bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/605071

Research applications of primary biodiversity databases in the digital age

Ball-Damerow, J.·Brenskelle, L.·Barve, N.·Soltis, P. S.·Sierwald, P.·Bieler, R.·LaFrance, R.·Arino, A. H.·Guralnick, R.
View original source ↗Export metadata ↓

Abstract

We are in the midst of unprecedented change--climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences and genetic barcodes. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing world.

Source connections

Explore related subjects

zoologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ball-Damerow, J., Brenskelle, L., Barve, N., Soltis, P. S., Sierwald, P., Bieler, R., LaFrance, R., Arino, A. H., Guralnick, R.. 2019-04-10. Research applications of primary biodiversity databases in the digital age. https://doi.org/10.1101/605071

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Impact of iron-enriched diets on the nutritional composition and microbiome diversity of house crickets (Acheta domesticus)

Iron deficiency (ID) and iron-deficiency anaemia (IDA) pose significant global health challenges. ID and IDA are particularly widespread in Sub-Saharan Africa and South Asian countries, where reliance on plant-based foods is high. Edible insects provide an alternative nutritious food source, rich in both protein and essential minerals and trace elements. Little is known about how dietary iron manipulation affects the trace element bioaccumulation and microbiome community composition of edible insects. This study examined the impact of dietary iron supplementation on the growth, survival, nutrient profile, and microbiome of Acheta domesticus. Experimental diets were formulated using iron (II) sulphate heptahydrate, resulting in final iron concentrations ranging from 333.45 mg Fe/kg (control diet) to 6923.39 mg Fe/kg (100 mM Fe diet). Iron supplementation significantly altered the cricket trace element profile, with iron levels increasing fivefold from basal 21.38 mg/kg to 118.34 mg/kg in the highest iron treatment group. Concurrently, manganese levels showed a strong negative correlation with dietary iron, while zinc and cadmium displayed non-significant downward trends. High-iron diets statistically altered dry matter, chitin, and TBARS, whereas carbohydrates, protein, glycogen, and lipids remained stable. Amino acid profiles shifted progressively, with branched-chain, sulphur-containing, and aromatic amino acids peaking in the 25 mM Fe group. In contrast, the diversity and overall structure of the microbial community remained unaffected across all treatments. In conclusion, tailoring dietary iron can significantly boost the iron content of Acheta domesticus without compromising host survival or altering core microbial structures. To optimize insect rearing strategies aimed at alleviating human micronutrient deficiencies, a feeding dose of 10-25 mmol Fe/kg is recommended.

zoology↗
bioRxiv2026

Tardigrades survive reversible dormancy during spaceflight: In-orbit revival, post-flight recovery, and transcriptomic responses

Long-duration space missions face substantial challenges, including limited resources and prolonged exposure to microgravity and radiation. Transporting organisms in a dormant state and reviving them at their destination could help overcome some of these limitations. However, the feasibility of this strategy has not been experimentally demonstrated in multicellular animals beyond Earth. Here, we investigated this possibility using tardigrades, microscopic invertebrates capable of entering a reversible state of dormancy. We demonstrate that dormant tardigrades can withstand near-absolute-zero temperatures (~12 mK), near-vacuum conditions (10-9 mbar), high doses of ionizing radiation (3000 Gy), and complete desiccation. We transported dormant tardigrades to the International Space Station (ISS). They were revived aboard the ISS, subsequently returned to a dormant state, and successfully revived again following their return to Earth. Approximately 45% of the space-flown tardigrades survived the 64-day experimental period. This included two dormancy-revival cycles, 18 days aboard the ISS, and prolonged periods without food or water. Importantly, surviving tardigrades retained their reproductive capacity. Transcriptomic analysis of ISS-exposed tardigrades revealed upregulation of genes associated with protein folding and stress responses, accompanied by downregulation of genes involved in energy metabolism and protein synthesis, providing insights into their molecular responses to the spaceflight environment. Together, these findings demonstrate the successful revival and re-induction of dormancy in a multicellular animal beyond Earth and establish an experimental foundation for exploring dormancy-based strategies for future long-duration space missions.

zoology↗
bioRxiv2026

A baseline for aquatic parasite diversity in West African mangroves: host-parasite records, DNA barcodes, and an experimental design for future use

Macroparasites represent a major fraction of biodiversity and biomass in marine ecosystems, yet remain substantially underrepresented in ecological surveys and food-web models, particularly in the Global South. This study addresses this geographic bias by providing the first comprehensive ecological survey of macroparasite communities of fishes in a West African Marine Protected Area (MPA) and adjacent Open-Access Area (OAA) characterised by mangrove forests. We collected 5,020 parasite specimens from 10 fish and one crab species in the Saloum Delta, Senegal, identifying 27 parasite species across all major taxa. Our findings include 15 new records for Senegal of which 11 are also new for West Africa. Additionally, 64% of host-parasite combinations constitute new host records. We provide 208 DNA barcodes, offering the first molecular data for 31% of these species globally and establishing a reference library for future DNA metabarcoding efforts in the region. Using sample size-corrected biodiversity indices and mixed-model analyses, we detected significant variations in parasite infracommunities and component communities between the MPA and OAA, demonstrating the feasibility of using comparative study designs to monitor fisheries impacts on parasite diversity in the Saloum Delta. Furthermore, the identification of trophically transmitted parasites provided evidence of unstudied food-web connections, e.g. predator-prey linkages between fishes and higher-trophic-level definitive hosts including birds and elasmobranchs. By integrating morphological identification, molecular data, and archiving of voucher specimens into publicly accessible, curated collections, this study establishes a new baseline for marine parasite biodiversity in West Africa and provides a methodological blueprint for surveying understudied regions.

zoology↗