentally removed vegetation on a separate study island in a naturally wet year. The experiment revealed similar inter-annual changes in selection on body size but not limb length. Conclusion Our results illustrate the dynamic nature of ecology driving natural selection on Anolis morphology and emphasize the importance of inter-annual environmental variation in shaping adaptive variation. In addition, results illustrate the utility of using remote sensing data to examine ecology's role in driving natural selection. PMID:19126226

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

PubMed

Roux, Fabrice; Colomé-Tatché, Maria; Edelist, Cécile; Wardenaar, René; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent; Jansen, Ritsert C; Johannes, Frank

2011-08-01

We extensively phenotyped 6000 Arabidopsis plants with experimentally perturbed DNA methylomes as well as a diverse panel of natural accessions in a common garden. We found that alterations in DNA methylation not only caused heritable phenotypic diversity but also produced heritability patterns closely resembling those of the natural accessions. Our findings indicate that epigenetically induced and naturally occurring variation in complex traits share part of their polygenic architecture and may offer complementary adaptation routes in ecological settings.

Quantifying Variations In Multi-parameter Models With The Photon Clean Method (PCM) And Bootstrap Methods

NASA Astrophysics Data System (ADS)

Carpenter, Matthew H.; Jernigan, J. G.

2007-05-01

We present examples of an analysis progression consisting of a synthesis of the Photon Clean Method (Carpenter, Jernigan, Brown, Beiersdorfer 2007) and bootstrap methods to quantify errors and variations in many-parameter models. The Photon Clean Method (PCM) works well for model spaces with large numbers of parameters proportional to the number of photons, therefore a Monte Carlo paradigm is a natural numerical approach. Consequently, PCM, an "inverse Monte-Carlo" method, requires a new approach for quantifying errors as compared to common analysis methods for fitting models of low dimensionality. This presentation will explore the methodology and presentation of analysis results derived from a variety of public data sets, including observations with XMM-Newton, Chandra, and other NASA missions. Special attention is given to the visualization of both data and models including dynamic interactive presentations. This work was performed under the auspices of the Department of Energy under contract No. W-7405-Eng-48. We thank Peter Beiersdorfer and Greg Brown for their support of this technical portion of a larger program related to science with the LLNL EBIT program.

Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

PubMed

Silla, Toomas; Kepp, Katrin; Tai, E Shyong; Goh, Liang; Davila, Sonia; Catela Ivkovic, Tina; Calin, George A; Voorhoeve, P Mathijs

2014-01-01

Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF<0.5%) of which 75% is not present in dbSNP137. UCEs association studies for complex human traits can use this information to model expected background variation and thus necessary power for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

Bounds on Lithospheric Thickness on Venus from Magellan Gravity and Topography Data

NASA Technical Reports Server (NTRS)

Johnson, Catherine L.; Sandwell, David

1997-01-01

The primary objective of the work executed under NAGW-4784 is to provide constraints on the thermal and tectonic evolution of Venus. Establishing thermal and tectonic evolution models requires not only geological, but geophysical constraints, in particular the nature of temporal and spatial variations in crustal and lithospheric thickness. The major topics of study completed under NAGW-4784 (described more fully below) are: (1) detailed analyses of the resolution of Magellan Line-Of-Site (LOS) Doppler data to establish the minimum resolvable wavelength in the gravity data; (2) calculations of the global strain field in the venusian lithosphere and comparisons with global strain patterns from geological mapping; (3) study of the geological history of coronae at E. Eistla Regio; (4) estimation of crustal and lithospheric thickness by modeling of topography at asymmetric and symmetric rift-like chasmata; (5) preliminary investigations of spatial versus temporal variations in lithospheric thickness. Both the PI and Co-I have presented papers based on these topics at national and international meetings (American Geophysical Union Meetings, Lunar and Planetary Science Conferences, Chapman Conference on the Geodynamics of Venus).

Seasonal variations of gene expression biomarkers in Mytilus galloprovincialis cultured populations: temperature, oxidative stress and reproductive cycle as major modulators.

PubMed

Jarque, Sergio; Prats, Eva; Olivares, Alba; Casado, Marta; Ramón, Montserrat; Piña, Benjamin

2014-11-15

The blue mussel Mytilus galloprovincialis has been used as monitoring organism in many biomonitoring programs because of its broad distribution in South European sea waters and its physiological characteristics. Different pollution-stress biomarkers, including gene expression biomarkers, have been developed to determine its physiological response to the presence of different pollutants. However, the existing information about basal expression profiles is very limited, as very few biomarker-based studies were designed to reflect the natural seasonal variations. In the present study, we analyzed the natural expression patterns of several genes commonly used in biomonitoring, namely ferritin, metallothionein, cytochrome P450, glutathione S-transferase, heat shock protein and the kinase responsive to stress KRS, during an annual life cycle. Analysis of mantle-gonad samples of cultured populations of M. galloprovincialis from the Delta del Ebro (North East Spain) showed natural seasonal variability of these biomarkers, pointing to temperature and oxidative stress as major abiotic modulators. In turn, the reproductive cycle, a process that can be tracked by VCLM7 expression, and known to be influenced by temperature, seems to be the major biotic factor involved in seasonality. Our results illustrate the influence of environmental factors in the physiology of mussels through their annual cycle, a crucial information for the correct interpretation of responses under stress conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

Flower color as a model system for studies of plant evo-devo.

PubMed

Sobel, James M; Streisfeld, Matthew A

2013-01-01

Even though pigmentation traits have had substantial impacts on the field of animal evolutionary developmental biology, they have played only relatively minor roles in plant evo-devo. This is surprising given the often direct connection between flower color and fitness variation mediated through the effects of pollinators. At the same time, ecological and evolutionary genetic studies have utilized the molecular resources available for the anthocyanin pathway to generate several examples of the molecular basis of putatively adaptive transitions in flower color. Despite this opportunity to synthesize experimental approaches in ecology, evolution, and developmental biology, the investigation of many fundamental questions in evo-devo using this powerful model is only at its earliest stages. For example, a long-standing question is whether predictable genetic changes accompany the repeated evolution of a trait. Due to the conserved nature of the biochemical and regulatory control of anthocyanin biosynthesis, it has become possible to determine whether, and under what circumstances, different types of mutations responsible for flower color variation are preferentially targeted by natural selection. In addition, because plants use anthocyanin and related compounds in vegetative tissue for other important physiological functions, the identification of naturally occurring transitions from unpigmented to pigmented flowers provides the opportunity to examine the mechanisms by which regulatory networks are co-opted into new developmental domains. Here, we review what is known about the ecological and molecular basis of anthocyanic flower color transitions in natural systems, focusing on the evolutionary and developmental features involved. In doing so, we provide suggestions for future work on this trait and suggest that there is still much to be learned from the evolutionary development of flower color transitions in nature.

Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes).

PubMed

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.

Eco-Geographical Diversification of Bitter Taste Receptor Genes (TAS2Rs) among Subspecies of Chimpanzees (Pan troglodytes)

PubMed Central

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires. PMID:22916235

Length Variation of Cag/Caa Trinucleotide Repeats in Natural Populations of Drosophila Melanogaster and Its Relation to the Recombination Rate

PubMed Central

Michalakis, Y.; Veuille, M.

1996-01-01

Eleven genes distributed along the Drosophila melanogaster chromosome 2 and showing exonic tandem repeats of glutamine codons (CAG or CAA) were surveyed for length variation in a sample of four European and African populations. Only one gene was monomorphic. Eight genes were polymorphic in all populations, with a total number of alleles varying between five and 12 for 120 chromosomes. The average heterozygozity per locus and population was 0.41. Selective neutrality in length variation could not be rejected under the assumptions of the infinite allele model. Significant population subdivision was found though no geographical pattern emerged, all populations being equally different. Significant linkage disequilibrium was found in four out of seven cases where the genetic distance between loci was <1 cM and was negligible when the distance was larger. There is evidence that these associations were established after the populations separated. An unexpected result was that variation at each locus was independent of the coefficient of exchange, although the latter ranged from zero to the relatively high value of 6.7%. This would indicate that background selection and selective hitchhiking, which are thought to affect levels of nucleotide substitution polymorphism, have no effect on trinucleotide repeat variation. PMID:8844158

Role of Vpma phase variation in Mycoplasma agalactiae pathogenesis

PubMed Central

Chopra-Dewasthaly, Rohini; Baumgartner, Martina; Gamper, Erika; Innerebner, Carmen; Zimmermann, Martina; Schilcher, Franz; Tichy, Alexander; Winter, Petra; Rosengarten, Renate; Spergser, Joachim

2015-01-01

Compared with other bacterial pathogens, the molecular mechanisms of mycoplasma pathogenicity are largely unknown. Several studies in the past have shown that pathogenic mycoplasmas are equipped with sophisticated genetic systems that allow them to undergo high-frequency surface antigenic variations. Although never clearly proven, these variable mycoplasma surface components are often implicated in host immune evasion and adaptation. Vpma surface lipoproteins of the ruminant pathogen Mycoplasma agalactiae are encoded on a genomic pathogenicity island–like locus and are considered as one of the well-characterized model systems of mycoplasma surface antigenic variation. The present study assesses the role of these phase-variable Vpmas in the molecular pathogenesis of M. agalactiae by testing the wild-type strain PG2 in comparison with the xer1-disrupted Vpma ‘phase-locked’ mutants in sheep infection models. The data clearly illustrate that although Xer1 recombinase is not a virulence factor of M. agalactiae and Vpma phase variation is not necessary for establishing an infection, it might critically influence the survival and persistence of the pathogen under natural field conditions, mainly due to a better capacity for dissemination and evoking systemic responses. This is the first study where mycoplasma ‘phase-locked’ mutants are tested in vivo to elucidate the role of phase variation during infection. PMID:22809092

Caenorhabditis elegans vulval cell fate patterning

NASA Astrophysics Data System (ADS)

Félix, Marie-Anne

2012-08-01

The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the network allow us to test the effect of parameter variation on the cell fate pattern output. Among the parameter sets that allow us to reach the wild-type pattern, two general developmental patterning mechanisms of the three fates can be found: sequential inductions and morphogen-based induction, the former being more robust to parameter variation. Experimentally, the vulval cell fate pattern is robust to stochastic and environmental challenges, and minor variants can be detected. The exception is the fate of the anterior cell, P3.p, which is sensitive to stochastic variation and spontaneous mutation, and is also evolving the fastest. Other vulval precursor cell fates can be affected by mutation, yet little natural variation can be found, suggesting stabilizing selection. Despite this fate pattern conservation, different Caenorhabditis species respond differently to perturbations of the system. In the quantitative models, different parameter sets can reconstitute their response to perturbation, suggesting that network variation among Caenorhabditis species may be quantitative. Network rewiring likely occurred at longer evolutionary scales.

Estimation of the Lithospheric Component Share in the Earth Natural Pulsed Electromagnetic Field Structure

NASA Astrophysics Data System (ADS)

Malyshkov, S. Y.; Gordeev, V. F.; Polyvach, V. I.; Shtalin, S. G.; Pustovalov, K. N.

2017-04-01

Article describes the results of the atmosphere and Earth’s crust climatic and ecological parameters integrated monitoring. The estimation is made for lithospheric component share in the Earth natural pulsed electromagnetic field structure. To estimate lithospheric component we performed a round-the-clock monitoring of the Earth natural pulsed electromagnetic field background variations at the experiment location and measured the Earth natural pulsed electromagnetic field under electric shields. Natural materials in a natural environment were used for shielding, specifically lakes with varying parameters of water conductivity. Skin effect was used in the experiment - it is the tendency of electromagnetic waves amplitude to decrease with greater depths in the conductor. Atmospheric and lithospheric component the Earth natural pulsed electromagnetic field data recorded on terrain was compared against the recorded data with atmosphere component decayed by an electric shield. In summary we have demonstrated in the experiment that thunderstorm discharge originating electromagnetic field decay corresponds to the decay calculated using Maxwell equations. In the absence of close lightning strikes the ratio of field intensity recorded on terrain to shielded field intensity is inconsistent with the ratio calculated for atmospheric sources, that confirms there is a lithospheric component present to the Earth natural pulsed electromagnetic field.

Robust resolution enhancement optimization methods to process variations based on vector imaging model

NASA Astrophysics Data System (ADS)

Ma, Xu; Li, Yanqiu; Guo, Xuejia; Dong, Lisong

2012-03-01

Optical proximity correction (OPC) and phase shifting mask (PSM) are the most widely used resolution enhancement techniques (RET) in the semiconductor industry. Recently, a set of OPC and PSM optimization algorithms have been developed to solve for the inverse lithography problem, which are only designed for the nominal imaging parameters without giving sufficient attention to the process variations due to the aberrations, defocus and dose variation. However, the effects of process variations existing in the practical optical lithography systems become more pronounced as the critical dimension (CD) continuously shrinks. On the other hand, the lithography systems with larger NA (NA>0.6) are now extensively used, rendering the scalar imaging models inadequate to describe the vector nature of the electromagnetic field in the current optical lithography systems. In order to tackle the above problems, this paper focuses on developing robust gradient-based OPC and PSM optimization algorithms to the process variations under a vector imaging model. To achieve this goal, an integrative and analytic vector imaging model is applied to formulate the optimization problem, where the effects of process variations are explicitly incorporated in the optimization framework. The steepest descent algorithm is used to optimize the mask iteratively. In order to improve the efficiency of the proposed algorithms, a set of algorithm acceleration techniques (AAT) are exploited during the optimization procedure.

Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species

PubMed Central

Árnason, Einar

2015-01-01

Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host’s apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection. PMID:26038731

Association mapping across numerous traits reveals patterns of functional variation in maize

USDA-ARS?s Scientific Manuscript database

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie funct...

Precipitation event tracking reveals that precipitation characteristics respond differently under seasonal, interannual, and anthropogenic forcing

NASA Astrophysics Data System (ADS)

Chen, C.; Chang, W.; Kong, W.; Wang, J.; Kotamarthi, V. R.; Stein, M.; Moyer, E. J.

2017-12-01

Change in precipitation characteristics is an especially concerning potential impact of climate change, and both model and observational studies suggest that increases in precipitation intensity are likely. However, studies to date have focused on mean accumulated precipitation rather than on the characteristics of individual events. We report here on a study using a novel rainstorm identification tracking algorithm (Chang et al. 2016) that allows evaluating changes in spatio-temporal characteristics of events. We analyze high-resolution precipitation from dynamically downscaled regional climate simulations over the continental U.S. (WRF driven by CCSM4) of present and future climate conditions. We show that precipitation events show distinct characteristic changes for natural seasonal and interannual variations and for anthropogenic greenhouse-gas forcing. In all cases, wetter seasons/years/future climate states are associated with increased precipitation intensity, but other precipitation characteristics respond differently to the different drivers. For example, under anthropogenic forcing, future wetter climate states involve smaller individual event sizes (partially offsetting their increased intensity). Under natural variability, however, wetter years involve larger mean event sizes. Event identification and tracking algorithms thus allow distinguishing drivers of different types of precipitation changes, and in relating those changes to large-scale processes.

Diurnal Solar Energy Conversion and Photoprotection in Rice Canopies1[OPEN

PubMed Central

Quick, W. Paul; von Caemmerer, Susanne; Furbank, Robert

2017-01-01

Genetic improvement of photosynthetic performance of cereal crops and increasing the efficiency with which solar radiation is converted into biomass has recently become a major focus for crop physiologists and breeders. The pulse amplitude modulated chlorophyll fluorescence technique (PAM) allows quantitative leaf level monitoring of the utilization of energy for photochemical light conversion and photoprotection in natural environments, potentially over the entire crop lifecycle. Here, the diurnal relationship between electron transport rate (ETR) and irradiance was measured in five cultivars of rice (Oryza sativa) in canopy conditions with PAM fluorescence under natural solar radiation. This relationship differed substantially from that observed for conventional short term light response curves measured under controlled actinic light with the same leaves. This difference was characterized by a reduced curvature factor when curve fitting was used to model this diurnal response. The engagement of photoprotective processes in chloroplast electron transport in leaves under canopy solar radiation was shown to be a major contributor to this difference. Genotypic variation in the irradiance at which energy flux into photoprotective dissipation became greater than ETR was observed. Cultivars capable of higher ETR at midrange light intensities were shown to produce greater leaf area over time, estimated by noninvasive imaging. PMID:27895208

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

PubMed

Hunter, Chad M; Huang, Wen; Mackay, Trudy F C; Singh, Nadia D

2016-04-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster

PubMed Central

Hunter, Chad M.; Huang, Wen; Mackay, Trudy F. C.; Singh, Nadia D.

2016-01-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. PMID:27035832

Implications of ecological energetics and biophysical and developmental constraints for life history variation in dinosaurs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunham, A.E.; Overall, K.L.; Forster, C.A.

1988-01-01

There has been much recent speculation concerning the nature of life history variation in dinosaurs (Case, 1978; Bakker, 1986; Horner, 1982, 1984a). The purpose of this paper is to review the data on dinosaur life histories and to examine the nature and magnitude of the demographic and physiological factors that must have constrained life history variation in this group. 145 refs., 8 figs., 3 tabs.

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value.

PubMed

Pacheco-Villalobos, David; Hardtke, Christian S

2012-06-05

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.

Morphological Variation in the Adult Hard Palate and Posterior Pharyngeal Wall

PubMed Central

Lammert, Adam; Proctor, Michael; Narayanan, Shrikanth

2013-01-01

Purpose Adult human vocal tracts display considerable morphological variation across individuals, but the nature and extent of this variation has not been extensively studied for many vocal tract structures. There exists a need to analyze morphological variation and, even more basically, to develop a methodology for morphological analysis of the vocal tract. Such analysis will facilitate fundamental characterization of the speech production system, with broad implications from modeling to explaining inter-speaker variability. Method A data-driven methodology to automatically analyze the extent and variety of morphological variation is proposed and applied to a diverse subject pool of 36 adults. Analysis is focused on two key aspects of vocal tract structure: the midsagittal shape of the hard palate and the posterior pharyngeal wall. Result Palatal morphology varies widely in its degree of concavity, but also in anteriority and sharpness. Pharyngeal wall morphology, by contrast, varies mostly in terms of concavity alone. The distribution of morphological characteristics is complex, and analysis suggests that certain variations may be categorical in nature. Conclusion Major modes of morphological variation are identified, including their relative magnitude, distribution and categorical nature. Implications of these findings for speech articulation strategies and speech acoustics are discussed. PMID:23690566

Genomic variation at the tips of the adaptive radiation of Darwin's finches.

PubMed

Chaves, Jaime A; Cooper, Elizabeth A; Hendry, Andrew P; Podos, Jeffrey; De León, Luis F; Raeymaekers, Joost A M; MacMillan, W Owen; Uy, J Albert C

2016-11-01

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site-associated DNA (RAD-seq), we characterized 32 569 single-nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta-like 1 homologue (DLK1) and high-mobility group AT-hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro- and macro-evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions. © 2016 John Wiley & Sons Ltd.

Evolutionary constraints or opportunities?

PubMed

Sharov, Alexei A

2014-09-01

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). Published by Elsevier Ireland Ltd.

Host-to-host variation of ecological interactions in polymicrobial infections

NASA Astrophysics Data System (ADS)

Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward; Das, Jayajit

2015-02-01

Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a maximum entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species.

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris.

PubMed

Aw, Rochelle; Barton, Geraint R; Leak, David J

2017-06-01

Clonal variation, wherein a range of specific productivities of secreted proteins are observed from supposedly identical transformants, is an accepted aspect of working with Pichia pastoris. It means that a significant number of transformants need to be tested to obtain a representative sample, and in commercial protein production, companies regularly screen thousands of transformants to select for the highest secretor. Here, we have undertaken a detailed investigation of this phenomenon by characterising clones transformed with the human serum albumin gene. The titers of nine clones, each containing a single copy of the human serum albumin gene (identified by qPCR), were measured and the clones grouped into three categories, namely, high-, mid- and low-level secretors. Transcriptomic analysis, using microarrays, showed that no regulatory patterns consistently correlated with titer, suggesting that the causes of clonal variation are varied. However, a number of physiological changes appeared to underlie the differences in titer, suggesting there is more than one biochemical signature for a high-secreting strain. An anomalous low-secreting strain displaying high transcript levels that appeared to be nutritionally starved further emphasises the complicated nature of clonal variation.

Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

NASA Astrophysics Data System (ADS)

Maier, E.; Buckenmaier, A.; Tollrian, R.; Nürnberger, B.

2012-06-01

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.

Use of natural variation to identify loci associated with relevant agronomic phenotypic traits

USDA-ARS?s Scientific Manuscript database

Analysis of natural allelic variation is a useful discovery tool to identify novel alleles in genes and pathways that are consistent with agronomic productivity and environmental stability. Switchgrass, a native perennial North American prairie grass and emerging biofuel feedstock species, is divide...

CORAL REEFS. Genomic determinants of coral heat tolerance across latitudes.

PubMed

Dixon, Groves B; Davies, Sarah W; Aglyamova, Galina A; Meyer, Eli; Bay, Line K; Matz, Mikhail V

2015-06-26

As global warming continues, reef-building corals could avoid local population declines through "genetic rescue" involving exchange of heat-tolerant genotypes across latitudes, but only if latitudinal variation in thermal tolerance is heritable. Here, we show an up-to-10-fold increase in odds of survival of coral larvae under heat stress when their parents come from a warmer lower-latitude location. Elevated thermal tolerance was associated with heritable differences in expression of oxidative, extracellular, transport, and mitochondrial functions that indicated a lack of prior stress. Moreover, two genomic regions strongly responded to selection for thermal tolerance in interlatitudinal crosses. These results demonstrate that variation in coral thermal tolerance across latitudes has a strong genetic basis and could serve as raw material for natural selection. Copyright © 2015, American Association for the Advancement of Science.

Abnormal Uterine Bleeding: American College of Nurse-Midwives.

PubMed

2016-07-01

Variations in uterine bleeding, termed abnormal uterine bleeding, occur commonly among women and often are physiologic in nature with no significant consequences. However, abnormal uterine bleeding can cause significant distress to women or may signify an underlying pathologic condition. Most women experience variations in menstrual and perimenstrual bleeding in their lifetimes; therefore, the ability of the midwife to differentiate between normal and abnormal bleeding is a key diagnostic skill. A comprehensive history and use of the PALM-COEIN classification system will provide clear guidelines for clinical management, evidence-based treatment, and an individualized plan of care. The purpose of this Clinical Bulletin is to define and describe classifications of abnormal uterine bleeding, review updated terminology, and identify methods of assessment and treatment using a woman-centered approach. © 2016 by the American College of Nurse-Midwives.

Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

PubMed

Tomar, Parul; Bhatia, Aatish; Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

2013-01-01

Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.

Sporulation Genes Associated with Sporulation Efficiency in Natural Isolates of Yeast

PubMed Central

Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

2013-01-01

Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes – HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast. PMID:23874994

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Evolutionary implications of the form of predator generalization for aposematic signals and mimicry in prey.

PubMed

Ruxton, Graeme D; Franks, Dan W; Balogh, Alexandra C V; Leimar, Olof

2008-11-01

Generalization is at the heart of many aspects of behavioral ecology; for foragers it can be seen as an essential feature of learning about potential prey, because natural populations of prey are unlikely to be perfectly homogenous. Aposematic signals are considered to aid predators in learning to avoid a class of defended prey. Predators do this by generalizing between the appearance of prey they have previously sampled and the appearance of prey they subsequently encounter. Mimicry arises when such generalization occurs between individuals of different species. Our aim here is to explore whether the specific shape of the generalization curve can be expected to be important for theoretical predictions relating to the evolution of aposematism and mimicry. We do this by a reanalysis and development of the models provided in two recent papers. We argue that the shape of the generalization curve, in combination with the nature of genetic and phenotypic variation in prey traits, can have evolutionary significance under certain delineated circumstances. We also demonstrate that the process of gradual evolution of Müllerian mimicry proposed by Fisher is particularly efficient in populations with a rich supply of standing genetic variation in mimetic traits.

Use of multiple regression models in the study of sandhopper orientation under natural conditions

NASA Astrophysics Data System (ADS)

Marchetti, Giovanni M.; Scapini, Felicita

2003-10-01

In sandhoppers (Amphipoda; Talitridae), typical dwellers of the supralittoral zone of sandy beaches, orientation with respect to the sun and landscape vision is adapted to the local direction of the shoreline. Variation of this behavioural adaptation can be related to the characteristics of the beach. Measures of orientation with respect to the shoreline direction can thus be made as a tool to assess beach stability versus changeability, once the sources of variation are correctly interpreted. Orientation of animals can be studied by statistical analysis of directions taken after release in nature. In this paper some new tools for exploring directional data are reviewed, with special emphasis on non-parametric smoothers and regression models. Results from a large study concerning one species of sandhoppers, Talitrus saltator (Montagu), from an exposed sandy beach in northeastern Tunisia are presented. Seasonal differences in orientation behaviour were shown with a higher scatter in autumn with respect to spring. The higher scatter shown in autumn depended both on intrinsic (sex) and external (climatic conditions and landscape visibility) factors and was related to the tendency of this species to migrate towards the dune anticipating winter conditions.

Ground-state properties of light kaonic nuclei signaling symmetry energy at high densities

NASA Astrophysics Data System (ADS)

Yang, Rongyao; Wei, Sina; Jiang, Weizhou

2018-01-01

A sensitive correlation between the ground-state properties of light kaonic nuclei and the symmetry energy at high densities is constructed under the framework of relativistic mean-field theory. Taking oxygen isotopes as an example, we see that a high-density core is produced in kaonic oxygen nuclei, due to the strongly attractive antikaon-nucleon interaction. It is found that the 1{S}1/2 state energy in the high-density core of kaonic nuclei can directly probe the variation of the symmetry energy at supranormal nuclear density, and a sensitive correlation between the neutron skin thickness and the symmetry energy at supranormal density is established directly. Meanwhile, the sensitivity of the neutron skin thickness to the low-density slope of the symmetry energy is greatly increased in the corresponding kaonic nuclei. These sensitive relationships are established upon the fact that the isovector potential in the central region of kaonic nuclei becomes very sensitive to the variation of the symmetry energy. These findings might provide another perspective to constrain high-density symmetry energy, and await experimental verification in the future. Supported by National Natural Science Foundation of China (11775049, 11275048) and the China Jiangsu Provincial Natural Science Foundation (BK20131286)

The cellular immune response of Daphnia magna under host-parasite genetic variation and variation in initial dose

PubMed Central

Auld, Stuart K. J. R; Edel, Kai H.; Little, Tom J.

2013-01-01

In invertebrate-parasite systems, the likelihood of infection following parasite exposure is often dependent on the specific combination of host and parasite genotypes (termed genetic specificity). Genetic specificity can maintain diversity in host and parasite populations and is a major component of the Red Queen hypothesis. However, invertebrate immune systems are thought to only distinguish between broad classes of parasite. Using a natural host-parasite system with a well-established pattern of genetic specificity, the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa, we found that only hosts from susceptible host-parasite genetic combinations mounted a cellular response following exposure to the parasite. These data are compatible with the hypothesis that genetic specificity is attributable to barrier defenses at the site of infection (the gut), and that the systemic immune response is general, reporting the number of parasite spores entering the hemocoel. Further supporting this, we found that larger cellular responses occurred at higher initial parasite doses. By studying the natural infection route, where parasites must pass barrier defenses before interacting with systemic immune responses, these data shed light on which components of invertebrate defense underlie genetic specificity. PMID:23025616

Final Report (BMWi Project No.: 02 E 10971): Joint project: Retention of radionuclides relevant for final disposal in natural clay rock and saline systems - Subproject 2: Geochemical behavior and transport of radionuclides in saline systems in the prese

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmeide, Katja; Fritsch, Katharina; Lippold, Holger

2016-02-29

The objective of this project was to study the influence of increased salinities on interaction processes in the system radionuclide – organics – clay – aquifer. For this, complexation, redox, sorption, and diffusion studies were performed under variation of the ionic strength (up to 4 mol kg -1) and the background electrolyte (NaCl, CaCl 2, MgCl 2).

[Effects of light intensity on Quercus liaotungensis seed germination and seedling growth].

PubMed

Yan, Xing-fu; Wang, Jian-li; Zhou, Li-biao

2011-07-01

This paper studied the effects of different shading (55.4%, 18.9%, 5.5%, 2.2%, 0.5% , and 0.3% natural sunlight) on the seed germination and seedling growth of Quercus liaotungensis. The seed germination rate and germination index were the highest (72.5% and 0.22, respectively) at 55.4% natural sunlight, declined with decreasing light intensity, and were the lowest (42.5% and 0.11, respectively) at 0.3% natural sunlight. Strong light had definite delaying effect on the germination. The index of germination vigor increased with decreasing light intensity, being the maximum at 0.5% natural sunlight. The delay of seed germination under strong light could be the selective tradeoff on varied seed fates. Strong light benefited the basal stem diameter and root system growth and dry mass accumulation of Q. liaotunensis seedling, but resulted in the minimum seedlings height (6.06 cm). Greater morphological plasticity was observed for the seedlings under different shading, which lent support to the higher adaptability of the seedlings to light environment. For example, the specific leaf area, specific shoot length, specific root length, and chlorophyll b and total chlorophyll contents were the maximum at 0.5% natural sunlight, being 142.57 cm2 x g(-1), 156.86 cm x g(-1), 271.87 cm x g(-1), 0.07 g x cm(-2), and 0.24 g x cm(-2), respectively, and the minimum at 55.4% natural sunlight, being 44.89 cm2 x g(-1), 52.84 cm x g(-1), 101.98 cm x g(-1), 0.04 g x cm(-2), and 0.15 g x cm(-2), respectively. The variation of the root/shoot ratio of Q. liaotungensis seedlings under different shading could be the effects of the combination of light intensity and water availability.

Impacts of Land Use Change on the Natural Flow Regime: A Case Study in the Meramec River Watershed in Eastern Missouri, USA

NASA Astrophysics Data System (ADS)

Wu, C. L.; Knouft, J.; Chu, M.

2017-12-01

The natural flow regime within a watershed can be considered as the expected temporal patterns of streamflow variation in the absence of human impacts. While ecosystems have evolved to function under these conditions, the natural flow regime of most rivers has been significantly altered by human activities. Land use change, including the development of agriculture and urbanization, is a primary cause of the loss of natural flow regimes. These changes have altered discharge volume, timing, and variability, and consequently affected the structure and functioning of river ecosystems. The Meramec River watershed is located in east central Missouri and changes in land use have been the primary factor impacting flow regimes across the watershed. In this study, a watershed model, the Soil and Water Assessment Tool (SWAT), was developed to simulate a long-term time series of streamflow (1978-2014) within the watershed. Model performance was evaluated using statistical metrics and graphical technique including R-squared, Nash-Sutcliffe efficiency, cumulative error, and 1:1-ratio comparison between observed and simulated variables. The calibrated and validated SWAT model was then used to quantify the responses of the watershed when it was a forested natural landscape. An Indicator of Hydrologic Alteration (IHA) approach was applied to characterize the flow regime under the current landcover conditions as well as the simulated natural flow regime under the no land use change scenario. Differences in intra- and inter-annual ecologically relevant flow metrics were then compared using SWAT model outputs in conjunction with the IHA approach based on model outputs from current and no land use change conditions. This study provides a watershed-scale understanding of effects of land use change on a river's flow variability and provides a framework for the development of restoration plans for heavily altered watersheds.

An integrative time-varying frequency detection and channel sounding method for dynamic plasma sheath

NASA Astrophysics Data System (ADS)

Shi, Lei; Yao, Bo; Zhao, Lei; Liu, Xiaotong; Yang, Min; Liu, Yanming

2018-01-01

The plasma sheath-surrounded hypersonic vehicle is a dynamic and time-varying medium and it is almost impossible to calculate time-varying physical parameters directly. The in-fight detection of the time-varying degree is important to understand the dynamic nature of the physical parameters and their effect on re-entry communication. In this paper, a constant envelope zero autocorrelation (CAZAC) sequence based on time-varying frequency detection and channel sounding method is proposed to detect the plasma sheath electronic density time-varying property and wireless channel characteristic. The proposed method utilizes the CAZAC sequence, which has excellent autocorrelation and spread gain characteristics, to realize dynamic time-varying detection/channel sounding under low signal-to-noise ratio in the plasma sheath environment. Theoretical simulation under a typical time-varying radio channel shows that the proposed method is capable of detecting time-variation frequency up to 200 kHz and can trace the channel amplitude and phase in the time domain well under -10 dB. Experimental results conducted in the RF modulation discharge plasma device verified the time variation detection ability in practical dynamic plasma sheath. Meanwhile, nonlinear phenomenon of dynamic plasma sheath on communication signal is observed thorough channel sounding result.

Environmental Noise, Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

PubMed Central

Steiner, Christopher F.

2012-01-01

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions. PMID:23284934

Trait Variation in Yeast Is Defined by Population History

PubMed Central

Warringer, Jonas; Zörgö, Enikö; Cubillos, Francisco A.; Zia, Amin; Gjuvsland, Arne; Simpson, Jared T.; Forsmark, Annabelle; Durbin, Richard; Omholt, Stig W.; Louis, Edward J.; Liti, Gianni; Moses, Alan; Blomberg, Anders

2011-01-01

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism. PMID:21698134

Trait variation in yeast is defined by population history.

PubMed

Warringer, Jonas; Zörgö, Enikö; Cubillos, Francisco A; Zia, Amin; Gjuvsland, Arne; Simpson, Jared T; Forsmark, Annabelle; Durbin, Richard; Omholt, Stig W; Louis, Edward J; Liti, Gianni; Moses, Alan; Blomberg, Anders

2011-06-01

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.

Equatorial electrojet and its response to external electromagnetic effects

NASA Astrophysics Data System (ADS)

Bespalov, P. A.; Savina, O. N.

2012-09-01

In the quiet low-latitude Earth's ionosphere, a sufficiently developed current system that is responsible for the Sq magnetic-field variations is formed in quiet Sun days under the action of tidal streams. The density of the corresponding currents is maximum in the midday hours at the equatorial latitudes, where the so-called equatorial electrojet is formed. In this work, we discuss the nature of the equatorial electrojet. This paper studies the value of its response to external effects. First of all, it is concerned with estimating the possibility of using the equatorial electrojet for generating low-frequency electromagnetic signals during periodic heating of the ionosphere by the heating-facility radiation. The equatorial electrojet can also produce electrodynamic response to the natural atmospheric processes, e.g., an acoustic-gravity wave.

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length.

PubMed

Cook, Daniel E; Zdraljevic, Stefan; Tanny, Robyn E; Seo, Beomseok; Riccardi, David D; Noble, Luke M; Rockman, Matthew V; Alkema, Mark J; Braendle, Christian; Kammenga, Jan E; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C

2016-09-01

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. Copyright © 2016 by the Genetics Society of America.

Physiological genomics of response to soil drying in diverse Arabidopsis accessions.

PubMed

Des Marais, David L; McKay, John K; Richards, James H; Sen, Saunak; Wayne, Tierney; Juenger, Thomas E

2012-03-01

Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural mutant screen to determine gene function. Here, we document physiological and transcriptomic response to soil drying in 17 natural accessions of Arabidopsis. By imposing ecologically realistic stress conditions, we found that acclimation in Arabidopsis involved a strong signature of increased investment in photosynthesis, carbohydrate turnover, and root growth. Our results extend previous work in the Columbia accession suggesting that abscisic acid signaling pathways play an important role in drought stress response. We also identified several mechanisms, including an increase in leaf nitrogen concentration and upregulation of two-component signaling relays, that were common to most natural accessions but had not been identified in studies using only the Columbia accession. Principal component analysis reveals strong correlations between suites of genes and specific physiological responses to stress. The functional variants we identified may represent adaptive mutations in natural habitats and useful variants for agronomic improvement of crop species.

Nature, nurture and evolution of intra-species variation in mosquito arbovirus transmission competence.

PubMed

Tabachnick, Walter J

2013-01-11

Mosquitoes vary in their competence or ability to transmit arthropod-borne viruses (arboviruses). Many arboviruses cause disease in humans and animals. Identifying the environmental and genetic causes of variation in mosquito competence for arboviruses is one of the great challenges in public health. Progress identifying genetic (nature) and environmental (nurture) factors influencing mosquito competence for arboviruses is reviewed. There is great complexity in the various traits that comprise mosquito competence. The complex interactions between environmental and genetic factors controlling these traits and the factors shaping variation in Nature are largely unknown. The norms of reaction of specific genes influencing competence, their distributions in natural populations and the effects of genetic polymorphism on phenotypic variation need to be determined. Mechanisms influencing competence are not likely due to natural selection because of the direct effects of the arbovirus on mosquito fitness. More likely the traits for mosquito competence for arboviruses are the effects of adaptations for other functions of these competence mechanisms. Determining these other functions is essential to understand the evolution and distributions of competence for arboviruses. This information is needed to assess risk from mosquito-borne disease, predict new mosquito-arbovirus systems, and provide novel strategies to mitigate mosquito-borne arbovirus transmission.

Physiological Genomics of Response to Soil Drying in Diverse Arabidopsis Accessions[W][OA

PubMed Central

Des Marais, David L.; McKay, John K.; Richards, James H.; Sen, Saunak; Wayne, Tierney; Juenger, Thomas E.

2012-01-01

Arabidopsis thaliana, like many species, is characterized by abundant genetic variation. This variation is rapidly being cataloged at the sequence level, but careful dissection of genetic variation in whole-organism responses to stresses encountered in the natural environment are lacking; this functional variation can be exploited as a natural mutant screen to determine gene function. Here, we document physiological and transcriptomic response to soil drying in 17 natural accessions of Arabidopsis. By imposing ecologically realistic stress conditions, we found that acclimation in Arabidopsis involved a strong signature of increased investment in photosynthesis, carbohydrate turnover, and root growth. Our results extend previous work in the Columbia accession suggesting that abscisic acid signaling pathways play an important role in drought stress response. We also identified several mechanisms, including an increase in leaf nitrogen concentration and upregulation of two-component signaling relays, that were common to most natural accessions but had not been identified in studies using only the Columbia accession. Principal component analysis reveals strong correlations between suites of genes and specific physiological responses to stress. The functional variants we identified may represent adaptive mutations in natural habitats and useful variants for agronomic improvement of crop species. PMID:22408074

Land management influences trade-offs and the total supply of ecosystem services in alpine grassland in Tibet, China.

PubMed

Wu, Junxi; Zhao, Yan; Yu, Chengqun; Luo, Liming; Pan, Ying

2017-05-15

Developing sustainable use patterns for alpine grassland in Tibet is the primary challenge related to conserving these vulnerable ecosystems of the 'world's third pole' and guaranteeing the well-being of local inhabitants. This challenge requires researchers to think beyond the methods of most current studies that are limited to a single aspect of conservation or productivity, and focus on balancing various needs. An analysis of trade-offs involving ecosystem services provides a framework that can be used to quantify the type of balancing needed. In this study, we measured variations in four types of ecosystem services under five types of grassland management including grazing exclusion, sowing, combined plowing and grazing exclusion, combined plowing and sowing, and natural grassland, from 2013 to 2015. In addition, we accessed the existence and changing patterns of ecosystem service trade-offs using Spearman coefficients and a trade-off index. The results revealed the existence of trade-offs among provisioning and regulating services. Plowing and sowing could convert the trade-off relationships into synergies immediately. Grazing exclusion reduced the level of trade-offs gradually over time. Thus, the combined plowing and sowing treatment promoted the total supply of multiple ecosystem services when compared with natural grassland. We argue that the variations in dry matter allocation to above- and belowground serve as one cause of the variation in trade-off relationships. Another cause for variation in trade-offs is the varied species competition between selection effects and niche complementarity. Our study provides empirical evidence that the effects of trade-offs among ecosystem services could be reduced and even converted into synergies by optimizing management techniques. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities.

PubMed

Morris, Jonathan R; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species' functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities

PubMed Central

Morris, Jonathan R.; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species’ functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems. PMID:26562676

Variation among genotypes in responses to increasing temperature in a marine parasite: evolutionary potential in the face of global warming?

PubMed

Berkhout, Boris W; Lloyd, Melanie M; Poulin, Robert; Studer, Anja

2014-11-01

Climates are changing worldwide, and populations are under selection to adapt to these changes. Changing temperature, in particular, can directly impact ectotherms and their parasites, with potential consequences for whole ecosystems. The potential of parasite populations to adapt to climate change largely depends on the amount of genetic variation they possess in their responses to environmental fluctuations. This study is, to our knowledge, the first to look at differences among parasite genotypes in response to temperature, with the goal of quantifying the extent of variation among conspecifics in their responses to increasing temperature. Snails infected with single genotypes of the trematode Maritrema novaezealandensis were sequentially acclimatised to two different temperatures, 'current' (15°C) and 'elevated' (20°C), over long periods. These temperatures are based on current average field conditions in the natural habitat and those predicted to occur during the next few decades. The output and activity of cercariae (free-swimming infective stages emerging from snails) were assessed for each genotype at each temperature. The results indicate that, on average, both cercarial output and activity are higher at the elevated acclimation temperature. More importantly, the output and activity of cercariae are strongly influenced by a genotype-by-temperature interaction, such that different genotypes show different responses to increasing temperature. Both the magnitude and direction (increase or decrease) of responses to temperature varied widely among genotypes. Therefore, there is much potential for natural selection to act on this variation, and predicting how the trematode M. novaezealandensis will respond to the climate changes predicted for the next century will prove challenging. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

A Variational Formulation of Macro-Particle Algorithms for Kinetic Plasma Simulations

NASA Astrophysics Data System (ADS)

Shadwick, B. A.

2013-10-01

Macro-particle based simulations methods are in widespread use in plasma physics; their computational efficiency and intuitive nature are largely responsible for their longevity. In the main, these algorithms are formulated by approximating the continuous equations of motion. For systems governed by a variational principle (such as collisionless plasmas), approximations of the equations of motion is known to introduce anomalous behavior, especially in system invariants. We present a variational formulation of particle algorithms for plasma simulation based on a reduction of the distribution function onto a finite collection of macro-particles. As in the usual Particle-In-Cell (PIC) formulation, these macro-particles have a definite momentum and are spatially extended. The primary advantage of this approach is the preservation of the link between symmetries and conservation laws. For example, nothing in the reduction introduces explicit time dependence to the system and, therefore, the continuous-time equations of motion exactly conserve energy; thus, these models are free of grid-heating. In addition, the variational formulation allows for constructing models of arbitrary spatial and temporal order. In contrast, the overall accuracy of the usual PIC algorithm is at most second due to the nature of the force interpolation between the gridded field quantities and the (continuous) particle position. Again in contrast to the usual PIC algorithm, here the macro-particle shape is arbitrary; the spatial extent is completely decoupled from both the grid-size and the ``smoothness'' of the shape; smoother particle shapes are not necessarily larger. For simplicity, we restrict our discussion to one-dimensional, non-relativistic, un-magnetized, electrostatic plasmas. We comment on the extension to the electromagnetic case. Supported by the US DoE under contract numbers DE-FG02-08ER55000 and DE-SC0008382.

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association.

PubMed

Kingston, S E; Martino, P; Melendy, M; Reed, F A; Carlon, D B

2018-03-01

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here, we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a 'climate change' common garden, where we raised temperature by 3°C, decreased pH by 0.2 units and limited food supply by filtering out planktonic particles >5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170 000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of >90% when effective sample size is 900. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Test system stability and natural variability of a Lemna gibba L. bioassay.

PubMed

Scherr, Claudia; Simon, Meinhard; Spranger, Jörg; Baumgartner, Stephan

2008-09-04

In ecotoxicological and environmental studies Lemna spp. are used as test organisms due to their small size, rapid predominantly vegetative reproduction, easy handling and high sensitivity to various chemicals. However, there is not much information available concerning spatial and temporal stability of experimental set-ups used for Lemna bioassays, though this is essential for interpretation and reliability of results. We therefore investigated stability and natural variability of a Lemna gibba bioassay assessing area-related and frond number-related growth rates under controlled laboratory conditions over about one year. Lemna gibba L. was grown in beakers with Steinberg medium for one week. Area-related and frond number-related growth rates (r(area) and r(num)) were determined with a non-destructive image processing system. To assess inter-experimental stability, 35 independent experiments were performed with 10 beakers each in the course of one year. We observed changes in growth rates by a factor of two over time. These did not correlate well with temperature or relative humidity in the growth chamber. In order to assess intra-experimental stability, we analysed six systematic negative control experiments (nontoxicant tests) with 96 replicate beakers each. Evaluation showed that the chosen experimental set-up was stable and did not produce false positive results. The coefficient of variation was lower for r(area) (2.99%) than for r(num) (4.27%). It is hypothesised that the variations in growth rates over time under controlled conditions are partly due to endogenic periodicities in Lemna gibba. The relevance of these variations for toxicity investigations should be investigated more closely. Area-related growth rate seems to be more precise as non-destructive calculation parameter than number-related growth rate. Furthermore, we propose two new validity criteria for Lemna gibba bioassays: variability of average specific and section-by-section segmented growth rate, complementary to average specific growth rate as the only validity criterion existing in guidelines for duckweed bioassays.

Test System Stability and Natural Variability of a Lemna Gibba L. Bioassay

PubMed Central

Scherr, Claudia; Simon, Meinhard; Spranger, Jörg; Baumgartner, Stephan

2008-01-01

Background In ecotoxicological and environmental studies Lemna spp. are used as test organisms due to their small size, rapid predominantly vegetative reproduction, easy handling and high sensitivity to various chemicals. However, there is not much information available concerning spatial and temporal stability of experimental set-ups used for Lemna bioassays, though this is essential for interpretation and reliability of results. We therefore investigated stability and natural variability of a Lemna gibba bioassay assessing area-related and frond number-related growth rates under controlled laboratory conditions over about one year. Methology/Principal Findings Lemna gibba L. was grown in beakers with Steinberg medium for one week. Area-related and frond number-related growth rates (r(area) and r(num)) were determined with a non-destructive image processing system. To assess inter-experimental stability, 35 independent experiments were performed with 10 beakers each in the course of one year. We observed changes in growth rates by a factor of two over time. These did not correlate well with temperature or relative humidity in the growth chamber. In order to assess intra-experimental stability, we analysed six systematic negative control experiments (nontoxicant tests) with 96 replicate beakers each. Evaluation showed that the chosen experimental set-up was stable and did not produce false positive results. The coefficient of variation was lower for r(area) (2.99%) than for r(num) (4.27%). Conclusions/Significance It is hypothesised that the variations in growth rates over time under controlled conditions are partly due to endogenic periodicities in Lemna gibba. The relevance of these variations for toxicity investigations should be investigated more closely. Area-related growth rate seems to be more precise as non-destructive calculation parameter than number-related growth rate. Furthermore, we propose two new validity criteria for Lemna gibba bioassays: variability of average specific and section-by-section segmented growth rate, complementary to average specific growth rate as the only validity criterion existing in guidelines for duckweed bioassays. PMID:18769541

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

Mate-finding as an overlooked critical determinant of dispersal variation in sexually-reproducing animals.

PubMed

Gilroy, James J; Lockwood, Julie L

2012-01-01

Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly 'fat-tailed' at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics.

PubMed

Nugent, B M; Stiver, K A; Alonzo, S H; Hofmann, H A

2016-10-01

The molecular mechanisms underlying phenotypic plasticity are not well understood. Identifying mechanisms underlying alternative reproductive tactics (ARTs) in species for which the behavioural and fitness consequences of this variation are well characterized provides an opportunity to integrate evolutionary and mechanistic understanding of the maintenance of variation within populations. In the ocellated wrasse Symphodus ocellatus, the behavioural phenotypes of three distinct male morphs (sneakers, satellites and nesting males), which arise from a single genome, have been thoroughly characterized. To determine the neuroendocrine and genomic mechanisms associated with discrete phenotypic variation and ARTs in S. ocellatus in their natural environment, we constructed a whole-brain de novo transcriptome and compared global patterns of gene expression between sexes and male morphs. Next, we quantified circulating cortisol and 11-ketotestosterone (11-kt), mediators of male reproductive behaviours, as well as stress and gonadal steroid hormone receptor expression in the preoptic area, ventral subpallial division of the telencephalon and dorsolateral telencephalon, critical brain regions for social and reproductive behaviours. We found higher levels of 11-kt in nesting males and higher levels of cortisol in sneaker males relative to other male morphs and females. We also identified distinct patterns of brain region-specific hormone receptor expression between males such that most hormone receptors are more highly expressed in satellites and nesting males relative to sneakers and females. Our results establish the neuroendocrine and molecular mechanisms that underlie ARTs in the wild and provide a foundation for experimentally testing hypotheses about the relationship between neuromolecular processes and reproductive success. © 2016 John Wiley & Sons Ltd.

Modeling Natural Variation through Distribution

ERIC Educational Resources Information Center

Lehrer, Richard; Schauble, Leona

2004-01-01

This design study tracks the development of student thinking about natural variation as late elementary grade students learned about distribution in the context of modeling plant growth at the population level. The data-modeling approach assisted children in coordinating their understanding of particular cases with an evolving notion of data as an…

Natural variation of rice blast resistance gene Pi-d2

USDA-ARS?s Scientific Manuscript database

Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (...

Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

USDA-ARS?s Scientific Manuscript database

Several groups have reported on massive accumulation of total carotenoids in cassava storage root (CSR). Naturally occurring color variation associated with carotenoid accumulation was observed in cassava (Manihot esculenta Crantz) storage root of landraces from Amazon. Here carotenoid profiles from...

Non-exponential kinetics of unfolding under a constant force.

PubMed

Bell, Samuel; Terentjev, Eugene M

2016-11-14

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

Non-exponential kinetics of unfolding under a constant force

NASA Astrophysics Data System (ADS)

Bell, Samuel; Terentjev, Eugene M.

2016-11-01

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

PubMed

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-04-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

Causes of variation among rice models in yield response to CO2 examined with Free-Air CO2 Enrichment and growth chamber experiments.

PubMed

Hasegawa, Toshihiro; Li, Tao; Yin, Xinyou; Zhu, Yan; Boote, Kenneth; Baker, Jeffrey; Bregaglio, Simone; Buis, Samuel; Confalonieri, Roberto; Fugice, Job; Fumoto, Tamon; Gaydon, Donald; Kumar, Soora Naresh; Lafarge, Tanguy; Marcaida Iii, Manuel; Masutomi, Yuji; Nakagawa, Hiroshi; Oriol, Philippe; Ruget, Françoise; Singh, Upendra; Tang, Liang; Tao, Fulu; Wakatsuki, Hitomi; Wallach, Daniel; Wang, Yulong; Wilson, Lloyd Ted; Yang, Lianxin; Yang, Yubin; Yoshida, Hiroe; Zhang, Zhao; Zhu, Jianguo

2017-11-01

The CO 2 fertilization effect is a major source of uncertainty in crop models for future yield forecasts, but coordinated efforts to determine the mechanisms of this uncertainty have been lacking. Here, we studied causes of uncertainty among 16 crop models in predicting rice yield in response to elevated [CO 2 ] (E-[CO 2 ]) by comparison to free-air CO 2 enrichment (FACE) and chamber experiments. The model ensemble reproduced the experimental results well. However, yield prediction in response to E-[CO 2 ] varied significantly among the rice models. The variation was not random: models that overestimated at one experiment simulated greater yield enhancements at the others. The variation was not associated with model structure or magnitude of photosynthetic response to E-[CO 2 ] but was significantly associated with the predictions of leaf area. This suggests that modelled secondary effects of E-[CO 2 ] on morphological development, primarily leaf area, are the sources of model uncertainty. Rice morphological development is conservative to carbon acquisition. Uncertainty will be reduced by incorporating this conservative nature of the morphological response to E-[CO 2 ] into the models. Nitrogen levels, particularly under limited situations, make the prediction more uncertain. Improving models to account for [CO 2 ] × N interactions is necessary to better evaluate management practices under climate change.

Mitochondrial Recombination Reveals Mito-Mito Epistasis in Yeast.

PubMed

Wolters, John F; Charron, Guillaume; Gaspary, Alec; Landry, Christian R; Fiumera, Anthony C; Fiumera, Heather L

2018-05-01

Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mito-nuclear interactions. Recombinant mtDNAs were generated to determine fitness components within high- and low-fitness mtDNAs. Based on phenotypic distributions of isogenic strains containing recombinant mtDNAs, we found that multiple loci contributed to mitotype fitness differences. These mitochondrial loci interacted in epistatic, nonadditive ways in certain environmental conditions. Mito-mito epistasis ( i.e. , nonadditive interactions between mitochondrial loci) influenced fitness in progeny from four different crosses, suggesting that mito-mito epistasis is a widespread phenomenon in yeast and other systems with recombining mtDNAs. Furthermore, we found that interruption of coadapted mito-mito interactions produced recombinant mtDNAs with lower fitness. Our results demonstrate that mito-mito epistasis results in functional variation through mitochondrial recombination in fungi, providing modes for adaptive evolution and the generation of mito-mito incompatibilities. Copyright © 2018 by the Genetics Society of America.

Variation under domestication in plants: 1859 and today

PubMed Central

Brown, Anthony H. D.

2010-01-01

Charles Darwin began The Origin of Species with a chapter entitled variation under domestication, which encapsulated decades of his research on a diverse array of animal and plant domesticated species. Variation in these species compared with that in their wild relatives, their origins and their selection by humans, formed a paradigm for his theory of the evolutionary origin of species by means of natural selection. This chapter, its subsequent expansion into a two-volume monograph, together with the rediscovery of Mendel's laws, later became the foundation of scientific plant breeding. In the period up to the present, several advances in genetics (such as artificial mutation, polyploidy, adaptation and genetic markers) have amplified the discipline with concepts and questions, the seeds of which are in Darwin's original words. Today, we are witnessing a flowering of genomic research into the process of domestication itself, particularly the specific major and minor genes involved. In one striking way, our view of domestic diversity contrasts with that in Darwin's writing. He stressed the abundance of diversity and the diversifying power of artificial selection, whereas we are concerned about dwindling genetic diversity that attends modern agriculture and development. In this context, it is paramount to strive for a deeper understanding of how farmer selection including both deliberate selection and unconscious selection, might generate and retain diversity. This knowledge is essential for devising in situ conservation measures. PMID:20643742

Does natural variation in diversity affect biotic resistance?

USGS Publications Warehouse

Harrison, Susan; Cornell, Howard; Grace, James B.

2015-01-01

Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

Long-Range Regulatory Polymorphisms Affecting a GABA Receptor Constitute a Quantitative Trait Locus (QTL) for Social Behavior in Caenorhabditis elegans

PubMed Central

Bendesky, Andres; Pitts, Jason; Rockman, Matthew V.; Chen, William C.; Tan, Man-Wah; Kruglyak, Leonid; Bargmann, Cornelia I.

2012-01-01

Aggregation is a social behavior that varies between and within species, providing a model to study the genetic basis of behavioral diversity. In the nematode Caenorhabditis elegans, aggregation is regulated by environmental context and by two neuromodulatory pathways, one dependent on the neuropeptide receptor NPR-1 and one dependent on the TGF-β family protein DAF-7. To gain further insight into the genetic regulation of aggregation, we characterize natural variation underlying behavioral differences between two wild-type C. elegans strains, N2 and CB4856. Using quantitative genetic techniques, including a survey of chromosome substitution strains and QTL analysis of recombinant inbred lines, we identify three new QTLs affecting aggregation in addition to the two known N2 mutations in npr-1 and glb-5. Fine-mapping with near-isogenic lines localized one QTL, accounting for 5%–8% of the behavioral variance between N2 and CB4856, 3′ to the transcript of the GABA neurotransmitter receptor gene exp-1. Quantitative complementation tests demonstrated that this QTL affects exp-1, identifying exp-1 and GABA signaling as new regulators of aggregation. exp-1 interacts genetically with the daf-7 TGF-β pathway, which integrates food availability and population density, and exp-1 mutations affect the level of daf-7 expression. Our results add to growing evidence that genetic variation affecting neurotransmitter receptor genes is a source of natural behavioral variation. PMID:23284308

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

PubMed Central

Famoso, Adam N.; Zhao, Keyan; Clark, Randy T.; Tung, Chih-Wei; Wright, Mark H.; Bustamante, Carlos; Kochian, Leon V.; McCouch, Susan R.

2011-01-01

Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype–genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice. PMID:21829395

Development and Characterization of a Reverse Genetic System for Studying Dengue Virus Serotype 3 Strain Variation and Neutralization

PubMed Central

Messer, William B.; Yount, Boyd; Hacker, Kari E.; Donaldson, Eric F.; Huynh, Jeremy P.; de Silva, Aravinda M.; Baric, Ralph S.

2012-01-01

Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis. PMID:22389731

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

Spatiotemporal variation of radon and carbon dioxide concentrations in an underground quarry: coupled processes of natural ventilation, barometric pumping and internal mixing.

PubMed

Perrier, Frédéric; Richon, Patrick

2010-04-01

Radon-222 and carbon dioxide concentrations have been measured during several years at several points in the atmosphere of an underground limestone quarry located at a depth of 18 m in Vincennes, near Paris, France. Both concentrations showed a seasonal cycle. Radon concentration varied from 1200 to 2000 Bq m(-3) in summer to about 800-1400 Bq m(-3) in winter, indicating winter ventilation rates varying from 0.6 to 2.5 x 10(-6) s(-1). Carbon dioxide concentration varied from 0.9 to 1.0% in summer, to about 0.1-0.3% in winter. Radon concentration can be corrected for natural ventilation using temperature measurements. The obtained model also accounts for the measured seasonal variation of carbon dioxide. After correction, radon concentrations still exhibit significant temporal variation, mostly associated with the variation of atmospheric pressure, with coupling coefficients varying from -7 to -26 Bq m(-3) hPa(-1). This variation can be accounted for using a barometric pumping model, coupled with natural ventilation in winter, and including internal mixing as well. After correction, radon concentrations exhibit residual temporal variation, poorly correlated between different points, with standard deviations varying from 3 to 6%. This study shows that temporal variation of radon concentrations in underground cavities can be understood to a satisfactory level of detail using non-linear and time-dependent modelling. It is important to understand the temporal variation of radon concentrations and the limitations in their modelling to monitor the properties of natural or artificial underground settings, and to be able to assess the existence of new processes, for example associated with the preparatory phases of volcanic eruptions or earthquakes. Copyright 2009 Elsevier Ltd. All rights reserved.

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

DOE PAGES

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.; ...

2016-06-08

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

Are Solar Activity Variations Amplified by the QBO: A Modeling Study

NASA Technical Reports Server (NTRS)

Mengel, J. G.; Mayr, H. G.; Drob, D. P.; Porter, H. S.; Bhartia, P. K. (Technical Monitor)

2002-01-01

Solar cycle activity effects (SCAE) in the lower and middle atmosphere, reported in several studies, are difficult to explain on the basis of the small changes in solar radiation that accompany the 11-year cycle. It is therefore natural to speculate that dynamical processes may come into play to produce a leverage. Such a leverage may be provided by the Quasi-Biennial Oscillation (QBO) in the zonal circulation of the stratosphere, which has been linked to solar activity variations. Driven primarily by wave mean flow interaction, the QBO period and its amplitude are variable but are also strongly influenced by the seasonal cycle in the solar radiation. This influence extends to low altitudes and is referred to as 'downward control'. Small changes in the solar radiative forcing may produce small changes in the period and phase of the QBO, but these in turn may produce measurable differences in the wind field. Thus, the QBO may be an amplifier of solar activity variations and a natural conduit of these variations to lower altitudes. To test this hypothesis, we conducted experiments with a 2D version of our Numerical Spectral Model that incorporates Hines' Doppler Spread Parameterization for small-scale gravity waves (GW). Solar cycle radiance variations (SCRV) are accounted for by changing the radiative heating rate on a logarithmic scale from 0.1% at the surface to 1% at 50 km to 10% at 100 km. With and without SCRV, but with the same GW flux, we then conduct numerical experiments to evaluate the magnitude of the SCAE in the zonal circulation. The numerical results indicate that, under certain conditions, the SCAE is significant and can extend to lower altitudes where the SCRV is small. For a modeled QBO period of 30 months, we find that the seasonal cycle in the solar forcing acts as a strong pacemaker to lock up the phase and period of the QBO. The SCAE then shows up primarily as a distinct but relatively weak amplitude modulation. But with a different QBO period between 30 and 34 (or less than 30, presumably) months, the seasonal phase lock is weak. Solar flux variations in the seasonal cycle then cause variations in the QBO period and phase. These amplify the SCAE to produce relatively large variations in the wind field. The SCAE in this case extends to mid-latitudes.

mtDNA recombination in a natural population.

PubMed

Saville, B J; Kohli, Y; Anderson, J B

1998-02-03

Variation in mtDNA has been used extensively to draw inferences in phylogenetics and population biology. In the majority of eukaryotes investigated, transmission of mtDNA is uniparental and clonal, with genotypic diversity arising from mutation alone. In other eukaryotes, the transmission of mtDNA is biparental or primarily uniparental with the possibility of "leakage" from the minority parent. In these cases, heteroplasmy carries the potential for recombination between mtDNAs of different descent. In fungi, such mtDNA recombination has long been documented but only in laboratory experiments and only under conditions in which heteroplasmy is ensured. Despite this experimental evidence, mtDNA recombination has not been to our knowledge documented in a natural population. Because evidence from natural populations is prerequisite to understanding the evolutionary impact of mtDNA recombination, we investigated the possibility of mtDNA recombination in an organism with the demonstrated potential for heteroplasmy in laboratory matings. Using nucleotide sequence data, we report here that the genotypic structure of mtDNA in a natural population of the basidiomycete fungus Armillaria gallica is inconsistent with purely clonal mtDNA evolution and is fully consistent with mtDNA recombination.

Comparative study on major bioactive components in natural, artificial and in-vitro cultured Calculus Bovis.

PubMed

Yan, Shi-Kai; Wu, Yan-Wen; Liu, Run-Hui; Zhang, Wei-Dong

2007-01-01

Major bioactive components in various Calculus Bovis, including natural, artificial and in-vitro cultured Calculus Bovis, were comparatively studied. An approach of high-performance liquid chromatography coupled with ultraviolet and evaporative light scattering detections (HPLC/UV/ELSD) was established to simultaneously determinate six bioactive components thereof, including five bile acids (cholic acid, deoxycholic acid, ursodeoxycholic, chenodeoxycholic acid, hyodeoxycholic acid) and bilirubin. ELSD and UV detector were applied to detect bile acids and bilirubin respectively. The assay was performed on a C(18) column with water-acetonitrile gradient elution and the investigated constituents were authenticated by comparing retention times and mass spectra with those of reference compounds. The proposed method was applied to analyze twenty-one Calculus Bovis extraction samples, and produced data with acceptable linearity, precision, repeatability and accuracy. The result indicated the variations among Calculus Bovis samples under different developmental conditions. Artificial and in-vitro cultured Calculus Bovis, especially in-vitro cultured ones, which contain total bioactive constituents no less than natural products and have the best batch-to-batch uniformity, suffice to be used as substitutes of natural Calculus Bovis.

Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest.

PubMed

Yang, Chunyan; Schaefer, Douglas A; Liu, Weijie; Popescu, Viorel D; Yang, Chenxue; Wang, Xiaoyang; Wu, Chunying; Yu, Douglas W

2016-08-24

Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a 'pure diversity' effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world's stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis.

Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

PubMed Central

Yang, Chunyan; Schaefer, Douglas A.; Liu, Weijie; Popescu, Viorel D.; Yang, Chenxue; Wang, Xiaoyang; Wu, Chunying; Yu, Douglas W.

2016-01-01

Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a ‘pure diversity’ effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world’s stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis. PMID:27553882

Interspecific variation in functional traits of oak seedlings (Quercus ilex, Quercus trojana, Quercus virgiliana) grown under artificial drought and fire conditions.

PubMed

Chiatante, D; Tognetti, R; Scippa, G S; Congiu, T; Baesso, B; Terzaghi, M; Montagnoli, A

2015-07-01

To face summer drought and wildfire in Mediterranean-type ecosystems, plants adopt different strategies that involve considerable rearrangements of biomass allocation and physiological activity. This paper analyses morphological and physiological traits in seedlings of three oak species (Quercus ilex, Quercus trojana and Quercus virgiliana) co-occurring under natural conditions. The aim of this study was to evaluate species-specific characteristics and the response of these oak seedlings to drought stress and fire treatment. Seedlings were kept in a growth chamber that mimicked natural environmental conditions. All three species showed a good degree of tolerance to drought and fire treatments. Differences in specific biomass allocation patterns and physiological traits resulted in phenotypic differences between species. In Q. ilex, drought tolerance depended upon adjustment of the allocation pattern. Q. trojana seedlings undergoing mild to severe drought presented a higher photosystem II (PSII) efficiency than control seedlings. Moreover, Q. trojana showed a very large root system, which corresponded to higher soil area exploitation, and bigger leaf midrib vascular bundles than the other two species. Morphological and physiological performances indicated Q. trojana as the most tolerant to drought and fire. These characteristics contribute to a high recruitment potential of Q. trojana seedlings, which might be the reason for the dominance of this species under natural conditions. Drought increase as a result of climate change is expected to favour Q. trojana, leading to an increase in its spatial distribution.

The evolution of phenotypes and genetic parameters under preferential mating

PubMed Central

Roff, Derek A; Fairbairn, Daphne J

2014-01-01

This article extends and adds more realism to Lande's analytical model for evolution under mate choice by using individual-based simulations in which females sample a finite number of males and the genetic architecture of the preference and preferred trait evolves. The simulations show that the equilibrium heritabilities of the preference and preferred trait and the genetic correlation between them (rG), depend critically on aspects of the mating system (the preference function, mode of mate choice, choosiness, and number of potential mates sampled), the presence or absence of natural selection on the preferred trait, and the initial genetic parameters. Under some parameter combinations, preferential mating increased the heritability of the preferred trait, providing a possible resolution for the lek paradox. The Kirkpatrick–Barton approximation for rG proved to be biased downward, but the realized genetic correlations were also low, generally <0.2. Such low values of rG indicate that coevolution of the preference and preferred trait is likely to be very slow and subject to significant stochastic variation. Lande's model accurately predicted the incidence of runaway selection in the simulations, except where preferences were relative and the preferred trait was subject to natural selection. In these cases, runaways were over- or underestimated, depending on the number of males sampled. We conclude that rapid coevolution of preferences and preferred traits is unlikely in natural populations, but that the parameter combinations most conducive to it are most likely to occur in lekking species. PMID:25077025

Evolutionary constraints or opportunities?

PubMed

Sharov, Alexei A

2014-04-22

Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term "constraint" has negative connotations, I use the term "regulated variation" to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch "on" or "off" preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). Copyright © 2014. Published by Elsevier Ireland Ltd.

Mutualists and antagonists drive among-population variation in selection and evolution of floral display in a perennial herb

PubMed Central

Ågren, Jon; Hellström, Frida; Toräng, Per; Ehrlén, Johan

2013-01-01

Spatial variation in the direction of selection drives the evolution of adaptive differentiation. However, few experimental studies have examined the relative importance of different environmental factors for variation in selection and evolutionary trajectories in natural populations. Here, we combine 8 y of observational data and field experiments to assess the relative importance of mutualistic and antagonistic interactions for spatial variation in selection and short-term evolution of a genetically based floral display dimorphism in the short-lived perennial herb Primula farinosa. Natural populations of this species include two floral morphs: long-scaped plants that present their flowers well above the ground and short-scaped plants with flowers positioned close to the ground. The direction and magnitude of selection on scape morph varied among populations, and so did the frequency of the short morph (median 19%, range 0–100%; n = 69 populations). A field experiment replicated at four sites demonstrated that variation in the strength of interactions with grazers and pollinators were responsible for among-population differences in relative fitness of the two morphs. Selection exerted by grazers favored the short-scaped morph, whereas pollinator-mediated selection favored the long-scaped morph. Moreover, variation in selection among natural populations was associated with differences in morph frequency change, and the experimental removal of grazers at nine sites significantly reduced the frequency of the short-scaped morph over 8 y. The results demonstrate that spatial variation in intensity of grazing and pollination produces a selection mosaic, and that changes in biotic interactions can trigger rapid genetic changes in natural plant populations. PMID:24145439

Mutualists and antagonists drive among-population variation in selection and evolution of floral display in a perennial herb.

PubMed

Agren, Jon; Hellström, Frida; Toräng, Per; Ehrlén, Johan

2013-11-05

Spatial variation in the direction of selection drives the evolution of adaptive differentiation. However, few experimental studies have examined the relative importance of different environmental factors for variation in selection and evolutionary trajectories in natural populations. Here, we combine 8 y of observational data and field experiments to assess the relative importance of mutualistic and antagonistic interactions for spatial variation in selection and short-term evolution of a genetically based floral display dimorphism in the short-lived perennial herb Primula farinosa. Natural populations of this species include two floral morphs: long-scaped plants that present their flowers well above the ground and short-scaped plants with flowers positioned close to the ground. The direction and magnitude of selection on scape morph varied among populations, and so did the frequency of the short morph (median 19%, range 0-100%; n = 69 populations). A field experiment replicated at four sites demonstrated that variation in the strength of interactions with grazers and pollinators were responsible for among-population differences in relative fitness of the two morphs. Selection exerted by grazers favored the short-scaped morph, whereas pollinator-mediated selection favored the long-scaped morph. Moreover, variation in selection among natural populations was associated with differences in morph frequency change, and the experimental removal of grazers at nine sites significantly reduced the frequency of the short-scaped morph over 8 y. The results demonstrate that spatial variation in intensity of grazing and pollination produces a selection mosaic, and that changes in biotic interactions can trigger rapid genetic changes in natural plant populations.

Survival of rapidly fluctuating natural low winter temperatures by High Arctic soil invertebrates.

PubMed

Convey, Peter; Abbandonato, Holly; Bergan, Frode; Beumer, Larissa Teresa; Biersma, Elisabeth Machteld; Bråthen, Vegard Sandøy; D'Imperio, Ludovica; Jensen, Christina Kjellerup; Nilsen, Solveig; Paquin, Karolina; Stenkewitz, Ute; Svoen, Mildrid Elvik; Winkler, Judith; Müller, Eike; Coulson, Stephen James

2015-12-01

The extreme polar environment creates challenges for its resident invertebrate communities and the stress tolerance of some of these animals has been examined over many years. However, although it is well appreciated that standard air temperature records often fail to describe accurately conditions experienced at microhabitat level, few studies have explicitly set out to link field conditions experienced by natural multispecies communities with the more detailed laboratory ecophysiological studies of a small number of 'representative' species. This is particularly the case during winter, when snow cover may insulate terrestrial habitats from extreme air temperature fluctuations. Further, climate projections suggest large changes in precipitation will occur in the polar regions, with the greatest changes expected during the winter period and, hence, implications for the insulation of overwintering microhabitats. To assess survival of natural High Arctic soil invertebrate communities contained in soil and vegetation cores to natural winter temperature variations, the overwintering temperatures they experienced were manipulated by deploying cores in locations with varying snow accumulation: No Snow, Shallow Snow (30 cm) and Deep Snow (120 cm). Air temperatures during the winter period fluctuated frequently between +3 and -24 °C, and the No Snow soil temperatures reflected this variation closely, with the extreme minimum being slightly lower. Under 30 cm of snow, soil temperatures varied less and did not decrease below -12 °C. Those under deep snow were even more stable and did not decline below -2 °C. Despite these striking differences in winter thermal regimes, there were no clear differences in survival of the invertebrate fauna between treatments, including oribatid, prostigmatid and mesostigmatid mites, Araneae, Collembola, Nematocera larvae or Coleoptera. This indicates widespread tolerance, previously undocumented for the Araneae, Nematocera or Coleoptera, of both direct exposure to at least -24 °C and the rapid and large temperature fluctuations. These results suggest that the studied polar soil invertebrate community may be robust to at least one important predicted consequence of projected climate change. Copyright © 2014 Elsevier Ltd. All rights reserved.

Naturally occurring variation in tadpole morphology and performance linked to predator regime

PubMed Central

Johnson, James B; Saenz, Daniel; Adams, Cory K; Hibbitts, Toby J

2015-01-01

Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic variations in the population and result in the evolution of reproductive barriers (ecological speciation) or phenotypic plasticity. We evaluated morphology and swimming performance in field collected Bronze Frog larvae (Lithobates clamitans) in ponds dominated by predatory fish and those dominated by invertebrate predators. Based on previous experimental findings, we hypothesized that tadpoles from fish-dominated ponds would have small bodies, long tails, and large tail muscles and that these features would facilitate fast-start speed. We also expected to see increased tail fin depth (i.e., the tail-lure morphology) in tadpoles from invertebrate-dominated ponds. Our results support our expectations with respect to morphology in affecting swimming performance of tadpoles in fish-dominated ponds. Furthermore, it is likely that divergent natural selection is playing a role in the diversification on morphology and locomotor performance in this system. PMID:26357533

Reconstructing Holocene hematite and goethite variations in the Indus Canyon to trace changes in the Asian monsoon system

NASA Astrophysics Data System (ADS)

Koehler, Cornelia; Clift, Peter; Pressling, Nicola; Limmer, David; Giosan, Liviu; Tabrez, Ali

2010-05-01

In order to study Holocene Asian monsoon variations, we reconstructed changes in chemical weathering by examining sediments from the Indus Canyon. During the late Holocene, the Asian monsoon system had periods of high and low intensities that influenced the civilisations living in its realm. For example, the demise of the Harappan civilisation has been linked to a weakened monsoon system around 4 ka. The sediments in the Indus Canyon, which originate from the River Indus and its Himalayan tributaries, provide an ideal, natural environmental archive of the South Asian monsoon system. In order to investigate the alternation between arid and humid monsoonal climatic conditions, variations are traced using the magnetic minerals hematite and goethite, which form under distinct environmental conditions: goethite is stable under humid conditions, whereas hematite forms from the dehydration of goethite under arid conditions. The two minerals are characterised and quantified using environmental magnetic measurements, as well as diffuse reflectance spectrometry. Combining both approaches will enable us to reconstruct variations in chemical weathering over time. Furthermore, because this is governed by temperature and the availability of moisture, our weathering record will allow us to understand monsoon variability during the Holocene and test whether summer rain intensity has been decreasing in SW Asia since 8 ka. In addition, the multi-component analysis of colour reflectance spectra identifies different mineral components including hematite/goethite, clay mineral mixtures, calcite and organics. We will present our results from the multi-sensor core logger equipped with a Minolta spectrometer, measuring both magnetic susceptibility and the optical properties of the split sediment cores. Initial results indicate the presence of hematite and goethite in the sediment. There is an increasing hematite content up the cores, indicating an aridification trend during the Holocene. The sediments are further analysed using the environmental magnetic proxies NRM, ARM and IRM to fully understand the mineral magnetic variations and to quantify hematite and goethite contributions. This work plays an integral part of a larger scale palaeoenvironmental project on Indus Canyon sediments.

GF-1 and Landsat observed a 40-year wetland spatiotemporal variation and its coupled environmental factors in Yangtze River estuary

NASA Astrophysics Data System (ADS)

Sun, Nan; Zhu, Weining; Cheng, Qian

2018-07-01

Wetlands are health indicators of aquatic ecosystems and also vulnerable to regional environmental and socio-economic changes. For exploring wetland spatiotemporal variations in estuarine and coastal regions of the Yangtze River, we extracted wetland information from 40-year time-series images of Landsat, GF-1, and other satellites, using the classification method of decision tree. Potential environmental and socio-economic factors which may drive wetland variations were analyzed. Results show that the wetland area in Yangtze River estuary has increased 663 km2, but it was only contributed by the increasing of human-made wetlands (767 km2), which were mostly caused by economic growth and constructions of human-made hydro-projects in Yangtze Delta. In comparison, natural wetlands, such as tidal flats and marshes, have decreased 163 km2. Land reclamation has changed these natural wetlands into reservoirs, aquaculture ponds and paddy fields. Wetlands in Shanghai and Qidong urban regions were mainly affected by human activities, while wetland variations in Chongming Island were mainly controlled by natural factors such as the upstream discharge, precipitation, diurnal variation of tidal level and long-term sea level rising. The general trend is that the natural wetland was transformed into the human-made wetland, and the human-made wetland was transformed into construction land.

Challenges in Physical Characterization of Dim Space Objects: What Can We Learn from NEOs

NASA Astrophysics Data System (ADS)

Reddy, V.; Sanchez, J.; Thirouin, A.; Rivera-Valentin, E.; Ryan, W.; Ryan, E.; Mokovitz, N.; Tegler, S.

2016-09-01

Physical characterization of dim space objects in cis-lunar space can be a challenging task. Of particular interest to both natural and artificial space object behavior scientists are the properties beyond orbital parameters that can uniquely identify them. These properties include rotational state, size, shape, density and composition. A wide range of observational and non-observational factors affect our ability to characterize dim objects in cis-lunar space. For example, phase angle (angle between Sun-Target-Observer), temperature, rotational variations, temperature, and particle size (for natural dim objects). Over the last two decades, space object behavior scientists studying natural dim objects have attempted to quantify and correct for a majority of these factors to enhance our situational awareness. These efforts have been primarily focused on developing laboratory spectral calibrations in a space-like environment. Calibrations developed correcting spectral observations of natural dim objects could be applied to characterizing artificial objects, as the underlying physics is the same. The paper will summarize our current understanding of these observational and non-observational factors and present a case study showcasing the state of the art in characterization of natural dim objects.