Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Digital Communications and Networking
Title: Webly Supervised Joint Embedding for Cross-Modal Image-Text Retrieval
Abstract: Cross-modal retrieval between visual data and natural language description remains a long-standing challenge in multimedia. While recent image-text retrieval methods offer great promise by learning deep representations aligned across modalities, most of these methods are plagued by the issue of training with small-scale datasets covering a limited number of images with ground-truth sentences. Moreover, it is extremely expensive to create a larger dataset by annotating millions of images with sentences and may lead to a biased model. Inspired by the recent success of webly supervised learning in deep neural networks, we capitalize on readily-available web images with noisy annotations to learn robust image-text joint representation. Specifically, our main idea is to leverage web images and corresponding tags, along with fully annotated datasets, in training for learning the visual-semantic joint embedding. We propose a two-stage approach for the task that can augment a typical supervised pair-wise ranking loss based formulation with weakly-annotated web images to learn a more robust visual-semantic embedding. Experiments on two standard benchmark datasets demonstrate that our method achieves a significant performance gain in image-text retrieval compared to state-of-the-art approaches.
Extracted statement — Has value: Visual
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae)
Abstract: The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa) and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera). The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ) / Maximum Likelihood (ML) analysis, and using SpeciesIdentifier). Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low (< 0.03) mean interspecific K2P distance that resulted in several incorrect identifications. A high (> 0.03) maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007–0.02), and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of) taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.
Extracted statement — Biogeographical region: Afrotropical
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera)
Abstract: Abstract. Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, was evaluated in a pilot study for discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated barcoding for a larger taxon set of 588 Australian sarcophagids. In total, 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be identified, but were included nonetheless as six unidentifiable taxa. A neighbour-joining tree was generated and nucleotide sequence divergences were calculated. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as monophyletic (99.2% of cases), with bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 1.12% and 2.81–11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for molecular identification of Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology.
Extracted statement — Biogeographical region: Australian
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits
Abstract: Abstract Background Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues. Results Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (&gt;95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected. Conclusions Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.
Extracted statement — Biogeographical region: Nearctic
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae)
Abstract: DNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. In this preliminary study, we tested the efficacy of a 615‐bp fragment of the cytochrome c oxidase I (COI) as a DNA barcode in the medically important family Simuliidae, or black flies. A total of 65 (25%) morphologically distinct species and sibling species in species complexes of the 255 recognized Nearctic black fly species were used to create a preliminary barcode profile for the family. Genetic divergence among congeners averaged 14.93% (range 2.83–15.33%), whereas intraspecific genetic divergence between morphologically distinct species averaged 0.72% (range 0–3.84%). DNA barcodes correctly identified nearly 100% of the morphologically distinct species (87% of the total sampled taxa), whereas in species complexes (13% of the sampled taxa) maximum values of divergence were comparatively higher (max. 4.58–6.5%), indicating cryptic diversity. The existence of sibling species in Prosimulium travisi and P. neomacropyga was also demonstrated, thus confirming previous cytological evidence about the existence of such cryptic diversity in these two taxa. We conclude that DNA barcoding is an effective method for species identification and discovery of cryptic diversity in black flies.
Extracted statement — Biogeographical region: Nearctic
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Revision of Nearctic Dasysyrphus Enderlein (Diptera: Syrphidae)
Abstract: Dasysyrphus Enderlein (Diptera: Syrphidae) has posed taxonomic challenges to researchers in the past, primarily due to their lack of interspecific diagnostic characters. In the present study, DNA data (mitochondrial cytochrome c oxidase sub-unit I—COI) were combined with morphology to help delimit species. This led to two species being resurrected from synonymy (D. laticaudus and D. pacificus) and the discovery of one new species (D. occidualis sp. nov.). An additional new species was described based on morphology alone (D. richardi sp. nov.), as the specimens were too old to obtain COI. Part of the taxonomic challenge presented by this group arises from missing type specimens. Neotypes are designated here for D. pauxillus and D. pinastri to bring stability to these names. An illustrated key to 13 Nearctic species is presented, along with descriptions, maps and supplementary data. A phylogeny based on COI is also presented and discussed.
Extracted statement — Biogeographical region: Nearctic
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: DNA Barcodes for the Northern European Tachinid Flies (Diptera: Tachinidae)
Abstract: This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.
Extracted statement — Biogeographical region: Palearctic
Research field: Ecology and Evolutionary Biology
Title: Disturbance-mediated competition and the spread of Phragmites australis in a coastal marsh
Abstract: In recent decades the grass Phragmites australis has been aggressively in- vading coastal, tidal marshes of North America, and in many areas it is now considered a nuisance species. While P. australis has historically been restricted to the relatively benign upper border of brackish and salt marshes, it has been expanding seaward into more phys- iologically stressful regions. Here we test a leading hypothesis that the spread of P. australis is due to anthropogenic modification of coastal marshes. We did a field experiment along natural borders between stands of P. australis and the other dominant grasses and rushes (i.e., matrix vegetation) in a brackish marsh in Rhode Island, USA. We applied a pulse disturbance in one year by removing or not removing neighboring matrix vegetation and adding three levels of nutrients (specifically nitrogen) in a factorial design, and then we monitored the aboveground performance of P. australis and the matrix vegetation. Both disturbances increased the density, height, and biomass of shoots of P. australis, and the effects of fertilization were more pronounced where matrix vegetation was removed. Clear- ing competing matrix vegetation also increased the distance that shoots expanded and their reproductive output, both indicators of the potential for P. australis to spread within and among local marshes. In contrast, the biomass of the matrix vegetation decreased with increasing severity of disturbance. Disturbance increased the total aboveground production of plants in the marsh as matrix vegetation was displaced by P. australis. A greenhouse experiment showed that, with increasing nutrient levels, P. australis allocates proportionally more of its biomass to aboveground structures used for spread than to belowground struc- tures used for nutrient acquisition. Therefore, disturbances that enrich nutrients or remove competitors promote the spread of P. australis by reducing belowground competition for nutrients between P. australis and the matrix vegetation, thus allowing P. australis, the largest plant in the marsh, to expand and displace the matrix vegetation. Reducing nutrient load and maintaining buffers of matrix vegetation along the terrestrial-marsh ecotone will, therefore, be important methods of control for this nuisance species.
Extracted statement — Habitat: Terrestrial
Research field: Ecology and Evolutionary Biology
Title: The vulnerability of habitats to plant invasion: disentangling the roles of propagule pressure, time and sampling effort
Abstract: Aim To quantify the vulnerability of habitats to invasion by alien plants having accounted for the effects of propagule pressure, time and sampling effort. Location New Zealand. Methods We used spatial, temporal and habitat information taken from 9297 herbarium records of 301 alien plant species to examine the vulnerability of 11 terrestrial habitats to plant invasions. A null model that randomized species records across habitats was used to account for variation in sampling effort and to derive a relative measure of invasion based either on all records for a species or only its first record. The relative level of invasion was related to the average distance of each habitat from the nearest conurbation, which was used as a proxy for propagule pressure. The habitat in which a species was first recorded was compared to the habitats encountered for all records of that species to determine whether the initial habitat could predict subsequent habitat occupancy. Results Variation in sampling effort in space and time significantly masked the underlying vulnerability of habitats to plant invasions. Distance from the nearest conurbation had little effect on the relative level of invasion in each habitat, but the number of first records of each species significantly declined with increasing distance. While Urban, Streamside and Coastal habitats were over-represented as sites of initial invasion, there was no evidence of major invasion hotspots from which alien plants might subsequently spread. Rather, the data suggest that certain habitats (especially Roadsides) readily accumulate alien plants from other habitats. Main conclusions Herbarium records combined with a suitable null model provide a powerful tool for assessing the relative vulnerability of habitats to plant invasion. The first records of alien plants tend to be found near conurbations, but this pattern disappears with subsequent spread. Regardless of the habitat where a species was first recorded, ultimately most alien plants spread to Roadside and Sparse habitats. This information suggests that such habitats may be useful targets for weed surveillance and monitoring.
Extracted statement — Habitat: Terrestrial
Research field: Ecology and Evolutionary Biology
Title: Hawaiian ant-flower networks. Nectar-thieving ants prefer undefended native over introduced plants with floral defense
Abstract: Ants are omnipresent in most terrestrial ecosystems, and plants have responded to their dominance by evolving traits that either facilitate positive interactions with ants or reduce negative ones. Because ants are generally poor pollinators, plants often protect their floral nectar against ants. Ants were historically absent from the geographically isolated Hawaiian archipelago, which harbors one of the most endemic floras in the world. We hypothesized that native Hawaiian plants lack floral features that exclude ants and therefore would be heavily exploited by introduced, invasive ants. To test this hypothesis, ant–flower interactions involving co-occurring native and introduced plants were observed in 10 sites on three Hawaiian Islands. We quantified the residual interaction strength of each pair of ant–plant species as the deviation of the observed interaction frequency from a null-model prediction based on available nectar sugar in a local plant community and local ant activity at sugar baits. As pred...
Extracted statement — Habitat: Terrestrial
Research field: Ecology and Evolutionary Biology
Title: How well do we understand the impacts of alien species on ecosystem services? A pan-European, cross-taxa assessment
Abstract: Recent comprehensive data provided through the DAISIE project (www.europe-aliens.org) have facilitated the development of the first pan-European assessment of the impacts of alien plants, vertebrates, and invertebrates – in terrestrial, freshwater, and marine environments – on ecosystem services. There are 1094 species with documented ecological impacts and 1347 with economic impacts. The two taxonomic groups with the most species causing impacts are terrestrial invertebrates and terrestrial plants. The North Sea is the maritime region that suffers the most impacts. Across taxa and regions, ecological and economic impacts are highly correlated. Terrestrial invertebrates create greater economic impacts than ecological impacts, while the reverse is true for terrestrial plants. Alien species from all taxonomic groups affect “supporting”, “provisioning”, “regulating”, and “cultural” services and interfere with human well-being. Terrestrial vertebrates are responsible for the greatest range of impacts, and these are widely distributed across Europe. Here, we present a review of the financial costs, as the first step toward calculating an estimate of the economic consequences of alien species in Europe.
Extracted statement — Habitat: Terrestrial
Research field: Ecology and Evolutionary Biology
Title: Land Use and Avian Species Diversity Along an Urban Gradient
Abstract: I examined the distribution and abundance of bird species across an urban gradient, and concomitant changes in community structure, by censusing summer resident bird populations at six sites in Santa Clara County, California (all former oak woodlands). These sites represented a gradient of urban land use that ranged from relatively undisturbed to highly developed, and included a biological preserve, recreational area, golf course, residential neighborhood, office park, and business district. The composition of the bird community shifted from predominantly native species in the undisturbed area to invasive and exotic species in the business district. Species richness, Shannon diversity, and bird biomass peaked at moderately disturbed sites. One or more species reached maximal densities in each of the sites, and some species were restricted to a given site. The predevelopment bird species (assumed to be those found at the most undisturbed site) dropped out gradually as the sites became more urban. These patterns were significantly related to shifts in habitat structure that occurred along the gradient, as determined by canonical correspondence analysis (CCA) using the environmental variables of percent land covered by pavement, buildings, lawn, grasslands, and trees or shrubs. I compared each formal site to four additional sites with similar levels of development within a two-county area to verify that the bird communities at the formal study sites were rep- resentative of their land use category.
Extracted statement — Hypothesis type: Urban
Research field: Ecology and Evolutionary Biology
Title: Inferring Process from Pattern in Plant Invasions: A Semimechanistic Model Incorporating Propagule Pressure and Environmental Factors
Abstract: Propagule pressure is intuitively a key factor in biological invasions: increased availability of propagules increases the chances of establishment, persistence, naturalization, and invasion. The role of propagule pressure relative to disturbance and various environmental factors is, however, difficult to quantify. We explored the relative importance of factors driving invasions using detailed data on the distribution and percentage cover of alien tree species on South Africa’s Agulhas Plain (2,160 km2). Classification trees based on geology, climate, land use, and topography adequately explained distribution but not abundance (canopy cover) of three widespread invasive species (Acacia cyclops, Acacia saligna, and Pinus pinaster). A semimechanistic model was then developed to quantify the roles of propagule pressure and environmental heterogeneity in structuring invasion patterns. The intensity of propagule pressure (approximated by the distance from putative invasion foci) was a much better predictor of canopy cover than any environmental factor that was considered. The influence of environmental factors was then assessed on the residuals of the first model to determine how propagule pressure interacts with environmental factors. The mediating effect of environmental factors was species specific. Models combining propagule pressure and environmental factors successfully predicted more than 70% of the variation in canopy cover for each species.
Extracted statement — Measure of invasion success: Cover