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Supplementary Info for manuscript "A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)" - F1000 Research
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Supplementary digital data for Exposure of Insects to Current Use Pesticide Residues in Soil and Vegetation along Spatial and Temporal Distribution in Agricultural Sites
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POLISHING OF AGRICULTURAL TERMS IN FICTION
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MOSAIKS-Togo-Agriculture
<p>Data for use in the MOSAIKS demonstration notebook</p>
Performance and environmental accounting of nutrient cycling models to estimate nitrogen emissions in agriculture and their sensitivity in life cycle assessment
<p>Abstract</p> <p>Purpose</p> <p>Several models are available in the literature to estimate agricultural emissions. From life cycle assessment (LCA) perspective, there is no standardized procedure for estimating emissions of nitrogen or other nutrients. This article aims to compare four agricultural models (PEF, SALCA, Daisy and Animo) with different complexity levels and test their suitability and sensitivity in LCA.</p> <p>Methods</p> <p>Required input data, obtained outputs, and main characteristics of the models are presented. Then, the performance of the models was evaluated according to their potential feasibility to be used in estimating nitrogen emissions in LCA using an adapted version of the criteria proposed by the United Nations Framework Convention on Climate Change (UNFCCC), and other relevant studies, to judge their suitability in LCA. Finally, nitrogen emissions from a case study of irrigated maize in Spain were estimated using the selected models and were tested in a full LCA to characterize the impacts.</p> <p>Results and discussion</p> <p>According to the set of criteria, the models scored, from best to worst: Daisy (77%), SALCA (74%), Animo (72%) and PEF (70%), being Daisy the most suitable model to LCA framework. Regarding the case study, the estimated emissions agreed to literature data for the irrigated corn crop in Spain and the Mediterranean, except N<sub>2</sub>O emissions. The impact characterization showed differences of up to 56% for the most relevant impact categories when considering nitrogen emissions. Additionally, an overview of the models used to estimate nitrogen emissions in LCA studies showed that many models have been used, but not always in a suitable or justified manner.</p> <p>Conclusions</p> <p>Although mechanistic models are more laborious, mainly due to the amount of input data required, this study shows that Daisy could be a suitable model to estimate emissions when fertilizer application is relevant for the environmental study. In addition, and due to LCA urgently needing a solid methodology to estimate nitrogen emissions, mechanistic models such as Daisy could be used to estimate default values for different archetype scenarios.</p>
Soil conditions drive belowground trait space in temperate agricultural grasslands
<p>Plant belowground organs perform essential functions, including water and nutrient uptake, anchorage, vegetative reproduction and recruitment of mutualistic soil microbiota. Recently, multivariate analyses showed that root traits of species can largely be linked to a 'conservation' and a 'collaboration' gradient. Here, we tested whether this species-level bidimensional belowground trait space also exists at the community level in grasslands. Furthermore, we tested whether the position of grassland communities in belowground trait space relates to environmental variables.</p> <p>For a total of 313 species, we collected data on eight belowground traits in greenhouse and common garden experiments and supplemented it with data on bud-bank size and specific leaf area from databases. We calculated community weighted means (CWMs) of these ten traits for 150 temperate grassland plots to investigate belowground plant-trait dimensionality and its variation along ten soil and land-use parameters.</p> <p>Using PCA, we found that about 55% of variance in CWMs was explained by two main dimensions, corresponding to a mycorrhizal 'collaboration' and a resource 'conservation' gradient. Frequently overlooked traits such as rooting depth, bud-bank size and root branching intensity were largely integrated in this trait space. The two plant-strategy gradients were partially dependent on each other, with communities that do 'outsourcing' of resource uptake to mycorrhizal fungi along the collaboration gradient also being more 'slow' along the conservation gradient. (i.e. high root tissue density and high root weight ratio). 'Outsourcing' communities were also more often deep-rooting and associated with soil parameters, such as low moisture and sand content, high topsoil pH, high C:N and low δ15N. 'Slow' communities had large bud banks and were associated with low land-use intensity, high topsoil pH, and low nitrate but high ammonium concentration in the soil. Surprisingly, we did not find an association of phosphorus availability with the mycorrhizal 'collaboration' gradient.</p> <p>In conclusion, the 'collaboration' and 'conservation' gradients previously identified among species scale up to the community level in grasslands, encompass more traits than previously described, and vary with the environment.</p>
Assessment of biogeographic variation in traits of Lewis flax (Linum lewisii) for use in restoration and agriculture
<p>Lewis flax (<i>Linum lewisii)</i> is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in <i>de novo</i> domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess bio-geographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain West region, the pre-variety germplasm Maple Grove (<i>L. </i><i>lewisii</i>) and the cultivar 'Appar' (<i>L. perenne</i>) and related this variation to collection site geography and climate. Results from linear mixed models suggest there is extensive phenotypic variation among populations of Lewis flax within the Intermountain West. Using a multivariate approach, we identify a key suite of traits that are related to latitude and climate and may facilitate adaptation, including flowering indeterminacy, seed mass, and stem number. These traits should be taken into account when considering the release of new germplasm for restoration efforts. We also find that Lewis flax seed contains desirably high amounts of <span>alpha</span>-linolenic acid and is otherwise mostly indistinguishable in fatty acid composition from oil-type varieties of domesticated flax (<i>L. usitatissimum</i>), making it a strong candidate for domestication. This study provides fundamental knowledge for future research into the ecology and evolution of Lewis flax, which will inform its use in both restoration and agriculture.</p>
Data set for combined influence of food availability and agricultural intensification on a declining aerial insectivore
<p>Aerial insectivores show worldwide population declines coinciding with shifts in agricultural practices. Increasing reliance on certain agricultural practices is thought to have led to an overall reduction in insect abundance that negatively affects aerial insectivore fitness. The relationship between prey availability and the fitness of insectivores may thus vary with the extent of agricultural intensity. It is therefore imperative to quantify the strength and direction of these associations. Here we used data from an 11-year study monitoring the breeding of Tree Swallows (<em>Tachycineta bicolor</em>) and the availability of Diptera (their main prey) across a gradient of agricultural intensification in southern Québec, Canada. This gradient was characterized by a shift in agricultural production, whereby landscapes composed of forage and pastures represented less agro-intensive landscapes and those focusing on large-scale arable row crop monocultures, such as corn (<em>Zea mays</em>) or soybean (<em>Glycine max</em>) that are innately associated with significant mechanization and agro-chemical inputs, represented more agro-intensive landscapes. We evaluated the landscape characteristics affecting prey availability, and how this relationship influences the fledging success, duration of the nestling period, fledgling body mass, and wing length as these variables are known to influence the population dynamics of this species. Diptera availability was greatest within predominately forested landscapes, while within landscapes dominated by agriculture, it was marginally greater in less agro-intensive areas. Of the measured fitness and body condition proxies, both fledging success and nestling body mass were positively related to prey availability. The impact of prey availability varied across the agricultural gradient as fledging success improved with increasing prey levels within forage landscapes yet declined in more agro-intensive landscapes. Finally, after accounting for prey availability, fledging success was lowest, nestling periods were the longest, and wing length of fledglings were shortest within more agro-intensive landscapes. Our results highlight the interacting roles that aerial insect availability and agricultural intensification have on the fitness of aerial insectivores, and by extension how food availability may interact with other aspects of breeding habitats to influence the population dynamics of predators.</p>
Periphyton carbon and nitrogen stable isotopes detect agricultural stressors in low-order streams
<p>Shifts in the stable isotope signatures of carbon (C) and nitrogen (N) in ecological materials have the potential to indicate environmental disturbances. This study examined the δ<sup>13</sup>C‰ and δ<sup>15</sup>N‰ ratios of stream water and periphyton from low-order streams in a landscape influenced by agricultural activities. Our key purpose was to assess the influence of best management practice (BMP) presence and age on C and N isotope values as a potential water-quality assessment. We collected stream water and periphyton from 19 streams within the Upper Delaware River watershed in New York, USA, in each of 4 management categories: 1) recently applied BMP treatments, 2) long-standing BMPs, 3) streams lacking BMPs, and 4) minimally disturbed reference streams. We sampled and analyzed water and periphyton for δ<sup>13</sup>C‰ and δ<sup>15</sup>N‰ in a repeated-measures design (BMP category ´ time) from April to November 2013. There were large seasonal differences in stream water δ<sup>13</sup>C-dissolved organic C (DIC)‰ and δ<sup>15</sup>NO<sub>3</sub>-N‰, with strong differences between reference and agricultural streams. Periphyton δ<sup>13</sup>C‰ and δ<sup>15</sup>N‰ values also differed strongly across streams draining land with agricultural activities, with 85% higher periphyton δ<sup>15</sup>N‰ signals in all agricultural categories vs reference streams. Periphyton diatom and chlorophyte taxonomic proportions showed the strongest relationship with periphyton δ<sup>13</sup>C‰ values, where diatoms were negatively associated with increasing δ<sup>13</sup>C‰. These results suggest that aqueous and periphytic stable isotopes were sensitive in detecting persistent effects of agriculture on these streams despite BMP mitigation, where nutrient (orthosphosphate, nitrite, and ammonia) levels were non-indicative. These results also suggest that BMPs may not have fully eliminated the negative impacts of agricultural stressors on water quality in impacted streams.</p>
Supplementary material 2 from: Kenis M, Agboyi LK, Adu-Acheampong R, Ansong M, Arthur S, Attipoe PT, Baba A-SM, Beseh P, Clottey VA, Combey R, Dzomeku I, Eddy-Doh MA, Fening KO, Frimpong-Anin K, Hevi W, Lekete-Lawson E, Nboyine JA, Ohene-Mensah G, Oppong-Mensah B, Nuamah HSA, van der Puije G, Mulema J (2022) Horizon scanning for prioritising invasive alien species with potential to threaten agriculture and biodiversity in Ghana. NeoBiota 71: 129-148. https://doi.org/10.3897/neobiota.71.72577
Risk scores for potential invasive alien plant pests in Ghana
Supplementary material 1 from: Kenis M, Agboyi LK, Adu-Acheampong R, Ansong M, Arthur S, Attipoe PT, Baba A-SM, Beseh P, Clottey VA, Combey R, Dzomeku I, Eddy-Doh MA, Fening KO, Frimpong-Anin K, Hevi W, Lekete-Lawson E, Nboyine JA, Ohene-Mensah G, Oppong-Mensah B, Nuamah HSA, van der Puije G, Mulema J (2022) Horizon scanning for prioritising invasive alien species with potential to threaten agriculture and biodiversity in Ghana. NeoBiota 71: 129-148. https://doi.org/10.3897/neobiota.71.72577
Guidelines for horizon scanning for plant pests potentially threatening Ghana
Data from: Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by DNA metabarcoding
<p>Gardens are important habitats for pollinators, providing floral resources and nesting sites. There are high levels of public support for growing 'pollinator-friendly' plants but whilst plant recommendation lists are available, they are usually inconsistent, poorly supported by scientific research and target a narrow group of pollinators. In order to supply the most appropriate resources, there is a clear need to understand foraging preferences, for a range of pollinators, across the season within horticultural landscapes.</p> <p>Using an innovative DNA metabarcoding approach, we investigated foraging preferences of four groups of pollinators in a large and diverse, horticultural, and agricultural landscape, across the flowering season and over two years, significantly improving on the spatial and temporal scale that can be achieved using observational studies.</p> <p>Bumblebees, honeybees, non-corbiculate bees, and hoverflies visited 191 plant taxa. Overall floral resources were shared between the different types of pollinators, but significant differences were seen between the plants used most abundantly by bees (Hymenoptera) and hoverflies (Diptera).</p> <p>Floral resource use by pollinators is strongly associated with seasonal changes in flowering plants, with pollinators relying on dominant plants found within each season, with preferences consistent across both years.</p> <p>The plants identified were categorised according to their native status to investigate the value of native and non-native plants. The majority of floral resources used were of native and near-native origin, but the proportion of horticultural and naturalised plants increased during late summer and autumn.</p> <p><em>Synthesis and applications: </em>We recommend that plant lists should distinguish between bees and hoverflies and provide evidence-based floral recommendations throughout the year that include native as well as non-native plants for use in the UK and Northern Europe. Specific management recommendations include reducing mowing to encourage plants such as dandelion <em>Taraxacum officinale</em>, buttercups <em>Ranunculus spp.</em>, and reducing scrub management to encourage bramble <em>Rubus fruticosus</em>.</p>
Supplementary material 1 from: Strokov AS, Potashnikov VY (2022) Environmental tradeoffs of agricultural growth in Russian regions and possible sustainable pathways for 2030. Russian Journal of Economics 8(1): 60-80. https://doi.org/10.32609/j.ruje.8.78331
Maps of main environmental indicators of Russian regional agricultural development
Supplementary material 2 from: Strokov AS, Potashnikov VY (2022) Environmental tradeoffs of agricultural growth in Russian regions and possible sustainable pathways for 2030. Russian Journal of Economics 8(1): 60-80. https://doi.org/10.32609/j.ruje.8.78331
The dataset on agricultural waste, nitrogen concentration, and GHG emissions in Russian regions
FIGURE 4 in First record of grey bush-cricket Platycleis albopunctata (Goeze, 1778) (Tettigoniidae: Tettigoniini) on the agricultural crops from Trans Himalaya India
FIGURE 4. (a & b). Collection sites of P. albopunctata.
FIGURE 1 in First record of grey bush-cricket Platycleis albopunctata (Goeze, 1778) (Tettigoniidae: Tettigoniini) on the agricultural crops from Trans Himalaya India
FIGURE 1. Platycleis albanctopunctata: A. Male, B. Female.
FIGURE 3 in First record of grey bush-cricket Platycleis albopunctata (Goeze, 1778) (Tettigoniidae: Tettigoniini) on the agricultural crops from Trans Himalaya India
FIGURE 3. Map showing distribution of P. albopunctata (Kargil, Ladakh).
Household Survey - Impacts of large-scale land acquisitions on smallholder agriculture and livelihoods in Tanzania
<p><strong>** Article & Dataset Currently Under Review **</strong></p> <p><strong>Dataset Overview</strong></p> <p>Our household dataset is associated with a pre-print article "Impacts of large-scale land acquisitions on smallholder agriculture and livelihoods in Tanzania". The household survey is designed for the purposes of policy evaluation with selection of households based on proximity to large-scale land acquisitions (treatment) and a set of households in similar socio-ecological contexts with no association to large-scale land acquisitions (control). Households were selected as a random sample in 35 villages surrounding LSLAs who provided responses to a questionnaire covering household income, assets, farming practices, health, food-security, and energy-use. </p> <p>Two datasets are provided. First, the "hh_dataset_rep.csv" providing household responses for variables used in this study. Second, the "hh_crops_rep.csv" provides detail on crops cultivated by each household, self-reported yields and farm-gate prices. Each variable is described in the "variable_descriptoin.xlsx". In addition to the datasets, we provide replication code for this study "lsla_mechanisms_rep.Rmd" as an R-Markdown file.</p> <p><strong>Article Abstract</strong></p> <p>Improving agricultural productivity is a major sustainability challenge of the 21<sup>st</sup> century. Large-scale land acquisitions (LSLAs) have important effects on both well-being and the environment in the Global South, but their impacts on agricultural productivity and subsequent effects on farm incomes or food-security are under-investigated. Prior studies lack data or methods to investigate the mechanistic nature of household change in agricultural practices that may vary due to LSLA conditions. To overcome this challenge, we use a novel household dataset and a quasi-experimental design to estimate household level changes in agricultural value driven by LSLAs in Tanzania. In addition, we use a causal mediation analysis to assess how contract farming arrangements, land loss, and adoption of new farming technologies around LSLAs influence agricultural productivity. We find that households near LSLAs produced 19.2% (95% CI: 3.5 – 37.2%) higher agricultural value, primarily due to increased crop prices and farmer selection of high-value crops. Importantly, effect sizes are positively and negatively mediated by different mechanisms. The presence of contract farming explains 18.1% (95% CI: 0.56%, 47%) of the effect size in agricultural value, whereas land loss reduces agricultural value by 26.8% (95% CI: -71.3%, -4.0%). We also estimate whether improvements in food-security and household incomes occur in proximity to LSLAs, as anticipated with higher agricultural value. However, we do not find increases in agricultural income and food security, which may be due to higher crop prices in proximity to LSLAs. Our results stand in contrast to assumptions that technological spillovers occur through LSLAs and are principal drivers of agrarian change, holding important implications for agricultural transformations. Instead access to output markets through contract farming enables greater agricultural value whereas land loss negatively affects the agricultural value of households. Governance strategies should focus on limiting negative impacts related to the loss of smallholder land rights enabling greater access to contract farming.</p> <p> </p>
Fig. 3 in Factors Affecting Avifaunal Diversity In Selected Agro-Ecosystems Of Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
Fig. 3. Distribution pattern of resident/migratory status of avifauna across seasons during the study period from January 2019 to April 2020.
Fig. 4 in Factors Affecting Avifaunal Diversity In Selected Agro-Ecosystems Of Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
Fig. 4. Comparative resident/migratory status and relative abundance of birds at Himachal Pradesh Agricultural University study site.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.