Science Enabled by Specimen Data

Pan, Y., J. García-Girón, and L. L. Iversen. 2023. Global change and plant-ecosystem functioning in freshwaters. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.12.013

Freshwater ecosystems are of worldwide importance for maintaining biodiversity and sustaining the provision of a myriad of ecosystem services to modern societies. Plants, one of the most important components of these ecosystems, are key to water nutrient removal, carbon storage, and food provision. Understanding how the functional connection between freshwater plants and ecosystems is affected by global change will be key to our ability to predict future changes in freshwater systems. Here, we synthesize global plant responses, adaptations, and feedbacks to present-day and future freshwater environments through trait-based approaches, from single individuals to entire communities. We outline the transdisciplinary knowledge benchmarks needed to further understand freshwater plant biodiversity and the fundamental services they provide.

Baltensperger, A., J. Hagelin, P. Schuette, A. Droghini, and K. Ott. 2022. High dietary and habitat diversity indicate generalist behaviors of northern bog lemmings Synaptomys borealis in Alaska, USA. Endangered Species Research 49: 145–158. https://doi.org/10.3354/esr01211

The northern bog lemming Synaptomys borealis (NBL) is a rare small mammal that is undergoing a federal Species Status Assessment (SSA) under the US Endangered Species Act. Despite a wide North American distribution, very little is known about NBL dietary or habitat needs, both of which are germane to the resiliency of this species to climate change. To quantify diet composition of NBL in Alaska, we used DNA metabarcoding from 59 archived specimens to describe the taxonomic richness and relative abundance of foods in recent diets. DNA analyses revealed a broad diet composed of at least 110 families and 92 genera of bryophytes (mosses and liverworts), graminoids, fungi, forbs, and woody shrubs. Nine bryophyte genera and Carex sedges composed the largest portions of NBL diets. To quantify habitat preference, we intersected 467 georeferenced occurrence records of NBL in Alaska with remotely sensed land cover classes and used a compositional analysis framework that accounts for the relative abundance of land cover types. We did not detect significant habitat preferences for specific land cover types, although NBL frequently occurred in evergreen forest, woody wetlands, and adjacent to water. Our research highlights the importance of bryophytes, among a high diversity of dietary components, and describes NBL as boreal habitat generalists. Results will inform the current federal SSA by quantifying the extent to which ecological constraints are likely to affect NBL in a rapidly changing boreal environment.

Kroonen, G., A. Jakob, A. I. Palmér, P. van Sluis, and A. Wigman. 2022. Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages S. Wichmann [ed.],. PLOS ONE 17: e0275744. https://doi.org/10.1371/journal.pone.0275744

Questions on the timing and the center of the Indo-European language dispersal are central to debates on the formation of the European and Asian linguistic landscapes and are deeply intertwined with questions on the archaeology and population history of these continents. Recent palaeogenomic studies support scenarios in which the core Indo-European languages spread with the expansion of Early Bronze Age Yamnaya herders that originally inhabited the East European steppes. Questions on the Yamnaya and Pre-Yamnaya locations of the language community that ultimately gave rise to the Indo-European language family are heavily dependent on linguistic reconstruction of the subsistence of Proto-Indo-European speakers. A central question, therefore, is how important the role of agriculture was among the speakers of this protolanguage. In this study, we perform a qualitative etymological analysis of all previously postulated Proto-Indo-European terminology related to cereal cultivation and cereal processing. On the basis of the evolution of the subsistence strategies of consecutive stages of the protolanguage, we find that one or perhaps two cereal terms can be reconstructed for the basal Indo-European stage, also known as Indo-Anatolian, but that core Indo-European, here also including Tocharian, acquired a more elaborate set of terms. Thus, we linguistically document an important economic shift from a mostly non-agricultural to a mixed agro-pastoral economy between the basal and core Indo-European speech communities. It follows that the early, eastern Yamnaya of the Don-Volga steppe, with its lack of evidence for agricultural practices, does not offer a perfect archaeological proxy for the core Indo-European language community and that this stage of the language family more likely reflects a mixed subsistence as proposed for western Yamnaya groups around or to the west of the Dnieper River.

Aguirre‐Liguori, J. A., A. Morales‐Cruz, and B. S. Gaut. 2022. Evaluating the persistence and utility of five wild Vitis species in the context of climate change. Molecular Ecology. https://doi.org/10.1111/mec.16715

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for the persistence of perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of samples from five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was to assess the relative potential of different CWR accessions to persist in the face of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load and a phenotype (resistance to Pierce’s Disease), we predicted that accessions from one species (V. mustangensis) are particularly well‐suited to persist in future climates. The second goal was to identify which CWR accessions may contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we evaluated whether CWR accessions have the allelic capacity to persist if moved to locations where grapevines (V. vinifera) are cultivated in the United States. We identified six candidates from V. mustangensis and hypothesized that they may prove useful for contributing alleles that can mitigate climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward assessing the genomic and bioclimatic characteristics of CWRs.

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).

Nygaard, M., A. Kopatz, J. M. D. Speed, M. D. Martin, T. Prestø, O. Kleven, and M. Bendiksby. 2022. Spatiotemporal monitoring of the rare northern dragonhead ( Dracocephalum ruyschiana , Lamiaceae) — SNP genotyping and environmental niche modeling herbarium specimens. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9187

The species we have studied the spatiotemporal genetic change in the northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We have added a temporal perspective to the monitoring of northern dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We have also assessed whether northern dragonhead has achieved its potential distribution in Norway. To obtain the genotype data from 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47), we applied a microfluidic array consisting of 96 SNP markers. To assess temporal genetic change, we compared our new genotype data with existing data from modern samples. We used sample metadata and observational records to model the species' environmental niche and potential distribution in Norway. Our results show that the SNP array successfully genotyped all included herbarium specimens. Hence, with the appropriate design procedures, the SNP array technology appears highly promising for genotyping old herbarium specimens. The captured genetic diversity correlates negatively with distance from Norway. The historical‐modern comparisons reveal similar genetic structure and diversity across space and limited genetic change through time in Norway, providing no signs of any regional bottleneck (i.e., spatiotemporal stasis). The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM results suggest that northern dragonhead has not fully achieved its potential distribution in Norway and corroborate that the species is anchored in warmer and drier habitats.

Hirabayashi, K., S. J. Murch, and L. A. E. Erland. 2022. Predicted impacts of climate change on wild and commercial berry habitats will have food security, conservation and agricultural implications. Science of The Total Environment 845: 157341. https://doi.org/10.1016/j.scitotenv.2022.157341

Climate change is now a reality and is altering ecosystems, with Canada experiencing 2–4 times the global average rate of warming. This will have a critical impact on berry cultivation and horticulture. Enhancing our understanding of how wild and cultivated berries will perform under changing climates will be essential to mitigating impacts on ecosystems, culture and food security. Our objective was to predict the impact of climate change on habitat suitability of four berry producing Vaccinium species: two species with primarily northern distributions (V. uliginosum, V. vitis-idaea), one species with a primarily southern distribution (V. oxycoccos), and the commercially cultivated V. macrocarpon. We used the maximum entropy (Maxent) model and the CMIP6 shared socioeconomic pathways (SSPs) 126 and 585 projected to 2041–2060 and 2061–2080. Wild species showed a uniform northward progression and expansion of suitable habitat. Our modeling predicts that suitable growing regions for commercial cranberries are also likely to shift with some farms becoming unsuitable for the current varieties and other regions becoming more suitable for cranberry farms. Both V. macrocarpon and V. oxycoccos showed a high dependence on precipitation-associated variables. Vaccinium vitis-idaea and V. uliginosum had a greater number of variables with smaller contributions which may improve their resilience to individual climactic events. Future competition between commercial cranberry farms and wild berries in protected areas could lead to conflicts between agriculture and conservation priorities. New varieties of commercial berries are required to maintain current commercial berry farms.

Pérez, G., M. Vilà, and B. Gallardo. 2022. Potential impact of four invasive alien plants on the provision of ecosystem services in Europe under present and future climatic scenarios. Ecosystem Services 56: 101459. https://doi.org/10.1016/j.ecoser.2022.101459

Invasive alien species (IAS) are one of the main threats to biodiversity conservation, with significant socio-economic and ecological impacts as they disrupt ecosystem services and compromise human well-being. Global change may exacerbate the impacts of IAS, since rising temperatures and human activities favour their introduction and range expansion. Therefore, anticipating the impacts of biological invasions is crucial to support decision-making for their management. In this work, the potential impacts of four invasive alien plant species: Ailanthus altissima, Baccharis halimifolia, Impatiens glandulifera and Pueraria montana, on the provision of three ecosystem services in Europe were evaluated under current and future climate change scenarios. Using a risk analysis protocol, we determined that the most affected services are food provisioning, soil erosion regulation and the maintenance of biological diversity. To evaluate future impacts, species distribution models were calibrated using bioclimatic, environmental and human impact variables. We found that most of continental Europe is suitable for the establishment of A. altissima, B. halimifolia and I. glandulifera, while the potential distribution of P. montana is more limited. Models anticipate a shift in the distribution range for the species towards the north and east of Europe under future scenarios. Bivariate analysis allowed the identification of trends for future impacts in ecosystem services by simultaneously visualising the potential distribution of invasive species and the provision of ecosystem services. Our models project an increase in critical and high impact areas on the analysed ecosystem services, with Western Europe and the British Isles as the most affected regions. In comparison, lower impacts are projected for the Mediterranean region, likely as a consequence of the northwards expansion of invaders. Measures need to be taken to mitigate the expansion and impact of invasive species as our work shows that it can jeopardise the provision of three key services in Europe.

To clarify biogeographic patterns of two mushroom species (Phallus merulinus and Geastrum courtecuissei) previously reported from Myanmar, sequence data of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were retrieved from GenBank. The BLAST search and phylogenetic analyses of Phallus indicated that P. merulinus and P. atrovolvatus from wide areas, including Australia, Myanmar, Thailand, Brazil, and French Guiana, cannot be distinguished molecularly. The species was, therefore, considered widespread across tropical to subtropical regions. In contrast, G. courtecuissei from Myanmar was tightly clustered exclusively with G. courtecuissei from Central and South America, supporting the idea of its disjunct distribution between Southeast Asia (Myanmar) and Central-South Americas.