Science Enabled by Specimen Data

Gillespie, L. J., P. C. Sokoloff, G. A. Levin, J. Doubt, and R. T. McMullin. 2024. Vascular plant, bryophyte, and lichen biodiversity of Agguttinni Territorial Park, Baffin Island, Nunavut, Canada: an annotated species checklist of a new Arctic protected area. Check List 20: 279–443.

Agguttinni Territorial Park is a large, newly established park on the east-central coast of Baffin Island in Nunavut, Canada. Previous knowledge of the plant and lichen biodiversity was limited and based mostly on collections made during the 1950 Baffin Island Expedition. We conducted a floristic inventory of the park in 2021 and re-examined previous collections. We recorded 141 species of vascular plants belonging to 25 families, 69 species of bryophytes in 27 families, and 93 species of lichens in 23 families. Most of the vascular plant and bryophyte species are new records for the park area, and some vascular plants, bryophytes, and lichens are newly reported for Baffin Island, Nunavut, or the Canadian Arctic or represent significant range extensions. Vascular plant species diversity varied greatly among localities, with inland valleys at the heads of fiords showing highest diversity and interior rocky barrens showing the lowest.

Rayos, A. L., M. A. M. Renner, and S. Y. W. Ho. 2024. The Neotropical endemic liverwort subfamily Micropterygioideae had circum‐Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous. Ecology and Evolution 14.

Lepidoziaceae are the third‐largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal‐vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157–240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American–Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum‐Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present‐day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.

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.

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.

Rautela, K., A. Kumar, S. K. Rana, A. Jugran, and I. D. Bhatt. 2024. Distribution, Chemical Constituents and Biological Properties of Genus Malaxis. Chemistry & Biodiversity.

The genus Malaxis (family Orchidaceae), comprises nearly 183 species available across the globe. The plants of this genus have long been employed in traditional medical practices because of their numerous biological properties, like the treatment of infertility, hemostasis, burning sensation, bleeding diathesis, fever, diarrhea, dysentery, febrifuge, tuberculosis, etc. Various reports highlight their phytochemical composition and biological activities. However, there is a lack of systematic review on the distribution, phytochemistry, and biological properties of this genus. Hence, this study aims to conduct a thorough and critical review of Malaxis species, covering data published from 1965 to 2022 with nearly 90 articles. Also, it examines different bioactive compounds, their chemistry, and pharmacotherapeutics as well as their traditional uses. A total of 191 unique compounds, including the oil constituents were recorded from Malaxis species. The highest active ingredients were obtained from Malaxis acuminata (103) followed by Malaxis muscifera (50) and Malaxis rheedei (33). In conclusion, this review offers an overview of the current state of knowledge on Malaxis species and highlights prospects for future research projects on them. Additionally, it recommends the promotion of domestication studies for rare medicinal orchids like Malaxis and the prompt implementation of conservation measures.

Zhang, H., W. Guo, and W. Wang. 2023. The dimensionality reductions of environmental variables have a significant effect on the performance of species distribution models. Ecology and Evolution 13.

How to effectively obtain species‐related low‐dimensional data from massive environmental variables has become an urgent problem for species distribution models (SDMs). In this study, we will explore whether dimensionality reduction on environmental variables can improve the predictive performance of SDMs. We first used two linear (i.e., principal component analysis (PCA) and independent components analysis) and two nonlinear (i.e., kernel principal component analysis (KPCA) and uniform manifold approximation and projection) dimensionality reduction techniques (DRTs) to reduce the dimensionality of high‐dimensional environmental data. Then, we established five SDMs based on the environmental variables of dimensionality reduction for 23 real plant species and nine virtual species, and compared the predictive performance of those with the SDMs based on the selected environmental variables through Pearson's correlation coefficient (PCC). In addition, we studied the effects of DRTs, model complexity, and sample size on the predictive performance of SDMs. The predictive performance of SDMs under DRTs other than KPCA is better than using PCC. And the predictive performance of SDMs using linear DRTs is better than using nonlinear DRTs. In addition, using DRTs to deal with environmental variables has no less impact on the predictive performance of SDMs than model complexity and sample size. When the model complexity is at the complex level, PCA can improve the predictive performance of SDMs the most by 2.55% compared with PCC. At the middle level of sample size, the PCA improved the predictive performance of SDMs by 2.68% compared with the PCC. Our study demonstrates that DRTs have a significant effect on the predictive performance of SDMs. Specifically, linear DRTs, especially PCA, are more effective at improving model predictive performance under relatively complex model complexity or large sample sizes.

Yim, C., E. S. Bellis, V. L. DeLeo, D. Gamba, R. Muscarella, and J. R. Lasky. 2023. Climate biogeography of Arabidopsis thaliana: Linking distribution models and individual variation. Journal of Biogeography.

Aim Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range‐wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity.LocationGlobal.TaxonArabidopsis thaliana (‘Arabidopsis’).MethodsWe fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current and future climates. We confronted model predictions with individual performance measured on 2194 herbarium specimens, and we asked whether predicted suitability was associated with life history and genomic variation measured on ~900 natural accessions.ResultsThe most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate‐associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late‐flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the centre of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well‐predicted by our native‐range model applied to certain regions but not others, suggesting it has colonized novel climates.Main ConclusionsIntegration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.

Rodríguez-Merino, A. 2023. Identifying and Managing Areas under Threat in the Iberian Peninsula: An Invasion Risk Atlas for Non-Native Aquatic Plant Species as a Potential Tool. Plants 12: 3069.

Predicting the likelihood that non-native species will be introduced into new areas remains one of conservation’s greatest challenges and, consequently, it is necessary to adopt adequate management measures to mitigate the effects of future biological invasions. At present, not much information is available on the areas in which non-native aquatic plant species could establish themselves in the Iberian Peninsula. Species distribution models were used to predict the potential invasion risk of (1) non-native aquatic plant species already established in the peninsula (32 species) and (2) those with the potential to invade the peninsula (40 species). The results revealed that the Iberian Peninsula contains a number of areas capable of hosting non-native aquatic plant species. Areas under anthropogenic pressure are at the greatest risk of invasion, and the variable most related to invasion risk is temperature. The results of this work were used to create the Invasion Risk Atlas for Alien Aquatic Plants in the Iberian Peninsula, a novel online resource that provides information about the potential distribution of non-native aquatic plant species. The atlas and this article are intended to serve as reference tools for the development of public policies, management regimes, and control strategies aimed at the prevention, mitigation, and eradication of non-native aquatic plant species.

Calvente, A., A. P. Alves da Silva, D. Edler, F. A. Carvalho, M. R. Fantinati, A. Zizka, and A. Antonelli. 2023. Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti. American Journal of Botany.

Premise: Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. Here we test global biogeographic boundaries for Neotropical Cactaceae using specimen‐based occurrences coupled with data from visual observations, as a means to tackle the known collection biases in the family.MethodsSpecies richness and record density were assessed for preserved specimens and human observations and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions based on data from 261,272 point records cleaned through automated and manual steps.Key ResultsWe find that areas in Mexico and southwestern USA, Eastern Brazil and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cacti bioregions, among which the most species‐rich are: northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, Mexico/Baja California.ConclusionsThe bioregionalization proposed shows biogeographical boundaries specific to cacti, and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert‐derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen‐science records, can complement traditional specimen‐based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.This article is protected by copyright. All rights reserved.

Luza, A. L., A. V. Rodrigues, L. Mamalis, and V. Zulian. 2023. Spatial distribution of the greater rhea, Rhea americana (Linnaeus, 1758), in Rio Grande do Sul, southern Brazil: citizen-science data, probabilistic mapping, and comparison with expert knowledge. Ornithology Research.

The popularization of citizen-science platforms has increased the amount of data available in a fine spatial and temporal resolution, which can be used to fill distribution knowledge gaps through probabilistic maps. In this study, we gathered expert-based information and used species distribution models to produce two independent maps of the greater rhea ( Rhea americana , Rheiformes, Rheidae) distribution in the state of Rio Grande do Sul, Brazil. We integrated municipality level detection/non-detection data from five citizen-science datasets into a Bayesian site occupancy model, accounting for false negatives, sampling effort, habitat covariates, and spatial autocorrelation. We addressed whether habitat (grassland and crop field cover, number of rural properties) and spatial autocorrelation explains the realized occurrence of the species and compared model-based and expert-based occurrence maps. The mean estimated percentage of occupied municipalities was 48% (239 out of 497 municipalities), whereas experts declared 21% of the municipalities (103) as occupied by the species. While both mapping approaches showed greater rhea presence in most municipalities of the Pampa biome, they disagreed in the majority of the municipalities in the Atlantic Forest, where more fieldwork must be undertaken. The greater rhea distribution was exclusively explained by the spatial autocorrelation component, suggesting that the species expanded its distribution towards the north of the state, reaching the Atlantic Forest, following deforestation and agriculture expansion.

Graham, C. D. K., E. J. Forrestel, A. L. Schilmiller, A. T. Zemenick, and M. G. Weber. 2023. Evolutionary signatures of a trade-off in direct and indirect defenses across the wild grape genus Vitis. Evolution.

Evolutionary correlations between chemical defense and protection by mutualist bodyguards have been long predicted, but tests of these pattern remain rare. We use a phylogenetic framework to test for evolutionary correlations indicative of trade-offs or synergisms between direct defense in the form of plant secondary metabolism, and indirect defense in the form of leaf domatia, across 33 species in the wild grape genus, Vitis. We also performed a bioassay with a generalist herbivore to associate our chemical phenotypes with herbivore palatability. Finally, we tested whether defensive traits correlate with the average abiotic characteristics of each species’ contemporary range and whether these correlations were consistent with plant defense theory. We found a negative evolutionary correlation between domatia size and the diversity of secondary metabolites in Vitis leaf tissue across the genus, and also that leaves with a higher diversity and richness of secondary metabolites were less palatable to a generalist herbivore, consistent with a trade-off in chemical and mutualistic defense investment. Predictions from plant defense theory were not supported by associations between investment in defense phenotypes and abiotic variables. Our work demonstrates an evolutionary pattern indicative of a trade-off between indirect and direct defense strategies across the Vitis genus.