Science Enabled by Specimen Data

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.

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.

Liang, S., Zhang, X., & Wei, R. (2022). Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Molecular Ecology. Portico. https://doi.org/10.1111/mec.16420 https://doi.org/10.1111/mec.16420

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long-distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns’ spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

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

Zhang, N., Liao, Z., Wu, S., Nobis, M. P., Wang, J., & Wu, N. (2021). Impact of climate change on wheat security through an alternate host of stripe rust. Food and Energy Security. doi:10.1002/fes3.356 https://doi.org/10.1002/fes3.356

In the 21st century, stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is still the most devastating disease of wheat globally. Despite the critical roles of the alternate host plants, the Berberis species, in the sexual reproduction and spread of Pst, the climate change impacts on t…

Vasconcelos, T., Boyko, J. D., & Beaulieu, J. M. (2021). Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography. doi:10.1111/jbi.14292 https://doi.org/10.1111/jbi.14292

Aim: Due to the sessile nature of flowering plants, movements to new geographical areas occur mainly during seed dispersal. Frugivores tend to be efficient dispersers because animals move within the boundaries of their preferable niches, so seeds are more likely to be transported to environments tha…

Alban, D. M., Biersma, E. M., Kadereit, J. W., & Dillenberger, M. S. (2021). Colonization of the Southern Hemisphere by Sagina and Colobanthus (Caryophyllaceae). Plant Systematics and Evolution, 308(1). doi:10.1007/s00606-021-01793-w https://doi.org/10.1007/s00606-021-01793-w

Colobanthus (23 species) and Sagina (30–33 species) together are sister to Facchinia. Whereas Facchinia is distributed in western Eurasia, Colobanthus is almost exclusively distributed in the Southern Hemisphere, and Sagina is distributed in both hemispheres with the highest species diversity in wes…

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…

Chu, X., Gugger, P. F., Li, L., Zhao, J., & Li, Q. (2021). Responses of an endemic species ( Roscoea humeana ) in the Hengduan Mountains to climate change. Diversity and Distributions. doi:10.1111/ddi.13397 https://doi.org/10.1111/ddi.13397

Aim: Adaptation, migration and extinction of species is closely associated with climate changes and shape the distribution of biodiversity. The adaptive responses of species in the biodiversity hotspot, the Hengduan Mountains, to climate change remain poorly understood. Location: The Hengduan Mount…