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Santa Rita Experimental Range site, station Santa Rita Experimental Range control treatment: pastures 8 and 22, study of plant cover of Opuntia engelmannii (cactus apple) in units of percent on a yearly timescale

The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant cover of Opuntia engelmannii (cactus apple) measurements in percent units and were aggregated to a yearly timescale.

Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures that were grazed and burned: pastures 2N and 6A, study of plant cover of Opuntia engelmannii (cactus apple) in units of percent on a yearly timescale

Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures where the mesquite were killed and the pastures were burned: pasture 2S, study of plant cover of Opuntia engelmannii (cactus apple) in units of percent on a yearly timescale

Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures where the existing mesquite were killed and the pastures were grazed: pastures 3, 5N, 5S, 6B and 12B, study of plant cover of Opuntia engelmannii (cactus apple) in units of percent on a yearly timescale

opencc-by-4.0Sep 2020View details →

Three-dimensional reconstructed canopies of apple cultivars grafted on different interstocks

Canopy architecture is important for a range of orchard ecosystem processes, including radiation interception and distribution within canopy, flowering, carbon assimilation, fruit yield and quality and pest and pathogen attacks in fruit trees. The canopy of fruit tree varies greatly from cultivar to cultivar, and can be manipulated by horticultural practices, such as rootstock, pruning, training etc. We collected canopy architectural data in ‘Fuji’ and ‘Gala’ apple cultivars which were grafted onto two rootstock/interstock combinations: M. micromalus/M. domestica cv. ‘Qinguan’, a vigorous interstock and M. micromalus/M26, a dwarf interstock. Allometric relationships at leaf and shoot scale were determined for all shoot types before harvests in 2011 and 2012, including bourse, bourse short shoot, bourse long shoot, vegetative short shoot, and vegetative long shoot. A dataset of 4351 records of leaf Euler angles were digitized for all shoot types. For 19 trees, their 3D distribution of the foliage within canopy was reconstructed by combining both the spatial locations of shoots (as measured from 3D digitizing) and foliage reconstruction based on allometric relationships and leaf angle distributions. We believe this dataset is a valuable resource for studies and models that require leaf angles and detailed 3D virtual canopies.

opencc-zeroDec 2020View details →

Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)

Many apple cultivars are subject to biennial fluctuations in flowering and fruiting. It is believed that this phenomenon is caused by a repressive effect of developing fruit on the initiation of flowers in the apex of proximal bourse shoots. However, the genetic pathways of floral initiation are incompletely described in apple, and the biological nature of floral repession by fruit is currently unknown. In this study, we characterize the transcriptional landscape of bourse shoot apices in the biennial cultivar, 'Honeycrisp', during the period of floral initiation, in trees bearing a high fruit load and in trees without fruit. Trees with high fruit load produced almost exclusively vegetative growth in the subsequent year, whereas the trees without fruit produced flowers on the majority of the potential flowering nodes. Using RNA-based sequence data, we documented gene expression at high resolution, identifying >11,000 transcripts that had not been previously annotated, and characterized expression profiles associated with vegetative growth and flowering. We also conducted a census of genes related to known flowering genes, organized the phylogenetic and syntenic relationships of these genes, and compared expression among homologs. Several genes closely related to AP1, FT, FUL, LFY, and SPLS were more strongly expressed in apices from non-bearing, floral-determined trees, consistent with their presumed floral-promotive roles. In contast, a homolog of TFL1 exhibited strong and persistent up-regulation only in apices from bearing, vegetative-determined trees, suggesting a roles in floral repression. Additionally, we identified four GIBBERELLIC ACID (GA) 2 OXIDASE genes that were expressed to relatively high levels in apices from bearing trees. These results define the flowering-related transcriptional landscape in apple, and strongly support previous studies implicating both gibberellins and TFL1 as key components in repression of flowering by fruit.

opencc-zeroDec 2020View details →

Enhancing ecosystem services in apple orchards: Nest boxes increase pest control by insectivorous birds

Ecological intensification in croplands aims to enhance biodiversity-based ecosystem services, helping to increase yield while reducing agricultural environmental impacts. Identifying ecological intensification tools of wide applicability and easily implemented by farmers is, therefore, an imperative. Here, we verify the efficiency of provisioning artificial nest boxes for insectivorous birds to reinforce pest biological control in apple orchards. The study was conducted in 24 cider-apple orchards in Asturias (NW Spain) over three years. We compared the effect of insectivorous birds between orchards with and without nest boxes occupied by different bird species, through insectivory estimates based on attack on a sentinel pest and measurements of arthropod abundance in apple trees. We also identified preys that birds of different species captured to feed nestlings. Bird occupancy of nest boxes was widespread, ranging 25.0-33.3% each year. Great tit was the dominant species, followed by blue tit and, occasionally, common redstart. Predation pressure on apple pests increased in orchards with nest boxes, as judged by the increased proportion of sentinel models attacked by birds (34.9% increase in 2018 and 41.1% in 2019), decreased biomass of tree-dwelling arthropods (-51.7%) and reduced probability of apple pest occurrence (from 57 to 40%), compared to orchards without nest boxes. Nesting species showed different predatory roles in apple orchards. Fewer attacks on sentinel pests but lower arthropod biomass was associated with blue tit rather than great tit. Besides, blue tit fed nestlings at a faster rate and included in their diet a higher proportion of apple pests than great tit, which preyed mostly on other herbivorous insects. Synthesis and applications. We demonstrated the usefulness of nest boxes for insectivorous birds in enhancing biological control of apple pests at a regional scale, identifying tit species as complementary predators of apple pests and herbivores. From the farmers' perspective, providing nest boxes in orchards may represent an efficient, easy to implement, cheap and attractive measure of ecological intensification, compatible with other actions fostering biodiversity in croplands.

opencc-zeroDec 2018View details →

Data from: Which frugivory‐related traits facilitated historical long‐distance dispersal in the custard apple family (Annonaceae)?

Aim Long-distance dispersal has contributed to the disjunct biogeographical distribution of rain forest plants – something that has fascinated biogeographers since Humboldt's time. However, the dispersal 'agent' for these tropical plant lineages remains puzzling. Here, we investigate which frugivory-related traits may have facilitated past intercontinental long-distance dispersal in the custard apple family (Annonaceae), a major vertebrate-dispersed tropical plant family. We hypothesize that long-distance dispersal was associated with the evolution of traits related to dispersal by large-bodied mammals (e.g. large, dull-coloured, 'megafaunal' fruits) and strong-flying, ocean-crossing birds and bats (e.g. dehiscent, moniliform or cauliflorous fruits). Location Global Taxon Annonaceae Methods We used a fossil-calibrated phylogenetic framework to infer the biogeographic history of 234 Annonaceae species (10%, covering nearly all genera) in relation to the evolution of 15 frugivory-related traits, using maximum likelihood and Bayesian inferences. Furthermore, we used linear and generalized linear models and phylogenetic simulations to test whether ancestral fruit traits during intercontinental dispersal were different from those of other lineages not involved in long-distance dispersal. Results We inferred the ancestral Annonaceae fruits to be small with a single or few small seeds and a small number of fruitlets. These fruits were most probably apocarpous, indehiscent and/or moniliform (i.e. long beads of fruitlets). Furthermore, most of the long-distance dispersal events in Annonaceae occurred via the expanded tropical forests in the Early Cenozoic ('geodispersal'), and were significantly associated with large (c. 3 cm long), dull-coloured fruits, and short stipes. Additionally, long-distance dispersal was also facilitated by dehiscent, moniliform and non-cauliflorous fruits. Main conclusions We suggest that the evolution of frugivory-related traits associated with dispersal by frugivores that frequently move across large distances and/or barriers, such as large-bodied mammals and strong-flying birds, has contributed to the disjunct tropical biogeographical distribution of Annonaceae, and probably of tropical rain forest plants more generally.

opencc-zeroDec 2014View details →

Data from: The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega-diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness.

opencc-zeroDec 2017View details →

Data from: Effectiveness of vole control by owls in apple orchards

1. Biological pest control is gaining greater acceptance as an important part of integrated pest management for sustainable agriculture. However, knowledge regarding biological control of rodent pests is limited, and its effectiveness in temperate areas has not been quantified. In traditional Japanese apple orchards, the Ural owl Strix uralensis breeds in tree hollows and preys on the Japanese field vole Microtus montebelli, a native pest species that can harm fruit production. In this study, we hypothesized that the Ural owl, a generalist predator, can act as a biological control agent by reducing vole densities in temperate orchards. 2. To quantify the pest control effects of breeding Ural owls, we first analysed the diet of individual owls nesting in apple tree hollows. Second, we installed nest boxes in orchards to attract breeding owl pairs and collected data on vole population changes around owl nests to compare with control areas. The population changes were analysed using a generalised linear mixed model to assess the effect of breeding owls within their breeding territory. The model took into account seasonal fluctuations in vole population size as well as surrounding land-use. We also examined vole populations around the owl nests in April, and the distance between nests and forested areas, to determine if these variables influenced nest site selection. 3. The primary prey of Ural owls breeding in orchards was voles, and the owls reduced vole populations within their estimated breeding territories by 63% (± SE: 53%–70%) compared with the predicted density without owls. Owls preferred to nest in orchards with higher vole population densities in April. Our findings also indicate that higher occupancy rates are possible by distributing nest boxes based on Ural owl breeding territory size (306 m radius circle in our study). 4. Synthesis and applications. As breeding Ural owls provided significant pest control effects within their breeding territories, the re-introduction of breeding Ural owl pairs within orchards will contribute to rodent pest control. Promoting the reproduction of native raptors in agricultural areas can be an option for developing integrated pest management while simultaneously maintaining regional biodiversity.04-Oct-2018

opencc-zeroDec 2017View details →

Data from: Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing

In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allowed the estimation of ploidy levels that were in accordance with flow cytometry results, and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purposes of characterizing a diverse apple gene bank and discuss the advantages and constraints of the two approaches.

opencc-zeroDec 2018View details →

Data from: Resource allocation trade-offs and the loss of chemical defences during apple domestication

Background and Aims: Most crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication. Methods: To provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary >26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays. Key Results: The results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths. Conclusions: The negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield–defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant–herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.

opencc-zeroDec 2012View details →

Data from: Postglacial recolonization history of the European crabapple (Malus sylvestris Mill.), a wild contributor to the domesticated apple

Understanding the way in which the climatic oscillations of the Quaternary Period have shaped the distribution and genetic structure of extant tree species provides insight into the processes driving species diversification, distribution and survival. Deciphering the genetic consequences of past climatic change is also critical for the conservation and sustainable management of forest and tree genetic resources, a timely endeavour as the Earth heads into a period of fast climate change. We used a combination of genetic data and ecological niche models to investigate the historical patterns of biogeographic range expansion of a wild fruit tree, the European crabapple (Malus sylvestris), a wild contributor to the domesticated apple. Both climatic predictions for the last glacial maximum and analyses of microsatellite variation indicated that M. sylvestris experienced range contraction and fragmentation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one genetic cluster spanning a large area in Western Europe and two other genetic clusters with a more limited distribution range in Eastern Europe, one around the Carpathian Mountains and the other restricted to the Balkan Peninsula. Approximate Bayesian computation appeared to be a powerful technique for inferring the history of these clusters, supporting a scenario of simultaneous differentiation of three separate glacial refugia. Admixture between these three populations was found in their suture zones. A weak isolation by distance pattern was detected within each population, indicating a high extent of historical gene flow for the European crabapple.

opencc-by-nc-sa-2.0Mar 2020View details →

100.DB.11 Venus Apple Thorvaldsen

This is a 3D model of a post-antique marble statue by Bertel Thorvaldsen in The Royal Collection of Paintings and Sculptures at the Statens Museum for Kunst, in Copenhagen, Denmark. The statue depicts Venus (Aphrodite), the Roman goddess of love, holding an apple. This apple represents the prize in the myth [The Judgment of Paris](www.theoi.com/Olympios/JudgementParis.html). The contrapposto figure looks down at the apple in her right hand. The left hand holds a cloth and rests upon a tree trunk. **Bibliography:** [Statens Museum for Kunst](https://collection.smk.dk/#/en/detail/KMS6004) # Ancient World 3D This model posting is part of [Ancient World 3D](https://exhibits.ulib.iupui.edu/aw3d/items/show/11), a project that provides curated 3D open access conteforClassical Studies. The [original model was posted by Statens Museum for Kunst](https://mmf.io/o/104928). This entry was composed by Rachel Moore (Dr. Elizabeth Thill, advisor, Cheyenne Eversole, curator). Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Nov 2023View details →

Offset-mode CT scan of an apple using table-top PHYWE scanner

This is an X-ray dataset from a table-top PHYWE instrument recorded at the CINEMAX Summer School on 3D Imaging, August 2021, Fuglsang Manor, Lolland, Denmark.The scanner was operated in offset mode, ie the centre-of-rotation was deliberately moved to the side to enable a larger field of view to image an object larger than the instrument's normal field of view, using a 360 degree scan. The object scanned is an apple collected in the Fuglsang Manor garden.The data contains, in the raw/ folder the raw projections and in the reconstruction/ folder the reconstructed slices computed by the instrument's own software.  These reconstructed slices do not contain the full apple and also shows double illumination from the offset scan geometry.The file settings.cto contain all required geometrical information to set up the geometry for reconstruction using other software.

FIGURES 36–41. Ologamasus spp., microphotographs. 36 in Two new species of the genus Ologamasus (Ologamasidae) from apple orchards in southern Brazil

FIGURES 36–41. Ologamasus spp., microphotographs. 36. Ologamasus margaridae, adult male, leg II, tibial spur and similar structure on tarsus; 37. Ologamasus tuberculatus, protonymph, dorsal pore gd4; 38. Ologamasus tuberculatus, deutonymph, podonotal shield and pore gd4; 39. Ologamasus tuberculatus, deutonymph, opisthonotal shield and pore gd9; 40. Ologamasus tuberculatus, adult female, dorsal pore gd4 pore; 41. Ologamasus tuberculatus, adult female, dorsal pore gd9.

FIGURES 32–35. Ologamasus tuberculatus n in Two new species of the genus Ologamasus (Ologamasidae) from apple orchards in southern Brazil

FIGURES 32–35. Ologamasus tuberculatus n. sp. Adult male. 32. Dorsal idiosoma; 33. Ventral idiosoma; 34. Lateral view of leg II; 35. Chelicera.

FIGURES 23–26. Ologamasus tuberculatus n in Two new species of the genus Ologamasus (Ologamasidae) from apple orchards in southern Brazil

FIGURES 23–26. Ologamasus tuberculatus n. sp. Deutonymph. 23. Dorsal idiosoma; 24. Ventral idiosoma; 25. Epistome; 26. Chelicera.

FIGURES 7–12. Ologamasus margaridae n in Two new species of the genus Ologamasus (Ologamasidae) from apple orchards in southern Brazil

FIGURES 7–12. Ologamasus margaridae n. sp. Adult female. 7. Dorsal idiosoma; 8. Ventral idiosoma; 9. Tritosternum; 10. Epistome; 11. Chelicera; 12. Palp.

FIGURES 13–17. Ologamasus margaridae n in Two new species of the genus Ologamasus (Ologamasidae) from apple orchards in southern Brazil

FIGURES 13–17. Ologamasus margaridae n. sp. Adult male. 13. Dorsal idiosoma; 14. Ventral idiosoma; 15. Leg II; 16. Chelicera; 17. Ventral view of palp.