Science Enabled by Specimen Data

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.

Li, L., Xu, X., Qian, H., Huang, X., Liu, P., Landis, J. B., Fu, Q., Sun, L., Wang, H., Sun, H., & Deng, T. (2022). Elevational patterns of phylogenetic structure of angiosperms in a biodiversity hotspot in eastern Himalaya. Diversity and Distributions. Portico. https://doi.org/10.1111/ddi.13513 https://doi.org/10.1111/ddi.13513

Aims The tropical niche conservatism (TNC) hypothesis and the out of the tropics (OTT) hypothesis propose mechanisms generating patterns of species diversity across warm-to-cold thermal gradients at large spatial scales. These two hypotheses both integrate ecological and biogeography-related evoluti…

Lin, H., Li, W., Lin, C., Wu, H., & Zhao, Y. (2022). International Biological Flora: Ginkgo biloba. Journal of Ecology. Portico. https://doi.org/10.1111/1365-2745.13856 https://doi.org/10.1111/1365-2745.13856

This account presents information on all aspects of the biology of Ginkgo biloba L. (Ginkgo, Maidenhair tree) that are relevant to understanding its ecological characteristics. The main topics are presented within the standard framework of the International Biological Flora: distribution, habitat, …

Xue, T., Gadagkar, S. R., Albright, T. P., Yang, X., Li, J., Xia, C., … Yu, S. (2021). Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation, 32, e01885. doi:10.1016/j.gecco.2021.e01885 https://doi.org/10.1016/j.gecco.2021.e01885

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

Grebennikov, K. (2021). Ecological niche modeling to assessment of potential distribution of Neodiprion abietis (Harris, 1841) (Insecta, Hymenoptera, Diprionidae) in Eurasia. International Journal of Agricultural Sciences and Technology, 1(1), 1–7. doi:10.51483/ijagst.1.1.2021.1-7 https://doi.org/10.51483/ijagst.1.1.2021.1-7

In the article first assesses the potential distribution in Eurasia of Neodiprion abietis (Harris, 1841) first time assessed. The species id a widely distributed in North America fir and spruce defoliator, intercepted in 2016 in the Netherlands. Analysis of the literature data on the known distribut…

Bidak, L. M., Heneidy, S. Z., Halmy, M. W. A., & El-Kenany, E. T. (2021). Sustainability potential for Ginkgo biloba L. plantations under climate change uncertainty: An ex-situ conservation perspective. Acta Ecologica Sinica. doi:10.1016/j.chnaes.2021.09.012 https://doi.org/10.1016/j.chnaes.2021.09.012

G. biloba is native to China and one of the oldest living species. It has high economic value and has been used for medicinal, ornamental and other purposes. The current study sought to assess the potential sustainability of the plantations of the endangered species under climate change scenarios. T…

Hui, Z., Zhou, X., Chevalier, M., Wei, X., Pan, Y., & Chen, Y. (2021). Miocene East Asia summer monsoon precipitation variability and its possible driving forces. Palaeogeography, Palaeoclimatology, Palaeoecology, 110609. doi:10.1016/j.palaeo.2021.110609 https://doi.org/10.1016/j.palaeo.2021.110609

The East Asian summer monsoon (EASM) precipitation is vital to hydrology, ecology and societal activities in the densely populated region of East Asia. However, its long-term evolution history and driving forces during the relatively warm Miocene remain unclear, even conflicting in some intervals. H…

Yi, S., Jun, C.-P., Jo, K., Lee, H., Kim, M.-S., Lee, S. D., … Lim, J. (2020). Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years. Scientific Reports, 10(1). doi:10.1038/s41598-020-74994-x https://doi.org/10.1038/s41598-020-74994-x

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Bazzicalupo, A. L., Whitton, J., & Berbee, M. L. (2019). Over the hills, but how far away? Estimates of mushroom geographic range extents. Journal of Biogeography. doi:10.1111/jbi.13617 https://doi.org/10.1111/jbi.13617

Aim: Geographic distributions of mushroom species remain poorly understood despite their importance for advancing our understanding of the habitat requirements, species interactions and ecosystem functions of this key group of organisms. Here, we estimate geographic range extents (maximum within‐spe…

Chase, B. M., Boom, A., Carr, A. S., Chevalier, M., Quick, L. J., Verboom, G. A., & Reimer, P. J. (2019). Extreme hydroclimate response gradients within the western Cape Floristic region of South Africa since the Last Glacial Maximum. Quaternary Science Reviews, 219, 297–307. doi:10.1016/j.quascirev.2019.07.006 https://doi.org/10.1016/j.quascirev.2019.07.006

The Cape Floristic Region (CFR) is one of the world's major biodiversity hotspots, and much work has gone into identifying the drivers of this diversity. Considered regionally in the context of Quaternary climate change, climate stability is generally accepted as being one of the major factors promo…