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DNA metabarcoding data of arthropods captured with different traps in the southwestern German agricultural landscape

<p>The dataset contains data on arthropods which was derived from DNA metabarcoding. The DNA metabarcoding was performed for samples from coloured canopy Malaise traps, caterpillar traps, branch sampling and blue and white pan traps. The traps were selected to capture predominantly flying insects, especially butterflies and hoverflies. They were placed as a defined set in four different habitat types: 'Forest (Beech and oak)', 'Centre of a short rotation coppice', 'Margin of a short rotation coppice' and 'Maize field'. There existed three replicates of each habitat type. The coloured canopy Malaise traps were equipped with blue, yellow and white cotton cloth panels (50 x 35 cm) and hung in a wooden frame four metres above ground. The caterpillar traps consisted of a dark-green plastic tarpaulin, which was stretched between trees and tapered towards the ground. At its lowest point, insects were collected with a capture bottle, which was attached to the tarpoulin with a fine gauze. The branch sampling was conducted by tabbing 100 tree branches and shaking ten trees at each site. In the corn fields, the shaking was replaced by another interval of tabbing. The blue and white pan traps were placed next to each other on a wooden table, one metre above ground. The pans were enlarged at the top with fine gauze to prevent from overfloating in the case of rain. All insects were captured and stored in 96.6% ethanol. The traps were operated in 15-day sampling intervals, each in June, July and August 2021. For DNA metabarcoding, the samples of each sampling interval and method were compiled. The DNA metabarcoding was performed following the method of Hausmann et al (2020): 'Toward a standardized quantitative and qualitative insect monitoring scheme. Ecology and Evolution, 10, 4009–4020'. Briefly, a lysis volume of 5-10 ml of the dried and homogenized composite samples was used for DNA extraction. The mitochondrial Cytochrome c Oxidase subunit I gene (COI) was amplified for species identification (see Leray et al. (2013): 'A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology, 10, 34' and Morinière et al. (2016): 'Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix. PLOS ONE, 11, e0155497'. The resulting metabarcoding data contains the OTU sequences from the samples and their corresponding identities from the Barcode of Life database (BOLD, Ratnasingham and Hebert 2007), the database of the National Center for Biotechnology Information (NCBI) and the Ribosomal Database Project (RDP) classifier. For the two databases, the overlap between the OTU sequence and the database entry determined the determination depth (97-100%: species, 95-97%: genus; 90-95%. family, 85-90%: order, 80-85%: class, 75-80%: phylum, &lt;75%: domain). Each taxonomic determination level of the RDP-classifier is additionally displayed with a bootstrap value. The table also provides data on the red list Germany and Bavaria for each entry.</p><p>The dataset is used in: Hoffmann, L. &amp; Stoll, S. (2025) Catch effectiveness, complementarity and costs of five sampling techniques for flying insects across different land use types. Insect Conservation and Diversity, 1–12. Available from: https://doi.org/10.1111/icad.12839</p>

DNA metabarcoding data of arthropods collected in different life stages of short rotation coppices (SRC)

<p>The dataset comprises presence data of arthropods, but also on the groups 'Annelida', 'Bacillariophyta', 'Ascomycota', 'Basidiomycota', 'Bryozoa', 'Chordata', 'Cnidaria', 'Echinodermata', 'Glomeromycota', 'Haptophyta', 'Mollusca', 'Mucoromycota', 'Nematoda', 'Nemertea', 'Ochrophyta', 'Oomycota', 'Porifera', 'Pseudomonadota', 'Rhodophyta', 'Rotifera' and 'Tardigrada'. The arthropods were collected in four different life stages of short rotation coppices (harvested, young (2 years), mature (3 years) and old (4 years)) using 3 different trapping techniques: branch sampling (BS), coloured canopy Malaise traps (MT) and pitfall traps (PIT). In each life stage, three sets of traps were placed (3 sites per life stage) and activated for two weeks, each in May, June, July and August. Once in a month, a branch sampling was conducted. In the branch sampling, 16 trees within a radius of 20m around the canopy Malaise traps were randomly selected and shaken for 10 s. Arthropods fell on a plastic tarpaulin of 1x1 m that was emptied into a collection bottle where the arthropods were stored in 96.7% ethanol.</p><p>The samples were analysed using DNA metabarcoding. In DNA metabarcoding, the Cytochrome Oxidase I-Region was targeted using the primers fwhF2 (forward) and fwhR2n (reverse) from Vamos et al 2017 (https://doi.org/10.3897/mbmg.1.14625) The sequences found in the samples were matched with sequences in the BOLD database. The sequences displayed are already grouped like it is known from OTUs. For this grouping, all sequences with a similarity of 97% were compiled, which means that the grouped sequences finally comprise different genetic variants of the same taxa. For each hit in the database, a plausibility check was performed by comparing the distribution range of a species (calculated from GBIF coordinates) and the trapping locations. For each detection of a sequence in a sample, the number of reads is also given. A flagging system helps the user to estimate the degree of uncertainty arising from each species hit.</p><p>This data and the data in the datasets "https://doi.org/10.15468/9pzhm6" and "https://doi.org/10.15468/9pzhm6" belongs to one study.</p>

DNA metabarcoding data of arthropods from lower mountain range regions in southwest Germany

<p>The dataset comprises presence data on arthropods, but also on the groups 'Annelida', 'Ascomycota', 'Basidiomycota', 'Mollusca', 'Mucoromycota', 'Nematoda' and 'Proteobacteria'. For each detection of an Observational Taxonomic Unit (OTU), the number of reads is also given, as well as further information about the species assigned. The species information was derived from a comparison of the detected DNA sequences with the BOLD database and the database of the National Center for Biotechnology Information (NCBI). Further, the Ribosomal Database Project (RDP) classifier was used to identify species. A consensus taxonomy compiles the species information dervied from the different databases and ranks the results according to their validity by using labels from A to C (Information on A, B, and C given at the description of the variables). The DNA metabarcoding process is decribed in detail in Uhler et al (2021): Relationship of insect biomass and richness with land use along a climate gradient (https://www.nature.com/articles/s41467-021-26181-3#Sec10 ). Since the samples were devided into large and small subsamples to improve the metabarcoding results, the data is given for each of the subsamples separately. The samples that went through DNA metabarcoding were derived from a Malaise trap experiment, for which five different types of Malaise traps were placed on a meadow and a forest clearing site each in three regions of southwest Germany (Nationalpark Hunsrück-Hochwald, Rhine-Main-Observatory, Steigerwald). The sites in the Hunsrück and the Rhine-Main-Observatory are part of the Long-term Ecological Research Network Germany (LTER-D). </p>

Indian Ocean Islands - Historic Freshwater Insect Taxa

Species occurrence records for freshwater aquatic insect taxa namely the EPT (Ephemeroptera, Plecoptera, Trichoptera) as well as freshwater diatom taxa from the Indian Ocean Islands (Madagascar, Mauritius, Seychelles). The species records have been collated from existing historical museum records and collections as well as from published scientific literature sources. The data set is a work in progress and more data will be added to it over time. The focus initially will be on Madagascar, followed by the smaller islands in no particular order. Detailed metadata can be found in the Freshwater Metadatabase (http://data.freshwaterbiodiversity.eu/metadb/bf_mdb_view.php?entryID=FAI_1).

Terrestrial Mollusca of Cuc Phuong National Park, Vietnam – Results from the 2019 VIETBIO inventory work. Collection data

Collection data of terrestrial Mollusca from the 2019 VIETBIO inventory work in Cuc Phuong National Park, Vietnam.

KSA Flora Survey 2013

Over 1000 stands from 10 major habitats in four regions in Saudi Arabia were surveyed to have a preliminary observation on the impact of invasive species. Vascular plants was recorded from 50 50 m2 quadrats belonging to infested localities across the Kingdom.

Updates on the taxonomy of the Neoserica calva group from continental Southeast Asia (Coleoptera, Scarabaeidae, Sericinae)

<p>Distribution data of a taxonomic revision (Neoserica calva group)</p>

An integrative taxonomy of cryptic Pachypus chafers

<p>The data set contains distribution data from an integrative taxonomic revision for the genus Pachypus Dejean, 1821, published in Scientific Reports (Title: An integrative taxonomy of cryptic Pachypus chafers using museomics, morphometrics, barcoding, and genomic DNA analysis (Coleoptera: Scarabaeidae: Pachypodinae)). </p>

SMNS Herpetologie

The herpetological collection at the SMNS comprises about 20,000 specimens from all over the world. Some of the material is historically valuable. After Baron Carl Ferdinand von Ludwig (1784-1847) and Duke Paul Wilhelm von Württemberg (1797-1860) had added their specimens, the herpetological collection grew further through material collected by Baron F. von Müller (collected between 1836-1896) and August Kappler (collected between 1832-1872). More detailed information is published in the type catalogue, that can be obtained from the curator. Important parts of the collection are tortoise, crocodiles and neotropical amphibians.<br><br> Through destruction of parts of the collection during the Second World War important information has been lost. It was necessary to reorganise and record the entire collection. In addition to collection-based research, studies on the ecology of South American frogs, toads and reptiles are conducted. Our knowledge of species composition and ecology of rainforests contrasts sharply with the speed that these habitats vanish from our planet. The analysis of such complex ecosystems can only be achieved step by step by looking at smaller systems within larger ones. In cooperation with the Natural History Museum at Lima (Museo de Historia Natural de la Universidad San Marcos), species composition and ecology of amphibians and reptiles in small pools within the Peruvian rainforest have been under investigation since 1977. These pools and streams are such 'smaller systems' that at least, on a temporary basis, offer ideal conditions to many species. A massive undertaking is to find out more about the food chains in these habitats. Most amphibians and reptiles are very sensitive to environmental change and are often at the centre of the food chain which makes them perfect indicators of an ecosystem. The identification of frogs and toads is often done by recording their call and subsequent analysis of the tapes which result in sonograms. On the other hand, to identify snakes, lizards and crocodiles it is often necessary to count rows of scales and for some species you have to look at their teeth with magnifying glass. This is of course difficult with wriggly, living and often poisonous animals and it is often easier to identify those as part of a scientific collection. Some of the specimens preserved in alcohol are over 200 years old and are used for taxonomic research as well as being available for the international research community. The entire collection is inventoried on a computer database.

GBOL Lonchaeidae

This dataset consist of the corresponding Lonchaeidae specimen data of Reimann &amp; Rulik (2024) out of the GBOL project. see for details: Reimann, A. &amp; Rulik, B. (2024): The Lonchaeidae (Diptera) of the GBOL project, with the description of a new Priscoearomyia species. Contributions to Entomology 74(2): 165-179. https://doi.org/10.3897/contrib.entomol.74.e127094

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