Onde aterrar? Conversa com Bruno Latour sobre colapso climático e pandemia

Phylogenetic relatedness, co-occurrence, and rhizomes increase lateral gene transfer among grasses 
Hibdige, et al., 2020

Background: Lateral gene transfer (LGT) has been documented in a broad range of eukaryotes, where it can promote adaptation. In plants, LGT of functional nuclear genes has been repeatedly reported in parasitic plants, ferns and grasses, but the exact extent of the phenomenon remains unknown. Systematic studies are now needed to identify the factors that govern the frequency of LGT among plants. Results: Here we scan the genomes of a diverse set of grass species that span more than 50 million years of divergence and include major crops. We identify protein coding LGT in a majority of them (13 out of 17). There is variation among species in the amount of LGT received, with rhizomatous species receiving more genes. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, we also observe genetic exchanges among distantly related species that diverged shortly after the origin of the grass family when they co-occur in the wild, pointing to a role of biogeography. The dynamics of successful LGT in grasses therefore appear to be dependent on both opportunity (co-occurrence and rhizomes) and compatibility (phylogenetic distance). Conclusion: Overall, we show that LGT is a widespread phenomenon in grasses, which is boosted by repeated contact among related lineages. The process has moved functional genes across the entire grass family into domesticated and wild species alike.

Time-calibrated phylogenetic tree of 17 model grass species used in this study (extracted from Christin et al. 2014; scale in million years - Myr). The direction of LGT between grass clades is shown with arrows whose size is proportional to the number of LGT. The black portion of pie charts on key nodes of the phylogeny indicates the quartet support for the observed topology based on a multigene coalescence analysis. The size of each pie chart is proportional to the number of species within the clade.

https://www.biorxiv.org/content/10.1101/2020.02.17.952150v1 
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Integrating agroecological production in a robust post-2020 Global Biodiversity Framework   

Wanger et al., 2020

https://www.nature.com/articles/s41559-020-1262-y

The 15th Conference of the Parties (COP) meeting to the Convention on Biological Diversity in China — now to be held in 2021 due to the coronavirus pandemic — will provide new opportunities for biodiversity conservation (https://go.nature.com/31YAVNF) through the decision on the post-2020 Global Biodiversity Framework (GBF). In short, the GBF is a global and solution-oriented framework aiming for transformative action by governments, civil society and businesses, to help biodiversity recover for the benefit of people and planet¹. Agriculture is the most extensive form of land use, occupying more than one-third of the global landmass, and imperilling 62% of all threatened species globally². Habitat conversion and conventional farming practices — including heavy use of agrochemicals — have negative effects on biodiversity³, even spilling into protected areas. However, if designed appropriately, agricultural landscapes can provide habitats for biodiversity, promote connectivity between protected areas, and increase the capacity of species to respond to environmental threats^4,5. While halting the loss of protected and intact nature is essential to halt species loss, bending the curve on biodiversity will require sustainable agriculture. We argue that the GBF must include conservation actions in agricultural landscapes based on agroecological principles (sensu High Level Panel of Experts⁶) in the three ‘2030 Action Targets’ (hereafter ‘Targets’) to reach its goals of biodiversity recovery. Agroecology is widely recognized as a necessary transformation in order to achieve food system sustainability.

Agroecological principles in the post-2020 Global Biodiversity Framework

Below, we elaborate on how agroecological production can help to support the GBF targets.

Target 1 — reduce the threats to biodiversity

Comprehensive spatial planning for diversified agriculture benefits biodiversity conservation and nature’s contributions to people (NCP)^7,8, when integrating multiple spatial scales from local to regional and multi-stakeholder participatory approaches. Diversified farmlands enhance biodiversity, biocontrol, pollination and reduce pathogen and pest impact⁷, thereby contributing to achieve conservation objectives in proximate protected areas, as more protected areas are seeing impact in intensive land use in surrounding areas⁹. Agroecological practices can considerably reduce the use of synthetic pesticides¹⁰, a major cause of biodiversity loss¹¹. A more effective use of fertilizers can reduce nutrient pollution and mitigate climate impacts by maintaining healthier, carbon-sequestering soil microbiota¹². Diversified cropping systems can further mitigate greenhouse gas emissions by, for example, non-crop tree diversification in agroforestry systems, thereby enhancing agrobiodiversity benefits^13,14.

Target 2 — meeting people’s needs through sustainable use and benefit sharing

Agroecological production is a comprehensive framework for the sustainable use of biodiversity that also supports productivity and resilience¹⁵. Farmers benefit from diversified systems through increased economic resilience, reduced dependency on agrochemical inputs, and in subsistence systems more diverse and nutritious foods^16,17,18. Moreover, agroecological production can reduce negative externalities and off-farm inputs, while increasing biodiversity and NCP^19,20. Trade-offs between agroecological approaches and yield are often assumed, but not inherent²¹. New crop varieties, crop combinations and technological innovations will only further reduce yield gaps between conventional and agroecological production^19,22, when the availability is fair and locally appropriate.

Target 3 — tools and solutions for implementation and mainstreaming

Eco-certification and agricultural policies — if well informed and implemented — provide important opportunities to encourage diversified farm and landscape measures for conservation^23,24. Corporate and government commitments to zero-deforestation and eco-labelling could be enhanced by coupling production and protection goals within innovative investment models that emphasize natural assets. Investing in diversified systems can mitigate environmental vulnerability by embedding resilience into supply chains²⁵. Promotion and equitable participation of indigenous peoples and local communities in decision-making processes is critical to incorporate their perspective on and knowledge about agroecological approaches. Lastly, an understanding of agroecological production, benefits for biodiversity conservation, food security, and overall better quality of life can help to shape new social norms for sustainability⁶.

A way forward for the post-2020 Global Biodiversity Framework and agroecology

A global transition from conventional to agroecological production will be critical to achieve the action targets and meet the GBF goals. Diversification at the field, farm and landscape scale holds large promises to make food systems more sustainable; however, farmers alone cannot achieve this major transformation. Action is required across the entire supply chain, from the processing industry to distributors to the consumers. Future research on agroecological production (Box 1) needs to (1) depart from traditional research approaches and increasingly engage in multi-stakeholder networks to define options that work in practice and across scales; (2) build on ‘theories of change’ and indicators to develop actionable strategies and quantify change; (3) support policy makers through easily accessible advisory services to promote change in the wider socioecological landscape, incentivize local innovation systems and increase budget allocations for agroecological transition; and (4) enable public and private funding for long-term research programmes more apt for the timescales that agroecological interventions operate on. By integrating agroecological principles and related future research, the GBF will be more robust in considering threats to biodiversity, people’s needs and identifying tools and solutions in support of its 2050 vision of ‘Living in harmony with nature’.

https://www.nature.com/articles/s41559-020-1262-y
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Intensive farming drives long-term shifts in avian community composition     
Hendershot et al., 2020

Agricultural practices constitute both the greatest cause of biodiversity loss and the greatest opportunity for conservation, given the shrinking scope of protected areas in many regions. Recent studies have documented the high levels of biodiversity—across many taxa and biomes—that agricultural landscapes can support over the short term. However, little is known about the long-term effects of alternative agricultural practices on ecological communities. Here we document changes in bird communities in intensive-agriculture, diversified-agriculture and natural-forest habitats in 4 regions of Costa Rica over a period of 18 years. Long-term directional shifts in bird communities were evident in intensive- and diversified-agricultural habitats, but were strongest in intensive-agricultural habitats, where the number of endemic and International Union for Conservation of Nature (IUCN) Red List species fell over time. All major guilds, including those involved in pest control, pollination and seed dispersal, were affected. Bird communities in intensive-agricultural habitats proved more susceptible to changes in climate, with hotter and drier periods associated with greater changes in community composition in these settings. These findings demonstrate that diversified agriculture can help to alleviate the long-term loss of biodiversity outside natural protected areas.

https://www.nature.com/articles/s41586-020-2090-6

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Farmer seed networks make a limited contribution to agriculture? Four common misconceptions 
Coomes et al., 2015.

Highlights

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Food and agricultural policy undervalues farmer seed networks.

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These networks are important globally in circulating planting material among farmers.

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We challenge four common misconceptions in policy and practice about seed networks.

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Farmer seed networks are efficient and open but also selective in seed provisioning.

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Commercialization and regulation are unlikely to eradicate farmer seed networks.

Abstract

The importance of seed provisioning in food security and nutrition, agricultural development and rural livelihoods, and agrobiodiversity and germplasm conservation is well accepted by policy makers, practitioners and researchers. The role of farmer seed networks is less well understood and yet is central to debates on current issues ranging from seed sovereignty and rights for farmers to GMOs and the conservation of crop germplasm. In this paper we identify four common misconceptions regarding the nature and importance of farmer seed networks today. (1) Farmer seed networks are inefficient for seed dissemination. (2) Farmer seed networks are closed, conservative systems. (3) Farmer seed networks provide ready, egalitarian access to seed. (4) Farmer seed networks are destined to weaken and disappear. We challenge these misconceptions by drawing upon recent research findings and the authors’ collective field experience in studying farmer seed systems in Africa, Europe, Latin America and Oceania. Priorities for future research are suggested that would advance our understanding of seed networks and better inform agricultural and food policy.

https://bit.ly/2WgR6lT

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The wisest and noblest teacher is nature itself.

Leonardo da Vinci
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 Increasing growth temperature alters the within-host competition of viral strains and influences virus genetic variation 
Alcaide et al., 2020

The emergence of viral diseases in plant crops hamper the sustainability of food production, and this may be boosted by global warming. Concurrently, mixed viral infections are becoming common in plants, of which epidemiology are unpredictable due to within-host virus-virus interactions. However, the extent in which the combined effect of variations in the abiotic components of the plant ecological niche (e.g., temperature) and the prevalence of mixed infections (i.e., within-host interactions among viruses) affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections, and show that two individual strains of pepino mosaic virus (PepMV) coexisted in a temperature-dependent continuum between neutral and antagonistic interactions in tomato plants. After a long-term infection, the mutational analysis of the evolved viral genomes revealed strain-specific single-nucleotide polymorphisms that were modulated by the interaction between the type of infection and temperature. Mathematical modeling allowed us to asses a thermal reaction norm for both strains, which indicated that viral replication rates were increased along with increasing temperature in mixed infections, with a remarkable strain-dependent effect. These results suggest that the growth temperature is an ecological driver of virus-virus interactions, with an effect on the genetic diversity of individual viruses co-infecting a host. This research provides insights into the effect that climate change will have on the evolutionary dynamics of viral populations.

(A) What is the effect of mixed viral infections on the fitness and genetic diversity of viral populations within a host? (B and C) Barplots exhibiting the viral load (RNA molecules / ng RNA total) of each PepMV (CH2 and EU) strain in tomato plants grown at 20 ºC and 30 ºC under single (black) and mixed infection (grey) condition. Viral accumulation was inferred by absolute quantification using RT-qPCR after 7 dpi (B) and60 dpi (C). 

https://www.biorxiv.org/content/10.1101/2020.07.06.190173v1

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I went to the woods because I wished to live deliberately, to front only the essential facts of life.

Henry David Thoreau 

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Native American gene flow into Polynesia predating Easter Island settlement      
Ioannidis et al., 2020

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas, while critics have argued that these botanical dispersals need not have been human mediated. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui). Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around ad 1200) contemporaneous with the settlement of remote Oceania. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.

https://www.nature.com/articles/s41586-020-2487-2
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Core microbiomes for sustainable agroecosystems      
Toju et al., 2018

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of ‘core microbiomes’, which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

https://www.nature.com/articles/s41477-018-0139-4
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The role of modularity in self-organisation dynamics in biological networks 
Siebert et al., 2020

Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting structure between different neurons, proteins or species influences the functioning of their respective systems. It is well-established that many biological networks are constructed in a highly hierarchical way with two main properties: short average paths that join two apparently distant nodes (neuronal, species, or protein patches) and a high proportion of nodes in modular aggregations. Although several hypotheses have been proposed so far, still little is known about the relation of the modules with the dynamical activity in such biological systems. Here we show that network modularity is a key ingredient for the formation of self-organising patterns of functional activity, independently of the topological peculiarities of the structure of the modules. In particular, we show that macroscopic spatial patterns at the modular scale can develop in this case, which may explain how spontaneous order in biological networks follows their modular structural organisation. Our results also show that Turing patterns on biological complex networks can be a signature of the presence of modular structure and consequently a possible protocol for community detection. We test our results on real-world networks to confirm the important role of modularity in creating macro-scale patterns. 

Modular vs. Small-world topology in Turing pattern formation. a) A Newman{Watts (NW) network with N = 125 nodes, and 660 edges, where patterns are absent. The colour of the nodes represents the concentration of the activator, ui(t), at long time. b) The dispersion relation of the NW network (red stars) overlain on the dispersion relation of the continuous case (blue curve), i.e. if the system was on a continuous domain and not on a network. Notice the absence of the unstable eigenvalues (inset) and the gap between the zero eigenvalue and the second smallest 2, known as the spectral gap. c) A modular network of the same size (same number of nodes and edges) as in a) where indeed Turing patterns are present. The ve modules are of the Erdos-R enyi (ER) family. The colour of the nodes again represents the concentration of the activator, ui(t), at long time. d) The dispersion relation of the modular network (red stars) overlain on the dispersion relation of the continuous domain (blue curve). Notice here the presence of unstable eigenvalues (inset) and that the eigenvalues are separated in two sets by an important gap, between the rst and second set of eigenvalues. The rst four non-zero one are denoted as the modular eigenvalues and the rest non-negative ones as the non-modular eigenvalues. The parameters of the Fitzhugh-Nagumo model are in both cases Du = 1, = 5:5, a = 0:7, b = 0:05; c = 1:7. Finally, note the di erent colormaps used between panels a) and c) to highlight the lack of patterns in the former.

https://arxiv.org/abs/2003.12311
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Curtis's botanical magazine
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https://archive.org/details/mobot31753002719729
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Agri‐environment schemes enhance pollinator richness and abundance but bumblebee reproduction depends on field size 

Geppert et al., 2020

1. Pollinators have experienced a dramatic decrease world‐wide due to agricultural intensification. In many countries, agri‐environment schemes (AES) have been introduced to counteract this current trend. However, until now, the relative importance of each AES for biodiversity and ecosystem services is still little understood and might change depending on landscape context. Complex landscape‐experiments are required to fill this knowledge gap, enabling the implementation of sustainable intensification of food production.
2. In our study, we compared the effectiveness of the two most popular AES in Germany, organic farming and flower strips, in supporting pollinators and flower resources. We selected nine landscapes along a gradient of increasing field size, (configurational heterogeneity), each with a triplet of winter wheat fields: one organic, one conventional with flower strip and one conventional without flower strip as a control. We surveyed insect‐pollinated plants and pollinators (bumblebees, solitary bees and hoverflies). Additionally, we placed bumblebee colonies in the field edges to monitor their growth (colony weight gain) and reproduction (queen production).
3. Flower strips stood out with the highest abundance and richness of pollinators. In contrast, bumblebee colony growth and plant richness benefited equally from organic and flower strip schemes. At the landscape scale, smaller fields had a positive effect on plant richness and bumblebee reproduction in flower strips. By contrast, bumblebee colonies in organic agriculture benefited most from large fields, as large organic fields provided much more flower resources than the narrow flower strips.
4. Synthesis and applications . Our results showed that both local and landscape management shaped pollinator communities and their reproduction. Overall, organic farming and flower strips appeared to be effective tools to mitigate flower shortage in conventional cereal fields, with organic farming supporting the highest flowering plant cover per field. Flower strips enhanced local pollinator richness most, but increased bumblebee reproduction only when the surrounding landscapes had small fields with long field borders. Therefore, our results reveal that European Union policies need to take into account that the effectiveness of agri‐environment schemes depends on the structure of the surrounding landscape. 

The effect of the interaction between management and mean field size in a 1,000‐m radius on colony queen brood cells (n  = 50). Different colours depict the management types, as indicated in the legend: CFS, conventional field edge with flower strip; CON, conventional field edge; ORG, organic field edge. The regression lines are based on the full model (link function: log). 

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2664.13682

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