Science Enabled by Specimen Data

Smith, A. B., S. J. Murphy, D. Henderson, and K. D. Erickson. 2023. Including imprecisely georeferenced specimens improves accuracy of species distribution models and estimates of niche breadth. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13628

Aim Museum and herbarium specimen records are frequently used to assess the conservation status of species and their responses to climate change. Typically, occurrences with imprecise geolocality information are discarded because they cannot be matched confidently to environmental conditions and are thus expected to increase uncertainty in downstream analyses. However, using only precisely georeferenced records risks undersampling of the environmental and geographical distributions of species. We present two related methods to allow the use of imprecisely georeferenced occurrences in biogeographical analysis. Innovation Our two procedures assign imprecise records to the (1) locations or (2) climates that are closest to the geographical or environmental centroid of the precise records of a species. For virtual species, including imprecise records alongside precise records improved the accuracy of ecological niche models projected to the present and the future, especially for species with c. 20 or fewer precise occurrences. Using only precise records underestimated loss of suitable habitat and overestimated the amount of suitable habitat in both the present and the future. Including imprecise records also improves estimates of niche breadth and extent of occurrence. An analysis of 44 species of North American Asclepias (Apocynaceae) yielded similar results. Main conclusions Existing studies examining the effects of spatial imprecision typically compare outcomes based on precise records against the same records with spatial error added to them. However, in real-world cases, analysts possess a mix of precise and imprecise records and must decide whether to retain or discard the latter. Discarding imprecise records can undersample the geographical and environmental distributions of species and lead to mis-estimation of responses to past and future climate change. Our method, for which we provide a software implementation in the enmSdmX package for R, is simple to use and can help leverage the large number of specimen records that are typically deemed “unusable” because of spatial imprecision in their geolocation.

Adhikari, P., Y.-H. Lee, A. Poudel, G. Lee, S.-H. Hong, and Y.-S. Park. 2023. Predicting the Impact of Climate Change on the Habitat Distribution of Parthenium hysterophorus around the World and in South Korea. Biology 12: 84. https://doi.org/10.3390/biology12010084

The global climate change, including increases in temperature and precipitation, may exacerbate the invasion by P. hysterophorus. Here, MaxEnt modeling was performed to predict P. hysterophorus distribution worldwide and in South Korea under the current and future climate global climate changes, including increases in temperature and precipitation. Under the current climate, P. hysterophorus was estimated to occupy 91.26%, 83.26%, and 62.75% of the total land area of Australia, South America, and Oceania, respectively. However, under future climate scenarios, the habitat distribution of P. hysterophorus would show the greatest change in Europe (56.65%) and would extend up to 65°N by 2081–2100 in South Korea, P. hysterophorus currently potentially colonizing 2.24% of the land area, particularly in six administrative divisions. In the future, P. hysterophorus would spread rapidly, colonizing all administrative divisions, except Incheon, by 2081–2100. Additionally, the southern and central regions of South Korea showed greater habitat suitability than the northern region. These findings suggest that future climate change will increase P. hysterophorus distribution both globally and locally. Therefore, effective control and management strategies should be employed around the world and in South Korea to restrict the habitat expansion of P. hysterophorus.

Gómez Díaz, J. A., A. Lira-Noriega, and F. Villalobos. 2023. Expanding protected areas in a Neotropical hotspot. International Journal of Sustainable Development & World Ecology: 1–15. https://doi.org/10.1080/13504509.2022.2163717

The region of central Veracruz is considered a biodiversity hotspot due to its high species richness and environmental heterogeneity, but only 2% of this region is currently protected. This study aimed to assess the current protected area system’s effectiveness and to identify priority conservation areas for expanding the existing protected area system. We used the distribution models of 1186 species from three kingdoms (Animalia, Plantae, and Fungi) together with ZONATION software, a conservation planning tool, to determine areas that could help expand the current network of protected areas. We applied three different parametrizations (including only species, using the boundary quality penalty, and using corridor connectivity). We found that protecting an additional 15% of the area would increase, between 16.2% and 19.3%, the protection of the distribution area of all species. We propose that the regions with a consensus of the three parametrizations should be declared as new protected areas to expand 374 km2 to the 216 km2 already protected. Doing so would double the protected surface in central Veracruz. The priority areas identified in this study have more species richness, carbon stock values, natural vegetation cover, and less human impact index than the existing protected areas. If our identified priority areas are declared protected, we could expect a future recovery of endangered species populations for Veracruz. The proposed new protected areas are planned and designed as corridors connecting currently isolated protected areas to promote biodiversity protection.

Wu, M., J. Huang, S. R. Manchester, H. Tang, Y. Gao, T. Wang, Z. Zhou, and T. Su. 2023. A new fossil record of Palaeosinomenium (Menispermaceae) from the Upper Eocene in the southeastern margin of the Tibetan Plateau and its biogeographic and paleoenvironmental implications. Review of Palaeobotany and Palynology 310: 104827. https://doi.org/10.1016/j.revpalbo.2022.104827

Palaeosinomenium Chandler (Menispermaceae) was established to accommodate the fossil endocarps that share similar morphological characteristics with the tribe Menispermeae in Menispermaceae. Previous fossil records suggested that Palaeosinomenium was distributed in North America, Europe, and East Asia before the Middle Eocene. A new fossil species, Palaeosinomenium hengduanensis Meng-Xiao Wu et Zhe-Kun Zhou sp. nov., was established based on an endocarp impression fossil from the Upper Eocene (35 ± 1 Ma) Shuanghe Formation, Jianchuan Basin, southwestern China. The new species is characterized by a horseshoe-shaped endocarp, an excavated central area, surrounded by a slightly asymmetrical C-shaped lateral ridge, and an elliptic aperture located near the longer endocarp limb. The fossil site is located in the modern distribution area of the living species Sinomenium acutum (Thunb.) Rehd. et Wils, a potential nearest living relative of the new species. The finding of P. hengduanensis supports that the divergence within the tribe Menispermeae might have occurred by the Late Eocene and the species similar to modern S. acutum appeared in the southeastern margin of the Tibetan Plateau as early as in the Late Eocene.

Sandoval-Martínez, J., E. I. Badano, F. A. Guerra-Coss, J. A. Flores Cano, J. Flores, S. M. Gelviz-Gelvez, and F. Barragán-Torres. 2023. Selecting tree species to restore forest under climate change conditions: Complementing species distribution models with field experimentation. Journal of Environmental Management 329: 117038. https://doi.org/10.1016/j.jenvman.2022.117038

The long-term success of forest restoration programs can be improved using climate-based species distribution models (SDMs) to predict which tree species will tolerate climate change. However, as SDMs cannot estimate if species will recruit at these habitats, determining whether their predictions apply to early life-cycle stages of trees is critical to support such a usage. For this, we propose sowing seeds of the focal tree species under the current climate and simulated climate change conditions in target restoration sites. Thus, using of SDMs to design climate-adaptive forest restoration programs would be supported if the differences in habitat occupancy probabilities of species they predict between the current and future climate concurs with the observed differences in recruitment rates of species when sowed under the current climate and simulated climate change conditions. To test this hypothesis, we calibrated SDMs for Vachellia pennatula and Prosopis laevigata, two pioneer tree species widely recommended to restore human-degraded drylands in Mexico, and transferred them to climate change scenarios. After that, we applied the experimental approach proposed above to validate the predictions of SDMs. These models predicted that V. pennatula will decrease its habitat occupancy probabilities across Mexico, while P. laevigata was predicted to keep out their current habitat occupancy probabilities, or even increase them, in climate change scenarios. The results of the field experiment supported these predictions, as recruitment rates of V. pennatula were lower under simulated climate change than under the current climate, while no differences were found for the recruitment rates of P. laevigata between these environmental conditions. These findings demonstrate that SDMs provide meaningful insights for designing climate-adaptive forest restoration programs but, before applying this methodology, predictions of these models must be validated with field experiments to determine whether the focal tree species will recruit under climate change conditions. Moreover, as the pioneer trees used to test our proposal seem to be differentially sensitive to climate change, this approach also allows establishing what species must be prescribed to restore forests with a view to the future and what species must be avoided in these practices.

Roberts, J., and S. Florentine. 2022. Biology, distribution and management of the globally invasive weed Solanum elaeagnifolium Cav (silverleaf nightshade): A global review of current and future management challenges. Weed Research. https://doi.org/10.1111/wre.12556

Solanum elaeagnifolium Cav (silverleaf nightshade) is a deep-rooted, multi-stemmed, perennial, herbaceous woody plant that has been observed to threaten agricultural and native biodiversity worldwide. It is widely agreed that without efficient integrated management, S. elaeagnifolium will continue to cause significant economic and environmental damage across multiple scales. It is estimated that the annual economic impact of S. elaeagnifolium in Australia exceeds AUD $62 million, with this figure likely to be much higher in other countries invaded by this plant. It can also tolerate a high level of abiotic stress and survive in a range of temperatures (below freezing point to 34°C) and areas with an average yearly rainfall between 250 and 600 mm. Its extensive deep taproot system is capable of regenerating asexually and with its many seed dispersal mechanisms; it can quickly spread and establish itself within a region. This makes containment and management of the species especially challenging. Previous management has largely been focused on biological control, competition, essential oils, grazing pressure, herbicide application and manual removal. Despite the large range of available management techniques, there has been little success in the long-term control of S. elaeagnifolium, and only a handful of methods such as essential oils and herbicide application have shown reasonable success for controlling this weed. Therefore, this review aims to synthesise the identified and potentially useful approaches to control S. elaeagnifolium that have been recorded in the literature which deal with its biology, distribution and management. It also explores previous and current management techniques to ascertain the research gaps and knowledge required to assist in the effective and economically sustainable management of this invasive weed.

Aguirre‐Liguori, J. A., A. Morales‐Cruz, and B. S. Gaut. 2022. Evaluating the persistence and utility of five wild Vitis species in the context of climate change. Molecular Ecology. https://doi.org/10.1111/mec.16715

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for the persistence of perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of samples from five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was to assess the relative potential of different CWR accessions to persist in the face of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load and a phenotype (resistance to Pierce’s Disease), we predicted that accessions from one species (V. mustangensis) are particularly well‐suited to persist in future climates. The second goal was to identify which CWR accessions may contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we evaluated whether CWR accessions have the allelic capacity to persist if moved to locations where grapevines (V. vinifera) are cultivated in the United States. We identified six candidates from V. mustangensis and hypothesized that they may prove useful for contributing alleles that can mitigate climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward assessing the genomic and bioclimatic characteristics of CWRs.

Gougherty, A. V., S. R. Keller, and M. C. Fitzpatrick. 2022. Do genetically informed distribution models improve range predictions in past climates? A case study with balsam poplar. Frontiers of Biogeography 14. https://doi.org/10.21425/f5fbg56931

Species distribution models (SDMs) are one of the most widely used approaches to predict changes in habitat suitability in response to climate change. However, as typically implemented, SDMs treat species as genetically uniform throughout their ranges and thereby ignore potentially important genetic differences between populations. While numerous studies have used SDMs to model genetically based subgroupings within species, the ability of such models to be transferred to new times has rarely been evaluated. Here, we used standard and genetically informed distribution models (gSDMs) to predict the future and past range of balsam poplar (Populus balsamifera L.). We then assessed model transferability of standard SDMs and gSDMs using balsam poplar fossil pollen and macrofossil occurrences. In general, standard and gSDMs performed similarly through time, with both predicting a northward expanding range from refugia as glaciers receded over the past 22 ky BP and declining suitable area in future climates. Both standard and gSDMs showed moderate abilities to distinguish balsam poplar fossils from pseudo-absences but tended to predict lower suitability at fossil sites during the Pleistocene-Holocene transition. Although gSDMs applied to balsam poplar did not prove more transferable than standard SDMs, they provided numerous unique insights, such as the change in suitable area of genetic clusters through time and potential refugial locations. We argue more research is needed to determine which species may benefit most from the gSDM approach and to test gSDMs with temporally or spatially independent occurrences, as is often recommended for standard SDMs.

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

Lu, L.-L., B.-H. Jiao, F. Qin, G. Xie, K.-Q. Lu, J.-F. Li, B. Sun, et al. 2022. Artemisia pollen dataset for exploring the potential ecological indicators in deep time. Earth System Science Data 14: 3961–3995. https://doi.org/10.5194/essd-14-3961-2022

Abstract. Artemisia, along with Chenopodiaceae, is the dominant component growing in the desert and dry grassland of the Northern Hemisphere. Artemisia pollen with its high productivity, wide distribution, and easy identification is usually regarded as an eco-indicator for assessing aridity and distinguishing grassland from desert vegetation in terms of the pollen relative abundance ratio of Chenopodiaceae/Artemisia (C/A). Nevertheless, divergent opinions on the degree of aridity evaluated by Artemisia pollen have been circulating in the palynological community for a long time. To solve the confusion, we first selected 36 species from nine clades and three outgroups of Artemisia based on the phylogenetic framework, which attempts to cover the maximum range of pollen morphological variation. Then, sampling, experiments, photography, and measurements were taken using standard methods. Here, we present pollen datasets containing 4018 original pollen photographs, 9360 pollen morphological trait measurements, information on 30 858 source plant occurrences, and corresponding environmental factors. Hierarchical cluster analysis on pollen morphological traits was carried out to subdivide Artemisia pollen into three types. When plotting the three pollen types of Artemisia onto the global terrestrial biomes, different pollen types of Artemisia were found to have different habitat ranges. These findings change the traditional concept of Artemisia being restricted to arid and semi-arid environments. The data framework that we designed is open and expandable for new pollen data of Artemisia worldwide. In the future, linking pollen morphology with habitat via these pollen datasets will create additional knowledge that will increase the resolution of the ecological environment in the geological past. The Artemisia pollen datasets are freely available at Zenodo (https://doi.org/10.5281/zenodo.6900308; Lu et al., 2022).