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

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.

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

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.

Influence of seed sowing rates on height, development and yield of the Russian varieties of oil-type sunflower in the Tashkent region of the Uzbekistan Republic

To obtain high yields of good quality of sunflower seeds, it is necessary to strictly observe scientifically justified cultivation technology, which combines techniques accounting both the biological features of the crop and the natural and climatic conditions of the region. But the role of varietal agricultural technology is also great, which takes into account the properties of a new variety and ensures the fullest realization of its productivity potential under these conditions. Research and development data are very important when introducing crops or varieties into new regions. In this regard, it became necessary to study and scientifically substantiate the optimal seed sowing rates of Russian sunflower varieties in irrigated conditions of the Uzbekistan Republic. The effect of seed sowing rates on the growth, development and yield of Russian oil sunflower varieties was studied in 2020– 2021 at the experimental station of the Tashkent State Agrarian University of Uzbekistan. The objects of the research were promising varieties Irtysh, Skormas (Russia) and the local variety Dilbar (Uzbekistan), which were cultivated at different seed sowing rates, providing a plant population of 40, 50, 60 and 70 thousand plants per ha. As a result of the studies, we found out, according to the complex of economically valuable traits, the best varieties of oil sunflower in the conditions of the Tashkent region are the middle maturing variety Dilbar of the local selection and the ultra-early maturing variety Skormas of the Russian selection, they formed the highest yield in the main crops on irrigation with a seed sowing rate of 50 thousand plant per ha – 4.35 and 4.09 t per ha, respectively. The Russian variety Irtysh is ultra-early maturing, the growing season is 86–88 days, it is less productive and can be considered as promising for repeated crops.

Handling temporality in human activity reasoning

Human-aware Artificial Intelligent systems are goal directed autonomous systems that are capable of interacting, collaborating, and teaming with humans. Activity reasoning is a formal reasoning approach that aims to provide common sense reasoning capabilities to these interactive and intelligent systems. This reasoning can be done by considering evidences –which may be conflicting–related to activities a human performs. In this context, it is important to consider the temporality of such evidence in order to distinguish activities and to analyse the relations between activities. Our approach is based on formal argumentation reasoning, specifically, Timed Argumentation Frameworks (TAF), which is an appropriate technique for dealing with inconsistencies in knowledge bases. Our approach involves two steps: local selection and global selection. In the local selection, a model of the world and of the human’s mind is constructed in form of hypothetical fragments of activities (pieces of evidences) by considering a set of observations. These hypothetical fragments have two kinds of relations: a conflict relation and a temporal relation. Based on these relations, the argumentation attack notion is defined. We define two forms of attacks namely the strong and the weak attack. The former has the same characteristics of attacks in TAF whereas for the latter the TAF approach has to be extended. For determining consistent sets of hypothetical fragments, that are part of an activity or are part of a set of non-conflicting activities, extension-based argumentation semantics are applied. In the global selection, the degrees of fulfillment of activities is determined. We study some properties of our approach and apply it to a scenario where a human performs activities with different temporal relations.

Multiscale selection in spatially structured populations

The spatial structure of natural populations is key to many of their evolutionary processes. Formal theories analysing the interplay between natural selection and spatial structure have mostly focused on populations divided into distinct, non-overlapping groups. Most populations, however, are not structured in this way, but rather (self-)organise into dynamic patterns unfolding at various spatial scales. Here, we present a mathematical framework that quantifies how patterns and processes at different spatial scales contribute to natural selection in such populations. To that end, we define the Local Selection Differential (LSD): a measure of the selection acting on a trait within a given local environment. Based on the LSD, natural selection in a population can be decomposed into two parts: the contribution of local selection, acting within local environments, and the contribution of interlocal selection, acting among them. Varying the size of the local environments subsequently allows one to measure the contribution of each length scale. To illustrate the use of this new multiscale selection framework, we apply it to two simulation models of the evolution of traits known to be affected by spatial population structure: altruism and pathogen transmissibility. In both models, the spatial decomposition of selection reveals that local and interlocal selection can have opposite signs, thus providing a mathematically rigorous underpinning to intuitive explanations of how processes at different spatial scales may compete. It furthermore identifies which length scales - and hence which patterns - are relevant for natural selection. The multiscale selection framework can thus be used to address complex questions on evolution in spatially structured populations.

Assessment of yield, plasticity and stability of spring barley cultivars grown in the European North of the Russian Federation

In recent years, modern agroclimatic environmental conditions in the European North of the Russian Federation are determined by constant fluctuations of biotic and abiotic factors, which require a high level of plasticity and stability of crop yield and quantitative characteristics from cultivars used in agricultural production. Therefore, determining the plant response to changing environmental factors in order to select the most promising breeding seeds, is an important task for breeders. The research was conducted on experimental field of N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, in the nursery of competitive variety testing in 20172019. Cultivars of spring barley of local selection were studied. Indicators of cultivar plasticity and stability were calculated by the method of S.A. Eberhart, W.A. Rassell (1966), the indicator of genetic flexibility by the method of R.A. Udachin (1990). Various weather conditions during the research period enabled to evaluate the breeding material comprehensively. The hydrothermal coefficient (according to G.T. Selyaninov) varied from 1.85 to 3.06 during the research years. Ten cultivar samples of spring barley were analyzed to identify a plastic stable genotype. As a result, a high level of stability was shown by samples k-037712 (Ϭ2 = 0.01), k-038404 (Ϭ2 = 0.02). Samples with a neutral genotype were identified: k-039257, k-036982 (bi 1) and a sample weakly responding to environmental changes k-038806 (bi = 0.23). The bi value is very close to 1 in Kotlassky cultivar, which shows a high ecological plasticity. Sample k-038806 has the lowest coefficient of linear regression (0.23), therefore, it is suitable for cultivation on unfertilized soils. The selected genetic sources will be used in breeding to develop highly productive cultivars of spring barley for the conditions of the European North of the Russian Federation.

Genetic Diversity of the Symbiotic Fungus Epichloë festucae in Naturally Occurring Host Grass Populations

Epichloë festucae is a common symbiont of the perennial and widely distributed cool season grass, Festuca rubra. The symbiosis is highly integrated involving systemic growth of the fungus throughout above-ground host parts and vertical transmission from plant to its offspring via host seeds. However, the nature of symbiosis is labile ranging from antagonistic to mutualistic depending on prevailing selection pressures. Both the loss of fungus in the maternal host lineage and horizontal transmission through sexual spores within the host population may partly explain the detected variation in symbiosis in wild grass populations. Epichloë species are commonly considered as pathogens when they produce sexual spores and partly castrate their host plant. This is the pathogenic end of the continuum from antagonistic to mutualistic interactions. Here we examined the population genetic structure of E. festucae to reveal the gene flow, importance of reproduction modes, and alkaloid potential of the symbiotic fungus in Europe. Epichloë-species are highly dependent on the host in survival and reproduction whilst benefits to the host are largely linked to defensive mutualism attributable to fungal-origin bioactive alkaloids that negatively affect vertebrate and/or invertebrate herbivores. We detected decreased genetic diversity in previously glaciated areas compared to non-glaciated regions during the last glacial maximum period and found three major genetic clusters in E. festucae populations: southern, northeastern and northwestern Europe. Sexual reproduction may have a higher role than expected in Spanish E. festucae populations due to the predominance of unique genotypes and presence of both mating types in the region. In contrast, asexual reproduction via host seeds predominates in the Faroe Island and Finland in northern Europe due to the presence of biased mating-type ratios and large dominant genotypes in the E. festucae populations within the region. A substantially larger variation of alkaloid genotypes was observed in the fungal populations than expected, although the variability of the alkaloid genotypes within populations is considerably lower in northern than Spanish populations in southern Europe. E. festucae populations consist of different combinations of alkaloid classes from the gene clusters of ergot alkaloid and indole-terpenes, and from pyrrolopyrazine alkaloid gene. We suggest that the postglacial distribution history of the host grass, prevailing reproduction strategies of E. festucae, and local selection pressures likely explain a large part of the genetic variation observed in fungal populations among geographic regions. The identified alkaloid genotypes can be used by turfgrass breeders to improve resistance against herbivores in red fescue varieties and to develop new sustainable cultivars in Europe.

Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates

Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st(Nei) = 0.673, P =0.001; G’st(Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological/or agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

Evaluation of meadow clover varieties in the foothill zone of the RSO — Alania

Relevance. The advantages of meadow clover, as a forage crop, is that it is a source of highly nutritious feed in monoculture and in grass mixtures, containing protein, macroand microelements, vitamins and carotenes. In the conditions of the foothill zone of the RSO — Alania, a new breeding material of meadow clover was studied. The possibilities of selection of breeding samples with high winter hardiness, feed and seed productivity are studied. The analysis of the most productive samples in terms of productivity and resistance to diseases was carried out. The research objective was to identify the most promising varieties of meadow clover for cultivation in specific natural and climatic conditions of the Republic of North Ossetia — Alania.Methods. Experimental studies were carried out on the experimental fields of the North Caucasus Research Institute of Mountain and Foothill Agriculture of the VNC RAS in the forest-steppe zone of the RSO — Alania. The soils of the experimental site are represented by leached chernozems on pebbles, they are characterized by a high content of gross and available nitrogen and phosphorus reserves. In terms of the content of mobile potassium, they are average in comparison with other soils. The arable layer contains from 3.3% to 4.7% of humus. The reaction of the soil solution in the upper horizons is neutral. The tab of experiments, phenological observations and statistical processing of the obtained data were carried out using generally accepted methods.Results. According to the duration of the period from the beginning of spring regrowth to the beginning of flowering at the first mowing, the studied varieties can be attributed to medium-ripe and late-ripe. То variety Vladikavkazsky the duration of the growing season was 65–70 days, to variety Daryal — 75–80 days, Farn — 70–75 days. Later matures include varieties Alan and Orlik. In the spring during the development periodand the beginning of regrowth there was no big difference between the varieties. The Daryal variety started growing earlier than everyone else, the difference was 5 days. The earliest flowering was observed in the Daryal variety, the difference between the studied varieties was from 10 to 20 days. In the varieties of meadow clover studied by us, the Alan variety surpasses other varieties in winter hardiness, productivity and biological yield. The highest plant height was found in samples of local selection Alan, Vladikavkazsky, Farn (within 68–72.4 cm), surpassing the standard variety Daryal by 7–11.4 cm.The seed yield of the samples had a weak positive correlation with the number of days from the beginning of spring regrowth to the beginning of flowering (r = 0.27).