1. Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus YDenis Kutnjak, Santiago F. Elena, Maja Ravnikar, 2017, original scientific article Abstract: RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).
IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
Keywords: Potato virus Y, experimental evolution, genetic drift, natural selection, sRNA deep sequencing
Published in DiRROS: 24.07.2024; Views: 148; Downloads: 67
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2. Cucujus cinnaberinus (Scopoli, 1763) at its terra typica in Slovenia : historical overview, distribution patterns and habitat selectionAl Vrezec, Špela Ambrožič Ergaver, Andrej Kobler, Andrej Kapla, Maarten De Groot, 2017, original scientific article Abstract: The saproxylic beetle, Cucujus cinnaberinus, has received increasing research attention in Europe since the adoption of the Habitats Directive and establishment of the Natura 2000 network. The history of the species has been investigated as well as the influence of abiotic and biotic variables on the distribution of C. cinnaberinus in Slovenia which is at the limit of its range and also terra typica for the species. The species was first described in 1763 by Joannes A. Scopoli in Carniola, a duchy of the Habsburg Monarchy. Today, most of the territory of Carniola is situated within Slovenia. C. cinnaberinus is particularly common in the eastern part of the country, but very scarce in the mountainous western part. According to historical and recent distribution patterns of C. cinnaberinus in the former Carniolan territory, the region of Ribnica-Kočevje in southern Slovenia is proposed as the most probable type locality of the species. Although the bulk of the C. cinnaberinus population in Slovenia is confined to the lowlands, the species has been found up to 1095 m a.s.l., albeit at a much lower abundance due to the influence of climate and forest structure. Although C. cinnaberinus is a quite an opportunistic species regarding host tree selection, it has been shown to exhibit a preference for Tilia, Populus and Robinia. It is suspected that the high abundance of C. cinnaberinus in lowland floodplain forests is due to the recent human-induced increase in preferred fast-growing and short-lived host trees, i.e. the planting of poplar trees and spread of invasive Black Locust (Robinia pseudoacacia) after the 1960s. In contrast, in montane forests, preferred host trees (e.g. Tilia) represent < 1 % of all growing stock. Although montane C. cinnaberinus populations are rare, they could still be important for the conservation of the species, since montane habitats cover the largest area within the species’ distribution range.
Keywords: saproxylic beetle, Natura 2000, type locality, Carniola, altitudinal distribution, host tree selection, macrohabitat, large-scale survey
Published in DiRROS: 24.07.2024; Views: 562; Downloads: 120
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3. Small but voracious : invasive generalist consumes more zooplankton in winter than native planktivoreŽiga Ogorelec, Alexander Brinker, Dietmar Straile, 2022, original scientific article Abstract: In recent years, Lake Constance has experienced an invasion and domination of three-spined stickleback (Gasterosteus aculeatus) in the pelagic zone, which has coincided with a decline in the native whitefish (Coregonus wartmanni) population. Similar massive invasions of sticklebacks into pelagic zones have been recognized also in marine areas or small lakes worldwide. However, their diet overlaps with native species is rarely evaluated, especially in the winter season, which often presents a bottleneck for fish survival. In this study, we compared the diet of pelagic sticklebacks with the diet of the substantially larger native whitefish in different seasons, to evaluate the threat of the recent stickleback invasion on whitefish populations. By monthly sampling of zooplankton and both fish species diets, we could demonstrate that sticklebacks select similar prey throughout most of the year and consume more prey than whitefish during the winter. With relations between prey availability and prey selection, interspecific and intraspecific seasonal diet variability and indices like a prey-specific index of relative importance, we discuss the importance of zooplankton species traits and abundance for whitefish and stickleback predation. This study shows that sticklebacks, despite their small size, represent a serious potential diet competitor to native planktivorous fish. Sticklebacks quickly adapt to new environments, and thus we advocate precautions regarding their introduction into similar lakes as Lake Constance, as this could cause irreversible ecological changes.
Keywords: Bythotrephes longimanus, Lake Constance, overwintering strategy, pelagic whitefish diet, planktivory, predator size, seasonal prey selection, stickleback invasion
Published in DiRROS: 18.07.2024; Views: 147; Downloads: 116
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4. A cross-benchmark examination of feature-based algorithm selector generalization in single-objective numerical optimizationGjorgjina Cenikj, Gašper Petelin, Tome Eftimov, 2024, original scientific article Abstract: The task of selecting the best optimization algorithm for a particular problem is known as algorithm selection (AS). This involves training a model using landscape characteristics to predict algorithm performance, but a key challenge remains: making AS models generalize effectively to new, untrained benchmark suites. This study assesses AS models’ generalizability in single-objective numerical optimization across diverse benchmark suites. Using Exploratory Landscape Analysis (ELA) and transformer-based (TransOpt) features, the research investigates their individual and combined effectiveness in AS across four benchmarks: BBOB, AFFINE, RANDOM, and ZIGZAG. AS models perform differently based on benchmark suite similarities in algorithm performance distributions and single-best solvers. When suites align, these models underperform against a baseline predicting mean algorithm performance; yet, they outperform the baseline when suites differ in performance distributions and solvers. The AS models trained using the ELA landscape features are better than the models trained using the TransOpt features on the BBOB and AFFINE benchmark suites, while the opposite is true for the RANDOM benchmark suite. Ultimately, the study reveals challenges in accurately capturing algorithm performance through problem landscape features (ELA or TransOpt), impacting AS model applicability.
Keywords: algorithm selection, multi-target regression, generalization, benchmarking
Published in DiRROS: 21.05.2024; Views: 293; Downloads: 395
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5. Međuodnos svojstava rasta i kvalitete drva na pokusnoj plohi arišaMirzeta Memišević Hodžić, Sulejman Sinanović, Dalibor Ballian, 2023, original scientific article Abstract: Larch (Larix decidua) showed good growth and adaptability to ecological conditions in Bosnia and Herzegovina. The research aims to determine the variability of the morphological traits of larch in the seed stand near Kakanj, the variability at the beginning of heartwood formation, and correlations among these properties.In the larch seed stand, established by seedlings 2+0 in 1979, an area of 0,45 hectares was set aside. The heights and breast height diameters of the trees were on that area were measured in 2002 and 2020, and the basal area and volume were calculated. In 2020, the trees were drilled at breast height with a Presler drill to measure the proportion of heartwood. Average values of all properties for 2002 and 2020 were calculated. The ten, five and one best trees were selected according to the properties of breast height diameter, height, basal area, volume, and the intensities of selection for these traits were calculated. The Pearson correlation coefficient among all investigated traits were calculated. The average breast height diameter of 41-year-old trees was 24,6 cm, average height 21,8 m, basal area 0.0499m2 and volume 0.3745 m3 (table 1), while in 2002. the average breast height diameter was 15,5 cm, height 18,2 m, basal area 0,020 m2, and volume 0,128 m3 (table 1). Between 2002 and 2020, there was an overtaking of trees in breast height diameter and height and thus the base and volume (table 2). The average larch tree starts heartwood formation at the age of 14 years (table 1). The earliest heart-wood formation occurs in the sixth year (tree 495) and the latest in the 32nd year (table 4). Pearson coefficient showed a high positive correlation between breast height diameter and height in 2002 (ta-ble 9), which means that trees with a good height increase also have a good thickness increase. As a result, the correlation between breast height diameter and basal area and breast height diameter and volume, height and basal area, height and volume, and basal area and volume are statistically signifi-cant. Pearson’s correlation coefficient for the year 2020 showed a negative correlation between the be-ginning of heartwood formation and all other traits (table 10), i.e., trees that formed heartwood earlier have higher values of growth traits.The results will be used in the selection processes of larch individuals with good height and thickness growth and early heartwood formation.
Keywords: European larch, morphological properties, core formation, selection
Published in DiRROS: 25.03.2024; Views: 364; Downloads: 230
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7. Arc length preserving $G^2$ Hermite interpolation of circular arcsEmil Žagar, 2023, original scientific article Abstract: In this paper, the problem of interpolation of two points, two corresponding tangent directions and curvatures, and the arc length sampled from a circular arc (circular arc data) is considered. Planar Pythagorean–hodograph (PH) curves of degree seven are used since they possess enough free parameters and are capable of interpolating the arc length in an easy way. A general approach using the complex representation of PH curves is presented first and the strong dependence of the solution on the general data is demonstrated. For circular arc data, a complicated system of nonlinear equations is reduced to a numerical solution of only one algebraic equation of degree 6 and a detailed analysis of the existence of admissible solutions is provided. In the case of several solutions, some criteria for selecting the most appropriate one are described and an asymptotic analysis is given. Numerical examples are included which confirm theoretical results.
Keywords: geometric interpolation, circular arc, arc length, Pythagorean-hodograph curve, solution selection
Published in DiRROS: 20.03.2024; Views: 284; Downloads: 138
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8. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beechMarjana Westergren, Juliette Archambeau, Marko Bajc, Rok Damjanić, Adélaïde Theraroz, Hojka Kraigher, Sylvie Oddou-Muratorio, Santiago C. González-Martínez, 2023, original scientific article Abstract: Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
Keywords: climate change, Fagus sylvatica, heritability, in situ adaptation, response to selection, selection gradients
Published in DiRROS: 12.12.2023; Views: 447; Downloads: 211
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9. PS-AAS : portfolio selection for automated algorithm selection in black-box optimizationAna Kostovska, Gjorgjina Cenikj, Diederick Vermetten, Anja Janković, Ana Nikolikj, Urban Škvorc, Peter Korošec, Carola Doerr, Tome Eftimov, 2023, published scientific conference contribution Keywords: automated algorithm selection, portfolio selection, black box optimization
Published in DiRROS: 11.12.2023; Views: 567; Downloads: 230
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10. Genomics and adaptation in forest ecosystemsCharalambos Neophytou, Katrin Heer, Pascal Miles, Martina Peter, Tanja Pyhäjärvi, Marjana Westergren, Christian Rellstab, Felix Gugerli, 2022, original scientific article Abstract: Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of “Genomics and Adaptation in Forest Ecosystems” brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.
Keywords: gene conservation, genetic diversity, local adaptation, pathogens, selection, mycorrhizal fungi
Published in DiRROS: 18.02.2022; Views: 825; Downloads: 610
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