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. https://doi.org/10.1111/jbi.14386
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.
Chen, K., P. K. Khine, Z. Yang, and H. Schneider. 2022. Historical plant records enlighten the conservation efforts of ferns and Lycophytes’ diversity in tropical China. Journal for Nature Conservation 68: 126197. https://doi.org/10.1016/j.jnc.2022.126197
Historical records, e.g., herbarium vouchers, contain information about species distribution since the early days of the scientific exploration of floras until today. These data provide crucial evidence to map the biodiversity of the area of interest and most importantly enable the evaluation of the conservation effectiveness for a given group of organisms. This study aimed to explore the ferns and lycophytes’ diversity of Xishuangbanna Dai Autonomous Prefecture in tropical China with special emphasis on conservation efforts provided by the currently established protected areas (PAs). Instead of relying exclusively on current observation, the database was compiled from digitalized herbarium vouchers and publications being explored with special attention on the temporal and spatial dimensions of collecting efforts. Utilizing the indices including species richness, weighed endemism, corrected weighted endemism, and beta diversity, hotspots of ferns and lycophytes’ diversity were identified. In turn, the proportion of hotspots located outside PAs was estimated as a measure of conservation gaps in Xishuangbanna. Our results revealed a long collecting history of ferns and lycophytes in Xishuangbanna and this prefecture accumulated a considerable number of historical records covering 20.2 % of Chinese and 3.6% of global fern diversity. The accumulation of historical records showed strong parallelism to the historical events shaping modern China. The spatial distribution of ferns and lycophytes in Xishuangbanna was characterized by a concentration of species richness in southern valleys and endemism in western and northern mountains. In terms of conservation, existing PAs showed higher effectiveness in the protection of species richness, whereas lower effectiveness was observed in the protection of endemism and beta diversity. Our research provided a key reference for understanding the diversity and conservation of ferns and lycophytes in Xishuangbanna, as well as highlighting the locality for future collecting and conservation efforts.
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. 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., 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. 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., 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. 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. &lt;i&gt;crestr&lt;/i&gt;: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844. 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., G. R. Holdgate, T. Reichgelt, D. R. Greenwood, A. P. Kershaw, and N. L. Schultz. 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
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.
Li, L., X. Xu, H. Qian, X. Huang, P. Liu, J. B. Landis, Q. Fu, et al. 2022. Elevational patterns of phylogenetic structure of angiosperms in a biodiversity hotspot in eastern Himalaya Y. Qu [ed.],. Diversity and Distributions. 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…
Zhang, N., Z. Liao, S. Wu, M. P. Nobis, J. Wang, and N. Wu. 2021. Impact of climate change on wheat security through an alternate host of stripe rust. Food and Energy Security 11. 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…
Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 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. 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…