Science Enabled by Specimen Data

Pang, S. E. H., Zeng, Y., De Alban, J. D. T., & Webb, E. L. (2022). Occurrence–habitat mismatching and niche truncation when modelling distributions affected by anthropogenic range contractions. Diversity and Distributions. Portico. https://doi.org/10.1111/ddi.13544 https://doi.org/10.1111/ddi.13544

Aims Human-induced pressures such as deforestation cause anthropogenic range contractions (ARCs). Such contractions present dynamic distributions that may engender data misrepresentations within species distribution models. The temporal bias of occurrence data—where occurrences represent distributions before (past bias) or after (recent bias) ARCs—underpins these data misrepresentations. Occurrence–habitat mismatching results when occurrences sampled before contractions are modelled with contemporary anthropogenic variables; niche truncation results when occurrences sampled after contractions are modelled without anthropogenic variables. Our understanding of their independent and interactive effects on model performance remains incomplete but is vital for developing good modelling protocols. Through a virtual ecologist approach, we demonstrate how these data misrepresentations manifest and investigate their effects on model performance. Location Virtual Southeast Asia. Methods Using 100 virtual species, we simulated ARCs with 100-year land-use data and generated temporally biased (past and recent) occurrence datasets. We modelled datasets with and without a contemporary land-use variable (conventional modelling protocols) and with a temporally dynamic land-use variable. We evaluated each model's ability to predict historical and contemporary distributions. Results Greater ARC resulted in greater occurrence–habitat mismatching for datasets with past bias and greater niche truncation for datasets with recent bias. Occurrence–habitat mismatching prevented models with the contemporary land-use variable from predicting anthropogenic-related absences, causing overpredictions of contemporary distributions. Although niche truncation caused underpredictions of historical distributions (environmentally suitable habitats), incorporating the contemporary land-use variable resolved these underpredictions, even when mismatching occurred. Models with the temporally dynamic land-use variable consistently outperformed models without. Main conclusions We showed how these data misrepresentations can degrade model performance, undermining their use for empirical research and conservation science. Given the ubiquity of ARCs, these data misrepresentations are likely inherent to most datasets. Therefore, we present a three-step strategy for handling data misrepresentations: maximize the temporal range of anthropogenic predictors, exclude mismatched occurrences and test for residual data misrepresentations.

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.

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.

Joshi, M. D., & Joshi, C. (2022). Areas of species diversity and endemicity of Nepal. Ecosphere, 13(3). Portico. https://doi.org/10.1002/ecs2.3969 https://doi.org/10.1002/ecs2.3969

In this study, we analyzed the distribution and the spatial pattern of species diversity of vascular plants in Nepal. The aim was to identify and evaluate the occurrence and status of species‐rich areas in Nepal using ecological and environmental drivers. We used 52,973 georeferenced herbarium specimen records, representing 2650 species collected from Nepal. Altogether, 41 environmental variables were used for model development and validation. We used MaxEnt to predict the distribution pattern. All the significant species distribution predictions were then used to develop a species richness and endemism pattern in Nepal. The High Mountain and Himalaya, particularly east and central Nepal, were found to be species diverse and endemically rich areas, whereas western Nepal had lower species richness. We observed that isothermality, slope, rugosity, potential evapotranspiration, precipitation of humid months, temperature annual range, mean diurnal range, and normalized difference in vegetation index of humid months were the most influential environmental and climatic variables. We observed that about 60% of the areas, which had highest richness and endemism values, are still not included in protected areas in Nepal. We quantitatively analyzed the species richness and endemicity patterns of Nepal and were able to identify 19 areas of high species diversity and endemicity, six of which are newly identified.

KHRAPOV, D., KOVAL, N., & YUNAKOV, N. (2022). Prediction of the distribution limits of Rhinomias forticornis (Boheman, 1842) (Coleoptera: Curculionidae: Entiminae) based on Remote Sensing. Journal of Insect Biodiversity, 31(1). https://doi.org/10.12976/jib/2022.31.1.3 https://doi.org/10.12976/jib/2022.31.1.3

Morphometry and diagnosis of Rhinomias forticornis (Boheman, 1842) are given. Distribution of Rhinomias forticornis is analyzed using known occurrences, original ecological data, correlative species distribution modeling with aspect on Last Glacial Maximum environment are given. To achieve a more re…

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…