Reviewing taxonomic bias in a megadiverse country: primary biodiversity data, cultural salience, and scientific interest of South African animals

Taxonomic bias, resulting in some taxa receiving more attention than others, has been shown to persist throughout history. Such bias in primary biodiversity data needs to be addressed because the data are vital to environmental management. This study reviews taxonomic bias in South African primary biodiversity data obtained from the Global Biodiversity Information Facility (GBIF). The focus was specifically on animal classes, and regression analysis was used to assess the influence of scientific interest and cultural salience on taxonomic bias. A higher resolution analysis of the two explanatory variables’ influence on taxonomic bias is conducted using a generalised linear model on a subset of herpetofaunal families from the focal classes. Furthermore, the potential effects of cultural salience and scientific interest on a taxon’s extinction risk are investigated. The findings show that taxonomic bias in South Africa’s primary biodiversity data has similarities with global scale taxonomic bias. Among animal classes, there is strong bias towards birds while classes such as Polychaeta and Maxillopoda are under-represented. Cultural salience has a stronger influence on taxonomic bias than scientific interest. It is, however, unclear how these explanatory variables may influence the extinction risk of taxa. We recommend that taxonomic bias can be reduced if primary biodiversity data collection has a range of targets that guide (but do not limit) accumulation of species occurrence records per habitat. Within this range, a lower target of species occurrence records accommodates species that are difficult to detect. The upper target means occurrence records for any species are less urgent but nonetheless useful and thus data collection efforts can focus on species with fewer occurrence records.

Contribution to a reference library of DNA barcodes of Colombian freshwater fishes

The Barcode of Life initiative was originally motivated by the large number of species, taxonomic difficulties and the limited number of expert taxonomists. Colombia has 1,610 freshwater fish species and comprises the second largest diversity of this group in the world. As genetic information continues to be limited, we constructed a reference collection of DNA sequences of Colombian freshwater fishes deposited in the Ichthyology Collection of the University of Antioquia (CIUA), thus joining the multiple efforts that have been made in the country to contribute to the knowledge of genetic diversity in order to strengthen the inventories of biological collections and facilitate the solution of taxonomic issues in the future. This study contributes to the knowledge on the DNA barcodes and occurrence records of 96 species of Colombian freshwater fishes. Fifty-seven of the species represented in this dataset were already available in the Barcode Of Life Data System (BOLD System), while 39 correspond to new species to the BOLD System. Forty-nine specimens were collected in the Atrato River Basin and 708 in the Magdalena-Cauca asin during the period 2010-2020. Two species (Loricariichthys brunneus (Hancock, 1828) and Poecilia sphenops Valenciennes, 1846) are considered exotic to the Atrato, Cauca and Magdalena Basins and four species (Oncorhynchus mykiss (Walbaum, 1792), Oreochromis niloticus (Linnaeus, 1758), Parachromis friedrichsthalii (Heckel, 1840) and Xiphophorus helleri Heckel, 1848) are exotic to the Colombian hydrogeographic regions. All specimens are deposited in CIUA and have their DNA barcodes made publicly available in the BOLD online database. The geographical distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

CATALOGUE OF AQUATIC MITES FROM THE MINHO RIVER (NW IBERIAN PENINSULA)

Acari are a subclass of chelicerate arthropods that includes mites and ticks. The present study focuses on the taxonomic diversity of aquatic mites in the Portuguese territory of the Minho Region. Our aim was to compile all available information and thus generate a list of species linking them to the site where they were recorded. Aquatic species were all those that live exclusively in the marine environment, deep sea, intertidal, freshwater, brackish water or in transitional environments with the terrestrial environment if their lifestyle is associated with the aquatic environment. Since the first records of Portuguese endemic mites by Lunblad in the 1950s several authors have contributed to accurately catalogue, record, and redescribe this vast group in Portugal and Minho consecutively. In our review in this work, we used the Global Biodiversity Information Facility (GBIF) to obtain previous occurrences supplemented by an extensive literature review and the book collection Süßwasserfauna von Mitteleuropa, among others. Additionally, we resorted to active sampling and by-catch sampling in the Portuguese section of the Rio Minho catchment area. The collected organisms represent 12 new records for the Minho River and among them 10 are new records for Portugal, which were deposited in the Natural History Museum of the Iberian Peninsula - NatMIP (“Museu de História Natural da Península Ibérica”), Vila Nova de Cerveira, Portugal.

European Journal of Taxonomy: a deeper look into a decade of data

The European Journal of Taxonomy (EJT) is a decade-old journal dedicated to the taxonomy of living and fossil eukaryotes. Launched in 2011, the EJT published exactly 900 articles (31 778 pages) from 2011 to 2021. The journal has been processed in its entirety by Plazi, liberating the data therein, depositing it into TreatmentBank, Biodiversity Literature Repository and disseminating it to partners, including the Global Biodiversity Information Facility (GBIF) using a combination of a highly automated workflow, quality control tools, and human curation. The dissemination of original research along with the ability to use and reuse data as freely as possible is the key to innovation, opening the corpus of known published biodiversity knowledge, and furthering advances in science. This paper aims to discuss the advantages and limitations of retro-conversion and to showcase the potential analyses of the data published in EJT and made findable, accessible, interoperable and reusable (FAIR) by Plazi. Among others, taxonomic and geographic coverage, geographical distribution of authors, citation of previous works and treatments, timespan between the publication and treatments with their cited works are discussed. Manually counted data were compared with the automated process, the latter being analysed and discussed. Creating FAIR data from a publication results in an average multiplication factor of 166 for additional access through the taxonomic treatments, figures and material citations citing the original publication in TreatmentBank, the Biodiversity Literature Repository and the Global Biodiversity Information Facility. Despite the advances in processing, liberating data remains cumbersome and has its limitations which lead us to conclude that the future of scientific publishing involves semantically enhanced publications.

Macrophyte diversity in rivers and streams of the Vologda Region and several other regions of Russia

The data paper contains the authors’ materials on the diversity of macrophytes, macroscopic plants regardless of their taxonomic position, in rivers and streams of East European Russia and Western Siberia. These data, collected on 247 rivers and 32 streams in 13 administrative regions of the Russian Federation, were provided as an occurrence dataset presented in the form of GBIF-mediated data. The main portion of the data was obtained in water objects of the Vologda Region (5201 occurrences). In addition, occurrences from the Arkhangelsk Region (347 occurrences), Khanty-Mansi Autonomous Okrug (159), Yaroslavl Region (132), Novgorod Region (97), Kostroma Region (41), Republic of Karelia (31), Sverdlovsk Region (29), Komi Republic (28), Orenburg Region (26), Chelyabinsk Region (22), Voronezh Region (22) and Tyumen Region (18) were given. The studies were carried out mainly in the southern and middle taiga and, to a lesser extent, in the northern taiga and the forest-steppe. The analysed watercourses belong to five drainage basins: the Azov Sea, the Baltic Sea, the White Sea, the Caspian Sea and the Kara Sea. The dataset contains materials on the diversity of Plantae (6094 occurrences) and Chromista (59 occurrences). This paper, in a standardised form, summarises mostly unpublished materials on the biodiversity of lotic ecosystems. The paper summarises the data obtained in long-term studies of phytodiversity in a range of rivers and streams of East European Russia and, fragmentarily, Western Siberia. A total of 6153 occurrences were included in the dataset. According to the GBIF taxonomic backbone, the dataset comprises 292 taxa, including 280 lower-rank taxa (species, subspecies, varieties) and 12 taxa identified to the genus level. All the occurrences are published openly through the Global Biodiversity Information Facility (GBIF) for the first time. Most of the data were stored in field diaries and, thus, by adding the data in GBIF, we believe that other researchers could benefit from it.

Predicting habitat suitability of critically endangered Nepenthes sumatrana

Nepenthes sumatrana is a tropical pitcher plant endemic to Sumatra. It has been categorised as critically endangered based on the IUCN Red List. It often occupies in lowland tropical forest of Sumatra. Its habitat has been threatened by land use conversion in the recent decade. Due to the high threats in the wild, the conservation efforts are necessarily required. It is not possible to assess all locations that are suitable for this species. In terms of addressing that issue, Species Distribution Modelling is considered as an alternative way to identify the regions that have the similar environmental conditions to where the species is known to occur. The occurrence records were derived from Global Biodiversity Information Facility and reliable scientific papers. Topography, soil, climate and land cover were used as predictors of the model. MaxEnt algorithm was used to predict the habitat suitability. MaxEnt produces a predictive model with the AUC value of 0.833 indicating that the model has a good performance. The suitable habitats are predicted in several different locations in Sumatra. The information about predicted suitability habitat would be useful to prioritize the protected areas of this species. Furthermore, our findings would be valuable for the discovery of unknown subpopulation.

Geographic Distribution of Colombian Spittlebugs (Hemiptera: Cercopidae) via Ecological Niche Modeling: A Prediction for the Main Tropical Forages' Pest in the Neotropics

Spittlebugs (Hemiptera: Cercopidae) are the main tropical pests in Central and South America of cultivated pastures. We aimed to estimate the potential distribution of Aeneolamia varia, A. lepidior, A. reducta, Prosapia simulans, Zulia carbonaria, and Z. pubescens throughout the Neotropics using ecological niche modeling. These six insect species are common in Colombia and cause large economic losses. Records of these species, prior to the year 2000, were compiled from human observations, specimens from CIAT Arthropod Reference Collection (CIATARC), Global Biodiversity Information Facility (GBIF), speciesLink (splink), and an extensive literature review. Different ecological niche models (ENMs) were generated for each species: Maximum Entropy (MaxEnt), generalized linear (GLM), multivariate adaptive regression spline (MARS), and random forest model (RF). Bioclimatic datasets were obtained from WorldClim and the 19 available variables were used as predictors. Future changes in the potential geographical distribution were simulated in ENMs generated based on climate change projections for 2050 in two scenarios: optimistic and pessimistic. The results suggest that (i) Colombian spittlebugs impose an important threat to Urochloa production in different South American countries, (ii) each spittlebug species has a unique geographic distribution pattern, (iii) in the future the six species are likely to invade new geographic areas even in an optimistic scenario, (iv) A. lepidior and A. reducta showed a higher number of suitable habitats across Colombia, Venezuela, Brazil, Peru, and Ecuador, where predicted risk is more severe. Our data will allow to (i) monitor the dispersion of these spittlebug species, (ii) design strategies for integrated spittlebug management that include resistant cultivars adoption to mitigate potential economic damage, and (iii) implement regulatory actions to prevent their introduction and spread in geographic areas where the species are not yet found.

Biodiversity of a boreal mire, including its hydrographic network (Shichengskoe mire, north-western Russia)

The paper is based on the dataset whose purpose was to deliver, in the form of GBIF-mediated data, diverse materials on the biodiversity of a large mire, Shichengskoe mire (Vologda Region, north-western Russia), including its various mire sites and intra-mire water bodies. The dataset was based on our materials collected for two decades (from 2000 to 2021) in different parts and biotopes of the Shichengskoe mire and complemented by scarce data obtained previously by other researchers. The data contain materials on the diversity of Animalia (2886 occurrences), Bacteria (22), Chromista (256), Fungi (111), Plantae (2463) and Protozoa (131). Within the study period, the most detailed and long-term biodiversity studies were carried out for higher plants and invertebrates. On the other hand, the data on the composition of lichens, protozoa, algae, basidiomycetes, some groups of invertebrates and, to a lesser extent, lichens and vertebrates are far less comprehensive and require further substantial research efforts. The list includes occurrences from both the peatland (mire sites and mire margins different in typology) and the objects of the mire hydrographic network. In a standardised form, this article summarises both already published (mainly in Russian) and unpublished materials. The paper summarises the results of long-term research on the biodiversity of a boreal mire, including its hydrographic network. A total of 5869 occurrences were included in the dataset published in the Global Biodiversity Information Facility (GBIF, gbif.org) for the first time. According to the GBIF taxonomic backbone, the dataset covers 1358 taxa, including 1250 lower-rank taxa (species, subspecies, varieties, forms) and 108 taxa identified to the genus level. Several species found in the Shichengskoe mire, mainly belonging to Bacteria, Chromista and Protozoa, have never been listed in GBIF for the territory of Russia before. The overwhelming majority of occurrences and identified species came from the territory of Shichengskiy Landscape Reserve. Due to our work, this Reserve is now the most studied regional reserve in the Vologda Region with respect to biodiversity. By the number of revealed species, it is close to two federal protected areas: Darwinskiy State Nature Biospheric Reserve and National Park "Russkiy Sever".

Geohistorical dataset of ten plant species introduced into Occitania (France)

The original dataset presented here is the result of the first near-exhaustive analysis performed on historical data concerning ten plant species introduced in and around Occitania (south-western France) since 1651. Research was carried out on the following species: Alnus incana, Buddleja davidii, Castanea sativa, Helianthus tuberosus, Impatiens glandulifera, Prunus cerasifera, Prunus laurocerasus, Reynoutria japonica, Robinia pseudoacacia and Spiraea japonica. The data file contains 199 occurrence data exclusively based on historical observations and records made between 1651 and 2004 and retrieved from 111 of the 640 literary sources consulted. All the records are associated with a year and 61% of them have associated spatial coordinates. Initially the EI2P-VALEEBEE research project focused on the introduction of these species into Occitania (95 occurrences, 47.7%), but mentions found beyond this territory - mainly in metropolitan France - are also reported. The creation of this dataset involved five stages: (1) selection of species, (2) consultation of historical sources, (3) recording of occurrences in the dataset, (4) dataset standardization/enrichment and Darwin core mapping, (5) data publication. Quality controls were conducted at each step. The dataset is available on the platform of the Global Biodiversity Information Facility (GBIF) at https://doi.org/10.15468/3kvaeh. It respects the internationally recognized FAIR Data Principles (Findable, Accessible, Interoperable and Reusable). The dataset will be progressively enriched by new data during the EI2P-VALEEBEE research project and future projects on invasive plant species conducted by the team.

Potential Impact of Climate Change on Six Economically Important Horticultural Crops in West Africa

Colocasia esculenta (taro), Ipomoea batatas (sweet potato), Abelmoschus esculentus (okra), Ananas cosmosus (pineapple), Musa paradisiaca (plantain), and Anacardium occidentale (cashew) are economically important horticultural crops in West Africa, which are widely grown across the region under rain fed conditions. They are very important set of crops that provides income for the individuals involved with it and thus contributing to economy of West African nation’s. For Predicting the potential future habitat suitability of these crops under different climate scenarios holds significance for their continuous cultivation and effective management. The Maxent model was used in this study to predict habitat suitability of these crops under current and future climatic conditions based on two representative concentration pathways (RCP4.5 and RCP8.5) for the years 2050s and 2070s. The data used were the occurrence records from Global Biodiversity Information Facility (GBIF) and WorldClim’s bioclimatic environmental predictor variables. The findings of this experiment showed that the habitat suitability of some crop species will =decrease and in some it will increase. Suitable habitat was predicted to decrease within the semi-arid and arid areas of the region, especially on those countries in northern part which includes Niger, Mali and Burkina Faso, as early as by 2070s. For species like okra, sweet potato and taro, there will be further decline as predicted under the higher emission scenario of RCP 8.5. The suitable habitat for cashew remained stable for future in all the models and scenarios used. This work provides the first theoretical guidance for possible future cultivation of these horticultural crops in the West Africa.