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.

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…

Orr, M. C., Hughes, A. C., Chesters, D., Pickering, J., Zhu, C.-D., & Ascher, J. S. (2020). Global Patterns and Drivers of Bee Distribution. Current Biology. doi:10.1016/j.cub.2020.10.053 https://doi.org/10.1016/j.cub.2020.10.053

Insects are the focus of many recent studies suggesting population declines, but even invaluable pollination service providers such as bees lack a modern distributional synthesis. Here, we combine a uniquely comprehensive checklist of bee species distributions and >5,800,000 public bee occurrence re…

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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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…

Chevalier, M., Chase, B. M., Quick, L. J., Dupont, L. M., & Johnson, T. C. (2020). Temperature change in subtropical southeastern Africa during the past 790,000 yr. Geology. doi:10.1130/g47841.1 https://doi.org/10.1130/G47841.1

Across the glacial-interglacial cycles of the late Pleistocene (~700 k.y.), temperature variability at low latitudes is often considered to have been negligible compared to changes in precipitation. However, a paucity of quantified temperature records makes this difficult to reliably assess. In this…

Chevalier, M. (2019). Enabling possibilities to quantify past climate from fossil assemblages at a global scale. Global and Planetary Change, 175, 27–35. doi:10.1016/j.gloplacha.2019.01.016 https://doi.org/10.1016/j.gloplacha.2019.01.016

The field of quantitative palaeoclimatology has made significant progress in the past decades. However, this progress has been spatially heterogeneous and strong discrepancies – both in terms of quality and density – exist between Europe and North America and the rest of the world. The need to balan…