Moussab/ORKG-training-evaluation-set huggingface dataset:
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 — Studied taxonomic group (Biology): Simuliidae
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 — Studied taxonomic group (Biology): Syrphidae
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Evaluation of DNA barcoding and identification of new haplomorphs in Canadian deerflies and horseflies
Abstract: This paper reports the first tests of the suitability of the standardized mitochondrial cytochrome c oxidase subunit I (COI) barcoding system for the identification of Canadian deerflies and horseflies. Two additional mitochondrial molecular markers were used to determine whether unambiguous species recognition in tabanids can be achieved. Our 332 Canadian tabanid samples yielded 650 sequences from five genera and 42 species. Standard COI barcodes demonstrated a strong A + T bias (mean 68.1%), especially at third codon positions (mean 93.0%). Our preliminary test of this system showed that the standard COI barcode worked well for Canadian Tabanidae: the target DNA can be easily recovered from small amounts of insect tissue and aligned for all tabanid taxa. Each tabanid species possessed distinctive sets of COI haplotypes which discriminated well among species. Average conspecific Kimura two‐parameter (K2P) divergence (0.49%) was 12 times lower than the average divergence within species. Both the neighbour‐joining and the Bayesian methods produced trees with identical monophyletic species groups. Two species, Chrysops dawsoni Philip and Chrysops montanus Osten Sacken (Diptera: Tabanidae), showed relatively deep intraspecific sequence divergences (∼10 times the average) for all three mitochondrial gene regions analysed. We suggest provisional differentiation of Ch. montanus into two haplotypes, namely, Ch. montanus haplomorph 1 and Ch. montanus haplomorph 2, both defined by their molecular sequences and by newly discovered differences in structural features near their ocelli.
Extracted statement — Studied taxonomic group (Biology): Tabanidae
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 — Studied taxonomic group (Biology): Tachinidae
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification
Abstract: Abstract A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae) based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences – almost 20% of the total – this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification. We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to BLAST against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.
Extracted statement — Studied taxonomic group (Biology): Tephritidae
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation
Abstract: Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.
Extracted statement — Studied taxonomic group (Biology): Zygaenidae
Research field: Ecology and Evolutionary Biology
Title: Germination patterns and implications for invasiveness in three Taraxacum (Asteraceae) species
Abstract: Luo J & Cardina J (2012). Germination patterns and implications for invasiveness in three Taraxacum (Asteraceae) species. Weed Research 52, 112–121. Summary The ability to germinate across different environments has been considered an important trait of invasive plant species that allows for establishment success in new habitats. Using two alien congener species of Asteraceae –Taraxacum officinale (invasive) and Taraxacum laevigatum laevigatum (non-invasive) – we tested the hypothesis that invasive species germinate better than non-invasives under various conditions. The germination patterns of Taraxacum brevicorniculatum, a contaminant found in seeds of the crop Taraxacum kok-saghyz, were also investigated to evaluate its invasive potential. In four experiments, we germinated seeds along gradients of alternating temperature, constant temperature (with or without light), water potential and following accelerated ageing. Neither higher nor lower germination per se explained invasion success for the Taraxacum species tested here. At alternating temperature, the invasive T. officinale had higher germination than or similar to the non-invasive T. laevigatum. Contrary to predictions, T. laevigatum exhibited higher germination than T. officinale in environments of darkness, low water potential or after the seeds were exposed to an ageing process. These results suggested a complicated role of germination in the success of T. officinale. Taraxacum brevicorniculatum showed the highest germination among the three species in all environments. The invasive potential of this species is thus unclear and will probably depend on its performance at other life stages along environmental gradients.
Extracted statement — Specific traits:  Germination
Research field: Ecology and Evolutionary Biology
Title: Re-colonisation rate differs between co-existing indigenous and invasive intertidal mussels following major disturbance
Abstract: The potential of introduced species to become invasive is often linked to their ability to colonise disturbed habitats rapidly. We studied the effects of major disturbance by severe storms on the indigenous mussel Perna perna and the invasive mussel Mytilus galloprovincialis in sympatric intertidal populations on the south coast of South Africa. At the study sites, these species dominate different shore levels and co-exist in the mid mussel zone. We tested the hypotheses that in the mid- zone P. perna would suffer less dislodgment than M. galloprovincialis, because of its greater tenacity, while M. galloprovincialis would respond with a higher re-colonisation rate. We estimated the per- cent cover of the 2 mussels in the mid-zone from photographs, once before severe storms and 3 times afterwards. M. galloprovincialis showed faster re-colonisation and 3 times more cover than P. perna 1 and 1.5 yr after the storms (when populations had recovered). Storm-driven dislodgment in the mid- zone was highest for the species that initially dominated at each site, conforming to the concept of compensatory mortality. This resulted in similar cover of the 2 species immediately after the storms. Thus, the storm wave forces exceeded the tenacity even of P. perna, while the higher recruitment rate of M. galloprovincialis can explain its greater colonisation ability. We predict that, because of its weaker attachment strength, M. galloprovincialis will be largely excluded from open coast sites where wave action is generally stronger, but that its greater capacity for exploitation competition through re-colonisation will allow it to outcompete P. perna in more sheltered areas (especially in bays) that are periodically disturbed by storms.
Extracted statement — Type of disturbance:  Storm
Research field: Ecology and Evolutionary Biology
Title: The role of propagule pressure, genetic diversity and microsite availability for Senecio vernalis invasion
Abstract: Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of invasive plants, a clear differentiation between initial emergence and subsequent survival to juvenile and adult stages is required.
Extracted statement — Measure of invasion success: Abundance
Research field: Ecology and Evolutionary Biology
Title: Invasive alien plants infiltrate bird-mediated shrub nucleation processes in arid savanna
Abstract: 1 The cultivation and dissemination of alien ornamental plants increases their potential to invade. More specifically, species with bird‐dispersed seeds can potentially infiltrate natural nucleation processes in savannas. 2 To test (i) whether invasion depends on facilitation by host trees, (ii) whether propagule pressure determines invasion probability, and (iii) whether alien host plants are better facilitators of alien fleshy‐fruited species than indigenous species, we mapped the distribution of alien fleshy‐fruited species planted inside a military base, and compared this with the distribution of alien and native fleshy‐fruited species established in the surrounding natural vegetation. 3 Abundance and diversity of fleshy‐fruited plant species was much greater beneath tree canopies than in open grassland and, although some native fleshy‐fruited plants were found both beneath host trees and in the open, alien fleshy‐fruited plants were found only beneath trees. 4 Abundance of fleshy‐fruited alien species in the natural savanna was positively correlated with the number of individuals of those species planted in the grounds of the military base, while the species richness of alien fleshy‐fruited taxa decreased with distance from the military base, supporting the notion that propagule pressure is a fundamental driver of invasions. 5 There were more fleshy‐fruited species beneath native Acacia tortilis than beneath alien Prosopis sp. trees of the equivalent size. Although there were significant differences in native plant assemblages beneath these hosts, the proportion of alien to native fleshy‐fruited species did not differ with host. 6 Synthesis. Birds facilitate invasion of a semi‐arid African savanna by alien fleshy‐fruited plants, and this process does not require disturbance. Instead, propagule pressure and a few simple biological observations define the probability that a plant will invade, with alien species planted in gardens being a major source of propagules. Some invading species have the potential to transform this savanna by overtopping native trees, leading to ecosystem‐level impacts. Likewise, the invasion of the open savanna by alien host trees (such as Prosopis sp.) may change the diversity, abundance and species composition of the fleshy‐fruited understorey. These results illustrate the complex interplay between propagule pressure, facilitation, and a range of other factors in biological invasions.
Extracted statement — Measure of invasion success: Abundance
Research field: Ecology and Evolutionary Biology
Title: Anthropogenic Disturbance Can Determine the Magnitude of Opportunistic Species Responses on Marine Urban Infrastructures
Abstract: Background Coastal landscapes are being transformed as a consequence of the increasing demand for infrastructures to sustain residential, commercial and tourist activities. Thus, intertidal and shallow marine habitats are largely being replaced by a variety of artificial substrata (e.g. breakwaters, seawalls, jetties). Understanding the ecological functioning of these artificial habitats is key to planning their design and management, in order to minimise their impacts and to improve their potential to contribute to marine biodiversity and ecosystem functioning. Nonetheless, little effort has been made to assess the role of human disturbances in shaping the structure of assemblages on marine artificial infrastructures. We tested the hypothesis that some negative impacts associated with the expansion of opportunistic and invasive species on urban infrastructures can be related to the severe human disturbances that are typical of these environments, such as those from maintenance and renovation works. Methodology/Principal Findings Maintenance caused a marked decrease in the cover of dominant space occupiers, such as mussels and oysters, and a significant enhancement of opportunistic and invasive forms, such as biofilm and macroalgae. These effects were particularly pronounced on sheltered substrata compared to exposed substrata. Experimental application of the disturbance in winter reduced the magnitude of the impacts compared to application in spring or summer. We use these results to identify possible management strategies to inform the improvement of the ecological value of artificial marine infrastructures. Conclusions/Significance We demonstrate that some of the impacts of globally expanding marine urban infrastructures, such as those related to the spread of opportunistic, and invasive species could be mitigated through ecologically-driven planning and management of long-term maintenance of these structures. Impact mitigation is a possible outcome of policies that consider the ecological features of built infrastructures and the fundamental value of controlling biodiversity in marine urban systems.
Extracted statement — Investigated species: Algae
Research field: Ecology and Evolutionary Biology
Title: Determinants of Caulerpa racemosa distribution in the north-western Mediterranean
Abstract: Predicting community susceptibility to invasion has become a priority for preserving biodiversity. We tested the hypothesis that the occurrence and abundance of the seaweed Caulerpa racemosa in the north-western (NW) Mediterranean would increase with increasing levels of human disturbance. Data from a survey encompassing areas subjected to different human influences (i.e. from urbanized to protected areas) were fitted by means of generalized linear mixed models, including descriptors of habitats and communities. The incidence of occurrence of C. racemosa was greater on urban than extra-urban or protected reefs, along the coast of Tuscany and NW Sardinia, respectively. Within the Marine Protected Area of Capraia Island (Tuscan Archipelago), the probability of detecting C. racemosa did not vary according to the degree of protection (partial versus total). Human influence was, however, a poor predictor of the seaweed cover. At the seascape level, C. racemosa was more widely spread within degraded (i.e. Posidonia oceanica dead matte or algal turfs) than in better preserved habitats (i.e. canopy-forming macroalgae or P. oceanica seagrass meadows). At a smaller spatial scale, the presence of the seaweed was positively correlated to the diversity of macroalgae and negatively to that of sessile invertebrates. These results suggest that C. racemosa can take advantage of habitat degradation. Thus, predicting invasion scenarios requires a thorough knowledge of ecosystem structure, at a hierarchy of levels of biological organization (from the landscape to the assemblage) and detailed information on the nature and intensity of sources of disturbance and spatial scales at which they operate.
Extracted statement — Investigated species: Algae