Science Enabled by Specimen Data

Zhao, J., X. Yu, W. J. Kress, Y. Wang, Y. Xia, and Q. Li. 2022. Historical biogeography of the gingers and its implications for shifts in tropical rain forest habitats. Journal of Biogeography 49: 1339–1351.

Aim The relationships between biome shifts and global environmental changes in temperate zone habitats have been extensively explored; yet, the historical dynamics of taxa found in the tropical rain forest (TRF) remain poorly known. This study aims to reconstruct the relationships between tropical rain forest shifts and global environmental changes through the patterns of historical biogeography of a pantropical family of monocots, the Zingiberaceae. Location Global. Taxon Zingiberaceae. Methods We sampled DNA sequences (nrITS, trnK, trnL-trnF and psbA-trnH) from GenBank for 77% of the genera, including 30% of species, in the Zingiberaceae. Global fossil records of the Zingiberaceae were collected from literatures. Rates of speciation, extinction and diversification were estimated based on phylogenetic data and fossil records through methods implemented in BAMM. Ancestral ranges were estimated using single-tree BioGeoBEARS and multiple-trees BioGeoBEARS in RASP. Dispersal rate through time and dispersal rate among regions were calculated in R based on the result of ancestral estimation. Results The common ancestor of the Zingiberaceae likely originated in northern Africa during the mid-Cretaceous, with later dispersal to the Asian tropics. Indo-Burma, rather than Malesia, was likely a provenance of the common ancestor of Alpinioideae–Zingiberoideae. Several abrupt shifts of evolutionary rates from the Palaeocene were synchronized with sudden global environmental changes. Main conclusions Integrating phylogenetic patterns with fossil records suggests that the Zingiberaceae dispersed to Asia through drift of the Indian Plate from Africa in the late Palaeocene. Formation of island chains, land corridors and warming temperatures facilitated the emigration of the Zingiberaceae to a broad distribution across the tropics. Moreover, dramatic fluctuations of the speciation rate of Zingiberoideae appear to have been synchronized with global climate fluctuations. In general, the evolutionary history of the Zingiberaceae broadens our understanding of the association between TRF shifts in distribution and past global environmental changes, especially the origin of TRF in Southeast Asia.

Gori, B., T. Ulian, H. Y. Bernal, and M. Diazgranados. 2022. Understanding the diversity and biogeography of Colombian edible plants. Scientific Reports 12.

Despite being the second most biodiverse country in the world, hosting more than 7000 useful species, Colombia is characterized by widespread poverty and food insecurity. Following the growing attention in Neglected and Underutilized Species, the present study will combine spatial and taxonomic analysis to unveil their diversity and distribution, as well as to advocate their potential as key resources for tackling food security in the country. The cataloguing of Colombian edible plants resulted in 3805 species. Among these, the most species-rich genera included Inga, Passiflora, Miconia, Solanum, Pouteria , Protium , Annona and Bactris . Biogeographic analysis revealed major diversity hotspots in the Andean humid forests by number of records, species, families, and genera. The departments of Antioquia, Boyacá, Meta, and Cundinamarca ranked first both in terms of number of unique georeferenced records and species of edible plants. Significant information gaps about species distribution were detected in the departments of Cesar, Sucre, Atlántico, Vichada, and Guainía, corresponding to the Caribe and Llanos bioregions, indicating the urgent need for focusing investigation in these areas. Furthermore, a significant level of geographic specificity was found in edible plant species’ distributions between 13 different bioregions and 33 departments, hinting the adoption of tailorized prioritisation protocols for the conservation and revitalization of such resources at the local level.

Ramirez-Villegas, J., C. K. Khoury, H. A. Achicanoy, M. V. Diaz, A. C. Mendez, C. C. Sosa, Z. Kehel, et al. 2022. State of ex situ conservation of landrace groups of 25 major crops. Nature Plants 8: 491–499.

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.

Cano, Á., F. W. Stauffer, T. Andermann, I. M. Liberal, A. Zizka, C. D. Bacon, H. Lorenzi, et al. 2022. Recent and local diversification of Central American understorey palms. Global Ecology and Biogeography 31: 1513–1525.

Aim Central America is largely covered by hyperdiverse, yet poorly understood, rain forests. Understorey palms are diverse components of these forests, but little is known about their historical assembly. It is not clear when palms in Central America reached present diversity levels and whether most species arrived from neighbouring regions or evolved locally. We addressed these questions using the most species-rich American palm clades indicative of rain forests. We reconstructed and compared their phylogenomic and biogeographical history with the diversification of 54 other plant lineages, to gain a better understanding of the processes that shaped the assembly of Central American rain forests. Location Central America. Time period Cretaceous to present. Major taxa studied Arecaceae: Arecoideae: Bactridinae, Chamaedoreeae, Geonomateae. Methods We sampled 218 species through fieldwork and living collections. We sequenced their genomic DNA using target sequence-capture procedures. Using 12 calibration points, we reconstructed dated phylogenies under three approaches (multispecies coalescent, maximum likelihood and Bayesian inference), conducted biogeographical analyses (dispersal–extinction–cladogenesis) and estimated phylogenetic diversity metrics. Results Dated phylogenies revealed intense diversification in Central America from 12 Ma. Local diversification events were four times more frequent than dispersal events, and we found strong phylogenetic clustering in relationship to Central America. Main conclusions Our results suggest that most understorey palm species that characterize the Central American rain forests today evolved locally after repeated dispersal events, mostly from South America. Understorey palms in Central American rain forests diversified primarily after closure of the Central American Seaway at c. 13 Ma, suggesting that the Great American Biotic Interchange was a major trigger for plant diversification in Central American rain forests. This recent diversification contrasts with the much earlier existence of rain forest palms in neighbouring South America since c. 58 Ma. We found similar timings of diversification in 54 other seed plant lineages, suggesting an unexpectedly recent assembly of the hyperdiverse Central American flora.

Williams, C. J. R., D. J. Lunt, U. Salzmann, T. Reichgelt, G. N. Inglis, D. R. Greenwood, W. Chan, et al. 2022. African Hydroclimate During the Early Eocene From the DeepMIP Simulations. Paleoceanography and Paleoclimatology 37.

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., D. R. Greenwood, S. Steinig, J. G. Conran, D. K. Hutchinson, D. J. Lunt, L. J. Scriven, and J. Zhu. 2022. Plant Proxy Evidence for High Rainfall and Productivity in the Eocene of Australia. Paleoceanography and Paleoclimatology 37.

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., J. R. Pirani, and A. Zizka. 2022. Ecological niche models and point distribution data reveal a differential coverage of the cacao relatives (Malvaceae) in South American protected areas. Ecological Informatics 69: 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.

Camacho, F., and G. Peyre. 2022. Red List and Vulnerability Assessment of the Páramo Vascular Flora in the Nevados Natural National Park (Colombia). Tropical Conservation Science 15: 194008292210869.

Background and research aims. The Andean páramo is renowned for its unique biodiversity and sensitivity to environmental threats. However, vulnerability assessments remain scarce, which hinders our capacity to prioritize and apply efficient conservation measures. To this end, we established the Red List of the páramo vascular flora from the Nevados National Natural Park and proposed conservation strategies for its threatened species. Methods. We performed International Union for Conservation of Nature (IUCN) Red List assessments by evaluating Criterion B, including sub-criteria B1–Extent of Occurrence and B2–Area of Occupancy, and using a systematic geographic-ecological approach for conditions a (Location analysis) and b (Continuing decline). We then executed a Conservation Gap Analysis to prioritize species for in- situ and/or ex-situ conservation. Results. Summing our 233 evaluated species with previous assessments, we completed the Red List of 262 páramo species and encountered 3% Threatened (7 VU, one EN), 44% Not Threatened (65 LC, 50 NT), and 53% Data Deficient. We acknowledged Lupinus ruizensis as Endangered and Aequatorium jamesonii, Carex jamesonii, Elaphoglossum cuspidatum, Miconia latifolia, Miconia alborosea, Pentacalia gelida, and Themistoclesia mucronata as Vulnerable. Conclusion. The eight threatened species should be included as target species in the PNN Nevados management plan 2023–2028 and regarded as national conservation priorities. Implications for Conservation. We recommend in-situ conservation for Medium-Priority species A. jamesonii, E. cuspidatum, and T. mucronata with thorough monitoring, paired with sub-population transfers for High-Priority species C. jamesonii. For the endemic L. ruizensis and P. gelida, we suggest combined in-situ/ex-situ strategies taking advantage of national germoplasm collections, like the seed bank of the Bogotá Botanical Garden José Celestino Mutis.

Chevalier, M. 2022. <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844.

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., Y.-P. Lin, S. Oba, Y. Yoshioka, and K. Hoshikawa. 2022. Prospects and potentials of underutilized leafy Amaranths as vegetable use for health-promotion. Plant Physiology and Biochemistry 182: 104–123.

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.