Science Enabled by Specimen Data

Ract, C., N. D. Burgess, L. Dinesen, P. Sumbi, I. Malugu, J. Latham, L. Anderson, et al. 2024. Nature Forest Reserves in Tanzania and their importance for conservation S. S. Romanach [ed.],. PLOS ONE 19: e0281408. https://doi.org/10.1371/journal.pone.0281408

Since 1997 Tanzania has undertaken a process to identify and declare a network of Nature Forest Reserves (NFRs) with high biodiversity values, from within its existing portfolio of national Forest Reserves, with 16 new NFRs declared since 2015. The current network of 22 gazetted NFRs covered 948,871 hectares in 2023. NFRs now cover a range of Tanzanian habitat types, including all main forest types—wet, seasonal, and dry—as well as wetlands and grasslands. NFRs contain at least 178 of Tanzania’s 242 endemic vertebrate species, of which at least 50% are threatened with extinction, and 553 Tanzanian endemic plant taxa (species, subspecies, and varieties), of which at least 50% are threatened. NFRs also support 41 single-site endemic vertebrate species and 76 single-site endemic plant taxa. Time series analysis of management effectiveness tracking tool (METT) data shows that NFR management effectiveness is increasing, especially where donor funds have been available. Improved management and investment have resulted in measurable reductions of some critical threats in NFRs. Still, ongoing challenges remain to fully contain issues of illegal logging, charcoal production, firewood, pole-cutting, illegal hunting and snaring of birds and mammals, fire, wildlife trade, and the unpredictable impacts of climate change. Increased tourism, diversified revenue generation and investment schemes, involving communities in management, and stepping up control measures for remaining threats are all required to create a network of economically self-sustaining NFRs able to conserve critical biodiversity values.

Lima, V. P., R. A. Ferreira de Lima, F. Joner, L. D’Orangeville, N. Raes, I. Siddique, and H. ter Steege. 2023. Integrating climate change into agroforestry conservation: A case study on native plant species in the Brazilian Atlantic Forest. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14464

Designing multispecies systems with suitable climatic affinity and identifying species' vulnerability under human‐driven climate change are current challenges to achieve successful adaptation of natural systems. To address this problem, we need to (1) identify groups of species with climatic similarity under climate scenarios and (2) identify areas with high conservation value under predicted climate change.To recognize species with similar climatic niche requirements that can be grouped for mixed cropping in Brazil, we employed ecological niche models (ENMs) and Spearman's ρ for overlap. We also used prioritization algorithms to map areas of high conservation value using two Shared Socioeconomic Pathways (SSP2‐4.5 and SSP5‐8.5) to assess mid‐term (2041–2060) and long‐term (2061–2080) climate change impacts.We identified 15 species groups with finer climatic affinities at different times depicted on hierarchical clustering dendrograms, which can be combined into agroecological agroforestry systems. Furthermore, we highlight the climatically suitable areas for these groups of species, thus providing an outlook of where different species will need to be planted over time to be conserved. In addition, we observed that climate change is predicted to modify the spatial association of these groups under different future climate scenarios, causing a mean negative change in species climatic similarity of 9.5% to 13.7% under SSP2‐4.5 scenario and 9.5% to 10.5% under SSP5‐8.5, for 2041–2060 and 2061–2080, respectively.Synthesis and applications. Our findings provide a framework for agroforestry conservation. The groups of species with finer climatic affinities identified and the climatically suitable areas can be combined into agroecological productive systems, and provide an outlook of where different species may be planted over time. In addition, the conservation priority zones displaying high climate stability for each species individually and all at once can be incorporated into Brazil's conservation plans by policymakers to prioritize specific sites. Lastly, we urge policymakers, conservation organizations and donors to promote interventions involving farmers and local communities, since the species' evaluated have proven to maintain landscapes with productive forest fragments and can be conserved in different Brazilian ecosystems.

Cousins-Westerberg, R., N. Dakin, L. Schat, G. Kadereit, and A. M. Humphreys. 2023. Evolution of cold tolerance in the highly stress-tolerant samphires and relatives (Salicornieae: Amaranthaceae). Botanical Journal of the Linnean Society. https://doi.org/10.1093/botlinnean/boad009

Low temperature constitutes one of the main barriers to plant distributions, confining many clades to their ancestrally tropical biome. However, recent evidence suggests that transitions from tropical to temperate biomes may be more frequent than previously thought. Here, we study the evolution of cold and frost tolerance in the globally distributed and highly stress-tolerant Salicornieae (Salicornioideae, Amaranthaceae s.l.). We first generate a phylogenetic tree comprising almost all known species (85-90%), using newly generated (n = 106) and published nuclear-ribosomal and plastid sequences. Next, we use geographical occurrence data to document in which clades and geographical regions cold-tolerant species occur and reconstruct how cold tolerance evolved. Finally, we test for correlated evolution between frost tolerance and the annual life form. We find that frost tolerance has evolved independently in up to four Northern Hemisphere lineages but that annuals are no more likely to evolve frost tolerance than perennials, indicating the presence of different strategies for adapting to cold environments. Our findings add to mounting evidence for multiple independent out-of-the-tropics transitions among close relatives of flowering plants and raise new questions about the ecological and physiological mechanism(s) of adaptation to low temperatures in Salicornieae.

Gharde, Y., R. P. Dubey, P. K. Singh, and J. S. Mishra. 2023. Littleseed canarygrass (Phalaris minor Retz.) a major weed of rice-wheat system in India is predicted to experience range contraction under future climate. International Journal of Pest Management: 1–12. https://doi.org/10.1080/09670874.2023.2199258

Modelling was carried out using maximum entropy model (MaxEnt) to explore and predict the invasion potential of littleseed canarygrass (Phalaris minor Retz.) in India under current as well as future climatic conditions under Representative Concentration Pathways (RCPs) 4.5 and 8.5 for the years 2050 and 2070. Mutually least correlated 8 bioclimatic variables along with soil and elevation data were used for the modelling over 223 occurrence locations of the species. Jackknife test revealed the significance of temperature derived variables viz. temperature seasonality, annual mean temperature and minimum temperature of the coldest month in governing the potential distribution of P. minor. Currently, 21% of India’s area is either highly (9%) or moderately (12%) suitable as habitat for P. minor. Our model predicts approximately 90% contraction in the area considered to be highly or moderately suitable climatically between 2050 and 2070 under both moderate and high emissions scenarios. Thus, under future climate, a significant niche shift by the species and decreased suitability was observed compared to the current distribution. The present study is first of its kind in exploring the invasion potential of alien invasive weed P. minor under climate change scenarios which is a current threat to rice-wheat system in Indo-Gangetic plains of India.

Reichgelt, T., A. Baumgartner, R. Feng, and D. A. Willard. 2023. Poleward amplification, seasonal rainfall and forest heterogeneity in the Miocene of the eastern USA. Global and Planetary Change 222: 104073. https://doi.org/10.1016/j.gloplacha.2023.104073

Paleoclimate reconstructions can provide a window into the environmental conditions in Earth history when atmospheric carbon dioxide concentrations were higher than today. In the eastern USA, paleoclimate reconstructions are sparse, because terrestrial sedimentary deposits are rare. Despite this, the eastern USA has the largest population and population density in North America, and understanding the effects of current and future climate change is of vital importance. Here, we provide terrestrial paleoclimate reconstructions of the eastern USA from Miocene fossil floras. Additionally, we compare proxy paleoclimate reconstructions from the warmest period in the Miocene, the Miocene Climatic Optimum (MCO), to those of an MCO Earth System Model. Reconstructed Miocene temperatures and precipitation north of 35°N are higher than modern. In contrast, south of 35°N, temperatures and precipitation are similar to today, suggesting a poleward amplification effect in eastern North America. Reconstructed Miocene rainfall seasonality was predominantly higher than modern, regardless of latitude, indicating greater variability in intra-annual moisture transport. Reconstructed climates are almost uniformly in the temperate seasonal forest biome, but heterogeneity of specific forest types is evident. Reconstructed Miocene terrestrial temperatures from the eastern USA are lower than modeled temperatures and coeval Atlantic sea surface temperatures. However, reconstructed rainfall is consistent with modeled rainfall. Our results show that during the Miocene, climate was most different from modern in the northeastern states, and may suggest a drastic reduction in the meridional temperature gradient along the North American east coast compared to today.

Heo, N., D. J. Leopold, M. V. Lomolino, S. Yun, and D. D. Fernando. 2022. Global and regional drivers of abundance patterns in the hart’s tongue fern complex (Aspleniaceae). Annals of Botany. https://doi.org/10.1093/aob/mcac129

Abstract Background and Aims The hart’s tongue fern (HTF) complex is a monophyletic group composed of five geographically segregated members with divergent abundance patterns across its broad geographic range. We postulated hierarchical systems of environmental controls in which climatic and land-use change drive abundance patterns at the global scale, while various ecological conditions function as finer-scale determinants that further increase geographic disparities at regional to local scales. Methods After quantifying the abundance patterns of the HTF complex, we estimated their correlations with global climate and land-use dynamics. Regional determinants were assessed using boosted regression tree models with 18 potential ecological variables. Moreover, we investigated long-term population trends in the U.S. to understand the interplay of climate change and anthropogenic activities on a temporal scale. Key Results Latitudinal climate shifts drove latitudinal abundance gradients, and regionally different levels of land-use change resulted in global geographic disparities in population abundance. At a regional scale, population isolation, which accounts for rescue effects, played an important role, particularly in Europe and East Asia where several hotspots occurred. Furthermore, the variables most strongly influencing abundance patterns greatly differed by region: precipitation seasonality in Europe, spatial heterogeneity of temperature and precipitation in East Asia, and magnitudes of past climate change, temperature seasonality, and edaphic conditions in North America. In the U.S., protected populations showed increasing trends compared to unprotected populations at the same latitude, highlighting the critical role of habitat protection in conservation measures. Conclusions Geographic disparities in the abundance patterns of HTF complex were determined by hierarchical systems of environmental controls, wherein climatic and land-use dynamics act globally but are modulated by various regional and local determinants operating at increasingly finer scales. We highlighted that fern conservation must be tailored to particular geographic contexts and environmental conditions by incorporating a better understanding of the dynamics acting at different spatiotemporal scales.

Führding‐Potschkat, P., H. Kreft, and S. M. Ickert‐Bond. 2022. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9168

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Catarino, S., D. Goyder, I. Darbyshire, E. Costa, R. Figueira, M. C. Duarte, and M. M. Romeiras. 2022. Species Diversity and Endemicity in the Angolan Leguminosae Flora. Frontiers in Ecology and Evolution 10. https://doi.org/10.3389/fevo.2022.871261

Angola has a great diversity of species and ecosystems and a high level of endemism. However, knowledge of the native flora remains very incomplete and outdated. Leguminosae is the largest family in the country, including many species which are of local or more regional economic importance. Based on an extensive review of bibliographic sources, natural history collections, and online databases, the checklist of Angolan Leguminosae plants was updated, including data on their native distribution, conservation status, and principal uses. The endemic taxa were the subject of additional investigation, including the main habitat, the number of collections preserved in herbaria, and the locality of the first collection. We identified 953 Leguminosae taxa occurring in Angola, of which 165 are endemic to the country. Among the 180 genera found, Crotalaria (136) and Indigofera (96) have the highest number of taxa. Almost half of the studied species have important applications, mainly in traditional medicine (385), forage (267), timber (188), and food (120). Nevertheless, only 27.7% have been assessed according to the IUCN Red List and 10 species are classified as threatened. Thirty-three endemics are known only from the type specimen, revealing the lack of knowledge on these species and the need for further field research. More than 30 type specimens were collected in the Serra da Chela, which highlights the importance of this region for biodiversity conservation.

Chevalier, M. 2022. <i>crestr</i>: 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.

Odorico, D., E. Nicosia, C. Datizua, C. Langa, R. Raiva, J. Souane, S. Nhalungo, et al. 2022. An updated checklist of Mozambique’s vascular plants. PhytoKeys 189: 61–80. https://doi.org/10.3897/phytokeys.189.75321

An updated checklist of Mozambique’s vascular plants is presented. It was compiled referring to several information sources such as existing literature, relevant online databases and herbaria collections. The checklist includes 7,099 taxa (5,957 species, 605 subspecies, 537 varieties), belonging to …