Browsing by Subject "ADAPTATION"

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  • Huttunen, Inese; Hyytiäinen, Kari; Huttunen, Markus; Sihvonen, Matti; Veijalainen, Noora; Korppoo, Marie; Heiskanen, Anna-Stiina (2021)
    This paper introduces a framework for extending global climate and socioeconomic scenarios in order to study agricultural nutrient pollution on an individual catchment scale. Our framework builds on and extends Representative Concentration Pathways (RCPs) and Shared Socioeconomic Pathways (SSPs) at the spatial and temporal scales that are relevant for the drivers of animal husbandry, manure recycling and the application of inorganic fertilisers in crop production. Our case study area is the Aura river catchment in South-West Finland, which discharges into the heavily eutrophic Baltic Sea. The Aura river catchment has intensive agriculture - both livestock and crop production. Locally adjusted and interpreted climate and socioeconomic scenarios were used as inputs to a field-level economic optimisation in order to study how farmers might react to the changing markets and climate conditions under different SSPs. The results on economically optimal fertilisation levels were then used as inputs to the spatially and temporally explicit nutrient loading model (VEMALA). Alternative manure recycling strategies that matched with SSP narratives were studied as means to reduce the phosphorus (P) overfertilisation in areas with high livestock density. According to our simulations, on average the P loads increased by 18% during 2071-2100 from the current level and the variation in P loads between scenarios was large (from & minus;14% to +50%). By contrast, the nitrogen (N) loads had decreased on average by & minus;9% (with variation from & minus;20% to +3%) by the end of the current century. Phosphorus loading was most sensitive to manure recycling strategies and the speed of climate change. Nitrogen loading was less sensitive to changes in climate and socioeconomic drivers. (c) 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (
  • Karges, Kathleen; Bellingrath-Kimura, Sonoko D.; Watson, Christine A.; Stoddard, Frederick L.; Halwani, Mosab; Reckling, Moritz (2022)
    Soybean is one of the five crops that dominate global agriculture, along with maize, wheat, cotton and rice. In Europe, soybean still plays a minor role and is cultivated mainly in the South and East. Very little is known about the potential for soybean in higher latitudes with relatively cool conditions. To investigate the agronomic potential and limitations of soybean for feed (high grain yield) and food (high protein content, e.g., for tofu production) in higher latitudes, an organic soybean cropping system experiment was carried out from 2015 to 2017 in northeastern Germany. The objectives were: (1) to identify food- and feed-grade soybean cultivars that are adapted to a central European climate in terms of protein, grain yield, and yield stability, (2) to explore the effect of irrigation on soybean protein and grain yield under relatively dry growing conditions, and (3) to determine the agro-economic potential of soybean cultivation for both feed and food markets. Three soybean cultivars were tested with and without irrigation. The soybean feed-grade cultivars 'Sultana' and 'Merlin' were better adapted to the growing cycle and temperature, providing higher and more stable yields (average 2700 kg ha(-1)) than the food-grade cultivar 'Protibus' (average 1300 kg ha(-1)). Irrigation increased soybean grain yields by 41% on average. In the year with sufficient precipitation, no additional irrigation was necessary. Gross margins of organic soybean ranged between 750 (sic) ha(-1) for the rainfed food-grade soybean and 2000 (sic) ha(-1) for the irrigated feed-grade soybean and were higher than other crops. We demonstrated a large agro-economic potential for soybean as a novel grain legume crop to diversify cropping systems and increase the production of protein crops in central Europe.
  • Truong Nguyen, Phuoc; Garcia-Valle, Santiago; Puigbo, Pere (2021)
    Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host-virus relationships.
  • Jurgilevich, Alexandra; Räsänen, Aleksi; Juhola, Sirkku (2021)
    Future climate risk is not only dependent on future climatic changes but also on how exposure and vulnerability develop in the future. There is a gap in understanding what drives future climate vulnerability, and how to account for its spatial emergence. This issue is particularly pertinent for cities due to the concentration of assets and population at risk, and rapid socio-economic and land use changes. We develop a mixed methods approach, which integrates quantitative, qualitative and participatory methods to (1) identify internal and external drivers of socio-economic development and land use change, (2) explore a range of future pathways using local socioeconomic scenarios, and (3) visualize changes in vulnerability indicators with the help of a participatory mapping exercise. We test the approach in the City of Helsinki with the timeframe up to 2050. Our results show the connections between the drivers and changes in vulnerability indicators, while maps developed in a stakeholder workshop visualize the potential spatial changes in indicators. Our approach of connecting indicators, drivers and adaptation/planning needs, as well as scenario analysis, provides a deeper understanding of vulnerability dynamics as a process and provides insights for different sectors of urban policy and planning.
  • Belachew, Kiflemariam Y.; Nagel, Kerstin A.; Poorter, Hendrik; Stoddard, Frederick L. (2019)
    Water deficit may occur at any stage of plant growth, with any intensity and duration. Phenotypic acclimation and the mechanism of adaptation vary with the evolutionary background of germplasm accessions and their stage of growth. Faba bean is considered sensitive to various kinds of drought. Hence, we conducted a greenhouse experiment in rhizotrons under contrasting watering regimes to explore shoot and root traits and drought avoidance mechanisms in young faba bean plants. Eight accessions were investigated for shoot and root morphological and physiological responses in two watering conditions with four replications. Pre-germinated seedlings were transplanted into rhizotron boxes filled with either air-dried or moist peat. The water-limited plants received 50-ml water at transplanting and another 50-ml water 4 days later, then no water was given until the end of the experimental period, 24 days after transplanting. The well-watered plants received 100 ml of water every 12 h throughout the experimental period. Root, stem, and leaf dry mass, their mass fractions, their dry matter contents, apparent specific root length and density, stomatal conductance, SPAD value, and Fv/Fm were recorded. Water deficit resulted in 3–4-fold reductions in shoot biomass, root biomass, and stomatal conductance along with 1.2–1.4-fold increases in leaf and stem dry matter content and SPAD values. Total dry mass and apparent root length density showed accession by treatment interactions. Accessions DS70622, DS11320, and ILB938/2 shared relatively high values of total dry mass and low values of stomatal conductance under water deficit but differed in root distribution parameters. In both treatments, DS70622 was characterized by finer roots that were distributed in both depth and width, whereas DS11320 and ILB938/2 produced less densely growing, thicker roots. French accession Mélodie/2 was susceptible to drought in the vegetative phase, in contrast to previous results from the flowering phase, showing the importance of timing of drought stress on the measured response. Syrian accession DS70622 explored the maximum root volume and maintained its dry matter production, with the difference from the other accessions being particularly large in the water-limited treatment, so it is a valuable source of traits for avoiding transient drought.
  • Asplund , Therese; Neset, Tina-Simone; Käyhkö, Janina; Wiréhn, Lotten; Juhola, Sirkku (2019)
    The use of digital tools and interactive technologies for farming systems has increased rapidly in recent years and is likely to continue to play a significant role in meeting future challenges. Particularly games and gaming are promising new and innovative communication strategies to inform and engage public and stakeholders with scientific research. This study offers an analysis of how a research based game on climate change maladaptation can support, but also hinder players’ sense-making processes. Through the analysis of eight gaming workshops, this study identifies challenges and support for the players’ sense-making. While it concludes that conceptual thinking of game content sometimes clashes with players’ everyday experiences and practice, possibly resulting in loss of credibility, this study also concludes that gaming may function as an eye-opener to new ways of thinking. Overall, this paper suggests that the communication of (social) science and agricultural practices through serious gaming has great potential but at the same time poses challenges due to different knowledge systems and interpretive frameworks among researchers and practitioners.
  • Rosa, Elena; Saastamoinen, Marjo (2020)
    Cold developmental conditions can greatly affect adult life history of ectotherms in seasonal habitats. Such effects are mostly negative, but sometimes adaptive. Here, we tested how cold conditions experienced during pupal development affect adult wing melanization of an insect ectotherm, the Glanville fritillary butterfly, Melitaea cinxia. We also assessed how in turn previous cold exposure and increased melanization can shape adult behaviour and fitness, by monitoring individuals in a seminatural set-up. We found that, despite pupal cold exposure inducing more melanization, wing melanization was not linked to adult thermoregulation preceding flight, under the conditions tested. Conversely, wing vibrating behaviour had a major role in producing heat preceding flight. Moreover, more melanized individuals were more mobile across the experimental set-up. This may be caused by a direct impact of melanization on flight ability or a more indirect impact of coloration on behaviours such as mate search strategies and/or eagerness to disperse to more suitable mating habitats. We also found that more melanized individuals of both sexes had reduced mating success and produced fewer offspring, which suggests a clear fitness cost of melanization. Whether the reduced mating success is dictated by impaired mate search behaviour, reduced physical condition leading to a lower dominance status or weakened visual signalling remains unknown. In conclusion, while there was no clear role of melanization in providing a thermal advantage under our seminatural conditions, we found a fitness cost of being more melanized, which potentially impacted adult space use behaviour. (c) 2020 The Authors. Published by Elsevier Ltd on behalf of The Association for the Study of Animal Behaviour. This is an open access article under the CC BY-NC-ND license ( licenses/by-nc-nd/4.0/).
  • Vizueta, Joel; Macias-Hernandez, Nuria; Arnedo, Miguel A.; Rozas, Julio; Sanchez-Gracia, Alejandro (2019)
    The coexistence of multiple eco-phenotypes in independently assembled communities makes island adaptive radiations the ideal framework to test convergence and parallelism in evolution. In the radiation of the spider genus Dysdera in the Canary Islands, species diversification occurs concomitant with repeated events of trophic specialization. These dietary shifts, to feed primarily on woodlice, are accompanied by modifications in morphology (mostly in the mouthparts), behaviour and nutritional physiology. To gain insight into the molecular basis of this adaptive radiation, we performed a comprehensive comparative transcriptome analysis of five Canary Island Dysdera endemics representing two evolutionary and geographically independent events of dietary specialization. After controlling for the potential confounding effects of hemiplasy, our differential gene expression and selective constraint analyses identified a number of genetic changes that could be associated with the repeated adaptations to specialized diet of woodlice, including some related to heavy metal detoxification and homeostasis, the metabolism of some important nutrients and venom toxins. Our results shed light on the genomic basis of an extraordinary case of dietary shift convergence associated with species diversification. We uncovered putative molecular substrates of convergent evolutionary changes at different hierarchical levels, including specific genes, genes with equivalent functions and even particular amino acid positions. This study improves our knowledge of rapid adaptive radiations and provides new insights into the predictability of evolution.
  • Renvik (Mähönen), Tuuli Anna; Manner, Joel; Vetik, Raivo; Sam, David; Jasinskaja-Lahti, Inga (2020)
    This survey study utilized a person-oriented approach to explore the patterns of socio-political integration among Russian-speaking minority group members in three neighboring countries in the Baltic area: Estonia (n = 482), Finland (n = 252), and Norway (n = 215). Three profiles were obtained in all countries: critical integration, separation, and assimilation. In the whole sample, critical integration was the most common acculturation profile. After the profiles were established, they were examined vis-a-vis citizenship and integration context to see, whether and to what extent, the objective (i.e., citizenship) and subjective (i.e., perceived social status and sense of belonging) socio-political integration of Russian-speakers corresponded with each other. Critical integration and separation were the most common profiles among participants holding national citizenship of the country of residence, while foreign citizenship was not related to any specific profile. Separation was rare among participants holding dual citizenship, but it was the most common profile among participants with undetermined citizenship. Also, intergroup context was associated with socio-political integration: critical integration and separation were the most common profiles of Russian-speakers in Estonia, critical integration and assimilation profiles in Finland, and assimilation profile in Norway. The results are discussed in relation to previous variable-oriented research and official integration policies of the countries studied.
  • Islam, Mohammad Mahmudul; Islam, Naimul; Habib, Ahasan; Mozumder, Mohammad Mojibul Hoque (2020)
    The present study aimed to map out the current threats and anticipated impacts of climate change on the most important hilsa shad (Tenualosa ilisha) fishery and the associated fishing communities based on fieldwork in six coastal fishing communities. To collect empirical data, individual interviews, focus group discussions, oral history, and key informant interviews were conducted. To supplement the empirical findings, time-series data of cyclones and sea-borne depressions in the Bay of Bengal were also analyzed. Analysis of secondary data regarding climate change-induced events and regional studies suggested that the biophysical conditions of the Bay of Bengal are likely to be aggravated in the future, potentially causing more frequent extreme events and affecting the livelihoods of coastal fishing communities in Bangladesh. The fisher respondents revealed that the main target hilsa shad fishery is particularly vulnerable to climate change in terms of alterations to migration patterns and breeding and growth performance. The fishers reported constant climate-related risks because they live in seafront locations, exposed to extreme events, and their occupation entails risky sea fishing. Fishers claimed that they often need return to the coast due to unsuitable weather conditions related to cyclones and frequent tropical depressions, which can cause financial losses or even causalities. Such events negatively affect fishers' livelihoods, and wellbeing. To cope with the impacts of climate change the fishers have adopted various strategies at both sea fishing and household levels. However, these strategies only support the fishers in terms of immediate survival; they are not enough for long-term resilience. To improve the resilience of the hilsa fishers, the study argues for the implementation the Small-Scale Fisheries Guidelines (SSF Guidelines), which call for longer-term development goals, including in the immediate relief phase, and rehabilitation, reconstruction, and recovery to reduce vulnerabilities to climate and anthropogenic risks.
  • Landreau, Armand; Juhola, Sirkku; Jurgilevich, Alexandra; Räsänen, Aleksi (2021)
    The assessments of future climate risks are common; however, usually, they focus on climate projections without considering social changes. We project heat risks for Finland to evaluate (1) what kind of differences there are in heat vulnerability projections with different scenarios and scales, and (2) how the use of socio-economic scenarios influences heat risk assessments. We project a vulnerability index with seven indicators downscaled to the postal code area scale for 2050. Three different scenario sets for vulnerability are tested: one with five global Shared Socioeconomic Pathways (SSPs) scenarios; the second with three European SSPs (EUSSPs) with data at the sub-national scale (NUTS2); and the last with the EUSSPs but aggregated data at the national scale. We construct projections of heat risk utilizing climatic heat hazard data for three different Representative Concentration Pathways (RCPs) and vulnerability and exposure data for five global SSPs up to 2100. In the vulnerability projections, each scenario in each dataset shows a decrease in vulnerability compared to current values, and the differences between the three scenario sets are small. There are evident differences both in the spatial patterns and in the temporal trends when comparing the risk projections with constant vulnerability to the projections with dynamic vulnerability. Heat hazard increases notably in RCP4.5 and RCP8.5, but a decrease of vulnerability especially in SSP1 and SSP5 alleviates risks. We show that projections of vulnerability have a considerable impact on future heat-related risk and emphasize that future risk assessments should include the combination of long-term climatic and socio-economic projections.
  • Autio, Antti; Johansson, Tino; Motaroki, Lilian; Minoia, Paola; Pellikka, Petri (2021)
    CONTEXT: Climate uncertainty challenges the livelihoods of smallholder farmers in sub-Saharan Africa. Awareness of climate-smart agricultural (CSA) practices and access to climate-smart technologies are key factors in determining the utilization of farm and land management practices that may simultaneously decrease greenhouse gas emissions, increase the adaptive capacity of farmers, and improve food security. OBJECTIVE: Understanding how biophysical and socio-economic constraints affect the adoption of CSA practices and technologies plays an essential role in policy and intervention planning. Our objective was to identify these constraints among smallholder farmers in Taita Taveta County of Southeast Kenya across varying agro-ecological zones. METHODS: We conducted a Climate-Smart Agriculture Rapid Appraisal that consisted of four mostly genderdisaggregated smallholder farmer workshops (102 participants), a household survey (65 participants), key informant interviews (16 informants), and four transect walks. RESULTS AND CONCLUSIONS: Our results indicate a dissonance in the perceived awareness of CSA practices and utilization of CSA technologies between state actors and farmers. State actors emphasize lack of awareness as a barrier to adoption, while farmers express knowledgeability regarding environmental change and climate-smart practices but are confined by limitations and restrictions posed by e.g. market mechanisms, land tenure issues,and lack of resources. These restrictions include e.g. uncertainty in product prices, lack of land ownership, scarcity of arable land, and simply lack of capital or willingness to invest. Farmers are further challenged by the emergence of new pests and human-wildlife conflicts. Our research findings are based on the contextual settings of Taita Taveta County, but the results indicate that adopting CSA practices and utilizing technologies, especially in sub-Saharan regions that are heavily based on subsistence agriculture with heterogenous agro-ecological zones, require localized and gender-responsive solutions in policy formation and planning of both agricultural extension services and development interventions that take into account the agency of the farmers. SIGNIFICANCE: This study contributes to existing climate change adaptation research by increasing our un- derstanding of how physical and socio-economic constraints can affect the adoption of new farm and land management practices, and how CSA-based intervention strategies could be restructured by local stakeholders to be more inclusive.
  • Méric, Guillaume; McNally, Alan; Pessia, Alberto; Mourkas, Evangelos; Pascoe, Ben; Mageiros, Leonardos; Vehkala, Minna Emilia; Corander, Jukka Ilmari; Shepard, Samuel K. (2018)
    Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.
  • Momigliano, Paolo; Jokinen, Henri; Calboli, Federico; Aro, Eero; Merilä, Juha (2019)
    Unobserved diversity, such as undetected genetic structure or the presence of cryptic species, is of concern for the conservation and management of global biodiversity in the face of threatening anthropogenic processes. For instance, unobserved diversity can lead to overestimation of maximum sustainable yields and therefore to overharvesting of the more vulnerable stock components within unrecognized mixed-stock fisheries. We used DNA from archival (otolith) samples to reconstruct the temporal (1976-2011) genetic makeup of two mixed-stock flounder fisheries in the angstrom land Sea (AS) and the Gulf of Finland (GoF). Both fisheries have hitherto been managed as a single stock of European flounders (Platichthys flesus), but were recently revealed to target two closely related species: the pelagic-spawning P. flesus and the newly described, demersal-spawning P. solemdali. While the AS and GoF fisheries were assumed to consist exclusively of P. solemdali, P. flesus dominated the GoF flounder assemblage (87% of total) in 1983, had disappeared (0%) by 1993, and remained in low proportions (10%-11%) thereafter. In the AS, P. solemdali dominated throughout the sampling period (>70%), and P. flesus remained in very low proportions after 1983. The disappearance of P. flesus from the GoF coincides in time with a dramatic (similar to 60%) decline in commercial landings and worsening environmental conditions in P. flesus' northernmost spawning ground, the Eastern Gotland Basin, in the preceding 4-6 years. These results are compatible with the hypothesis that P. flesus in the GoF is a sink population relying on larval subsidies from southern spawning grounds and the cause of their disappearance is a cessation of larval supply. Our results highlight the importance of uncovering unobserved genetic diversity and studying spatiotemporal changes in the relative contribution of different stock components, as well as the underlying environmental causes, to manage marine resources in the age of rapid anthropogenic change.
  • Savilammi, Tiina; Papakostas, Spiros; Leder, Erica H.; Vollestad, L. Asbjorn; Debes, Paul V.; Primmer, Craig R. (2021)
    Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.
  • McFarlane, S. Eryn; Ålund, Murielle; Sirkiä, Päivi M.; Qvarnström, Anna (2018)
    Variation in relative fitness of competing recently formed species across heterogeneous environments promotes coexistence. However, the physiological traits mediating such variation in relative fitness have rarely been identified. Resting metabolic rate (RMR) is tightly associated with life history strategies, thermoregulation, diet use, and inhabited latitude and could therefore moderate differences in fitness responses to fluctuations in local environments, particularly when species have adapted to different climates in allopatry. We work in a long-term study of collared (Ficedula albicollis) and pied flycatchers (Ficedula hypoleuca) in a recent hybrid zone located on the Swedish island of Oland in the Baltic Sea. Here, we explore whether differences in RMR match changes in relative performance of growing flycatcher nestlings across environmental conditions using an experimental approach. The fitness of pied flycatchers has previously been shown to be less sensitive to the mismatch between the peak in food abundance and nestling growth among late breeders. Here, we find that pied flycatcher nestlings have lower RMR in response to higher ambient temperatures (associated with low food availability). We also find that experimentally relaxed nestling competition is associated with an increased RMR in this species. In contrast, collared flycatcher nestlings did not vary their RMR in response to these environmental factors. Our results suggest that a more flexible nestling RMR in pied flycatchers is responsible for the better adaptation of pied flycatchers to the typical seasonal changes in food availability experienced in this hybrid zone. Generally, subtle physiological differences that have evolved when species were in allopatry may play an important role to patterns of competition, coexistence, or displacements between closely related species in secondary contact.
  • Salgado, Ana L.; Suchan, Tomasz; Pellissier, Loic; Rasmann, Sergio; Ducrest, Anne-Lyse; Alvarez, Nadir (2016)
    Elevation gradients impose large differences in abiotic and biotic conditions over short distances, in turn, likely driving differences in gene expression more than would genetic variation per se, as natural selection and drift are less likely to fix alleles at such a narrow spatial scale. As elevation increases, the pressure exerted on plants by herbivores and on arthropod herbivores by predators decreases, and organisms spanning the elevation gradient are thus expected to show lower levels of defence at high elevation. The alternative hypothesis, based on the optimal defence theory, is that defence allocation should be higher in low-resource habitats such as those at high elevation, due to higher costs associated with tissue replacement. In this study, we analyse variation with elevation in (i) defence compound content in the plant Lotus corniculatus and (ii) gene expression associated with defence against predators in the specific phytophagous moth, Zygaena filipendulae. Both species produce cyanogenic glycosides (CNglcs) such as lotaustralin and linamarin as defence mechanisms, with the moth, in addition, being able to sequester CNglcs from its host plant. Specifically, we tested the assumption that the defence-associated phenotype in plants and the gene expression in the insect herbivore should covary between low-and high-elevation environments. We found that L. corniculatus accumulated more CNglcs at high elevation, a result in agreement with the optimal defence theory. By contrast, we found that the levels of expression in the defence genes of Z. filipendulae larvae were not related to the CNglc content of their host plant. Overall, expression levels were not correlated with elevation either, with the exception of the UGT33A1 gene, which showed a marginally significant trend towards higher expression at high elevation when using a simple statistical framework. These results suggest that the defence phenotype of plants against herbivores, and subsequent herbivore sequestration machineries and de novo production, are based on a complex network of interactions.
  • Hiltunen, Teppo; Cairns, Johannes; Frickel, Jens; Jalasvuori, Matti; Laakso, Jouni; Kaitala, Veijo; Kuenzel, Sven; Karakoc, Emre; Becks, Lutz (2018)
    Recognizing when and how rapid evolution drives ecological change is fundamental for our understanding of almost all ecological and evolutionary processes such as community assembly, genetic diversification and the stability of communities and ecosystems. Generally, rapid evolutionary change is driven through selection on genetic variation and is affected by evolutionary constraints, such as tradeoffs and pleiotropic effects, all contributing to the overall rate of evolutionary change. Each of these processes can be influenced by the presence of multiple environmental stressors reducing a population's reproductive output. Potential consequences of multistressor selection for the occurrence and strength of the link from rapid evolution to ecological change are unclear. However, understanding these is necessary for predicting when rapid evolution might drive ecological change. Here we investigate how the presence of two stressors affects this link using experimental evolution with the bacterium Pseudomonas fluorescens and its predator Tetrahymena thermophila. We show that the combination of predation and sublethal antibiotic concentrations delays the evolution of anti-predator defence and antibiotic resistance compared with the presence of only one of the two stressors. Rapid defence evolution drives stabilization of the predator-prey dynamics but this link between evolution and ecology is weaker in the two-stressor environment, where defence evolution is slower, leading to less stable population dynamics. Tracking the molecular evolution of whole populations over time shows further that mutations in different genes are favoured under multistressor selection. Overall, we show that selection by multiple stressors can significantly alter eco-evolutionary dynamics and their predictability.
  • Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz (2017)
    Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.
  • Kalendar, Ruslan; Sabot, Francois; Rodriguez, Fernando; Karlov , Gennady I.; Natali, Lucia; Alix, Karine (2021)
    Multiple changes that occur constantly in the plant genome allow an organism to develop from a single-celled embryo to a multicellular organism. A significant part of these changes is associated with the recombination activity of numerous classes of interspersed repeats. These numerous families of interspersed repeats were often called "junk DNA" as they were not associated with vital protein-coding processes (1). Transposable elements (TEs), such as DNA transposons and retrotransposons, are the main part of these interspersed repeats (2). DNA transposons can rightfully be called true mobile elements, the activity of which can occur at any stage of cell development and manifest itself at any moment and stage of the organism's development. The diverse families of retrotransposons are highly abundant genetic elements that are related to retroviruses (3). Although retrotransposons are not true mobile elements like DNA transposons, retrotransposable elements (RTEs) form a variety of chromosomal structures, such as centromeric and telomeric regions (4), and are the main intergenic part of the genome (5). Retrotransposons move to new chromosomal locations via an RNA intermediate that is converted into extrachromosomal DNA by the encoded reverse transcriptase/RNaseH enzymes prior to reinsertion into the genome. This replicative mode of transposition can rapidly increase the copy number of elements and can thereby greatly increase plant genome size. RTEs can be clustered into distinct families each traceable to a single ancestral sequence or a closely related group of ancestral sequences. In contrast to multigene families, which are defined based on their biological role, repetitive families are usually defined based on their active ancestors (called master or source genes) and on their generation mechanisms. Over time, individual elements from repetitive families may acquire diverse biological roles. Some RTEs can provide evolutionary advantages to the host and increase their chances of survival (6). While the view that RTEs are beneficial to the host is not new, recent progress in the field has placed RTEs squarely in the center of the ongoing debate on eukaryotic evolution. To advance this important research field, in the Research Topic "Mobile Elements and Plant Genome Evolution, Comparative Analyses, and Computational Tools" we focus on the role of mobile elements with host genome evolution, discovery, and comparative and genome-wide profiling analysis of transposable elements. Different retrotransposon families, each with its own lineage and structure, may have been active at distinct phases in the evolution of a species. Retrotransposon sequences bear the promoters that bind the nuclear factors of transcription initialization and initiate RNA synthesis by polymerases II or III. In the article entitled "Additional ORFs in Plant LTR-Retrotransposons" by Vicient C.M. and Casacuberta J.M., LTR-retrotransposons that carry additional, not retrotransposon-specific open reading frames (aORF), were discovered and analyzed. This discovery expands on the unique potential of LTR-retrotransposons as evolutionary tools, as LTR-retrotransposons can be used to deliver new gene variants within a genome. The presence of a unique aORF in some characterized LTR-retrotransposon families like maize Grande, rice RIRE2, or Silene Retand, are just as typical as retrovirus gene transduction. As dispersed and ubiquitous mobile elements, the life cycle of replicative transposition leads to genome rearrangements that affect cellular function (7). Transposable elements are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. The research group led by Kashkush K., reported the potential impact of miniature transposable element insertions on the expression of wheat genes in different wheat species in the articles entitled "The Evolutionary Dynamics of a Novel Miniature Transposable Element in the Wheat Genome" and "Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome". The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, which leads to "genomic stress" (8). TEmediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. TEs also contribute to genome plasticity and have a dramatic impact on the genetic diversity and evolution of the wheat genome. Using transposon display (9) and genome-wide profiling analysis of insertional polymorphisms of transposable elements (10), the authors discovered large genomic rearrangement events, such as deletions and introgressions in the wheat genome. High-throughput bioinformatics with next-generation sequencing (NGS) were key tools in these studies (11). Chromosomal rearrangements, gene duplications, and transposable element content may have a large impact on genomic structure, which could generate new phenotypic traits (7). In the article entitled "Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa", de Carvalho J.F. et al investigated structural variants and repetitive content between two accessions of Brassica rapa genomes and genome-size variation among a core collection using comparative genomics and cytogenetic approaches. Large genomic variants with a chromosome length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu' belonging to different cultigroups of B. rapa highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability. Transposable elements are also the driving force in the evolution of epigenetic regulation and have a long-term impact on genomic instability and evolution. Remnants of RTEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation. RTEs are dynamic and play a role in chromosome crossing over recognition and in DNA recombination between homologous chromosomes. In the article entitled "Sequencing Multiple Cotton Genomes Reveals Complex Structures and Lays Foundation for Breeding", Wang X. et al revealed that post-polyploidization of cotton genome instability resulted in numerous genomic structural changes, DNA inversion and translocation, illegitimate recombinations, accumulation of repetitive sequences, and functional innovation accompanied by elevated evolutionary rates of genes. This genome study also revealed the evolutionary past of cotton plants, which were recursively affected by polyploidization, with a decaploidization contributing to the formation of the genus Gossypium, and a neo-tetraploidization contributing to the formation of the currently widely cultivated cotton plants. The centromere is a unique part of the chromosome that combines a conserved function with extreme variability in its DNA sequence. In the article entitled "Functional Allium fistulosum centromeres comprise arrays of a long satellite repeat, insertions of retrotransposons and chloroplast DNA" Kirov G.I., et al studied the largest plant genomic organization of the functional centromere in large-sized chromosomes in Allium fistulosum and A. cepa. Long, high-copy repeats are associated with insertions of retrotransposons and plastidial DNA, and the landscape of the centromeric regions of these species possess insertions of plastidial DNA. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution. As such, the Spinacia genus serves as an ideal model to investigate the evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. This was studied in the article entitled "Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution" by Li N., et al. Major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative, sugar beet, were elucidated in the evolutionary processes of sex chromosome evolution using NGS data. The differences of repetitive DNA sequences correlate with the formation of sex chromosomes and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes, as heteromorphic sex chromosomes existed exclusively in Spinacia tetrandra.