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Science Enabled by Specimen Data

Raggi, L., C. Zucchini, E. Sayde, D. Gigante, and V. Negri. 2024. Priority areas for the establishment of genetic reserves to actively protect key crop wild relative species in Italy. Global Ecology and Conservation 50: e02836. https://doi.org/10.1016/j.gecco.2024.e02836

Crop Wild Relatives (CWR) are wild plant taxa genetically close to a crop. Being a precious source of genetic variability and of traits for crop improvement, CWR have a high socio-economic value and are identified among the main plant genetic resources. Alarming enough, the inter- and intraspecific diversity, as well as their habitat diversity, is under threat of irremediable loss. Italy is the second richest country in Europe in terms of plant species number; applying the taxon group concept 5712 have been recently identified as CWR. The aims of the present research are to identify the best sites for: i) the institution of genetic reserves to actively protect CWR species of the key crop genera as Allium, Brassica and Triticum and ii) performing new collection missions to reach adequate ex situ conservation of target species. Georeferenced data were retrieved from different online databases. CAPFITOGEN tools were initially used to develop an ecogeographic land characterisation map (ELC) of Italy. Geographical distribution data were assembled for 379 populations of 18 CWR taxa. Results of the complementarity analysis showed that 10 protected areas provide coverage of the 46.4% of the target conservation units and include 66.7% of the priority CWR taxa investigated. Alarming enough, only 7.4% of the 379 populations are currently conserved ex situ; among the 18 ecogeographic land characterisation categories only 3 are covered by ex situ conservation. This is the first study where most suitable protected areas for the institution of genetic reserves are proposed for Italy for the protection of multiple CWR taxa of key genera; this is relevant also considering the global value of many of the related crop such as different wheat species, cabbages, rape, garlic and onion. Being already dedicated to habitat and species conservation, the identified sites are optimal candidates for the institution of genetic reserves. Results will hopefully also guide new collecting missions that are urgently needed to strength ex situ conservation of such precious genetic resources.

Grether, G. F., A. E. Finneran, and J. P. Drury. 2023. Niche differentiation, reproductive interference, and range expansion. Ecology Letters. https://doi.org/10.1111/ele.14350

Understanding species distributions and predicting future range shifts requires considering all relevant abiotic factors and biotic interactions. Resource competition has received the most attention, but reproductive interference is another widespread biotic interaction that could influence species ranges. Rubyspot damselflies (Hetaerina spp.) exhibit a biogeographic pattern consistent with the hypothesis that reproductive interference has limited range expansion. Here, we use ecological niche models to evaluate whether this pattern could have instead been caused by niche differentiation. We found evidence for climatic niche differentiation, but the species that encounters the least reproductive interference has one of the narrowest and most peripheral niches. These findings strengthen the case that reproductive interference has limited range expansion and also provide a counterexample to the idea that release from negative species interactions triggers niche expansion. We propose that release from reproductive interference enables species to expand in range while specializing on the habitats most suitable for breeding.

Grigoropoulou, A., S. A. Hamid, R. Acosta, E. O. Akindele, S. A. Al‐Shami, F. Altermatt, G. Amatulli, et al. 2023. The global EPTO database: Worldwide occurrences of aquatic insects. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13648

Motivation Aquatic insects comprise 64% of freshwater animal diversity and are widely used as bioindicators to assess water quality impairment and freshwater ecosystem health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater biodiversity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database, which includes worldwide geo-referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO). Main type of variables contained A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the corresponding drainage basin and sub-catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the protection status of their location. Spatial location and grain The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m precision at the equator) in the World Geodetic System 1984 (WGS84) coordinate reference system. Time period and grain Sampling years span from 1951 to 2021. Ninety-nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub-datasets, exact dates can be retrieved upon communication with the data contributors. Major taxa and level of measurement Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification. Software format The entire tab-separated value (.csv) database can be downloaded and visualized at https://glowabio.org/project/epto_database/. Fifty individual datasets are also available at https://fred.igb-berlin.de, while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors.

Reichgelt, T., A. Baumgartner, R. Feng, and D. A. Willard. 2023. Poleward amplification, seasonal rainfall and forest heterogeneity in the Miocene of the eastern USA. Global and Planetary Change 222: 104073. https://doi.org/10.1016/j.gloplacha.2023.104073

Paleoclimate reconstructions can provide a window into the environmental conditions in Earth history when atmospheric carbon dioxide concentrations were higher than today. In the eastern USA, paleoclimate reconstructions are sparse, because terrestrial sedimentary deposits are rare. Despite this, the eastern USA has the largest population and population density in North America, and understanding the effects of current and future climate change is of vital importance. Here, we provide terrestrial paleoclimate reconstructions of the eastern USA from Miocene fossil floras. Additionally, we compare proxy paleoclimate reconstructions from the warmest period in the Miocene, the Miocene Climatic Optimum (MCO), to those of an MCO Earth System Model. Reconstructed Miocene temperatures and precipitation north of 35°N are higher than modern. In contrast, south of 35°N, temperatures and precipitation are similar to today, suggesting a poleward amplification effect in eastern North America. Reconstructed Miocene rainfall seasonality was predominantly higher than modern, regardless of latitude, indicating greater variability in intra-annual moisture transport. Reconstructed climates are almost uniformly in the temperate seasonal forest biome, but heterogeneity of specific forest types is evident. Reconstructed Miocene terrestrial temperatures from the eastern USA are lower than modeled temperatures and coeval Atlantic sea surface temperatures. However, reconstructed rainfall is consistent with modeled rainfall. Our results show that during the Miocene, climate was most different from modern in the northeastern states, and may suggest a drastic reduction in the meridional temperature gradient along the North American east coast compared to today.

Führding‐Potschkat, P., H. Kreft, and S. M. Ickert‐Bond. 2022. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9168

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Chevalier, M. 2022. <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844. https://doi.org/10.5194/cp-18-821-2022

Abstract. Statistical climate reconstruction techniques are fundamental tools to study past climate variability from fossil proxy data. In particular, the methods based on probability density functions (or PDFs) can be used in various environments and with different climate proxies because they rely on elementary calibration data (i.e. modern geolocalised presence data). However, the difficulty of accessing and curating these calibration data and the complexity of interpreting probabilistic results have often limited their use in palaeoclimatological studies. Here, I introduce a new R package (crestr) to apply the PDF-based method CREST (Climate REconstruction SofTware) on diverse palaeoecological datasets and address these problems. crestr includes a globally curated calibration dataset for six common climate proxies (i.e. plants, beetles, chironomids, rodents, foraminifera, and dinoflagellate cysts) associated with an extensive range of climate variables (20 terrestrial and 19 marine variables) that enables its use in most terrestrial and marine environments. Private data collections can also be used instead of, or in combination with, the provided calibration dataset. The package includes a suite of graphical diagnostic tools to represent the data at each step of the reconstruction process and provide insights into the effect of the different modelling assumptions and external factors that underlie a reconstruction. With this R package, the CREST method can now be used in a scriptable environment and thus be more easily integrated with existing workflows. It is hoped that crestr will be used to produce the much-needed quantified climate reconstructions from the many regions where they are currently lacking, despite the availability of suitable fossil records. To support this development, the use of the package is illustrated with a step-by-step replication of a 790 000-year-long mean annual temperature reconstruction based on a pollen record from southeastern Africa.

Yousefi, M., A. Mahmoudi, A. Kafash, A. Khani, and B. Kryštufek. 2022. Biogeography of rodents in Iran: species richness, elevational distribution and their environmental correlates. Mammalia 86: 309–320. https://doi.org/10.1515/mammalia-2021-0104

Abstract Rodent biogeographic studies are disproportionately scarce in Iran, however, they are an ideal system to understand drivers of biodiversity distributions in the country. The aims of the present research are to determine (i) the pattern of rodent richness across the country, (ii) quantify th…

Boulad, N., S. Al Shogoor, W. Sahwan, N. Al-Ouran, and B. Schütt. 2021. Systematic Conservation Planning as a Tool for the Assessment of Protected Areas Network in Jordan. Land 11: 56. https://doi.org/10.3390/land11010056

The present study aims to use systematic conservation planning to analyse and review the national protected areas (PAs) network in Jordan. The analysis included the application of three modules: the environmental risk surface (ERS), the relative biodiversity index (RBI), and the application of Marxa…

Vasconcelos, T., J. D. Boyko, and J. M. Beaulieu. 2021. Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography. https://doi.org/10.1111/jbi.14292

Aim: Due to the sessile nature of flowering plants, movements to new geographical areas occur mainly during seed dispersal. Frugivores tend to be efficient dispersers because animals move within the boundaries of their preferable niches, so seeds are more likely to be transported to environments tha…

Alban, D. M., E. M. Biersma, J. W. Kadereit, and M. S. Dillenberger. 2021. Colonization of the Southern Hemisphere by Sagina and Colobanthus (Caryophyllaceae). Plant Systematics and Evolution 308. https://doi.org/10.1007/s00606-021-01793-w

Colobanthus (23 species) and Sagina (30–33 species) together are sister to Facchinia. Whereas Facchinia is distributed in western Eurasia, Colobanthus is almost exclusively distributed in the Southern Hemisphere, and Sagina is distributed in both hemispheres with the highest species diversity in wes…