Science Enabled by Specimen Data

Tang, T., Y. Zhu, Y.-Y. Zhang, J.-J. Chen, J.-B. Tian, Q. Xu, B.-G. Jiang, et al. 2024. The global distribution and the risk prediction of relapsing fever group Borrelia: a data review with modelling analysis. The Lancet Microbe.

Background The recent discovery of emerging relapsing fever group Borrelia (RFGB) species, such as Borrelia miyamotoi, poses a growing threat to public health. However, the global distribution and associated risk burden of these species remain uncertain. We aimed to map the diversity, distribution, and potential infection risk of RFGB.MethodsWe searched PubMed, Web of Science, GenBank, CNKI, and eLibrary from Jan 1, 1874, to Dec 31, 2022, for published articles without language restriction to extract distribution data for RFGB detection in vectors, animals, and humans, and clinical information about human patients. Only articles documenting RFGB infection events were included in this study, and data for RFGB detection in vectors, animals, or humans were composed into a dataset. We used three machine learning algorithms (boosted regression trees, random forest, and least absolute shrinkage and selection operator logistic regression) to assess the environmental, ecoclimatic, biological, and socioeconomic factors associated with the occurrence of four major RFGB species: Borrelia miyamotoi, Borrelia lonestari, Borrelia crocidurae, and Borrelia hermsii; and mapped their worldwide risk level.FindingsWe retrieved 13 959 unique studies, among which 697 met the selection criteria and were used for data extraction. 29 RFGB species have been recorded worldwide, of which 27 have been identified from 63 tick species, 12 from 61 wild animals, and ten from domestic animals. 16 RFGB species caused human infection, with a cumulative count of 26 583 cases reported from Jan 1, 1874, to Dec 31, 2022. Borrelia recurrentis (17 084 cases) and Borrelia persica (2045 cases) accounted for the highest proportion of human infection. B miyamotoi showed the widest distribution among all RFGB, with a predicted environmentally suitable area of 6·92 million km2, followed by B lonestari (1·69 million km2), B crocidurae (1·67 million km2), and B hermsii (1·48 million km2). The habitat suitability index of vector ticks and climatic factors, such as the annual mean temperature, have the most significant effect among all predictive models for the geographical distribution of the four major RFGB species.InterpretationThe predicted high-risk regions are considerably larger than in previous reports. Identification, surveillance, and diagnosis of RFGB infections should be prioritised in high-risk areas, especially within low-income regions.FundingNational Key Research and Development Program of China.

Hebets, E. A., M. Oviedo-Diego, F. Cargnelutti, F. Bollatti, L. Calbacho-Rosa, C. I. Mattoni, P. Olivero, et al. 2023. A scientist’s guide to Solifugae: how solifuges could advance research in ecology, evolution, and behaviour. Zoological Journal of the Linnean Society.

Despite having >1200 described species and despite their nearly worldwide distribution and prevalence in many xeric ecosystems, relative to many other arachnid groups, we know little about the natural history and behaviour of animals in the order Solifugae (camel spiders, sun spiders, sun scorpions, etc.). Here, we review the current solifuge literature through the lens of conceptual research areas in ecology, evolution, and behaviour and propose ways in which solifuges can contribute to research in specific subfields, as follows: (i) ecology: community and trophic dynamics; connecting food webs; habitat specialization; and biodiversity and conservation; (ii) evolution: speciation and diversification; activity cycles and associated traits; adaptations for speed; and living in extreme environments; and (iii) behaviour and sensory systems: sleep, quiescence, and diapause; sensory systems and sensory ecology; learning and cognition; and mating systems, sexual selection, and sexual conflict. This resource can provide a starting point for identifying research programmes that will simultaneously contribute basic natural history information about this under-studied group and provide a broader understanding of fundamental concepts and theories across the life sciences. We hope that scientists will take this review as a challenge to develop creative ways of leveraging the unique features of solifuges to advance scientific knowledge and understanding.

Vieira, M. D. C., J. Manger, B. White, J. D. Berson, F. Dempster, and T. A. Evans. 2023. Estimating biocontrol agent spread: A case study using introduced dung beetles. Ecological Entomology.

Insect biological control agents may be released in relatively few locations; thus, the rate of spread is critical to predicting the spatial distribution of the agent.Exotic dung beetles have been introduced into Australia since the 1960s to bury dung, reduce bush fly populations, increase pasture productivity and improve livestock health.We use a stochastic cellular automata model to predict the historical occupancy and abundance of introduced dung beetles in the South West agricultural region of Western Australia. The model predicts the spread of four species of dung beetles in six‐month time steps for 10 years following initial release. Our model includes release locations, species‐specific ecological parameters, dung resource availability and weather variables.The average rate of spread varied between species from a high of ca. 79 km/year (Euoniticellus intermedius) to a low of 28 km/year (Onthophagus taurus). Thus, after 10 years, the area of spread varied between 99,175 and 34,175 km2 and abundance varied from 88,100 to 4,189 beetles/km2.These findings provide an estimate of the spread patterns of dung beetles. The model can be used to guide future dung beetle release programmes in Australia and elsewhere.

Al-Khalaf, A. A., M. G. Nasser, and E. M. Hosni. 2023. Global Potential Distribution of Sarcophaga dux and Sarcophaga haemorrhoidalis under Climate Change. Diversity 15: 903.

Climate change has a direct impact on biodiversity, affecting ecosystems and altering their balance. Many taxa, including insects, are likely to be affected by climate change in terms of geographic distribution. Sarcophagid flies, such as Sarcophaga dux and Sarcophaga haemorrhoidalis, are important flies because of their apparent ecological, forensic, and medical significance. Global habitat suitability varies as a result of climate change. In wildlife management, models that predict species’ spatial distribution are being used more and more, which emphasizes the need for reliable methods to evaluate their accuracy. Consequently, the statistical robustness of maximum entropy was implemented in Maxent to model the current and future global distribution of both flies, involving occurrence data of 155 and 87 points for S. dux and S. haemorrhoidalis, respectively. Based on the Pearson correlation and Jackknife test, five bioclimatic variables were used for current and future predictive models. For future models, two representative concentration pathways (RCPs), 2.6 and 8.5, for 2050 and 2070 were applied. Both statistical parameters, AUC and TSS, were used to assess the resulting models with values equal to 0.80 (±0.01) and 0.9, respectively, for S. dux and equal to 0.86 (±0.01) and 0.92 for S. haemorrhoidalis. The resulting models for S. dux showed high and very high suitability in Europe, Tropical Africa, India, Canada, the United States from Alaska to Florida, Brazil, and Australia. In the case of S. haemorrhoidalis Europe and North and South America displayed low to medium suitability, but North Africa, including Egypt; Tropical Africa; Asia, including Saudi Arabia, India, and China; and Australia showed increased suitability. Decision-makers are put in conflict with their duties to avert destruction in the economic, medical, and ecological sectors by such anticipated models, and use these predictive models as a cornerstone for building a control strategy for such forensically important flies at local spatial scales.

Lopes, D., E. de Andrade, A. Egartner, F. Beitia, M. Rot, C. Chireceanu, V. Balmés, et al. 2023. FRUITFLYRISKMANAGE: A Euphresco project for Ceratitis capitata Wiedemann (Diptera: Tephritidae) risk management applied in some European countries. EPPO Bulletin.

Ceratitis capitata (Wiedemann), the Mediterranean fruit fly or medfly, is one of the world's most serious threats to fresh fruits. It is highly polyphagous (recorded from over 300 hosts) and capable of adapting to a wide range of climates. This pest has spread to the EPPO region and is mainly present in the southern part, damaging Citrus and Prunus. In Northern and Central Europe records refer to interceptions or short‐lived adventive populations only. Sustainable programs for surveillance, spread assessment using models and control strategies for pests such as C. capitata represent a major plant health challenge for all countries in Europe. This article includes a review of pest distribution and monitoring techniques in 11 countries of the EPPO region. This work compiles information that was crucial for a better understanding of pest occurrence and contributes to identifying areas susceptible to potential invasion and establishment. The key outputs and results obtained in the Euphresco project included knowledge transfer about early detection tools and methods used in different countries for pest monitoring. A MaxEnt software model resulted in risk maps for C. capitata in different climatic regions. This is an important tool to help decision making and to develop actions against this pest in the different partner countries.

Hamer, M., M. Kgatla, and B. Petersen. 2023. An assessment of collection specimen data for South African mountain plants and invertebrates. Transactions of the Royal Society of South Africa: 1–19.

South Africa is considered a megadiverse country, with exceptionally high plant and relatively high animal species richness and endemism. The country’s species have been surveyed and studied for over 200 years, resulting in extensive natural science collections and a vast number of scientific papers and books. This study assessed whether existing data portals provide access to occurrence data and investigated the extent of the data in Global Biodiversity Information Facility and its completeness for plants and selected invertebrate taxa. The main focus was preserved specimen data, but some observation data from iNaturalist were also considered for selected analyses. Records that include species-level identification and co-ordinates were mapped in QGIS to show the coverage of collection localities across the country. The records that fall within the mountain range spatial layer were then extracted and counted to identify density of records per mountain range for various taxa. Forty percent of plant records are from mountain localities, and the Atlantic Cape Fold Mountains had the highest density of records. Table Mountain has been extensively collected for plants and invertebrates. A large proportion of the records for invertebrates lacked species-level identification and co-ordinates, resulting in a low number of records for analyses. The accessible data are only a relatively small subset of existing collections, and digitisation and data upgrading is considered a high priority before collecting gaps can be addressed by targeted surveys.

Bento, M., H. Niza, A. Cartaxana, S. Bandeira, J. Paula, and A. M. Correia. 2023. Mind the Gaps: Taxonomic, Geographic and Temporal Data of Marine Invertebrate Databases from Mozambique and São Tomé and Príncipe. Diversity 15: 70.

One of the best ways to share and disseminate biodiversity information is through the digitization of data and making it available via online databases. The rapid growth of publicly available biodiversity data is not without problems which may decrease the utility of online databases. In this study we analyze taxonomic, geographic and temporal data gaps, and bias related to existing data on selected marine invertebrate occurrences along the coastline of two African countries, Mozambique and São Tomé and Príncipe. The final marine invertebrate dataset comprises of 19.910 occurrences, but 32% of the original dataset occurrences were excluded due to data gaps. Most marine invertebrates in Mozambique were collected in seagrasses, whereas in São Tomé and Príncipe they were mostly collected offshore. The dataset has a temporal coverage from 1816 to 2019, with most occurrences collected in the last two decades. This study provides baseline information relevant to a better understanding of marine invertebrate biodiversity data gaps and bias in these habitats along the coasts of these countries. The information can be further applied to complete marine invertebrate data gaps contributing to design informed sampling strategies and advancing refined datasets that can be used in management and conservation plans in both countries.

Moreno, I., J. M. W. Gippet, L. Fumagalli, and P. J. Stephenson. 2022. Factors affecting the availability of data on East African wildlife: the monitoring needs of conservationists are not being met. Biodiversity and Conservation.

Understanding the status and abundance of species is essential for effective conservation decision-making. However, the availability of species data varies across space, taxonomic groups and data types. A case study was therefore conducted in a high biodiversity region—East Africa—to evaluate data biases, the factors influencing data availability, and the consequences for conservation. In each of the eleven target countries, priority animal species were identified as threatened species that are protected by national governments, international conventions or conservation NGOs. We assessed data gaps and biases in the IUCN Red List of Threatened Species, the Global Biodiversity Information Facility and the Living Planet Index. A survey of practitioners and decision makers was conducted to confirm and assess consequences of these biases on biodiversity conservation efforts. Our results showed data on species occurrence and population trends were available for a significantly higher proportion of vertebrates than invertebrates. We observed a geographical bias, with higher tourism income countries having more priority species and more species with data than lower tourism income countries. Conservationists surveyed felt that, of the 40 types of data investigated, those data that are most important to conservation projects are the most difficult to access. The main challenges to data accessibility are excessive expense, technological challenges, and a lack of resources to process and analyse data. With this information, practitioners and decision makers can prioritise how and where to fill gaps to improve data availability and use, and ensure biodiversity monitoring is improved and conservation impacts enhanced.

Pazmiño-Palomino, A., C. Reyes-Puig, and A. Del Hierro. 2022. How could climate change influence the distribution of the black soldier fly, Hermetia illucens (Linnaeus) (Diptera, Stratiomyidae)? Biodiversity Data Journal 10.

The black soldier fly, Hermetiaillucens (Linnaeus, 1758), is a saprophagous species used to decompose organic matter. This study proposes a distribution model of H.illucens to illustrate its current and future distribution. The methodology includes data collection from the Global Biodiversity Information Facility (GBIF), complemented with iNaturalist, manual expert curation of occurrence records, six species distribution models algorithms and one ensemble model. The average temperature of the driest annual quarter and the precipitation of the coldest annual quarter were the key variables influencing the potential distribution of H.illucens. The distribution range is estimated to decrease progressively and their suitable habitats could change dramatically in the future due to global warming. On the other hand, current optimal habitats would become uninhabitable for the species, mainly at low latitudes. Under this scenario, the species is projected to move to higher latitudes and elevations in the future. The results of this study provide data on the distribution of H.illucens, facilitating its location, management and sustainable use in current and future scenarios.

Lule, S. A., R. Gibb, D. Kizito, G. Nakanjako, J. Mutyaba, S. Balinandi, L. Owen, et al. 2022. Widespread exposure to Crimean-Congo haemorrhagic fever in Uganda might be driven by transmission from Rhipicephalus ticks: Evidence from cross-sectional and modelling studies. Journal of Infection.

BackgroundCrimean-Congo haemorrhagic fever (CCHF) is a widespread tick-borne viral infection, present across Africa and Eurasia, which might pose a cryptic public health problem in Uganda. We aimed to understand the magnitude and distribution of CCHF risk in humans, livestock and ticks across Uganda by synthesising epidemiological (cross-sectional) and ecological (modelling) studies.MethodsWe conducted a cross-sectional study at three urban abattoirs receiving cattle from across Uganda. We sampled humans (n = 478), livestock (n = 419) and ticks (n = 1065) and used commercially-available kits to detect human and livestock CCHF virus (CCHFV) antibodies and antigen in tick pools. We developed boosted regression tree models to evaluate the correlates and geographical distribution of expected tick and wildlife hosts, and of human CCHF exposures, drawing on continent-wide data.FindingsThe cross-sectional study found CCHFV IgG/IgM seroprevalence in humans of 10·3% (7·8–13·3), with antibody detection positively associated with reported history of tick bite (age-adjusted odds ratio = 2·09 (1·09–3·98)). Cattle had a seroprevalence of 69·7% (65·1–73·4). Only one Hyalomma tick (CCHFV-negative) was found. However, CCHFV antigen was detected in Rhipicephalus (5·9% of 304 pools) and Amblyomma (2·9% of 34 pools) species. Modelling predicted high human CCHF risk across much of Uganda, low environmental suitability for Hyalomma, and high suitability for Rhipicephalus and Amblyomma.InterpretationOur epidemiological and ecological studies provide complementary evidence that CCHF exposure risk is widespread across Uganda. We challenge the idea that Hyalomma ticks are consistently the principal reservoir and vector for CCHFV, and postulate that Rhipicephalus might be important for CCHFV transmission in Uganda, due to high frequency of infected ticks and predicted environmental suitability.FundingUCL Global Challenges Research Fund (GCRF) and Pan-African Network on Emerging and Re-Emerging Infections (PANDORA-ID-NET) funded by the European and Developing Countries Clinical Trials Partnership (EDCTP) under the EU Horizon 2020 Framework Programme for Research and Innovation.