Science Enabled by Specimen Data

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.

Heo, N., M. V. Lomolino, J. E. Watkins, S. Yun, J. Weber-Townsend, and D. D. Fernando. 2022. Evolutionary history of the Asplenium scolopendrium complex (Aspleniaceae), a relictual fern with a northern pan-temperate disjunct distribution. Biological Journal of the Linnean Society. https://doi.org/10.1093/biolinnean/blac080

Abstract Asplenium scolopendrium is distributed in northern temperate forests with many global biogeographic disjunctions. The species complex of A. scolopendrium has been generated by spatial segregation coupled with divergent evolution. We elucidated the biogeographic history of the A. scolopendrium complex by exploring its origin, dispersal and evolution, thus providing insights into the evolutionary history of the Tertiary floras with northern pan-temperate disjunct distributions. The results revealed that all infraspecific taxa descended from a widely distributed common ancestor in the Northern Hemisphere. This pan-temperate ancestral population formed by unidirectional westward dispersal from European origins primarily during the Early Eocene when the Earth’s climate was much warmer than today. The splitting of European, American and East Asian lineages occurred during the Early Miocene due to geo-climatic vicariances. Polyploidy events in the American ancestral populations created additional reproductive barriers. The star-shaped haplotypes in each continent indicated that local disjunctions also led to derived genotypes with potential to diverge into different taxa. This intracontinental lineage splitting is likely related to latitudinal range shift and habitat fragmentation caused by glacial cycles and climate change during the Pleistocene. The evolutionary history of the A. scolopendrium complex supported the Boreotropical hypothesis exhibiting range expansion during the Early Eocene Climatic Optimum.

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).

Pereira, R. F. P., J. Rocha, P. Nunes, T. Fernandes, A. P. Ravishankar, R. Cruz, M. Fernandes, et al. 2022. Vicariance Between Cercis siliquastrum L. and Ceratonia siliqua L. Unveiled by the Physical–Chemical Properties of the Leaves’ Epicuticular Waxes. Frontiers in Plant Science 13. https://doi.org/10.3389/fpls.2022.890647

Classically, vicariant phenomena have been essentially identified on the basis of biogeographical and ecological data. Here, we report unequivocal evidences that demonstrate that a physical–chemical characterization of the epicuticular waxes of the surface of plant leaves represents a very powerful strategy to get rich insight into vicariant events. We found vicariant similarity between Cercis siliquastrum L. (family Fabaceae, subfamily Cercidoideae) and Ceratonia siliqua L. (family Fabaceae, subfamily Caesalpinoideae). Both taxa converge in the Mediterranean basin (C. siliquastrum on the north and C. siliqua across the south), in similar habitats (sclerophyll communities of maquis) and climatic profiles. These species are the current representation of their subfamilies in the Mediterranean basin, where they overlap. Because of this biogeographic and ecological similarity, the environmental pattern of both taxa was found to be very significant. The physical–chemical analysis performed on the epicuticular waxes of C. siliquastrum and C. siliqua leaves provided relevant data that confirm the functional proximity between them. A striking resemblance was found in the epicuticular waxes of the abaxial surfaces of C. siliquastrum and C. siliqua leaves in terms of the dominant chemical compounds (1-triacontanol (C30) and 1-octacosanol (C28), respectively), morphology (intricate network of randomly organized nanometer-thick and micrometer-long plates), wettability (superhydrophobic character, with water contact angle values of 167.5 ± 0.5° and 162 ± 3°, respectively), and optical properties (in both species the light reflectance/absorptance of the abaxial surface is significantly higher/lower than that of the adaxial surface, but the overall trend in reflectance is qualitatively similar). These results enable us to include for the first time C. siliqua in the vicariant process exhibited by C. canadensis L., C. griffithii L., and C. siliquastrum.

Ramirez-Villegas, J., C. K. Khoury, H. A. Achicanoy, M. V. Diaz, A. C. Mendez, C. C. Sosa, Z. Kehel, et al. 2022. State of ex situ conservation of landrace groups of 25 major crops. Nature Plants 8: 491–499. https://doi.org/10.1038/s41477-022-01144-8

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation. By analysing the state of representation of traditional varieties of 25 major crops in ex situ repositories, this study demonstrates conservation progress made over more than a half-century and identifies the gaps remaining to be filled.

Sanczuk, P., E. De Lombaerde, S. Haesen, K. Van Meerbeek, M. Luoto, B. Van der Veken, E. Van Beek, et al. 2022. Competition mediates understorey species range shifts under climate change. Journal of Ecology 110: 1813–1825. https://doi.org/10.1111/1365-2745.13907

Biological communities are reshuffling owing to species range shifts in response to climate change. This process inherently leads to novel assemblages of interacting species. Yet, how climatic change and local dynamics in biotic interactions jointly affect range shifts is still poorly understood.We combine a unique long‐term transplant competition‐exclusion experiment with species distribution models (SDMs) to test the effects of biotic interactions on understorey species range shifts under climate change in European temperate forests. Using a time‐series of 18 years of individual‐level demographic data of four common understorey plant species transplanted beyond their cold range edge to plots with and without interspecific competition, we built integral projection models (IPMs) and analysed the effects of competition on five key vital rates and population growth. We assessed the results of the transplant experiment in the context of the modelled species’ current and future potential distributions.We find that species’ population performances in the transplant experiment decreased with lower predicted habitat suitability from the SDMs. The population performance at the transplant sites was mediated by biotic interactions with the local plant community: for two species with intermediate levels of predicted habitat suitability at the transplant sites, competition effects could explicitly differentiate between net population growth (λ > 1) or shrinkage (λ < 1).Synthesis: Our findings contest the long‐standing idea that at cold range edges, mainly abiotic factors structure species’ distributions. We conclude that biotic interactions, through acting on local population dynamics, may impact species distributions at the continental scale. Hence, predicting climate‐change impacts on biodiversity redistributions ultimately requires us to also integrate dynamics in biotic interactions.

Pirie, M. D., R. Blackhall‐Miles, G. Bourke, D. Crowley, I. Ebrahim, F. Forest, M. Knaack, et al. 2022. Preventing species extinctions: A global conservation consortium for Erica. PLANTS, PEOPLE, PLANET 4: 335–344. https://doi.org/10.1002/ppp3.10266

Societal Impact Statement Human-caused habitat destruction and transformation is resulting in a cascade of impacts to biological diversity, of which arguably the most fundamental is species extinctions. The Global Conservation Consortia (GCC) are a means to pool efforts and expertise across national boundaries and between disciplines in the attempt to prevent such losses in focal plant groups. GCC Erica coordinates an international response to extinction threats in one such group, the heaths, or heathers, of which hundreds of species are found only in South Africa's spectacularly diverse Cape Floristic Region. Summary Effectively combating the biodiversity crisis requires coordinated conservation efforts. Botanic Gardens Conservation International (BGCI) and numerous partners have established Global Conservation Consortia (GCC) to collaboratively develop and implement comprehensive conservation strategies for priority threatened plant groups. Through these networks, institutions with specialised collections and staff can leverage ongoing work to optimise impact for threatened plant species. The genus Erica poses a challenge similar in scale to that of the largest other GCC group, Rhododendron, but almost 700 of the around 800 known species of Erica are concentrated in a single biodiversity hotspot, the Cape Floristic Region (CFR) of South Africa. Many species are known to be threatened, suffering the immediate impacts of habitat destruction, invasive species, changes in natural fire regimes and climate change. Efforts to counter these threats face general challenges: disproportionate burden of in situ conservation falling on a minority of the community, limited knowledge of species-rich groups, shortfalls in assessing and monitoring threat, lack of resources for in situ and limitations of knowledge for ex situ conservation efforts and in communicating the value of biological diversity to a public who may never encounter it in the wild. GCC Erica brings together the world's Erica experts, conservationists and the botanical community, including botanic gardens, seed banks and organisations in Africa, Madagascar, Europe, the United States, Australia and beyond. We are collaboratively pooling our unique sets of skills and resources to address these challenges in working groups for conservation prioritisation, conservation in situ, horticulture, seed banking, systematic research and outreach.

Bywater‐Reyes, S., R. M. Diehl, A. C. Wilcox, J. C. Stella, and L. Kui. 2022. A Green New Balance: Interactions among riparian vegetation plant traits and morphodynamics in alluvial rivers. Earth Surface Processes and Landforms 47: 2410–2436. https://doi.org/10.1002/esp.5385

The strength of interactions between plants and river processes is mediated by plant traits and fluvial conditions, including above‐ground biomass, stem density and flexibility, channel and bed material properties, and flow and sediment regimes. In many rivers, concurrent changes in 1) the composition of riparian vegetation communities as a result of exotic species invasion and 2) shifts in hydrology have altered physical and ecological conditions in a manner that has been mediated by feedbacks between vegetation and morphodynamic processes. We review how Tamarix, which has invaded many U.S. Southwest waterways, and Populus species, woody pioneer trees that are native to the region, differentially affect hydraulics, sediment transport, and river morphology. We draw on flume, field, and modeling approaches spanning the individual seedling to river‐corridor scales. In a flume study, we found differences in the crown morphology, stem density, and flexibility of Tamarix compared to Populus influenced near‐bed flow velocities in a manner that favored aggradation associated with Tamarix. Similarly, at the patch and corridor scales, observations confirmed increased aggradation with increased vegetation density. Furthermore, long‐term channel adjustments were different for Tamarix‐ versus Populus‐dominated reaches, with faster and greater geomorphic adjustments for Tamarix. Collectively, our studies show how plant‐trait differences between Tamarix and Populus, from individual seedlings to larger spatial and temporal scales, influence the co‐adjustment of rivers and riparian plant communities. These findings provide a basis for predicting changes in alluvial riverine systems which we conceptualize as a Green New Balance model that considers how channels may adjust to changes in plant traits and community structure in additional to alterations in flow and sediment supply. We offer suggestions regarding how the Green New Balance can be used in management and invasive species management.

Chevalier, M. 2022. &amp;lt;i&amp;gt;crestr&amp;lt;/i&amp;gt;: 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.

Filartiga, A. L., A. Klimeš, J. Altman, M. P. Nobis, A. Crivellaro, F. Schweingruber, and J. Doležal. 2022. Comparative anatomy of leaf petioles in temperate trees and shrubs: the role of plant size, environment and phylogeny. Annals of Botany 129: 567–582. https://doi.org/10.1093/aob/mcac014

Background and Aims Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting ability of the leaf as well as transport of water, nutrients and biochemical signals. Despite the high diversity in petiole size, shape and anatomy, little information is availabl…