| 1. |
- Atherton, Sarah, et al.
(författare)
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Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding
- 2020
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Ingår i: Biodiversity Data Journal. - : Sarah Atherton. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm3 sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.
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| 2. |
- Audisio, Paolo, et al.
(författare)
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Fauna Europaea : Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea)
- 2015
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Fauna Europaea provides a public web-service with an index of scientific names (including synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Coleoptera represent a huge assemblage of holometabolous insects, including as a whole more than 200 recognized families and some 400,000 described species worldwide. Basic information is summarized on their biology, ecology, economic relevance, and estimated number of undescribed species worldwide. Little less than 30,000 species are listed from Europe. The Coleoptera 2 section of the Fauna Europaea database (Archostemata, Myxophaga, Adephaga and Polyphaga excl. the series Elateriformia, Scarabaeiformia, Staphyliniformia and the superfamily Curculionoidea) encompasses 80 families (according to the previously accepted family-level systematic framework) and approximately 13,000 species. Tabulations included a complete list of the families dealt with, the number of species in each, the names of all involved specialists, and, when possible, an estimate of the gaps in terms of total number of species at an European level. A list of some recent useful references is appended. Most families included in the Coleoptera 2 Section have been updated in the most recent release of the Fauna Europaea index, or are ready to be updated as soon as the FaEu data management environment completes its migration from Zoological Museum Amsterdam to Berlin Museum fur Naturkunde.
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| 3. |
- Brown, Brian, et al.
(författare)
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A new white-spotted Megaselia Rondani (Diptera: Phoridae) from western North America
- 2019
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background The phorid fly genus Megaselia Rondani is a large, poorly-known taxon whose species are found worldwide. New information A new species of Megaselia Rondani, M. simunorum, is described from both urban and rural sites in southern California. With a large area of white colour on the posterior part of the abdominal dorsum, it closely resembles the much more common species M. sulphurizona, but M. simunorum has distinctly thicker ventral setae on the abdomen and a differently-shaped white spot.
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| 4. |
- de Jong, Yde, et al.
(författare)
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PESI - a taxonomic backbone for Europe
- 2015
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 3, s. 1-51
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Tidskriftsartikel (refereegranskat)abstract
- Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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| 5. |
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| 6. |
- Haemig, Paul D, et al.
(författare)
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Ecology and phylogeny of birds foraging at outdoor restaurants in Sweden
- 2015
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Birds frequently visit the outdoor serving areas of restaurants to feed on scraps of food and leftovers. Although this feeding association between humans and birds is widespread and could have significant effects, both positive and negative, for all taxa involved, the authors know of no published studies that have investigated restaurant bird communities. To lay the foundation for future research, the authors conducted a basic study of birds at 80 outdoor restaurants in Sweden, identifying which species and taxonomic clades of birds visited the restaurants and comparing restaurant birds in urban and rural environments. New information: Thirteen species of birds visited the outdoor restaurants. Eight of these species were predominant, i.e. accounting for 51% or more of bird presence (sum of minutes of all individual birds) at one or more restaurants. Every restaurant studied had a predominant species, but species often differed from each other in frequency of predominance in different landscapes. No endangered species were seen visiting restaurants. However, three farmland bird species (House Sparrow Passer domesticus, White Wagtail Motacilla alba, Eurasian Tree Sparrow Passer montanus), whose numbers are reported to be declining in the countryside, were predominant at the majority of restaurants in rural areas, suggesting that rural restaurants might be able to contribute to the conservation of these species. The thirteen species of restaurant-visiting birds belonged to five monophyletic clades. Ninety percent of all restaurants had, as their predominant species, birds from either Clade A (Passeridae, Motacillidae, Fringillidae) or Clade C (Corvidae). Statistical testing revealed that Clade A and Clade C were distributed differently in environments along the urban-rural gradient. At all spatial scales measured, birds of Clade C were predominant at the majority of restaurants in urban areas, while birds of Clade A were the predominant clade at the majority of restaurants in rural areas. The authors use this evidence, and observations of birds foraging in association with other primates, to hypothesize that the outdoor serving areas of modern restaurants may be helping to preserve and nurture ancient human-bird symbioses that have been part of human ecology since antiquity.
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| 7. |
- Haenel, Quiterie, et al.
(författare)
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NGS-based biodiversity and community structure analysis of meiofaunal eukaryotes in shell sand from Hållö island, Smögen, and soft mud from Gullmarn Fjord, Sweden
- 2017
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Ingår i: Biodiversity Data Journal. - : Oleksandr Holovachov. - 1314-2828 .- 1314-2836. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- © Haenel Q et al. Aim: The aim of this study was to assess the biodiversity and community structure of Swedish meiofaunal eukaryotes using metabarcoding. To validate the reliability of the metabarcoding approach, we compare the taxonomic resolution obtained using the mitochondrial cytochrome oxidase 1 (COI) 'mini-barcode' and nuclear 18S small ribosomal subunit (18S) V1-V2 region, with traditional morphology-based identification of Xenacoelomorpha and Nematoda. Location: 30 samples were analysed from two ecologically distinct locations along the west coast of Sweden. 18 replicate samples of coarse shell sand were collected along the northeastern side of Hållö island near Smögen, while 12 replicate samples of soft mud were collected in the Gullmarn Fjord near Lysekil.
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Holovachov, Oleksandr
(författare)
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Nematodes from terrestrial and freshwater habitats in the Arctic
- 2014
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 2:e1165
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Forskningsöversikt (refereegranskat)abstract
- We present an updated list of terrestrial and freshwater nematodes from all regions of the Arctic, for which records of properly identified nematode species are available: Svalbard, Jan Mayen, Iceland, Greenland, Nunavut, Northwest territories, Alaska, Lena River estuary, Taymyr and Severnaya Zemlya and Novaya Zemlya. The list includes 391 species belonging to 146 genera, 54 families and 10 orders of the phylum Nematoda.
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| 12. |
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| 13. |
- Humala, Andrei E, et al.
(författare)
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Ichneumonidae (Hymenoptera) species new to the fauna of Norway.
- 2014
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; :2, s. e1047-
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Tidskriftsartikel (refereegranskat)abstract
- The present paper contains new distributional records for 61 species of ichneumon wasps (Hymenoptera, Ichneumonidae) previously unknown for Norway, six of them are reported from Scandinavia for the first time.
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| 14. |
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| 15. |
- Karlsson, Dave, et al.
(författare)
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The data of the Swedish Malaise Trap Project, a countrywide inventory of Sweden's insect fauna
- 2020
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Despite Sweden's strong entomological tradition, large portions of its insect fauna remain poorly known. As part of the Swedish Taxonomy Initiative, launched in 2002 to document all multi-cellular species occurring in the country, the first taxonomically-broad inventory of the country's insect fauna was initiated, the Swedish Malaise Trap Project (SMTP). In total, 73 Malaise traps were deployed at 55 localities representing a wide range of habitats across the country. Most traps were run continuously from 2003 to 2006 or for a substantial part of that time period. The total catch is estimated to contain 20 million insects, distributed over 1,919 samples (Karlsson et al. 2020). The samples have been sorted into more than 300 taxonomic units, which are made available for expert identification. Thus far, more than 100 taxonomists have been involved in identifying the sorted material, recording the presence of 4,000 species. One third of these had not been recorded from Sweden before and 700 have tentatively been identified as new to science.Here, we describe the SMTP dataset, published through the Global Biodiversity Information Facility (GBIF). Data on the sorted material are available in the "SMTP Collection Inventory" dataset. It currently includes more than 130,000 records of taxonomically-sorted samples. Data on the identified material are published using the Darwin Core standard for sample-based data. That information is divided up into group-specific datasets, as the sample set processed for each group is different and in most cases non-overlapping. The current data are divided into 79 taxonomic datasets, largely corresponding to taxonomic sorting fractions. The orders Diptera and Hymenoptera together comprise about 90% of the specimens in the material and these orders are mainly sorted to family or subfamily. The remaining insect taxa are mostly sorted to the order level. In total, the 79 datasets currently available comprise around 165,000 specimens, that is, about 1% of the total catch. However, the data are now accumulating rapidly and will be published continuously. The SMTP dataset is unique in that it contains a large proportion of data on previously poorly-known taxa in the Diptera and Hymenoptera.
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| 16. |
- Karlsson, Dave, et al.
(författare)
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The Swedish Malaise Trap Project: a 15 year retrospective on a countrywide inventory.
- 2020
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The Swedish Malaise Trap Project (SMTP) is one of the most ambitious insect inventories ever attempted. The project was designed to target poorly known insect groups across a diverse range of habitats in Sweden. The field campaign involved the deployment of 73 Malaise traps at 55 localities across the country for three years (2003-2006). Over the past 15 years, the collected material has been hand sorted by trained technicians into over 300 taxonomic fractions suitable for expert attention. The resulting collection is a tremendous asset for entomologists around the world, especially as we now face a desperate need for baseline data to evaluate phenomena like insect decline and climate change. Here, we describe the history, organisation, methodology and logistics of the SMTP, focusing on the rationale for the decisions taken and the lessons learned along the way. The SMTP represents one of the early instances of community science applied to large-scale inventory work, with a heavy reliance on volunteers in both the field and the laboratory. We give estimates of both staff effort and volunteer effort involved. The project has been funded by the Swedish Taxonomy Initiative; in total, the inventory has cost less than 30 million SEK (approximately 3.1 million USD). Based on a subset of the samples, we characterise the size and taxonomic composition of the SMTP material. Several different extrapolation methods suggest that the material comprises around 20 million specimens in total. The material is dominated by Diptera (75% of the specimens) and Hymenoptera (15% of specimens). Amongst the Diptera, the dominant groups are Chironomidae (37% of specimens), Sciaridae (15%), Phoridae (13%), Cecidomyiidae (9.5%) and Mycetophilidae (9.4%). Within Hymenoptera, the major groups are Ichneumonidae (44% of specimens), Diaprioidea (19%), Braconidae (9.6%), Platygastroidea (8.5%) and Chalcidoidea (7.9%). The taxonomic composition varies with latitude and season. Several Diptera and Hymenoptera groups are more common in non-summer samples (collected from September to April) and in the North, while others show the opposite pattern. About 1% of the total material has been processed and identified by experts so far. This material represents over 4,000 species. One third of these had not been recorded from Sweden before and almost 700 of them are new to science. These results reveal the large amounts of taxonomic work still needed on Palaearctic insect faunas. Based on the SMTP experiences, we discuss aspects of planning and conducting future large-scale insect inventory projects using mainly traditional approaches in relation to more recent approaches that rely on molecular techniques.
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| 17. |
- Leidenberger, Sonja, et al.
(författare)
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Host records and geographical distribution of Corynosoma magdaleni, C. semerme and C. strumosum (Acanthocephala: Polymorphidae)
- 2020
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- A literature survey was conducted to investigate the host and geographical distribution patterns of three Corynosoma species (Acanthocephala: Polymorphidae), viz. C. magdaleni, C. semerme and C. strumosum. All three species appear to be restricted to the Northern Hemisphere. Occurrence records of C. magdaleni are limited to the Northern Atlantic coasts, while C. semerme has a circumpolar distribution. The geographical range of Corynosoma strumosum encompasses the distributions of the other two species, but also extends into warmer southern regions. Some Corynosoma populations are living with their definitive hosts in very isolated locations, such as in the brackish Baltic Sea or different freshwater lakes (e.g. Lake Saimaa). All three species have a heteroxenous life cycle, comprising a peracaridan intermediate host, a fish paratenic host and a mammalian definitive host. Occasionally, an acanthocephalan may enter an accidental host, from which it is unable to complete its life cycle. The host records reported here are categorised by type, i.e. intermediate, paratenic, definitive or accidental. While most of the definitive hosts are shared amongst the three Corynosoma species, C. strumosum showed the broadest range of paratenic hosts, which reflects its more extensive geographical distribution. One aim of this study and extensive literature summary is to guide future sampling efforts therewith contribute to throw more light on the on-going species and morphotype discussion for this interesting parasite species.
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| 18. |
- Leidenberger, Sonja, et al.
(författare)
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The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research
- 2016
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Ingår i: Biodiversity Data Journal. - : Pensoft Publishers. - 1314-2836 .- 1314-2828. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Background During the last years, more and more online portals were generated and are now available for ecologists to run advanced models with extensive data sets. Some examples are the Biodiversity Virtual e-Laboratory (BioVel) Portal (https://portal.biovel.eu) for ecological niche modelling and the Mobyle SNAP Workbench (https://snap.hpc.ncsu.edu) for evolutionary and population genetics analysis. Such portals have the main goal to facilitate the run of advanced models, through access to large-capacity computers or servers. In this study, we present the Analysis Portal (www.analysisportal.se), which is a part of the Swedish LifeWatch e-infrastructure for biodiversity research that combines a variety of Swedish web services to perform different kinds of dataprocessing. New information For the first time, the Swedish Analysis Portal for integrated analysis of species occurrence data is described in detail. It was launched in 2013 and today, over 60 Million Swedish species observation records can be assessed, visualized and analyzed via the portal. Datasets can be assembled using sophisticated filtering tools, and combined with environmental and climatic data from a wide range of providers. Different validation tools, for example the official Swedish taxon concept database Dyntaxa, ensure high data quality. Results can be downloaded in different formats as maps, tables, diagrams and reports.
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| 19. |
- Mathew, Cherian, et al.
(författare)
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A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control
- 2014
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 2:e4221, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.
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| 20. |
- Mitroiu, Mircea-Dan, et al.
(författare)
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Fauna Europaea: Hymenoptera - Apocrita (excl. Ichneumonoidea).
- 2015
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Ingår i: Biodiversity data journal. - 1314-2828 .- 1314-2836. ; :3
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Tidskriftsartikel (refereegranskat)abstract
- Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, 'Hymenoptera - Apocrita (excluding Ichneumonoidea)' comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.
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| 21. |
- Reshchikov, Alexey
(författare)
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New species of Lathrolestes Förster (Hymenoptera : Ichneumonidae) from Côte d'Ivoire.
- 2013
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; :1, s. e1005-
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Tidskriftsartikel (refereegranskat)abstract
- Lathrolestesivoriensis sp. n. is described from Côte d'Ivoire. This is the second record of the genus from the Afrotropical region and the first record of the genus and the subfamily for the country. Illustrated re-description of Lathrolestesruwenzoricus (Benoit, 1955) is also provided.
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| 22. |
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| 23. |
- Retter, Alice, et al.
(författare)
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Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding
- 2019
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Ingår i: Biodiversity Data Journal. - 1314-2828 .- 1314-2836. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. New information The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description.
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| 24. |
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| 25. |
- Stålstedt, Jeanette, et al.
(författare)
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Checklist of terrestrial Parasitengona mites in Fennoscandia with new species- and distribution records (Acariformes: Prostigmata)
- 2019
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The knowledge of terrestrial Parasitengona in Fennoscandia lies far behind that of their aquatic counterparts, the water mites (Hydrachnidia). Based on new inventories, we provide primary data and an annotated checklist of terrestrial Parasitengona in Fennoscandia including 107 species. Out of these, nineteen species are new findings for the region and five are species potentially new for science. Twenty-three species are new for Norway, fourteen for Finland and eleven for Sweden. The known recorded fauna today of terrestrial Parasitengona is 80 species for Norway, 54 for Sweden and 48 for Finland. Primary data include georeferenced locality data as well as collecting techniques and microhabitat to increase the knowledge on species' habitat requirements.
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| 26. |
- Vasconcelos, Sasha
(författare)
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The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths
- 2024
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Ingår i: Biodiversity data journal. - 1314-2836 .- 1314-2828. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. New information The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).
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| 27. |
- Anton, Victor, et al.
(författare)
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An open-source, citizen science and machine learning approach to analyse subsea movies
- 2021
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background The increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that= are efficient, publicly available and easy to use. Such tools are starting to be developed for wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research. New information This paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.
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| 28. |
- Berov, D., et al.
(författare)
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Current distribution of Zostera seagrass meadows along the Bulgarian Black Sea coast (SW Black Sea, Bulgaria) (2010-2020)
- 2022
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Background The current distribution of Zostera spp. seagrass meadows along the Bulgarian Black Sea coast was studied. We used a combination of historical and recent observations of the habitat along the studied coastline. Remote sensing data (satellite images, sonar sidescans) was groundtruthed with georeferenced drop camera observations, scuba diving sampling and georeferenced scuba diving photo and video transects. New information Тhe total area of the habitat type ‘MB548 - Black Sea seagrass meadows on lower infralittoral sands’ (EUNIS habitat type list 2019) in the study area is 916.9 ha, of which only 17.9 ha are in man-made sheltered environments (harbours). All seagrass meadows identified in 1978-79 were also located during the current survey, despite the increased eutrophication pressure and overall degradation of benthic habitats in the western Black Sea during the 1980s and early 1990s. © Berov D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 29. |
- Citeli, N., et al.
(författare)
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Snake richness in urban forest fragments from Niterói and surroundings, state of Rio de Janeiro, southeastern Brazil
- 2016
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Background The Atlantic Forest is a hotspot for biodiversity, an area which houses high species richness and endemism, but with high level of threat. With reference to the herpetofauna, until recently there has been no detailed information regarding diversity of snakes recorded in the Atlantic Forest, the number of endemic species and their distribution ranges. While these basic data were missing, large areas of original forest have continued to be lost to increased urbanization and human population, representing a severe threat to the biodiversityNew information We recorded 28 snake species in our study area. Dipsadidae was the richest family with 14 species, followed by Colubridae (eight species), Boidae (two species), Viperidae (two species), and Anomalepididae, Elapidae and Typhlopidae (one species each). Most species were forest inhabitants (61%), of which 13 are endemic to the Atlantic Forest. There were no clearly defined species clusters regarding species composition. None of the species recorded in Niterói are listed as threatened in the Brazilian Redlist. However, most of them are strongly associated with forested areas and, perhaps, are not adapted to live in small fragments. Thus, more initiatives should be implemented to evaluate the true conservation status of these species in order to better protect them. © Citeli N et al.
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| 30. |
- Dahlgren, Thomas G., 1963, et al.
(författare)
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Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Cnidaria
- 2016
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 4:e9277
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Tidskriftsartikel (refereegranskat)abstract
- We present data from a DNA taxonomy register of the abyssal Cnidaria collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise ‘AB01’ to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration area ‘UK-1’ in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. This is the second paper in a series to provide regional taxonomic data for a region that is undergoing intense deep-sea mineral exploration for high-grade polymetallic nodules. Data were collected from the UK-1 exploration area following the methods described in Glover et al. (2015b).
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| 31. |
- Forshage, Mattias, et al.
(författare)
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Checklist of British and Irish Hymenoptera - Cynipoidea.
- 2017
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Ingår i: Biodiversity data journal. - 1314-2828. ; :5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The British and Irish checklist of Cynipoidea is revised, considerably updating the last complete checklist published in 1978. Disregarding uncertain identifications, 220 species are now known from Britain and Ireland, comprising 91 Cynipidae (including two established non-natives), 127 Figitidae and two Ibaliidae.NEW INFORMATION: One replacement name is proposed, Kleidotoma thomsoni Forshage, for the secondary homonym Kleidotoma tetratoma Thomson, 1861 (nec K. tetratoma (Hartig, 1841)).
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| 32. |
- Glover, Adrian G, et al.
(författare)
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Abyssal fauna of the UK-1 polymetallic nodule exploration claim, Clarion-Clipperton Zone, central Pacific Ocean: Echinodermata.
- 2016
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Ingår i: Biodiversity data journal. - 1314-2828. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- We present data from a DNA taxonomy register of the abyssal benthic Echinodermata collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise 'AB01' to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration claim 'UK-1' in the eastern Clarion-Clipperton Zone (CCZ), central Pacific Ocean abyssal plain. Morphological and genetic data are presented for 17 species (4 Asteroidea, 4 Crinoidea, 2 Holothuroidea and 7 Ophiuroidea) identified by a combination of morphological and genetic data. No taxa matched previously published genetic sequences, but 8 taxa could be assigned to previously-described species based on morphology, although here we have used a precautionary approach in taxon assignments to avoid over-estimating species ranges. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.
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| 33. |
- Murillo-Ramos, Leidys, et al.
(författare)
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A database and checklist of geometrid moths (Lepidoptera) from Colombia
- 2021
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 9, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- Background Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs - Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015–2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only.
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| 34. |
- Norris, Daniel H., et al.
(författare)
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On the diversity and richness of understory bryophytes at Nectandra Cloud Forest Reserve, Costa Rica
- 2017
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Background A survey of the understory bryophytes in the Nectandra Cloud Forest Preserve yielded 1083 specimens distributed among 55 families, represented by 74 genera of mosses, 75 genera of liverworts and 3 of hornworts. We studied and analyzed the bryophytic distribution on six types of substrates: 1) corticolous, 2) epiphyllous, 3) saxicolous, 4) terricolous, 5) aquatic and 6) lignicolous. The richness and composition of bryophyte genera are compared to those of other previous bryophyte surveys from 4 other sites with different oceanic exposures, climatic and geographic conditions in Costa Rica. New information This is a report of the first extensive general survey of bryophytes at the Nectandra Reserve, a premontane cloud forest located on the Atlantic slope of Costa Rica, an area much less studied compared to the Monteverde cloud forest on the Pacific slope.
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| 35. |
- Oskyrko, Oleksandra, et al.
(författare)
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Unravelling the origin of the common wall lizards (Podarcis muralis) in south-eastern Europe using mitochondrial evidence
- 2022
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The origin of the common wall lizards (Podarcis muralis) populations in south-eastern Europe (namely in Bulgaria and Romania), representing the north-eastern range border of this species, was addressed using mitochondrial DNA. We compared cytochrome b sequences from Bulgaria and Romania with those from the contiguous range in Central Europe that are available from previous studies. We recorded five main haplogroups in Bulgaria and Romania, belonging to the Central Balkan clade. However, haplogroup III was recorded in more localities than previously found. Additionally, signs of haplotype admixture were identified in several populations along the Danube River. The presence of the Southern Alps haplotype in one population from Otopeni, Bucharest (Romania) and its close phylogenetic relationships to north Italy populations suggests human-mediated introductions of this wall lizard clade in Romania. Our results confirm that P.
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| 36. |
- Ribeiro, C. V. R., et al.
(författare)
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UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)
- 2021
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. New information We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs. © 2021. Ribeiro C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 37. |
- Roslin, Tomas
(författare)
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Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve
- 2015
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundComprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada.New informationThe existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.
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| 38. |
- Ruete, Alejandro
(författare)
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Displaying bias in sampling effort of data accessed from biodiversity databases using ignorance maps
- 2015
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Ingår i: Biodiversity Data Journal. - 1314-2828. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background Open-access biodiversity databases including mainly citizen science data make temporally and spatially extensive species’ observation data available to a wide range of users. Such data have limitations however, which include: sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. These limitations are not always recorded, while any technical assessment or scientific research based on such data should include an evaluation of the uncertainty of its source data and researchers should acknowledge this information in their analysis. The here proposed maps of ignorance are a critical and easy way to implement a tool to not only visually explore the quality of the data, but also to filter out unreliable results. New information I present simple algorithms to display ignorance maps as a tool to report the spatial distribution of the bias and lack of sampling effort across a study region. Ignorance scores are expressed solely based on raw data in order to rely on the fewest assumptions possible. Therefore there is no prediction or estimation involved. The rationale is based on the assumption that it is appropriate to use species groups as a surrogate for sampling effort because it is likely that an entire group of species observed by similar methods will share similar bias. Simple algorithms are then used to transform raw data into ignorance scores scaled 0-1 that are easily comparable and scalable. Because of the need to perform calculations over big datasets, simplicity is crucial for web-based implementations on infrastructures for biodiversity information. With these algorithms, any infrastructure for biodiversity information can offer a quality report of the observations accessed through them. Users can specify a reference taxonomic group and a time frame according to the research question. The potential of this tool lies in the simplicity of its algorithms and in the lack of assumptions made about the bias distribution, giving the user the freedom to tailor analyses to their specific needs.
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| 39. |
- Wiklund, Helena, 1965, et al.
(författare)
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Checklist of newly-vouchered annelid taxa from the Clarion-Clipperton Zone, central Pacific Ocean, based on morphology and genetic delimitation
- 2023
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Ingår i: Biodiversity Data Journal. - 1314-2836. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background We present a checklist of annelids from recent United Kingdom Seabed Resources (UKSR) expeditions (Abyssal Baseline -ABYSSLINE project) to the eastern abyssal Pacific Clarion-Clipperton Zone (CCZ) polymetallic nodule fields, based on DNA species delimitation, including imagery of voucher specimens, Darwin Core (DwC) data and links to vouchered specimen material and new GenBank sequence records. This paper includes genetic and imagery data for 129 species of annelids from 339 records and is restricted to & COPY; Wiklund H et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. material that is, in general, in too poor a condition to describe formally at this time, but likely contains many species new to science. We make these data available both to aid future taxonomic studies in the CCZ that will be able to link back to these genetic data and specimens and to better underpin ongoing ecological studies of potential deep-sea mining impacts using the principles of FAIR (Findable, Accessible, Interoperable, Reusuable) data and specimens that will be available for all. New information We include genetic, imagery and all associated metadata in Darwin Core format for 129 species of annelids from the Clarion-Clipperton Zone, eastern abyssal Pacific, with 339 records.
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