Crossbreeding reveals the scale and genetic architecture of local adaptation in a predominantly selfing Hordeum spontaneum

2022 ◽  
Vol 1 (1) ◽  
Author(s):  
S Volis ◽  
I Shulgina ◽  
B Dyuzgenbekova
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Spatial Scales ◽  
Hordeum Spontaneum ◽  
Term Effect ◽  
Negev Desert ◽  
Experimental Conditions ◽  
Local Selection ◽  
Wide Range ◽  
F2 Generation

Environmental variation can be large across a wide range of spatial scales resulting in complex patterns of local adaptation across species ranges. We analyzed the scale, genetic mechanism and direct climatic causes of local adaptation in a widely distributed grass Hordeum spontaneum. We performed artificial crosses of maternal plants representing the same Negev desert population with plants originating elsewhere. Pollen donors were plants from other Negev desert populations, non-desert Israeli populations sampled along an aridity gradient, and accessions covering the entire species range. Our study included planting of inter-population hybrids under favorable and simulated desert experimental conditions, followed by analysis of their performance, variation in adaptive traits and relationship with climatic parameters at sampling locations. The combined results of parental phenotypic variation and performance of hybrids were consistent with local selection, reflecting the importance of both regional and local climates. The adaptive genetic differentiation of barley desert populations had a complex architecture. None of the three effects (additive, dominance and epistasis) were fully responsible for this differentiation. Although genetic effects not related to extrinsic selection appear to contribute to genetic differentiation in barley, epistatic effects arising from local selection clearly predominated. The short-term effect of gene flow by pollen was generally negative, indicating that a majority of the new allele combinations created by recombination were maladaptive. However, the long-term effect of occasional pollen flow from other desert populations appears to be positive, as some new recombined genotypes were superior in fitness to the maternal plants even in the F2 generation.

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

scholarly journals Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257461
Author(s):  
Antonios Kominakis ◽  
Eirini Tarsani ◽  
Ariadne L. Hager-Theodorides ◽  
Ioannis Mastranestasis ◽  
Dimitra Gkelia ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Candidate Genes ◽  
Local Adaptation ◽  
Ecological Niches ◽  
P Value ◽  
Positional Candidate ◽  
Island Populations ◽  
Significant Marker ◽  
Genome Wide ◽  
Wide Range

In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of ‘mainland-island’ populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.

TEMPERATURES AND ECOLOGICAL—GENETIC DIFFERENTIATION AFFECTING THE GERMINATION OF HORDEUM SPONTANEUM CARYOPSES HARVESTED FROM THREE POPULATIONS: THE NEGEV DESERT AND OPPOSING SLOPES ON MEDITERRANEAN MOUNT CARMEL

1994 ◽  
Vol 42 (3) ◽  
pp. 183-195 ◽  
Author(s):  
Yitzchak Gutterman ◽  
Eviatar Nevo
Keyword(s):  
Genetic Differentiation ◽  
Low Temperatures ◽  
Hordeum Spontaneum ◽  
Negev Desert ◽  
Ecological Significance ◽  
Wild Type ◽  
Dry Storage ◽  
Long Time ◽  
Cultivated Barley ◽  
Storage Temperatures

Ecological—genetic differentiation and dry storage temperatures regulate the germination of caryopses of Hordeum spontaneum, the wild type of cultivated barley. Freshly harvested caryopses of H. spontaneum in their spikelets (dispersal units) did not germinate, but separated embryos did. After dry storage for more than 68 days at high temperatures, caryopses in their dispersal units germinated. The degree of after-ripening (dormancy) was found to differ in the 3 local populations tested in this study. The highest germination occurred in caryopses collected from the northern-facing slope of Nahal Oren, Mount Carmel, the most humid habitat tested. An intermediate result was from the opposite southern-facing slope, and the lowest germination was observed in those from the Negev Desert near Sede Boker. The germination level of caryopses from spikelets stored dry at low temperatures such as −18 °C remained poor for a long time. The ecological significance of this study is discussed.

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

2019 ◽  
Author(s):  
Christopher John ◽  
Greg M. Swain ◽  
Robert P. Hausinger ◽  
Denis A. Proshlyakov
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Heme Iron ◽  
Chemical Transformations ◽  
Experimental Conditions ◽  
Strongly Coupled ◽  
Non Heme Iron ◽  
Reversible Redox ◽  
Wide Range ◽  
Complex Structural

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semi-empirical computational methods, demonstrating that the Fe (III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and 171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

scholarly journals Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

2021 ◽  
Vol 22 (15) ◽  
pp. 7879
Author(s):  
Yingxia Gao ◽  
Yi Zheng ◽  
Léon Sanche
Keyword(s):  
Condensed Phase ◽  
Genetic Material ◽  
High Energy ◽  
Dna Lesions ◽  
Low Energy ◽  
Experimental Investigations ◽  
Experimental Conditions ◽  
Strand Breaks ◽  
Sequence Of Events ◽  
Wide Range

The complex physical and chemical reactions between the large number of low-energy (0–30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

scholarly journals Review of the Upright Balance Assessment Based on the Force Plate

2021 ◽  
Vol 18 (5) ◽  
pp. 2696
Author(s):  
Baoliang Chen ◽  
Peng Liu ◽  
Feiyun Xiao ◽  
Zhengshi Liu ◽  
Yong Wang
Keyword(s):  
Postural Balance ◽  
Force Plate ◽  
Assessment Method ◽  
Balance Assessment ◽  
Experimental Conditions ◽  
Methodological Research ◽  
Assessment Tests ◽  
Wide Range ◽  
Foot Posture ◽  
Plate System

Quantitative assessment is crucial for the evaluation of human postural balance. The force plate system is the key quantitative balance assessment method. The purpose of this study is to review the important concepts in balance assessment and analyze the experimental conditions, parameter variables, and application scope based on force plate technology. As there is a wide range of balance assessment tests and a variety of commercial force plate systems to choose from, there is room for further improvement of the test details and evaluation variables of the balance assessment. The recommendations presented in this article are the foundation and key part of the postural balance assessment; these recommendations focus on the type of force plate, the subject’s foot posture, and the choice of assessment variables, which further enriches the content of posturography. In order to promote a more reasonable balance assessment method based on force plates, further methodological research and a stronger consensus are still needed.

scholarly journals On the generation of internal waves by river plumes in subcritical initial conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
R. Mendes ◽  
J. C. B. da Silva ◽  
J. M. Magalhaes ◽  
B. St-Denis ◽  
D. Bourgault ◽  
...  
Keyword(s):  
Numerical Modeling ◽  
Internal Waves ◽  
Coastal Waters ◽  
Initial Conditions ◽  
Spatial Scales ◽  
River Plumes ◽  
Wide Range ◽  
Near Shore ◽  
Generation Mechanisms ◽  
Douro River

AbstractInternal waves (IWs) in the ocean span across a wide range of time and spatial scales and are now acknowledged as important sources of turbulence and mixing, with the largest observations having 200 m in amplitude and vertical velocities close to 0.5 m s−1. Their origin is mostly tidal, but an increasing number of non-tidal generation mechanisms have also been observed. For instance, river plumes provide horizontally propagating density fronts, which were observed to generate IWs when transitioning from supercritical to subcritical flow. In this study, satellite imagery and autonomous underwater measurements are combined with numerical modeling to investigate IW generation from an initial subcritical density front originating at the Douro River plume (western Iberian coast). These unprecedented results may have important implications in near-shore dynamics since that suggest that rivers of moderate flow may play an important role in IW generation between fresh riverine and coastal waters.

scholarly journals Provenance Trials of the Mexican Spruces in Nursery Conditions: Three Species Endangered by Climatic Variation

2020 ◽  
Vol 3 (1) ◽  
pp. 12
Author(s):  
José Marcos Torres-Valverde ◽  
José Ciro Hernández-Díaz ◽  
Artemio Carrillo-Parra ◽  
Eduardo Mendoza-Maya ◽  
Christian Wehenkel
Keyword(s):  
Cluster Analysis ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Quantitative Traits ◽  
Climatic Factors ◽  
Climatic Variation ◽  
Climatic Variables ◽  
Provenance Trials ◽  
Survival And Growth ◽  
Picea Species

The three Mexican spruces’ distributions are fragmented, which could lead to phenological, morphological and genetic differentiation, partially caused by local adaptation. In this study, we examined the effect that climatic variables had on the survival and growth of 5641 Picea seedlings, coming from eight seed provenances of three species and produced in identical nursery conditions. The respective responses of each species and provenance can be considered as a proxy of the genetic differentiation and adaptation of each population. A cluster analysis revealed: (i) significant differences in genetic quantitative traits among the three Picea species and (ii) significant correlations between genetic quantitative traits and climatic factors.

scholarly journals Comparison of Satellite and Drone-Based Images at Two Spatial Scales to Evaluate Vegetation Regeneration after Post-Fire Treatments in a Mediterranean Forest

2021 ◽  
Vol 11 (12) ◽  
pp. 5423
Author(s):  
Jose Luis Martinez ◽  
Manuel Esteban Lucas-Borja ◽  
Pedro Antonio Plaza-Alvarez ◽  
Pietro Denisi ◽  
Miguel Angel Moreno ◽  
...  
Keyword(s):  
Vegetation Cover ◽  
Spatial Scales ◽  
Soil Surface ◽  
Plant Biodiversity ◽  
Mediterranean Forests ◽  
Experimental Conditions ◽  
Vegetation Growth ◽  
Surface Conditions ◽  
Vegetation Regeneration ◽  
Forest Managers

The evaluation of vegetation cover after post-fire treatments of burned lands is important for forest managers to restore soil quality and plant biodiversity in burned ecosystems. Unfortunately, this evaluation may be time consuming and expensive, requiring much fieldwork for surveys. The use of remote sensing, which makes these evaluation activities quicker and easier, have rarely been carried out in the Mediterranean forests, subjected to wildfire and post-fire stabilization techniques. To fill this gap, this study evaluates the feasibility of satellite (using LANDSAT8 images) and drone surveys to evaluate changes in vegetation cover and composition after wildfire and two hillslope stabilization treatments (log erosion barriers, LEBs, and contour-felled log debris, CFDs) in a forest of Central Eastern Spain. Surveys by drone were able to detect the variability of vegetation cover among burned and unburned areas through the Visible Atmospherically Resistant Index (VARI), but gave unrealistic results when the effectiveness of a post-fire treatment must be evaluated. LANDSAT8 images may be instead misleading to evaluate the changes in land cover after wildfire and post-fire treatments, due to the lack of correlation between VARI and vegetation cover. The spatial analysis has shown that: (i) the post-fire restoration strategy of landscape managers that have prioritized steeper slopes for treatments was successful; (ii) vegetation growth, at least in the experimental conditions, played a limited influence on soil surface conditions, since no significant increases in terrain roughness were detected in treated areas.

scholarly journals Towards Reduced CNNs for De-Noising Phase Images Corrupted with Speckle Noise

Photonics ◽  
2021 ◽  
Vol 8 (7) ◽  
pp. 255
Author(s):  
Marie Tahon ◽  
Silvio Montresor ◽  
Pascal Picart
Keyword(s):  
Phase Error ◽  
Speckle Noise ◽  
Experimental Conditions ◽  
Benchmark Data ◽  
Wide Range ◽  
Phase Images ◽  
Different Depths ◽  
Phase Data ◽  
Do So

Digital holography is a very efficient technique for 3D imaging and the characterization of changes at the surfaces of objects. However, during the process of holographic interferometry, the reconstructed phase images suffer from speckle noise. In this paper, de-noising is addressed with phase images corrupted with speckle noise. To do so, DnCNN residual networks with different depths were built and trained with various holographic noisy phase data. The possibility of using a network pre-trained on natural images with Gaussian noise is also investigated. All models are evaluated in terms of phase error with HOLODEEP benchmark data and with three unseen images corresponding to different experimental conditions. The best results are obtained using a network with only four convolutional blocks and trained with a wide range of noisy phase patterns.

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