Science Enabled by Specimen Data

Ramirez-Villegas, J., Khoury, C. K., Achicanoy, H. A., Diaz, M. V., Mendez, A. C., Sosa, C. C., Kehel, Z., Guarino, L., Abberton, M., Aunario, J., Awar, B. A., Alarcon, J. C., Amri, A., Anglin, N. L., Azevedo, V., Aziz, K., Capilit, G. L., Chavez, O., Chebotarov, D., … Zavala, C. (2022). State of ex situ conservation of landrace groups of 25 major crops. Nature Plants. https://doi.org/10.1038/s41477-022-01144-8 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.

Williams, C. J. R., Lunt, D. J., Salzmann, U., Reichgelt, T., Inglis, G. N., Greenwood, D. R., Chan, W., Abe‐Ouchi, A., Donnadieu, Y., Hutchinson, D. K., Boer, A. M., Ladant, J., Morozova, P. A., Niezgodzki, I., Knorr, G., Steinig, S., Zhang, Z., Zhu, J., Huber, M., & Otto‐Bliesner, B. L. (2022). African hydroclimate during the early Eocene from the DeepMIP simulations. Paleoceanography and Paleoclimatology. Portico. https://doi.org/10.1029/2022pa004419 https://doi.org/10.1029/2022pa004419

The early Eocene (∼56‐48 million years ago) is characterised by high CO2 estimates (1200‐2500 ppmv) and elevated global temperatures (∼10 to 16°C higher than modern). However, the response of the hydrological cycle during the early Eocene is poorly constrained, especially in regions with sparse data coverage (e.g. Africa). Here we present a study of African hydroclimate during the early Eocene, as simulated by an ensemble of state‐of‐the‐art climate models in the Deep‐time Model Intercomparison Project (DeepMIP). A comparison between the DeepMIP pre‐industrial simulations and modern observations suggests that model biases are model‐ and geographically dependent, however these biases are reduced in the model ensemble mean. A comparison between the Eocene simulations and the pre‐industrial suggests that there is no obvious wetting or drying trend as the CO2 increases. The results suggest that changes to the land sea mask (relative to modern) in the models may be responsible for the simulated increases in precipitation to the north of Eocene Africa. There is an increase in precipitation over equatorial and West Africa and associated drying over northern Africa as CO2 rises. There are also important dynamical changes, with evidence that anticyclonic low‐level circulation is replaced by increased south‐westerly flow at high CO2 levels. Lastly, a model‐data comparison using newly‐compiled quantitative climate estimates from palaeobotanical proxy data suggests a marginally better fit with the reconstructions at lower levels of CO2.

Reichgelt, T., Greenwood, D. R., Steinig, S., Conran, J. G., Hutchinson, D. K., Lunt, D. J., Scriven, L. J., & Zhu, J. (2022). Plant Proxy Evidence for High Rainfall and Productivity in the Eocene of Australia. Paleoceanography and Paleoclimatology. Portico. https://doi.org/10.1029/2022pa004418 https://doi.org/10.1029/2022pa004418

During the early to middle Eocene, a mid‐to‐high latitudinal position and enhanced hydrological cycle in Australia would have contributed to a wetter and “greener” Australian continent where today arid to semi‐arid climates dominate. Here, we revisit 12 southern Australian plant megafossil sites from the early to middle Eocene to generate temperature, precipitation and seasonality paleoclimate estimates, net primary productivity (NPP) and vegetation type, based on paleobotanical proxies and compare to early Eocene global climate models. Temperature reconstructions are uniformly subtropical (mean annual, summer, and winter mean temperatures 19–21 °C, 25–27 °C and 14–16 °C, respectively), indicating that southern Australia was ∼5 °C warmer than today, despite a >20° poleward shift from its modern geographic location. Precipitation was less homogeneous than temperature, with mean annual precipitation of ∼60 cm over inland sites and >100 cm over coastal sites. Precipitation may have been seasonal with the driest month receiving 2–7× less than mean monthly precipitation. Proxy‐model comparison is favorable with an 1680 ppm CO2 concentration. However, individual proxy reconstructions can disagree with models as well as with each other. In particular, seasonality reconstructions have systemic offsets. NPP estimates were higher than modern, implying a more homogenously “green” southern Australia in the early to middle Eocene, when this part of Australia was at 48–64 °S, and larger carbon fluxes to and from the Australian biosphere. The most similar modern vegetation type is modern‐day eastern Australian subtropical forest, although distance from coast and latitude may have led to vegetation heterogeneity.

Colli-Silva, M., Pirani, J. R., & Zizka, A. (2022). Ecological niche models and point distribution data reveal a differential coverage of the cacao relatives (Malvaceae) in South American protected areas. Ecological Informatics, 101668. https://doi.org/10.1016/j.ecoinf.2022.101668 https://doi.org/10.1016/j.ecoinf.2022.101668

For many regions, such as in South America, it is unclear how well the existent protected areas network (PAs) covers different taxonomic groups and if there is a coverage bias of PAs towards certain biomes or species. Publicly available occurrence data along with ecological niche models might help to overcome this gap and to quantify the coverage of taxa by PAs ensuring an unbiased distribution of conservation effort. Here, we use an occurrence database of 271 species from the cacao family (Malvaceae) to address how South American PAs cover species with different distribution, abundance, and threat status. Furthermore, we compared the performance of online databases, expert knowledge, and modelled species distributions in estimating species coverage in PAs. We found 79 species from our survey (29% of the total) lack any record inside South American PAs and that 20 out of 23 species potentially threatened with extinction are not covered by PAs. The area covered by South American PAs was low across biomes, except for Amazonia, which had a relative high PA coverage, but little information on species distribution within PA available. Also, raw geo-referenced occurrence data were underestimating the number of species in PAs, and projections from ecological niche models were more prone to overestimating the number of species represented within PAs. We discuss that the protection of South American flora in heterogeneous environments demand for specific strategies tailored to particular biomes, including making new collections inside PAs in less collected areas, and the delimitation of more areas for protection in more known areas. Also, by presenting biasing scenarios of collection effort in a representative plant group, our results can benefit policy makers in conserving different spots of tropical environments highly biodiverse.

Li, D., Li, Z., Wang, X., Wang, L., Li, Y., & Liu, D. (2022). Increasing risk of aphids spreading plant viruses in maize fields on both sides of China’s Heihe‐Tengchong line under climate change. Pest Management Science. Portico. https://doi.org/10.1002/ps.6932 https://doi.org/10.1002/ps.6932

BACKGROUND In the coming decades, geographical distribution patterns of farmland organisms may undergo drastic changes due to climate change, with significant implications for global food security. In China, Rhopalosiphum maidis and its spread of sugarcane mosaic virus (ScMV) can become an increasingly serious threat to maize (Zea mays) production. We conducted ecological niche modeling for Z. mays, R. maidis, and ScMV under current and future (2041–2060 and 2081–2100) climate scenarios by using MaxEnt software to explore changes in this system. RESULTS The Heihe-Tengchong line (an imaginary separation line of human population density) can divide China into main (east of the line) and secondary (west of the line) habitats for the three species. With climate change, rapid expansion in suitable areas is projected for ScMV and the aphid vector R. maidis. Taking species interactions into consideration, our overlaying analyses show that most areas east of the Heihe-Tengchong line (optimal for maize and suitable for R. maidis) will become increasingly highly suitable for ScMV, suggesting that the prevention and control of this plant virus and its aphid vector in China's main maize-growing areas (e.g. northeast) will become an increasing challenge in the future. CONCLUSION Climate change will profoundly affect ScMV–vector–maize interactions, which may contribute favorably to invasion of this virus into new areas. Our comprehensive and in-depth analyses on shifts in this multi-species system under climate change provide useful and insightful information for devising strategies for the prevention and control of plant viruses and aphid vectors on maize in the future. © 2022 Society of Chemical Industry.

Bywater‐Reyes, S., Diehl, R. M., Wilcox, A. C., Stella, J. C., & Kui, L. (2022). A Green New Balance: interactions among riparian vegetation plant traits and morphodynamics in alluvial rivers. Earth Surface Processes and Landforms. Portico. https://doi.org/10.1002/esp.5385 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). <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past, 18(4), 821–844. https://doi.org/10.5194/cp-18-821-2022 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.

Sarker, U., Lin, Y.-P., Oba, S., Yoshioka, Y., & Hoshikawa, K. (2022). Prospects and potentials of underutilized leafy Amaranths as vegetable use for health-promotion. Plant Physiology and Biochemistry. https://doi.org/10.1016/j.plaphy.2022.04.011 https://doi.org/10.1016/j.plaphy.2022.04.011

Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as ‘hidden hunger.’ Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail.

Sluiter, I. R. K., Holdgate, G. R., Reichgelt, T., Greenwood, D. R., Kershaw, A. P., & Schultz, N. L. (2022). A new perspective on Late Eocene and Oligocene vegetation and paleoclimates of South-eastern Australia. Palaeogeography, Palaeoclimatology, Palaeoecology, 596, 110985. https://doi.org/10.1016/j.palaeo.2022.110985 https://doi.org/10.1016/j.palaeo.2022.110985

We present a composite terrestrial pollen record of latest Eocene through Oligocene (35.5–23 Ma) vegetation and climate change from the Gippsland Basin of south-eastern Australia. Climates were overwhelmingly mesothermic through this time period, with mean annual temperature (MAT) varying between 13 and 18 °C, with an average of 16 °C. We provide evidence to support a cooling trend through the Eocene–Oligocene Transition (EOT), but also identify three subsequent warming cycles through the Oligocene, leading to more seasonal climates at the termination of the Epoch. One of the warming episodes in the Early Oligocene appears to have also occurred at two other southern hemisphere sites at the Drake Passage as well as off eastern Tasmania, based on recent research. Similarities with sea surface temperature records from modern high southern latitudes which also record similar cycles of warming and cooling, are presented and discussed. Annual precipitation varied between 1200 and 1700 mm/yr, with an average of 1470 mm/yr through the sequence. Notwithstanding the extinction of Nothofagus sg. Brassospora from Australia and some now microthermic humid restricted Podocarpaceae conifer taxa, the rainforest vegetation of lowland south-eastern Australia is reconstructed to have been similar to present day Australian Evergreen Notophyll Vine Forests existing under the sub-tropical Köppen-Geiger climate class Cfa (humid subtropical) for most of the sequence. Short periods of cooler climates, such as occurred through the EOT when MAT was ~ 13 °C, may have supported vegetation similar to modern day Evergreen Microphyll Fern Forest. Of potentially greater significance, however, was a warm period in the Early to early Late Oligocene (32–26 Ma) when MAT was 17–18 °C, accompanied by small but important increases in Araucariaceae pollen. At this time, Araucarian Notophyll/Microphyll Vine Forest likely occurred regionally.

Afonin, A. N., Baranova, O. G., Fedorova, Y. A., Abramova, L. M., Boshko, T. F., Kotsareva, N. V., Li, Yu. S., Milyutina, E. A., Pikalova, N. A., Prokhorov, V. E., & Senator, S. A. (2022). ECOLOGICAL AND GEOGRAPHICAL POTENTIAL OF <i>AMBROSIA ARTEMISIIFOLIA</i> L. DISTRIBUTION TO THE NORTH OF THE EUROPEAN RUSSIA BASED ON A COMPARISON OF THE NORTHERN BOUNDARIES OF THE PRIMARY AND SECONDARY RANGES. Russian Journal of Biological Invasions, 15(1), 2–12. https://doi.org/10.35885/1996-1499-15-1-2-12 https://doi.org/10.35885/1996-1499-15-1-2-12

В ходе экспедиционных исследований уточнена современная фактическая граница натурализации Аmbrosia artemisiifolia на Европейской территории России. Эта граница проходит по югу Брянской, Курской и Саратовской, северу Воронежской областей. Общая протяжённость экспедиционных маршрутов составила около 8900 км, количество обследованных точек – 777. В целях выявления потенциала дальнейшего продвижения вида на север проведён сравнительный эколого-географический анализ и моделирование распространения амброзии на севере её вторичного ареала на Европейской территории России и первичного – в Канаде. Выявлено, что основным фактором, лимитирующим продвижение вида на север, служит недостаточная теплообеспеченность периода созревания семян. Для определения эколого-географической ниши амброзии была составлена глобальная карта распределения сумм активных температур с порогом выше 10 °С за период от даты перехода длины дня через 14 часов после летнего солнцестояния до устойчивого перехода осенних температур через 0 °С (САТфп). Было определено значение САТфп на самых северных точках натурализации Аmbrosia artemisiifolia на Европейской территории России и в Канаде. Сравнение эколого-географических границ по фактору теплообеспеченности на Европейской территории России и в Канаде показало, что реализованная видом эколого-географическая ниша на Североамериканском континенте в настоящее время в целом шире, чем на Европейской территории России. Рассмотрены возможные причины, по которым амброзия не освоила всю потенциальную экологическую нишу на Европейской территории России, сделаны предположения о возможности дальнейшего продвижения вида на север. Амброзия по фактору теплообеспеченности на Европейской территории России может продвинуться дальше на север – в Брянскую, Орловскую, Липецкую, Тамбовскую, Саратовскую, Оренбургскую, южную половину Пензенской, юг Ульяновской, Самарской областей и Башкортостана. Дополнительные проблемы с продвижением вида в северо-восточном направлении на Европейской территории России могут быть обусловлены сопряжённым неблагоприятным воздействием дополнительного фактора – недостаточной влагообеспеченности, поскольку от Саратовской области и восточнее амброзия на северном пределе распространения находится в зоне экологического пессимума одновременно по показателям тепло- и влагообеспеченности.