Science Enabled by Specimen Data

Smith, A. B., S. J. Murphy, D. Henderson, and K. D. Erickson. 2023. Including imprecisely georeferenced specimens improves accuracy of species distribution models and estimates of niche breadth. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13628

Aim Museum and herbarium specimen records are frequently used to assess the conservation status of species and their responses to climate change. Typically, occurrences with imprecise geolocality information are discarded because they cannot be matched confidently to environmental conditions and are thus expected to increase uncertainty in downstream analyses. However, using only precisely georeferenced records risks undersampling of the environmental and geographical distributions of species. We present two related methods to allow the use of imprecisely georeferenced occurrences in biogeographical analysis. Innovation Our two procedures assign imprecise records to the (1) locations or (2) climates that are closest to the geographical or environmental centroid of the precise records of a species. For virtual species, including imprecise records alongside precise records improved the accuracy of ecological niche models projected to the present and the future, especially for species with c. 20 or fewer precise occurrences. Using only precise records underestimated loss of suitable habitat and overestimated the amount of suitable habitat in both the present and the future. Including imprecise records also improves estimates of niche breadth and extent of occurrence. An analysis of 44 species of North American Asclepias (Apocynaceae) yielded similar results. Main conclusions Existing studies examining the effects of spatial imprecision typically compare outcomes based on precise records against the same records with spatial error added to them. However, in real-world cases, analysts possess a mix of precise and imprecise records and must decide whether to retain or discard the latter. Discarding imprecise records can undersample the geographical and environmental distributions of species and lead to mis-estimation of responses to past and future climate change. Our method, for which we provide a software implementation in the enmSdmX package for R, is simple to use and can help leverage the large number of specimen records that are typically deemed “unusable” because of spatial imprecision in their geolocation.

Ecke, F., B. A. Han, B. Hörnfeldt, H. Khalil, M. Magnusson, N. J. Singh, and R. S. Ostfeld. 2022. Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses. Nature Communications 13. https://doi.org/10.1038/s41467-022-35273-7

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species’ synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world. Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.

Pelletier, D., and J. R. K. Forrest. 2022. Pollen specialisation is associated with later phenology in Osmia bees (Hymenoptera: Megachilidae). Ecological Entomology. https://doi.org/10.1111/een.13211

Species exhibit a range of specialisation in diet and other niche axes, with specialists typically thought to be more efficient in resource use but more vulnerable to extinction than generalists. Among herbivorous insects, dietary specialists seem more likely to lack acceptable host plants during the insect's feeding stage, owing to fluctuations in host‐plant abundance or phenology. Like other herbivores, bee species vary in host breadth from pollen specialisation (oligolecty) to generalisation (polylecty).Several studies have shown greater interannual variation in flowering phenology for earlier‐flowering plants than later‐flowering plants, suggesting that early‐season bees may experience substantial year‐to‐year variation in the floral taxa available to them.It was therefore reasoned that, among bees, early phenology could be a more viable strategy for generalists, which can use resources from multiple floral taxa, than for specialists. Consequently, it was expected that the median dates of collection of adult specimens to be earlier for generalist species than for specialists. To test this, phenology data and pollen diet information on 67 North American species of the bee genus Osmia was obtained.Controlling for latitude and phylogeny, it was found that dietary generalisation is associated with significantly earlier phenology, with generalists active, on average, 11–14 days earlier than specialists.This result is consistent with the generalist strategy being more viable than the specialist strategy for species active in early spring, suggesting that dietary specialisation may constrain the evolution of bee phenology—or vice versa.

Christman, M. E., L. R. Spears, J. B. U. Koch, T.-T. T. Lindsay, J. P. Strange, C. L. Barnes, and R. A. Ramirez. 2022. Captive Rearing Success and Critical Thermal Maxima of Bombus griseocollis (Hymenoptera: Apidae): A Candidate for Commercialization? J. Brunet [ed.],. Journal of Insect Science 22. https://doi.org/10.1093/jisesa/ieac064

Abstract Commercialized bumble bees (Bombus) are primary pollinators of several crops within open field and greenhouse settings. However, the common eastern bumble bee (Bombus impatiens Cresson, 1863) is the only species widely available for purchase in North America. As an eastern species, concerns have been expressed over their transportation outside of their native range. Therefore, there is a need to identify regionally appropriate candidates for commercial crop pollination services, especially in the western U.S.A. In this study, we evaluated the commercialization potential of brown-belted bumble bees (Bombus griseocollis De Geer, 1773), a broadly distributed species throughout the U.S.A., by assessing nest initiation and establishment rates of colonies produced from wild-caught gynes, creating a timeline of colony development, and identifying lab-reared workers’ critical thermal maxima (CTMax) and lethal temperature (ecological death). From 2019 to 2021, 70.6% of the wild-caught B. griseocollis gynes produced brood in a laboratory setting. Of these successfully initiated nests, 74.8% successfully established a nest (produced a worker), providing guidance for future rearing efforts. Additionally, lab-reared workers produced from wild-caught B. griseocollis gynes had an average CTMax of 43.5°C and an average lethal temperature of 46.4°C, suggesting B. griseocollis can withstand temperatures well above those commonly found in open field and greenhouse settings. Overall, B. griseocollis should continue to be evaluated for commercial purposes throughout the U.S.A.

Liu, S., S. Xia, D. Wu, J. E. Behm, Y. Meng, H. Yuan, P. Wen, et al. 2022. Understanding global and regional patterns of termite diversity and regional functional traits. iScience: 105538. https://doi.org/10.1016/j.isci.2022.105538

Our understanding of broad-scale biodiversity and functional trait patterns is largely based on plants, and relatively little information is available on soil arthropods. Here, we investigated the distribution of termite diversity globally and morphological traits and diversity across China. Our analyses showed increasing termite species richness with decreasing latitude at both the globally, and within-China. Additionally, we detected obvious latitudinal trends in the mean community value of termite morphological traits on average, with body size and leg length decreasing with increasing latitude. Furthermore, temperature, NDVI and water variables were the most important drivers controlling the variation in termite richness, and temperature and soil properties were key drivers of the geographic distribution of termite morphological traits. Our global termite richness map is one of the first high resolution maps for any arthropod group and especially given the functional importance of termites, our work provides a useful baseline for further ecological analysis.

Inman, R. D., T. C. Esque, and K. E. Nussear. 2022. Dispersal limitations increase vulnerability under climate change for reptiles and amphibians in the southwestern United States. The Journal of Wildlife Management. https://doi.org/10.1002/jwmg.22317

Species conservation plans frequently rely on information that spans political and administrative boundaries, especially when predictions are needed of future habitat under climate change; however, most species conservation plans and their requisite predictions of future habitat are often limited in geographical scope. Moreover, dispersal constraints for species of concern are not often incorporated into distribution models, which can result in overly optimistic predictions of future habitat. We used a standard modeling approach across a suite of 23 taxa of amphibians and reptiles in the North American deserts (560,024 km2 across 13 ecoregions) to assess impacts of climate change on habitat and combined landscape population dispersal simulations with species distribution modeling to reduce the risk of predicting future habitat in areas that are not available to species given their dispersal abilities. We used 3 general circulation models and 2 representative concentration pathways (RCPs) to represent multiple scenarios of future habitat potential and assess which study species may be most vulnerable to changes forecasted under each climate scenario. Amphibians were the most vulnerable taxa, but the most vulnerable species tended to be those with the lowest dispersal ability rather than those with the most specialized niches. Under the most optimistic climate scenario considered (RCP 2.6; a stringent scenario requiring declining emissions from 2020 to near zero emissions by 2100), 76% of the study area may experience a loss of >20% of the species examined, while up to 87% of the species currently present may be lost in some areas under the most pessimistic climate scenario (RCP 8.5; a scenario wherein greenhouse gases continue to increase through 2100 based on trajectories from the mid‐century). Most areas with high losses were concentrated in the Arizona and New Mexico Plateau ecoregion, the Edwards Plateau in Texas, and the Southwestern Tablelands in New Mexico and Texas, USA. Under the most pessimistic climate scenario, all species are predicted to lose some existing habitat, with an average of 34% loss of extant habitat across all species. Even under the most optimistic scenario, we detected an average loss of 24% of extant habitat across all species, suggesting that changing climates may influence the ranges of reptiles and amphibians in the Southwest.

Lee, W.-H., J.-W. Song, S.-H. Yoon, and J.-M. Jung. 2022. Spatial Evaluation of Machine Learning-Based Species Distribution Models for Prediction of Invasive Ant Species Distribution. Applied Sciences 12: 10260. https://doi.org/10.3390/app122010260

Recent advances in species distribution models (SDMs) associated with artificial intelligence (AI) and increased volumes of available data for model variables have allowed reliable evaluation of the potential distribution of any species. A reliable SDM requires suitable occurrence records and variables with optimal model structures. In this study, we developed three different machine learning-based SDMs [MaxEnt, random forest (RF), and multi-layer perceptron (MLP)] to predict the global potential distribution of two invasive ants under current and future climates. These SDMs showed that the potential distribution of Solenopsis invicta would be expanded by climatic change, whereas it would not significantly change for Anoplolepis gracilipes. The models were compared using model performance metrics, and the optimal model structure and spatial projection were selected. The MaxEnt exhibited high performance, while the MLP model exhibited low performance, with the largest variation by climate change. Random forest showed the smallest potential distribution area, but it was robust considering the number of occurrence records and changes in model variables. All the models showed reliable performance, but the difference in performance and projection size suggested that optimal model selection based on data availability, model variables, study objectives, or an ensemble approach was necessary to develop a comprehensive SDM to minimize modeling uncertainty. We expect that this study will help with the use of AI-based SDMs for the evaluation and risk assessment of invasive ant species.

Roberts, J., and S. Florentine. 2022. Biology, distribution and management of the globally invasive weed Solanum elaeagnifolium Cav (silverleaf nightshade): A global review of current and future management challenges. Weed Research. https://doi.org/10.1111/wre.12556

Solanum elaeagnifolium Cav (silverleaf nightshade) is a deep-rooted, multi-stemmed, perennial, herbaceous woody plant that has been observed to threaten agricultural and native biodiversity worldwide. It is widely agreed that without efficient integrated management, S. elaeagnifolium will continue to cause significant economic and environmental damage across multiple scales. It is estimated that the annual economic impact of S. elaeagnifolium in Australia exceeds AUD $62 million, with this figure likely to be much higher in other countries invaded by this plant. It can also tolerate a high level of abiotic stress and survive in a range of temperatures (below freezing point to 34°C) and areas with an average yearly rainfall between 250 and 600 mm. Its extensive deep taproot system is capable of regenerating asexually and with its many seed dispersal mechanisms; it can quickly spread and establish itself within a region. This makes containment and management of the species especially challenging. Previous management has largely been focused on biological control, competition, essential oils, grazing pressure, herbicide application and manual removal. Despite the large range of available management techniques, there has been little success in the long-term control of S. elaeagnifolium, and only a handful of methods such as essential oils and herbicide application have shown reasonable success for controlling this weed. Therefore, this review aims to synthesise the identified and potentially useful approaches to control S. elaeagnifolium that have been recorded in the literature which deal with its biology, distribution and management. It also explores previous and current management techniques to ascertain the research gaps and knowledge required to assist in the effective and economically sustainable management of this invasive weed.

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

Lu, L.-L., B.-H. Jiao, F. Qin, G. Xie, K.-Q. Lu, J.-F. Li, B. Sun, et al. 2022. Artemisia pollen dataset for exploring the potential ecological indicators in deep time. Earth System Science Data 14: 3961–3995. https://doi.org/10.5194/essd-14-3961-2022

Abstract. Artemisia, along with Chenopodiaceae, is the dominant component growing in the desert and dry grassland of the Northern Hemisphere. Artemisia pollen with its high productivity, wide distribution, and easy identification is usually regarded as an eco-indicator for assessing aridity and distinguishing grassland from desert vegetation in terms of the pollen relative abundance ratio of Chenopodiaceae/Artemisia (C/A). Nevertheless, divergent opinions on the degree of aridity evaluated by Artemisia pollen have been circulating in the palynological community for a long time. To solve the confusion, we first selected 36 species from nine clades and three outgroups of Artemisia based on the phylogenetic framework, which attempts to cover the maximum range of pollen morphological variation. Then, sampling, experiments, photography, and measurements were taken using standard methods. Here, we present pollen datasets containing 4018 original pollen photographs, 9360 pollen morphological trait measurements, information on 30 858 source plant occurrences, and corresponding environmental factors. Hierarchical cluster analysis on pollen morphological traits was carried out to subdivide Artemisia pollen into three types. When plotting the three pollen types of Artemisia onto the global terrestrial biomes, different pollen types of Artemisia were found to have different habitat ranges. These findings change the traditional concept of Artemisia being restricted to arid and semi-arid environments. The data framework that we designed is open and expandable for new pollen data of Artemisia worldwide. In the future, linking pollen morphology with habitat via these pollen datasets will create additional knowledge that will increase the resolution of the ecological environment in the geological past. The Artemisia pollen datasets are freely available at Zenodo (https://doi.org/10.5281/zenodo.6900308; Lu et al., 2022).