Large and small herbivores have strong effects on tundra vegetation in Scandinavia and Alaska

1. Large and small mammalian herbivores are present in most vegetated areas in the Arctic and often have large impacts on plant community composition and ecosystem functioning. The relative importance of different herbivores and especially how their specific impact on the vegetation varies across the Arctic is however poorly understood.
2. Here, we investigate how large and small herbivores influence vegetation density and plant community composition in four arctic vegetation types in Scandinavia and Alaska. We used a unique set of exclosures, excluding only large (reindeer and muskoxen) or all mammalian herbivores (also voles and lemmings) for at least 20 years.
3. We found that mammalian herbivores in general decreased leaf area index, NDVI, and abundance of vascular plants in all four locations, even though the strength of the effect and which herbivore type caused these effects differed across locations. In three locations, herbivore presence caused contrasting plant communities, but not in the location with lowest productivity. Large herbivores had a negative effect on plant height, whereas small mammalian herbivores increased species diversity by decreasing dominance of the initially dominating plant species. Above‐ or belowground disturbances caused by herbivores were found to play an important role in shaping the vegetation in all locations.
4. Synthesis: Based on these results, we conclude that both small and large mammalian herbivores influence vegetation in Scandinavia and Alaska in a similar way, some of which can mitigate effects of climate change. We also see important differences across locations, but these depend rather on local herbivore and plant community composition than large biogeographical differences among continents.

     

Impacts of soil temperature,phenology and plant community composition on invertebrate herbivory in a natural warming experiment

Species and community-level responses to warming are well documented, with plants and invertebrates known to alter their range, phenology or composition as temperature increases. The effects of warming on biotic interactions are less clearly understood, but can have consequences that cascade through ecological networks. Here, we used a natural soil temperature gradient of 5–35°C in the Hengill geothermal valley, Iceland, to investigate the effects of temperature on plant community composition and plant–invertebrate interactions. We quantified the level of invertebrate herbivory on the plant community across the temperature gradient and the interactive effects of temperature, plant phenology (i.e. development stage) and vegetation community composition on the probability of herbivory for three ubiquitous plant species, Cardamine pratensis, Cerastium fontanum and Viola palustris. We found that the percentage cover of graminoids and forbs increased, while the amount of litter decreased, with increasing soil temperature. Invertebrate herbivory also increased with soil temperature at the plant community level, but this was underpinned by different effects of temperature on herbivory for individual plant species, mediated by the seasonal development of plants and the composition of the surrounding vegetation. This illustrates the importance of considering the development stage of organisms in climate change research given the variable effects of temperature on susceptibility to herbivory at different ontogenetic stages.     

Response to genomic selection: The Bulmer effect and the potential of genomic selection when the number of phenotypic records is limiting

Background

Over the last ten years, genomic selection has developed enormously. Simulations and results on real data suggest that breeding values can be predicted with high accuracy using genetic markers alone. However, to reach high accuracies, large reference populations are needed. In many livestock populations or even species, such populations cannot be established when traits are difficult or expensive to record, or when the population size is small. The value of genomic selection is then questionable.

Methods

In this study, we compare traditional breeding schemes based on own performance or progeny information to genomic selection schemes, for which the number of phenotypic records is limiting. Deterministic simulations were performed using selection index theory. Our focus was on the equilibrium response obtained after a few generations of selection. Therefore, we first investigated the magnitude of the Bulmer effect with genomic selection.

Results

Results showed that the reduction in response due to the Bulmer effect is the same for genomic selection as for selection based on traditional BLUP estimated breeding values, and is independent of the accuracy of selection. The reduction in response with genomic selection is greater than with selection based directly on phenotypes without the use of pedigree information, such as mass selection. To maximize the accuracy of genomic estimated breeding values when the number of phenotypic records is limiting, the same individuals should be phenotyped and genotyped, rather than genotyping parents and phenotyping their progeny. When the generation interval cannot be reduced with genomic selection, large reference populations are required to obtain a similar response to that with selection based on BLUP estimated breeding values based on own performance or progeny information. However, when a genomic selection scheme has a moderate decrease in generation interval, relatively small reference population sizes are needed to obtain a similar response to that with selection on traditional BLUP estimated breeding values.

Conclusions

When the trait of interest cannot be recorded on the selection candidate, genomic selection schemes are very attractive even when the number of phenotypic records is limited, because traditional breeding requires progeny testing schemes with long generation intervals in those cases.     

Simulating switchgrass biomass production across ecoregions using the DAYCENT model

The production potential of switchgrass (Panicum virgatum L.) has not been estimated in a Mediterranean climate on a regional basis and its economic and environmental contribution as a biofuel crop remains unknown. The objectives of the study were to calibrate and validate a biogeochemical model, DAYCENT, and to predict the biomass yield potential of switchgrass across the Central Valley of California. Six common cultivars were calibrated using published data across the US and validated with data generated from four field trials in California (2007–2009). After calibration, the modeled range of yields across the cultivars and various management practices in the US (excluding California) was 2.4–41.2 Mg ha^?1 yr^?1, generally compatible with the observed yield range of 1.3–33.7 Mg ha^?1 yr^?1. Overall, the model was successfully validated in California; the model explained 66–90% of observed yield variation in 2007–2009. The range of modeled yields was 2.0–41.4 Mg ha^?1 yr^?1, which corresponded to the observed range of 1.3–41.1 Mg ha^?1 yr^?1. The response to N fertilizer and harvest frequency on yields were also reasonably validated. The model estimated that Alamo (21–23 Mg ha^?1 yr^?1) and Kanlow (22–24 Mg ha^?1 yr^?1) had greatest yield potential during the years after establishment. The effects of soil texture on modeled yields tended to be consistent for all cultivars, but there were distinct climatic (e.g., annual mean maximum temperature) controls among the cultivars. Our modeled results suggest that early stand maintenance of irrigated switchgrass is strongly dependent on available soil N; estimated yields increased by 1.6–5.5 Mg ha^?1 yr^?1 when residual soil mineral N was sufficient for optimal re‐growth. Therefore, management options of switchgrass for regional biomass production should be ecotype‐specific and ensure available soil N maintenance.     

Climate limitation at the cold edge: contrasting perspectives from species distribution modelling and a transplant experiment

The role of climate in determining range margins is often studied using species distribution models (SDMs), which are easily applied but have well-known limitations, e.g. due to their correlative nature and colonization and extinction time lags. Transplant experiments can give more direct information on environmental effects, but often cover small spatial and temporal scales. We simultaneously applied a SDM using high-resolution spatial predictors and an integral projection (demographic) model based on a transplant experiment at 58 sites to examine the effects of microclimate, light and soil conditions on the distribution and performance of a forest herb, Lathyrus vernus, at its cold range margin in central Sweden. In the SDM, occurrences were strongly associated with warmer climates. In contrast, only weak effects of climate were detected in the transplant experiment, whereas effects of soil conditions and light dominated. The higher contribution of climate in the SDM is likely a result from its correlation with soil quality, forest type and potentially historic land use, which were unaccounted for in the model. Predicted habitat suitability and population growth rate, yielded by the two approaches, were not correlated across the transplant sites. We argue that the ranking of site habitat suitability is probably more reliable in the transplant experiment than in the SDM because predictors in the former better describe understory conditions, but that ranking might vary among years, e.g. due to differences in climate. Our results suggest that L. vernus is limited by soil and light rather than directly by climate at its northern range edge, where conifers dominate forests and create suboptimal conditions of soil and canopy-penetrating light. A general implication of our study is that to better understand how climate change influences range dynamics, we should not only strive to improve existing approaches but also to use multiple approaches in concert.     

Facultative mutualisms: A double‐edged sword for foundation species in the face of anthropogenic global change

Ecosystems worldwide depend on habitat‐forming foundation species that often facilitate themselves with increasing density and patch size, while also engaging in facultative mutualisms. Anthropogenic global change (e.g., climate change, eutrophication, overharvest, land‐use change), however, is causing rapid declines of foundation species‐structured ecosystems, often typified by sudden collapse. Although disruption of obligate mutualisms involving foundation species is known to precipitate collapse (e.g., coral bleaching), how facultative mutualisms (i.e., context‐dependent, nonbinding reciprocal interactions) affect ecosystem resilience is uncertain. Here, we synthesize recent advancements and combine these with model analyses supported by real‐world examples, to propose that facultative mutualisms may pose a double‐edged sword for foundation species. We suggest that by amplifying self‐facilitative feedbacks by foundation species, facultative mutualisms can increase foundation species’ resistance to stress from anthropogenic impact. Simultaneously, however, mutualism dependency can generate or exacerbate bistability, implying a potential for sudden collapse when the mutualism's buffering capacity is exceeded, while recovery requires conditions to improve beyond the initial collapse point (hysteresis). Thus, our work emphasizes the importance of acknowledging facultative mutualisms for conservation and restoration of foundation species‐structured ecosystems, but highlights the potential risk of relying on mutualisms in the face of global change. We argue that significant caveats remain regarding the determination of these feedbacks, and suggest empirical manipulation across stress gradients as a way forward to identify related nonlinear responses.     

Anti-type II collagen immune complex-induced granulocyte reactivity is associated with joint erosions in RA patients with anti-collagen antibodies

IntroductionRheumatoid arthritis (RA) patients with autoantibodies against collagen type II (CII) are characterized by acute RA onset with elevated inflammatory measures and early joint erosions as well as increased production of tumor necrosis factor-α (ΤΝF-α) by peripheral blood mononuclear cells (PBMC) stimulated by anti-CII immune complexes (IC) in vitro. Polymorphonuclear granulocytes (PMN) are abundant in RA synovial fluids, where they might interact directly with anti-CII IC in the articular cartilage, but no studies have investigated PMN responses towards anti-CII IC. The aim was to investigate whether PMN react towards anti-CII IC, and to what extent such reactivity might relate to the clinical acute onset RA phenotype associated with elevated levels of anti-CII.MethodsPMN and PBMC isolated from healthy donors were stimulated with IC made with a set of 72 baseline patient sera (24 anti-CII positive, 48 anti-CII negative) chosen from a clinically well-characterized RA cohort with two-year radiological follow-up with Larsen scoring. PMN expression of cluster of differentiation (CD)11b, CD66b, CD16 and CD32 was measured by flow cytometry, whereas PMN production of myeloperoxidase (MPO) and interleukin (IL)-17, and PBMC production of ΤΝF-α was measured with enzyme linked immunosorbent assay.ResultsPMN expression of CD11b, CD66b and MPO, and PBMC production of ΤΝF-α were upregulated whereas PMN expression of CD16 and CD32 were downregulated by anti-CII IC. CD16, CD66b, and MPO production correlated to serum anti-CII levels (Spearman’s ρ = 0.315, 0.675 and 0.253, respectively). CD16 was associated with early joint erosions (P = 0.024, 0.034, 0.046 at baseline, one and two years) and CD66b was associated with changes in joint erosions (P = 0.017 and 0.016, at one and two years compared to baseline, respectively). CD66b was associated with baseline C-reactive protein and PBMC production of ΤΝF-α was associated with baseline erythrocyte sedimentation rate, in accordance with our earlier findings. No clinical associations were observed for MPO or IL-17.ConclusionPMN responses against anti-CII IC are more closely associated with early joint erosions than are PBMC cytokine responses. PMN reactivity against anti-CII IC may contribute to joint destruction in newly diagnosed RA patients with high levels of anti-CII.     

Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.     

Qualitative Analyses of Polishing and Precoating FIB Milled Crystals for MicroED

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Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

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