cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4734174
title: Training Data for SLGPT

description: Training Corpus for SLGPT. The upload contains: (1) Slforge Generated Simulink Models : Synthetic Simulink Models (2) Source of Real World Simulink Models The .txt file is a combined text file that contains all the real world Simulink models based on SLGPT's experimental setup.
DOI: 10.5281/zenodo.4734173
title: Training Data for SLGPT

description: Training Corpus for SLGPT. The upload contains: (1) Slforge Generated Simulink Models : Synthetic Simulink Models (2) Source of Real World Simulink Models The .txt file is a combined text file that contains all the real world Simulink models based on SLGPT's experimental setup.
DOI: 10.12761/sgn.2018.10265
title: Functional and phylogenetic diversity of bird assemblages are filtered by different biotic factors on tropical mountains

description: It is not yet clear whether similar mechanisms influence the assembly of ecological communities across different continents. Here, we investigated the functional and phylogenetic diversity of bird assemblages along elevational gradients in two biogeographic regions in order to identify how these are driven by biotic factors, such as food resources and vegetation structure, and abiotic factors, such as ambient temperature and precipitation. We recorded bird species abundances on 18 and 30 plots in the Ecuadorian Andes and on Mount Kilimanjaro, respectively. We measured ten functional morphological traits, related to bird feeding and movement, and utilized bird phylogenies to compare observed values and null-model corrected effect sizes of functional and phylogenetic diversity along elevational gradients and between biogeographic regions. Furthermore, we assessed how observed values and effect sizes of functional and phylogenetic diversity were associated with the underlying gradients in available food resources, vegetation structure, temperature and precipitation. Functional and phylogenetic diversity were generally higher in species assemblages in the Ecuadorian Andes than on Mount Kilimanjaro. Both observed values and effect sizes of functional and phylogenetic diversity decreased significantly with increasing elevation in both biogeographic regions. Functional diversity consistently increased with increasing resource availability, whereas phylogenetic diversity increased with increasing vegetation heterogeneity and canopy closure in both biogeographic regions. Temperature and precipitation were not significantly associated with functional and phylogenetic diversity. Our results suggest that in both mountain systems the diversity of functional traits in bird species assemblages is the result of environmental filtering by available food resources, whereas phylogenetic diversity is primarily limited by vegetation structure. These findings suggest important differences in the main drivers of functional and phylogenetic diversity. We conclude that biotic factors might be more important for driving bird diversity patterns than abiotic factors and that a loss of resource availability and vegetation structure, e.g. through human impacts, is likely to trigger changes in community assembly on tropical mountains.
DOI: 10.12761/sgn.2018.10268
title: Functional responses of avian frugivores to variation in fruit resources between natural and fragmented forests

description: Observations of plant-bird interactions: We sampled plant-frugivore networks at six study sites covering all three elevations (1000, 2000 and 3000 m) and two habitat types (natural and fragmented forest). Every study site comprised three plots, resulting in a total of 18 study plots. Each plot was sampled once in the more humid and once in the less humid season per year over two years (2014 and 2015). During each observation period, we observed each plot for 25 h on four consecutive days between dawn and noon. Each study plot was observed for a total of 100 h, resulting in 300 h for every study site and 1800 h for all 18 study plots. We recorded plant-frugivore interaction events by direct observations with binoculars within a 30 x 100 m transect within each plot. We walked freely through the plot and observed each fruiting plant species for a similar amount of time. The study plots ran along steep slopes, which enabled the observation of frugivore activity in the canopy. Only legitimate seed dispersal events were considered, therefore only interactions with swallowed, pecked or transported fruits of a fruiting plant were recorded. Seed predation events were excluded from the analysis (less than 1% of the observed interactions). In order to quantify resource switching between natural and fragmented forests, we selected the subset of bird species that occurred in both interaction networks (i.e., natural and fragmented forest) at each elevation (i.e., 63 species out of 133 species from all interaction networks). We then excluded those birds that were recorded just in a single interaction event in either of the two forest types. Consequently, plant species considered in this analysis were those ones consumed by the subset of birds for each habitat type at each elevation. This resulted in a total number of 52 bird species feeding on 83 plant species that we used for all subsequent analyses. Most bird species were present at only one elevation; only four out of the 52 species were recorded at two different elevations. Species morphological traits and metrics of functional diversity. We measured traits of all fleshy-fruited plant species based on plant individuals collected on the study plots. Fruit length, width and mass were measured on 15 fruits per plant species to obtain average fruit traits per plant species. In the field, we estimated the height of every individual fruiting plant to calculate the average height of each fruiting plant species. Bill and wing traits of birds were measured on four specimens (two female and two male) of each species in museum collections (Natural History Museum, Berlin, Germany; Museo Ecuatoriano de Ciencias Naturales, Quito, Ecuador; Zoological Research Museum Alexander Koenig, Bonn, Germany; Zoological Museum of the University of Copenhagen, Denmark). Bird body mass was compiled from Dunning (2007).
DOI: 10.5517/ccdc.csd.cc24d7tm
title: CCDC 1977980: Experimental Crystal Structure Determination

description: Related Article: Elena A. Malinina, Svetlana E. Korolenko, Aleksey S. Kubasov, Lyudmila V. Goeva, Varvara V. Avdeeva, Nikolay T. Kuznetsov|2020|Polyhedron|184|114566|doi:10.1016/j.poly.2020.114566
DOI: 10.12761/sgn.2014.1
title: Gallegos et al. 2014 Secondary dispersal by ants promotes forest regeneration after deforestation

description: We studied the effects of secondary dispersal on seed predation, germination and seedling recruitment of the primarily bird-dispersed tree Clusia trochiformis in a tropical montane forest in Bolivia. We carried out exclosure experiments that allowed or excluded access to seeds by vertebrates in three habitat types (forest interior, degraded habitat close to and degraded habitat far from the forest margin) in a spatial block design at six sites. We offered a total of 1,440 seeds (both with and without an aril) and marked half of them with a thread to follow their fate after 48 h and after 1 month.
DOI: 10.12761/sgn.2014.2
title: Illumina metabarcoding pipeline for fungal ITS

description: High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (i) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding, (ii) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments, (iii) and is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus avoiding a black-box approach and giving the user maximum control over data treatment. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
DOI: 10.12761/sgn.2014.3
title: A host jump from monocots to dicots is associated with high gene loss rather than gene gain in the smut fungus Melanopsichium pennsylvanicum

description: A host jump from monocots to dicots is associated with high gene loss rather than gene gain in the smut fungus Melanopsichium pennsylvanicum.
DOI: 10.12761/sgn.2014.4
title: Foraging preferences of hummingbirds on artificial and natural flowers; 2011-2012; Costa Rica

description: 1. In plant-pollinator networks, the floral morphology of food plants is an important determinant of the interaction niche of pollinators. Studies on foraging preferences of pollinators combining experimental and observational approaches may help to understand the mechanisms behind patterns of interactions and niche partitioning within pollinator communities. 2. In this study, we tested whether morphological floral traits were associated with foraging preferences of hummingbirds for artificial and natural flower types in Costa Rica. We performed field experiments with artificial feeders, differing in length and curvature of flower types, to quantify the hummingbirds' interaction niche under unlimited nectar resources. To quantify the interaction niche under real-world conditions of limited nectar resources, we measured foraging preferences of hummingbirds for a total of 34 plant species. 3. Artificial feeders were visited by Eupherusa nigriventris and Phaethornis guy in the pre-montane forest, and Lampornis calolaemus in the lower montane forest. Under experimental conditions, all three hummingbird species overlapped their interaction niches and showed a preference for the short artificial flower type over the long-straight and the long-curved flower types. Under natural conditions, the two co-occurring hummingbird species preferred to feed on plant species with floral traits corresponding to their bill morphology. The short-billed hummingbird E. nigriventris preferred to feed on short and straight flowers, whereas the long- and curved-billed P. guy preferred long and curved natural flowers. The medium-size billed species L. calolaemus preferred to feed on flowers of medium length and did not show preferences for plant species with specific corolla curvature. 4. Our results show that floral morphological traits constrain access by short-billed hummingbird species to nectar resources. Morphological constraints, therefore, represent one important mechanism structuring trophic networks. In addition, other factors, such as competition and differences in resource quantity or quality, define the interaction niches of consumer species in real-world communities, enforcing patterns of niche segregation between co-occurring consumer species. This suggests that experimental studies are needed to disentangle effects of morphological constraints from those of competition for resources in plant-pollinator interactions and other types of trophic interactions.
DOI: 10.12761/sgn.2014.5
title: Ursus arctos coding sequences (CDS)

description: Ursus arctos coding sequences (CDS)
DOI: 10.12761/sgn.2015.1
title: The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina

description: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota. The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represent the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned. The current study provides some basic insights into the evolution of Agaricomycotina and ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. The genome sequence of X. dendrorhous will extremely facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
DOI: 10.12761/sgn.2015.3
title: Functional structure and specialization in three tropical plant-hummingbird interaction networks across an elevational gradient in Costa Rica

description: Understanding causes of variation in multispecies assemblages along spatial environmental gradients is a long-standing research topic in ecology and biogeography. Ecological networks comprising interacting species of plants and pollinators are particularly suitable for testing effects of environmental gradients on the functional structure and specialization in multispecies assemblages. In this study, we investigated patterns in functional assemblage structure and specialization of hummingbirds at the individual and species level along a tropical elevational gradient. We mist-netted hummingbirds at three elevations in Costa Rica in seven temporally distinct sampling periods and used the pollen carried by hummingbird individuals to construct plant-hummingbird networks at each elevation. We measured four functional traits of hummingbird species and quantified different metrics of functional community structure. We tested the effect of elevation on functional metrics of hummingbird assemblages and specialization within the networks, employing the variability across sampling periods and hummingbird species to compare the respective metrics among elevations. Hummingbird species and individuals were more specialized at low and mid elevations than at the highest elevation. This pattern corresponded to a more even and over-dispersed assemblage structure at the lower elevations throughout the year and suggests a high level of floral resource partitioning in functionally diversified communities. In contrast, an uneven and clustered functional structure of the highland assemblage across all sampling periods suggests that this assemblage was structured by environmental filtering and by niche expansion of hummingbird individuals and species at this elevation. We conclude that high degrees of specialization on specific floral resources might be crucial for the coexistence of hummingbird species in diversified lowland communities. Spatial variation in animal resource use may be a crucial driver of spatial patterns in the functional structure of diversified species assemblages also in other types of ecological networks.
DOI: 10.12761/sgn.2015.2
title: Morphological traits determine specialization and resource use in plant-hummingbird networks in the neotropics

description: Ecological communities are organized in complex ecological networks. Trait-based analyses of the structure of these networks in highly diversified species assemblages are crucial for improving our understanding of the ecological and evolutionary processes causing specialization in mutualistic networks. In this study, we assessed the importance of morphological traits for structuring plant-hummingbird networks in Neotropical forests by using a novel combination of quantitative analytical approaches. We recorded the visitation of hummingbirds to plant species over an entire year at three different elevations in Costa Rica and constructed quantitative networks based on interaction frequencies. Three morphological traits were measured in hummingbirds (bill length, bill curvature, and body mass) and plants (corolla length, curvature, and volume). We tested the effects of avian morphological traits and abundance on ecological specialization of hummingbird species. All three morphological traits of hummingbirds were positively associated with ecological specialization, especially bill curvature. We tested whether interaction strength in the networks was associated with the degree of trait matching between corresponding pairs of morphological traits in plant and hummingbird species and explore whether this was related to resource handling times by hummingbird species. We found strong and significant associations between interaction strength and the degree of trait matching. Moreover, the degree of trait matching, particularly between bill and corolla length, was associated with the handling time of nectar resources by hummingbirds. Our findings show that bill morphology structures tropical plant-hummingbird networks and patterns of interactions are closely associated with morphological matches between plant and bird species and the efficiency of hummingbirds' resource use. These results are consistent with the findings of seminal studies in plant-hummingbird systems from the neotropics. We conclude that trait-based analyses of quantitative networks contribute to a better mechanistic understanding of the causes of specialization in ecological networks and could be valuable for studying processes of complementary trait evolution in highly diversified species assemblages.
DOI: 10.12761/sgn.2015.4
title: FastQFS A Tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing

description: Next generation sequencing (NGS) technologies generate huge amounts of sequencing data. Several microbial genome projects, in particular fungal whole genome sequencing, have used NGS techniques, because of their cost efficiency. However, NGS techniques also demand for computational tools to process and analyze massive datasets. Implementation of few data processing steps, including quality and length filters, often leads to a remarkable improvement in the accuracy and quality of data analyses. Choosing appropriate parameters for this purpose is not always straightforward, as these will vary with the dataset. In this study we present the FastQFS (Fastq Quality Filtering and Statistics) tool, which can be used for both read filtering and filtering parameters assessment. There are several tools available, but an important asset of FastQFS is that it provides the information of filtering parameters that fit best to the raw dataset, prior to computationally expensive filtering. It generates statistics of reads meeting different quality and length thresholds, and also the expected coverage depth of the genome which would be left after applying different filtering parameters. The FastQFS tool will help researchers to make informed decisions on NGS reads filtering parameters, avoiding time-consuming optimization of filtering criteria.
DOI: 10.12761/sgn.2015.5
title: Model results for DFG Project: WE4519/1-1: N trace gas emissions from tropical savanna ecosystems and responses to global changes

description: LandscapeDNDC simulation results for the years 1960-2100 for tropical savanna of Australia. DFG Projekt 4519/1-1, Christian Werner. Data is provided as daily, yearly and decadal netCDF files with a resolution of 0.16x0.16 degrees.
DOI: 10.12761/sgn.2015.6
title: Comparative genomics including the early-diverging smut fungus Ceraceosorus bombacis reveals signatures of parallel evolution within plant and animal pathogens of fungi and oomycetes

description: Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, genome of Ce. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 megabases encodes for 8024 proteins, of which 576 are putative secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in Ce. bombacis compared to other Ustilaginomycotina genomes. Metabolic pathway analyses reveal the absence of genes encoding for nitrite and nitrate reductase in the genome of human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, but only nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed in obligate biotrophs and hemi-biotrophs of fungal and oomycete pathogens. Furthermore, it was also found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories within smuts, but also among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
DOI: 10.12761/sgn.2015.7
title: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Background Downy mildews are the most specious group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. Results Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the dEER-motif in effector translocation. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolutionary trajectories of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. Conclusions The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.