549 results match your criteria Biodiversity data journal[Journal]


Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.

Biodivers Data J 2019 13;7:e33303. Epub 2019 Mar 13.

Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America Florida Museum of Natural History, University of Florida Gainesville, FL United States of America.

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. Read More

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http://dx.doi.org/10.3897/BDJ.7.e33303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426826PMC

Using Malaise traps for collecting Lepidoptera (Insecta), with notes on the preparation of Macrolepidoptera from ethanol.

Biodivers Data J 2019 20(7):e32192. Epub 2019 Feb 20.

Vietnam National Museum of Nature, VAST, Hanoi, Vietnam Vietnam National Museum of Nature, VAST Hanoi Vietnam.

The present paper deals with the potential of employing Malaise traps for collecting butterflies and moths for morphological analysis and presents a protocol for preparing Macrolepidoptera from Malaise trap samples that were preserved in ethanol. About 80 specimens of Lepidoptera, including Nymphalidae, Geometridae, Hesperiidae, Erebidae, Noctuidae, Pyralidae and Tortricidae, were mounted, following the protocol. All specimens with robust wings and contrasting wing patterns were well suited for the study of external morphology, regardless of the family. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426827PMC
February 2019

Connecting data and expertise: a new alliance for biodiversity knowledge.

Biodivers Data J 2019 8;7:e33679. Epub 2019 Mar 8.

VertNet, Bariloche, Argentina VertNet Bariloche Argentina.

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Read More

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http://dx.doi.org/10.3897/BDJ.7.e33679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420472PMC
March 2019
2 Reads

Stream benthic macroinvertebrates abundances over a 6-year monitoring period of an Italian glacier-fed stream.

Biodivers Data J 2019 6;7:e33576. Epub 2019 Mar 6.

Institute for Alpine Environment, EURAC Research, Bolzano, Italy Institute for Alpine Environment, EURAC Research Bolzano Italy.

Background: Aquatic macroinvertebrates are widely used as bioindicators for water quality assessments involving different kinds of disruptive factors, such as hydrological regime variations or pollutant spills. Recently, they demonstrated to be effective in monitoring effects of climate change in alpine stream and rivers. Indeed, since the distribution of macroinvertebrates in glacier-fed streams has been succesfully investigated and described by several authors, the discrepancy in presence/absence and quantity of specific taxa from the established models may represent an early warning of the effects of climatic changes occurring in alpine riverine ecosystems. Read More

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http://dx.doi.org/10.3897/BDJ.7.e33576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416225PMC

A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides.

Biodivers Data J 2019 1;7:e32342. Epub 2019 Mar 1.

Natural History Museum, London, United Kingdom Natural History Museum London United Kingdom.

The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Read More

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http://dx.doi.org/10.3897/BDJ.7.e32342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408422PMC
March 2019
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First record of Han & Klotz, 2015 (Decapoda, Atyidae) from the Ryukyu Islands, Japan.

Biodivers Data J 2019 1;7:e30507. Epub 2019 Mar 1.

Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Matsudo, Japan Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo Matsudo Japan.

Background: The freshwater shrimp, Han & Klotz, has been known only from Taiwan and Panay Island, Philippines.

New Information: An adult was collected from a river on Ishigaki Island, Ryukyu Islands, Japan. This is the first record of the species in Japan and the northernmost specimen-supported record to date. Read More

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http://dx.doi.org/10.3897/BDJ.7.e30507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408424PMC

An online global database of Hemiptera-Phytoplasma-Plant biological interactions.

Biodivers Data J 2019 26(7):e32910. Epub 2019 Feb 26.

Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America Illinois Natural History Survey, University of Illinois Champaign, Illinois United States of America.

Background: Phytoplasmas are phloem-limited plant pathogenic bacteria in the class Mollicutes transmitted by sap-feeding insect vectors of the Order Hemiptera. Vectors still have not yet been identified for about half of the 33 known phytoplasma groups and this has greatly hindered efforts to control the spread of diseases affecting important crops. Extensive gaps of knowledge on actual phytoplasma vectors and on the plant disease epidemiology prevent our understanding of the basic underlying biological mechanisms that facilitate interactions between insects, phytoplasmas and their host plants. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400871PMC
February 2019

A benchmark dataset of herbarium specimen images with label data.

Biodivers Data J 2019 8(7):e31817. Epub 2019 Feb 8.

Royal Botanic Gardens Kew, Surrey, United Kingdom Royal Botanic Gardens Kew Surrey United Kingdom.

Background: More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Read More

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http://dx.doi.org/10.3897/BDJ.7.e31817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396854PMC
February 2019
2 Reads

Reference DNA barcodes and other mitochondrial markers for identifying Caribbean Octocorals.

Biodivers Data J 2019 20(7):e30970. Epub 2019 Feb 20.

Smithsonian Tropical Research Institute, Balboa, Panama Smithsonian Tropical Research Institute Balboa Panama.

DNA barcoding is a useful tool for documenting the diversity of metazoans. The most commonly used barcode markers, 16S and COI, are not considered suitable for species identification within some "basal" phyla of metazoans. Nevertheless metabarcoding studies of bulk mixed samples commonly use these markers and may obtain sequences for "basal" phyla. Read More

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http://dx.doi.org/10.3897/BDJ.7.e30970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393399PMC
February 2019

The Lyell Collection at the Earth Sciences Department, Natural History Museum, London (UK).

Authors:
Consuelo Sendino

Biodivers Data J 2019 19(7):e33504. Epub 2019 Feb 19.

Natural History Museum, London, United Kingdom Natural History Museum London United Kingdom.

Background: This paper provides a quantitative and general description of the Lyell Collection kept in the Department of Earth Sciences at the Natural History Museum of London. This collection started to be built by the eminent British geologist Sir Charles Lyell (1797-1875) in 1846 when the first specimen reached the Museum. The last one entered in 1980 donated by one of Lyell's heirs. Read More

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http://dx.doi.org/10.3897/BDJ.7.e33504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391367PMC
February 2019

Sample checklist of Gastropoda and Bivalvia in Cham Islands, Vietnam.

Biodivers Data J 2019 19(7):e32930. Epub 2019 Feb 19.

Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay, Hanoi Vietnam.

Background: Cham Islands (Cu Lao Cham) is a group of 8 small islands in the Quang Nam province, Central Vietnam. There is only one study that mentioned the diversity of marine molluscs in this area. However, the data on species composition have not been digitised and not stored or shared for other purposes. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391368PMC
February 2019
2 Reads

New record of (Hymenoptera: Scelionidae) parasitising (Hemiptera: Pentatomidae) in the United States of America.

Biodivers Data J 2019 19(7):e30124. Epub 2019 Feb 19.

United States Department of Agriculture, Agricultural Research Service, Crop Protection & Management Research Laboratory, Tifton, GA, United States of America United States Department of Agriculture, Agricultural Research Service, Crop Protection & Management Research Laboratory Tifton, GA United States of America.

Background: A parasitoid wasp, Johnson, was recorded parasitising eggs of the invasive stink bug (Stål), in the United States. This is the first record of this species parasitising eggs of .

New Information: First record of parasitising eggs in the United States and first record of in Alabama. Read More

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http://dx.doi.org/10.3897/BDJ.7.e30124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391366PMC
February 2019
1 Read

Distribution and diversity patterns of herpetofauna in the Pantabangan-Carranglan Watershed, Nueva Ecija, Caraballo Mountain Range, Philippines.

Biodivers Data J 2019 14(7):e31638. Epub 2019 Feb 14.

Adjunct Faculty, Institute of Graduate Studies, University of the Philippines Los Baños, Los Baños, Laguna, Philippines Adjunct Faculty, Institute of Graduate Studies, University of the Philippines Los Baños Los Baños, Laguna Philippines.

The recent extensive survey conducted in the Pantabangan-Carranglan Watershed, located in the Caraballo Mountain Range during the rainy season (October to November) resulted in the recording of fifty-nine (59) species of amphibians and reptiles (17 frogs, 14 skinks, 3 agamids, 6 gekkonid lizards, 2 varanids and 17 snakes). Out of 59 species, 42 species were Philippine endemics and 25 species are recorded only from the Luzon faunal region. Habitat analysis and mapping showed seven habitat types including lowland dipterocarp forest, grassland, lower montane forest, upper montane forest, pine forest, agricultural areas and riparian habitats. Read More

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http://dx.doi.org/10.3897/BDJ.7.e31638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384284PMC
February 2019

The PPEAO experimental fishing dataset: Fish from West African estuaries, lagoons and reservoirs.

Biodivers Data J 2019 14(7):e31374. Epub 2019 Feb 14.

LEMAR, IRD, Univ BREST, CNRS, Ifremer, Plouzané, France LEMAR, IRD, Univ BREST, CNRS, Ifremer Plouzané France.

Background: This paper describes a dataset of fish, crustacean and mollusc occurrences extracted from the "Experimental Fishing" section of the IRD's PPEAO information system. PPEAO stands for "Fish communities and artisanal fisheries of West African estuarine, lagoon and freshwater ecosystems". This database contains information collected using two different methods: experimental fishing and surveys of the artisanal fisheries that exploit these ecosystems. Read More

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http://dx.doi.org/10.3897/BDJ.7.e31374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384281PMC
February 2019
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A new species of (Coleoptera: Chrysomelidae), discovered and described on a field course to Kuala Belalong, Brunei.

Biodivers Data J 2019 31(7):e32555. Epub 2019 Jan 31.

Taxon Expeditions, Leiden, Netherlands Taxon Expeditions Leiden Netherlands.

Background: is a genus of very small flea beetles living in the leaf litter layer of Asian forests, easily sampled with Winkler extraction. The genus is presumably very rich in species, but their taxonomy is hampered by their small size and morphological uniformity.

New Information: On a 'taxon expedition'-style field course at Kuala Belalong Field Studies Centre in Brunei Darussalam (Borneo), a new species, n. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367309PMC
January 2019

Dragonfly biodiversity 90 years ago in an Alpine region: The Odonata historical collection of the MUSE (Trento, Italy).

Biodivers Data J 2019 31(7):e32391. Epub 2019 Jan 31.

MUSE - Science Museum of Trento, Trento, Italy MUSE - Science Museum of Trento Trento Italy.

Background: Historical collections of natural science museums play a fundamental role in documenting environmental changes and patterns of biodiversity transformation. This considered, they should have a pivotal role to plan conservation and management actions.The MUSE - Science Museum of Trento is an Italian regional museum preserving about 5. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367308PMC
January 2019

A world dataset on the geographic distributions of Solenidae razor clams (Mollusca: Bivalvia).

Biodivers Data J 2019 31(7):e31375. Epub 2019 Jan 31.

Institute of Marine Science, University of Auckland, Auckland 1142, New Zealand Institute of Marine Science, University of Auckland Auckland 1142 New Zealand.

Background: Using this dataset, we examined the global geographical distributions of Solenidae species in relation to their endemicity, species richness and latitudinal ranges and then predicted their distributions under future climate change using species distribution modelling techniques (Saeedi et al. 2016a, Saeedi et al. 2016b). Read More

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http://dx.doi.org/10.3897/BDJ.7.e31375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367310PMC
January 2019

Photo images, 3D/CT data and mtDNA of the freshwater mussels (Bivalvia: Unionidae) in the Kyushu and Ryukyu Islands, Japan, with SEM/EDS analysis of the shell.

Biodivers Data J 2019 28(7):e32114. Epub 2019 Jan 28.

Yamashina Institute for Ornithology, Konoyama, Japan Yamashina Institute for Ornithology Konoyama Japan.

Background: Freshwater mussels (Bivalvia: Unionidae), which are keystone species of freshwater ecosystems, are in global decline. In addition to ecological/genetic studies, morphological examinations are needed to help provide information for the development of additional freshwater mussel studies and eventually conservation efforts for freshwater ecosystems.The microscopic structure, which can be obtained by scanning electron microscopy (SEM) and elemental composition, which can be obtained with energy dispersive X-ray spectrometry (EDS), of mollusc shells are of interest to malacologists. Read More

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http://dx.doi.org/10.3897/BDJ.7.e32114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361872PMC
January 2019

Checklist of bees (Hymenoptera: Apoidea) from small diversified vegetable farms in south-western Montana.

Biodivers Data J 2019 28(7):e30062. Epub 2019 Jan 28.

Department of Ecology, Montana State University, Bozeman, United States of America Department of Ecology, Montana State University Bozeman United States of America.

Background: Over three years (2013-2015), we sampled bees using nets and bowl traps on four diversified vegetable farms in Gallatin County, Montana, USA, as part of a study evaluating the use of wildflower strips for supporting wild bees and crop pollination services on farmlands (Delphia et al. In prep). We document 202 species and morphospecies from 32 genera within five families, of which 25 species represent the first published state records for Montana. Read More

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http://dx.doi.org/10.3897/BDJ.7.e30062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361878PMC
January 2019

First records of the Common Eastern Bumble Bee, Cresson (Hymenoptera: Apidae, Apinae, Bombini) from the Prairies Ecozone in Canada.

Biodivers Data J 2019 10(7):e30953. Epub 2019 Jan 10.

Royal Saskatchewan Museum, Regina, Canada Royal Saskatchewan Museum Regina Canada.

Background: In Canada, the Common Eastern Bumble Bee ( Cresson) is native to southern Ontario and Quebec, but since being developed as a managed commercial pollinator, it has been exported to several other provinces for use in greenhouse and field crop settings. This has enabled this species to become established outside its natural range and it is now established in eastern Canada (New Brunswick, Nova Scotia, Prince Edward Island) and British Columbia. To date, the species has not been detected via field capture in the prairie provinces. Read More

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http://dx.doi.org/10.3897/BDJ.7.e30953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356050PMC
January 2019
1 Read

COPIOUS: A gold standard corpus of named entities towards extracting species occurrence from biodiversity literature.

Biodivers Data J 2019 22(7):e29626. Epub 2019 Jan 22.

The National Centre for Text Mining, University of Manchester, Manchester, United Kingdom The National Centre for Text Mining, University of Manchester Manchester United Kingdom.

Species occurrence records are very important in the biodiversity domain. While several available corpora contain only annotations of species names or habitats and geographical locations, there is no consolidated corpus that covers all types of entities necessary for extracting species occurrence from biodiversity literature. In order to alleviate this issue, we have constructed the COPIOUS corpus-a gold standard corpus that covers a wide range of biodiversity entities. Read More

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http://dx.doi.org/10.3897/BDJ.7.e29626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351503PMC
January 2019

Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature.

Biodivers Data J 2019 16(7):e28737. Epub 2019 Jan 16.

Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam Netherlands.

Background: A considerable portion of primary biodiversity data is digitally locked inside published literature which is often stored as pdf files. Large-scale approaches to biodiversity science could benefit from retrieving this information and making it digitally accessible and machine-readable. Nonetheless, the amount and diversity of digitally published literature pose many challenges for knowledge discovery and retrieval. Read More

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http://dx.doi.org/10.3897/BDJ.7.e28737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344444PMC
January 2019
1 Read

rMyCoPortal - an R package to interface with the Mycology Collections Portal.

Biodivers Data J 2019 14(7):e31511. Epub 2019 Jan 14.

University of Illinois Urbana-Champaign, Champaign, United States of America University of Illinois Urbana-Champaign Champaign United States of America.

The understanding of the biodiversity and biogeographical distribution of fungi is still limited. The small number of online databases and the large effort required to access existing data have prevented their use in research articles. The Mycology Collections Portal was established in 2012 to help alleviate these issues and currently serves data online for over 4. Read More

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https://bdj.pensoft.net/article/31511/
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http://dx.doi.org/10.3897/BDJ.7.e31511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341041PMC
January 2019
2 Reads

DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project.

Biodivers Data J 2019 15(7):e31432. Epub 2019 Jan 15.

SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany.

We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Read More

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http://dx.doi.org/10.3897/BDJ.7.e31432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342863PMC
January 2019

The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia.

Biodivers Data J 2018 19(6):e29927. Epub 2018 Dec 19.

SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany.

The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Read More

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http://dx.doi.org/10.3897/BDJ.6.e29927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306476PMC
December 2018

Species conservation profiles of a random sample of world spiders IV: Scytodidae to Zoropsidae.

Biodivers Data J 2018 14(6):e30842. Epub 2018 Dec 14.

LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki Helsinki Finland.

Background: The IUCN Red List of Threatened Species is the most widely used information source on the extinction risk of species. One of the uses of the Red List is to evaluate and monitor the state of biodiversity and a possible approach for this purpose is the Red List Index (RLI). For many taxa, mainly hyperdiverse groups, it is not possible within available resources to assess all known species. Read More

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http://dx.doi.org/10.3897/BDJ.6.e30842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303285PMC
December 2018

The highest altitudinal record of the Mountain coati (Gray, 1865) for Ecuador.

Biodivers Data J 2018 14(6):e29160. Epub 2018 Dec 14.

Proyecto Paisajes Vida Silvestre - Ministerio del Ambiente del Ecuador - Programa de las Naciones Unidas para el Desarrollo, Quito, Ecuador Proyecto Paisajes Vida Silvestre - Ministerio del Ambiente del Ecuador - Programa de las Naciones Unidas para el Desarrollo Quito Ecuador.

The Mountain coati is a species of carnivorous mammal, several aspects of its ecology and natural history remain unknown. In Ecuador, its presence is reported in high Andean forest and paramo between 1,300 and 3,700 m a.s. Read More

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http://dx.doi.org/10.3897/BDJ.6.e29160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303284PMC
December 2018

Wet collections accession: a workflow based on a large stonefly (Insecta, Plecoptera) donation.

Biodivers Data J 2018 7(6):e30256. Epub 2018 Dec 7.

Illinois Natural History Survey, Champaign, United States of America Illinois Natural History Survey Champaign United States of America.

This study details a workflow used to accession a large stonefly (Plecoptera) collection resulting from several donations. The eastern North American material of Kenneth W. Stewart (deceased, University of North Texas), the entire collection of Stanley W. Read More

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http://dx.doi.org/10.3897/BDJ.6.e30256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294822PMC
December 2018

(Coleoptera: Carabidae) is established in California.

Biodivers Data J 2018 4(6):e30763. Epub 2018 Dec 4.

Oregon Department of Agriculture, Salem, United States of America Oregon Department of Agriculture Salem United States of America.

Background: The ground beetle Bembidion (Neja) ambiguum Dejean is native to Europe and north Africa, in the Mediterranean region.

New Information: We report it from North America for the first time, from five localities around San Francisco Bay, California. The earliest record is from 2012. Read More

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http://dx.doi.org/10.3897/BDJ.6.e30763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290041PMC
December 2018

A DNA barcode-assisted annotated checklist of the spider (Arachnida, Araneae) communities associated to white oak woodlands in Spanish National Parks.

Biodivers Data J 2018 29(6):e29443. Epub 2018 Nov 29.

Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028, Barcelona, Spain Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona Spain.

Background: A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Read More

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https://bdj.pensoft.net/article/29443/
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http://dx.doi.org/10.3897/BDJ.6.e29443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284012PMC
November 2018
25 Reads

Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier.

Biodivers Data J 2018 28(6):e29232. Epub 2018 Nov 28.

University of Arizona, Tucson, United States of America University of Arizona Tucson United States of America.

When phenotypic characters are described in the literature, they may be constrained or clarified with additional information such as the location or degree of expression, these terms are called "modifiers". With effort underway to convert narrative character descriptions to computable data, ontologies for such modifiers are needed. Such ontologies can also be used to guide term usage in future publications. Read More

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http://dx.doi.org/10.3897/BDJ.6.e29232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281706PMC
November 2018
1 Read

An interactive key to Central European species of the species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species.

Biodivers Data J 2018 14(6):e27722. Epub 2018 Nov 14.

Department of Invertebrates, Natural History Museum Bern, Bern, Switzerland Department of Invertebrates, Natural History Museum Bern Bern Switzerland.

Background: Parasitoid wasps of the genus play an important role in biological pest control, however, the genus includes a large number of cryptic species, which makes reliable identification difficult. The latest identification key dates back to Graham (1969) and since then many new species have been described and nomenclatural changes proposed.

New Information: Here we present an interactive and fully illustrated identification key in Xper3 for 27 species of the species group as well as for 18 similar species. Read More

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http://dx.doi.org/10.3897/BDJ.6.e27722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249333PMC
November 2018
2 Reads

Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production.

Biodivers Data J 2018 7(6):e29616. Epub 2018 Nov 7.

University of Massachusetts at Boston, Boston, United States of America University of Massachusetts at Boston Boston United States of America.

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses. Read More

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https://bdj.pensoft.net/articles.php?id=29616
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http://dx.doi.org/10.3897/BDJ.6.e29616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235995PMC
November 2018
12 Reads

A preliminary checklist of soil ants (Hymenoptera: Formicidae) of Colombian Amazon.

Biodivers Data J 2018 7(6):e29278. Epub 2018 Nov 7.

Instituto Amazónico de Investigaciones Científicas SINCHI, Leticia, Colombia Instituto Amazónico de Investigaciones Científicas SINCHI Leticia Colombia.

Background: This paper presents an updated list of soil ants of the Colombian Amazon collected in three different river basins: the Amazon, the Caquetá and the Putumayo. The list includes 10 subfamilies, 60 genera and 218 species collected from TSBF monoliths at four different depths (Litter, 0 - 10 cm, 10 - 20 cm and 20 - 30 cm). This updated list increases considerably the knowledge of edaphic macrofauna of the region, due to the limited published information about soil ant diversity in the Colombian Amazon region. Read More

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http://dx.doi.org/10.3897/BDJ.6.e29278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235997PMC
November 2018
2 Reads

A story of data won, data lost and data re-found: the realities of ecological data preservation.

Biodivers Data J 2018 7(6):e28073. Epub 2018 Nov 7.

Atlas of Living Australia, CSIRO, Canberra, Australia Atlas of Living Australia, CSIRO Canberra Australia.

This paper discusses the process of retrieval and updating legacy data to allow on-line discovery and delivery. There are many pitfalls of institutional and non-institutional ecological data conservation over the long term. Interruptions to custodianship, old media, lost knowledge and the continuous evolution of species names makes resurrection of old data challenging. Read More

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http://dx.doi.org/10.3897/BDJ.6.e28073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235994PMC
November 2018
10 Reads

Data Leakage and Loss in Biodiversity Informatics.

Biodivers Data J 2018 7(6):e26826. Epub 2018 Nov 7.

Museum of Vertebrate Zoology, University of California, Berkeley, United States of America Museum of Vertebrate Zoology, University of California Berkeley United States of America.

The field of biodiversity informatics is in a massive, "grow-out" phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy applications, the question arises as to how these existing and available data records can be mobilized most efficiently and effectively. This situation led to our analysis of several large-scale biodiversity datasets regarding birds and plants, detecting information gaps and documenting data "leakage" or attrition, in terms of data on taxon, time, and place, in each data record. Read More

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http://dx.doi.org/10.3897/BDJ.6.e26826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235996PMC
November 2018
21 Reads

A list of bees from three locations in the Northern Rockies Ecoregion (NRE) of western Montana.

Biodivers Data J 2018 30(6):e27161. Epub 2018 Oct 30.

USDA-ARS Pollinating Insects Research Unit, Logan, United States of America USDA-ARS Pollinating Insects Research Unit Logan United States of America.

Background: Wild bees that were collected in conjunction with a larger study are presented as a checklist of species for the Northern Rockies Ecoregion of Montana, USA. Over the course of four field seasons (2013-2016), 281 species and morphospecies in 32 genera and five families were collected using insect nets, and identified. This paper addresses the distinct lack of studies monitoring bee species in Montana and contributes to a basic understanding of fauna in the northern Rocky Mountains. Read More

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http://dx.doi.org/10.3897/BDJ.6.e27161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220116PMC
October 2018

On the identity of a U.S. intercepted Dejean (Coleoptera: Curculionidae) with avocado ().

Biodivers Data J 2018 2(6):e26362. Epub 2018 Nov 2.

Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom Department of Life Sciences, Natural History Museum London SW7 5BD United Kingdom.

Background: The multimillion-dollar avocado industry is threatened by a number of serious insect pests, including at least seven species of Curculionidae. Of these, three species are known to develop and feed on avocados: Barber, Barber and (Klug); the first two are of economic importance. Recently, a series of unrecognised was intercepted with avocado and other commodities by the USDA at various southern U. Read More

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http://dx.doi.org/10.3897/BDJ.6.e26362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226545PMC
November 2018
11 Reads

Species conservation profiles of a random sample of world spiders III: Oecobiidae to Salticidae.

Biodivers Data J 2018 2(6):e27004. Epub 2018 Aug 2.

Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland Finnish Museum of Natural History, University of Helsinki Helsinki Finland.

Background: The IUCN Red List of Threatened Species is the most widely used information source on the extinction risk of species. One of the uses of the Red List is to evaluate and monitor the state of biodiversity and a possible approach for this purpose is the Red List Index (RLI). For many taxa, mainly hyperdiverse groups, it is not possible within available resources to assess all known species. Read More

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http://dx.doi.org/10.3897/BDJ.6.e27004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086925PMC

Resolving "orphaned" non-specific structures using machine learning and natural language processing methods.

Biodivers Data J 2018 10(6):e26659. Epub 2018 Aug 10.

University of Arizona, Tucson, United States of America University of Arizona Tucson United States of America.

Scholarly publications of biodiversity literature contain a vast amount of information in human readable format. The detailed morphological descriptions in these publications contain rich information that can be extracted to facilitate analysis and computational biology research. However, the idiosyncrasies of morphological descriptions still pose a number of challenges to machines. Read More

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http://dx.doi.org/10.3897/BDJ.6.e26659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207837PMC
August 2018
16 Reads

A new record of Avrainvillea cf. erecta (Berkeley) A. Gepp & E. S. Gepp (Bryopsidales, Chlorophyta) from urbanized estuaries in the Hawaiian Islands.

Biodivers Data J 2018 5(6):e21617. Epub 2018 Oct 5.

University of Hawai'i at Mānoa, Honolulu, United States of America University of Hawai'i at Mānoa Honolulu United States of America.

Background: A second species in the siphonous green algal genus was recently discovered off the island of O'ahu in the Main Hawaiian Islands. Specimens were collected from Honolulu Harbor, including its entrance channel, and near Ke'ehi Harbor. These locations are both in Mālama Bay on O'ahu's south shore in or adjacent to urbanized estuaries, respectively. Read More

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https://bdj.pensoft.net/articles.php?id=21617
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http://dx.doi.org/10.3897/BDJ.6.e21617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6185993PMC
October 2018
15 Reads

Visualizing natural history collection data provides insight into collection development and bias.

Authors:
Vaughn Shirey

Biodivers Data J 2018 3(6):e26741. Epub 2018 Oct 3.

Department of Entomology, The Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Department of Entomology, The Academy of Natural Sciences of Drexel University Philadelphia United States of America.

Natural history collections contain estimated billions of records representing a large body of knowledge about the diversity and distribution of life on Earth. Assessments of various forms of bias within the aggregated data associated with specimens in these collections have been conducted across temporal, taxonomic, and spatial domains. Considering that these biases are the sum of biases across all contributing collections to aggregate datasets, the assessment of bias at the collection level is warranted. Read More

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http://dx.doi.org/10.3897/BDJ.6.e26741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180142PMC
October 2018

Aggregated occurrence records of the federally endangered Poweshiek skipperling ().

Biodivers Data J 2018 27(6):e29081. Epub 2018 Sep 27.

Central Michigan University and Institute for Great Lakes Research, Mount Pleasant, United States of America Central Michigan University and Institute for Great Lakes Research Mount Pleasant United States of America.

Background: Primary biodiversity data records that are open access and available in a standardised format are essential for conservation planning and research on policy-relevant time-scales. We created a dataset to document all known occurrence data for the Federally Endangered Poweshiek skipperling butterfly [ (Parker, 1870; Lepidoptera: Hesperiidae)]. The Poweshiek skipperling was a historically common species in prairie systems across the upper Midwest, United States and Manitoba, Canada. Read More

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http://dx.doi.org/10.3897/BDJ.6.e29081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172292PMC
September 2018
1 Read

OpenNahele: the open Hawaiian forest plot database.

Biodivers Data J 2018 27(6):e28406. Epub 2018 Sep 27.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.

Background: This data paper provides a description of OpenNahele, the open Hawaiian forest plot database. OpenNahele includes 530 forest plots across the Hawaiian archipelago containing 43,590 individuals of 185 native and alien tree, shrub and tree fern species across six islands. We include estimates of maximum plant size (D95 and D) for 58 woody plant species, a key functional trait associated with dispersal distance and competition for light. Read More

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http://dx.doi.org/10.3897/BDJ.6.e28406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172291PMC
September 2018
13 Reads

Evaluation of the population dynamics of microalgae isolated from the state of Chiapas, Mexico with respect to the nutritional quality of water.

Biodivers Data J 2018 26(6):e28496. Epub 2018 Sep 26.

Universidad Autónoma de México, Cuernavaca, Mexico Universidad Autónoma de México Cuernavaca Mexico.

As Chiapas state, México, counts on an extensive hydrography with diverse nutrimental and climatic characteristics, it therefore allows isolating and identifying microalgae with bioenergetics potential. For this purpose, samples from 8 locations were collected, corresponding to 6 rivers, a wastewater and a springwater. The isolation of microalgae was developed for 4 weeks with 12:12 light/dark cycles. Read More

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http://dx.doi.org/10.3897/BDJ.6.e28496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170526PMC
September 2018

Macrobenthic fauna from an upwelling coastal area of Peru (Warm Temperate South-eastern Pacific province -Humboldtian ecoregion).

Biodivers Data J 2018 10(6):e28937. Epub 2018 Sep 10.

Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, Washington, DC, United States of America Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute Washington, DC United States of America.

Background: A total of 162 species and subspecies of marine macroinvertebrates were recorded in the submerged soft and hard substrates around the PERU LNG marine terminal and surrounding area, in the central coast of Peru, 167 km south of Lima, Peru. The collection of specimens was carried out from June 2011 to June 2015 as part of the research studies conducted by the Biodiversity Monitoring and Assessment Program (BMAP) around the marine terminal. The area is part of the Humboldt Current Large Marine Ecosystem, one of the most important upwelling systems in the world. Read More

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http://dx.doi.org/10.3897/BDJ.6.e28937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160799PMC
September 2018

New records of sharks (Elasmobranchii) from the Andaman and Nicobar Archipelago in India with notes on current checklists.

Biodivers Data J 2018 10(6):e28593. Epub 2018 Sep 10.

James Cook University, Queensland, Australia James Cook University Queensland Australia.

The diversity of sharks occurring off the Andaman and Nicobar Archipelago in India has received increased attention in recent years. Yet, available checklists are out of date, often with inaccurate information and a number of commercially important species have not been documented through research and fish landing surveys. Here we report on shark species examined during fish landing surveys conducted from January 2017 to April 2018. Read More

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http://dx.doi.org/10.3897/BDJ.6.e28593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160849PMC
September 2018
2 Reads

Two species of Surcouf (Diptera: Calliphoridae) new to India, with data on larval behaviour and morphology.

Biodivers Data J 2018 10(6):e27736. Epub 2018 Sep 10.

Natural History Museum, London, United Kingdom Natural History Museum London United Kingdom.

Surcouf (Diptera: Calliphoridae) is an Old World genus of blow flies, the larvae of which feed on egg masses in the foam nests of various species of rhacophorid tree frogs. Here, we provide the first records for India (West Bengal, Eastern India) of Séguy, 1948 and Rognes, 2015, together with new information on the behaviour and morphology of their larvae. Active surface swimming to disperse from infested nests is documented in blow fly larvae for the first time, as is the presence of a large internal air sac presumably acting as a floating aid. Read More

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http://dx.doi.org/10.3897/BDJ.6.e27736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160781PMC
September 2018
1 Read

The spider fauna from Uruguay River islands: understanding its role in a biological corridor.

Biodivers Data J 2018 28(6):e27319. Epub 2018 Aug 28.

Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400, Montevideo, Uruguay Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225. CP 11400 Montevideo Uruguay.

Biological corridors are connections which link habitats in a regional scale, allowing the gene flow between populations. The Uruguay River comprises riverside and insular riparian forests along subtropical to temperate zones passing through different biogeographic provinces. The aim of this study was to characterise the spider fauna from the Uruguay River islands highlighting their connection role for the spider community of riparian forest. Read More

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http://dx.doi.org/10.3897/BDJ.6.e27319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160865PMC
August 2018
3 Reads

New records of a critically endangered shrew from Mexican cloud forests (Soricidae, ) and prospects for future field research.

Biodivers Data J 2018 14(6):e26667. Epub 2018 Aug 14.

Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México Ciudad de Mexico Mexico.

The Nelson´s small-eared shrew, (Merriam, 1895), is a critically endangered species, endemic to cloud forests in Los Tuxtlas, a mountain range along the Gulf of Mexico coast. This species is only known from the type locality and its surroundings. Here we present new records that extend its distribution approximately 7 km southeast of the type locality and report more specimens near to the type locality. Read More

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http://dx.doi.org/10.3897/BDJ.6.e26667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160866PMC