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.

Tackett, M., C. Berg, T. Simmonds, O. Lopez, J. Brown, R. Ruggiero, and J. Weber. 2022. Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9382

Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of Triodanis perfoliata, a widespread mix‐mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between a breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R2 = .63, p = .01, n = 9 populations), and we found significant population structuring (FST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environments appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that T. perfoliata experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that the breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.

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.

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.

Canavan, S., Z. T. Brym, G. Brundu, K. Dehnen-Schmutz, D. Lieurance, T. Petri, W. H. Wadlington, et al. 2022. Cannabis de-domestication and invasion risk. Biological Conservation 274: 109709. https://doi.org/10.1016/j.biocon.2022.109709

Cultivated plants provide food, fiber, and energy but they can escape, de-domesticate, colonize agroecosystems as weeds, and disrupt natural ecosystems as invasive species. Escape and invasion depend on traits of the species, type and rate of domestication, and cultivation context. Understanding this “de-domestication invasion process” is critical for managing conservation efforts to reduce unintended consequences of cultivated species in novel areas. Cannabis (Cannabis sativa L.) is an ideal case study to explore this process because it was one of the earliest plants to co-evolve with humans, has a crop to weed history, and has been introduced and cultivated globally. Moreover, recent liberalization of cannabis cultivation and use policies have raised concerns about invasion risk. Here, we synthesize knowledge on cannabis breeding, cultivation, and processing relevant to invasion risk and outline research and management priorities to help overcome the research deficit on the invasion ecology of the species. Understanding the transition of cannabis through the de-domestication-invasion process will inform policy and minimize agricultural and environmental risks associated with cultivation of domesticated species.

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).

Coca‐de‐la‐Iglesia, M., N. G. Medina, J. Wen, and V. Valcárcel. 2022. Evaluation of the tropical‐temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae. American Journal of Botany. https://doi.org/10.1002/ajb2.16059

(no abstract available)

Contreras-Medina, R., M. Santiago-Alvarado, D. Espinosa, G. Rivas, and I. Luna-Vega. 2022. Distributional patterns and conservation of the genus Habromys (Rodentia: Cricetidae) in Mesoamerica. Studies on Neotropical Fauna and Environment: 1–17. https://doi.org/10.1080/01650521.2022.2085071

We analyzed the geographical distribution of Habromys species based on distributional data from museum specimens, web databases, and literature. We recorded species-presence data of each species in 0.5° × 0.5° grid cells and biogeographic provinces in Mexico and Central America. We analyzed the association between vegetation types and land use. We carried out species distribution models of most species of Habromys and those tree species frequently harboring these mice, finding a high distributional congruence among mice and trees. Species of Habromys occur throughout the montane systems of Mexico and northern Central America, so they can be considered characteristic elements of the Neotropical montane cloud forests. All species of the genus occur in Mexico, whereas Guatemala and El Salvador have only one species. Although all species of Habromys are highly restricted and considered rare species, only one (H. simulatus) is currently protected by Mexican laws. We assigned two species to a high and four to the critical conservation risk. Habromys species contribute to the recognition of Mesoamerica as a biodiversity hotspot.

Amaral, D. T., I. A. S. Bonatelli, M. Romeiro-Brito, E. M. Moraes, and F. F. Franco. 2022. Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas. Biological Conservation 273: 109677. https://doi.org/10.1016/j.biocon.2022.109677

Mapping biodiversity patterns across taxa and environments is crucial to address the evolutionary and ecological dimensions of species distribution, suggesting areas of particular importance for conservation purposes. Within Cactaceae, spatial diversity patterns are poorly explored, as are the abiotic factors that may predict these patterns. We gathered geographic and genetic data from 921 cactus species by exploring both the occurrence and genetic databases, which are tightly associated with drylands, to evaluate diversity patterns, such as phylogenetic diversity and endemism, paleo-, neo-, and superendemism, and the environmental predictor variables of such patterns in a global analysis. Hotspot areas of cacti diversity are scattered along the Neotropical and Nearctic regions, mainly in the desertic portion of Mesoamerica, Caribbean Island, and the dry diagonal of South America. The geomorphological features of these regions may create a complexity of areas that work as locally buffered zones over time, which triggers local events of diversification and speciation. Desert and dryland/dry forest areas comprise paleo- and superendemism and may act as both museums and cradles of species, displaying great importance for conservation. Past climates, topography, soil features, and solar irradiance seem to be the main predictors of distinct endemism types. The hotspot areas that encompass a major part of the endemism cells are outside or poorly covered by formal protection units. The current legally protected areas are not able to conserve the evolutionary diversity of cacti. Given the rapid anthropogenic disturbance, efforts must be reinforced to monitor biodiversity and the environment and to define/plan current and new protected areas.

Rewicz, A., M. Myśliwy, T. Rewicz, W. Adamowski, and M. Kolanowska. 2022. Contradictory effect of climate change on American and European populations of Impatiens capensis Meerb. - is this herb a global threat? Science of The Total Environment 850: 157959. https://doi.org/10.1016/j.scitotenv.2022.157959

AimsThe present study is the first-ever attempt to generate information on the potential present and future distribution of Impatiens capensis (orange balsam) under various climate change scenarios. Moreover, the differences in bioclimatic preferences of native and non-native populations were evaluated.LocationGlobal.TaxonAngiosperms.MethodsA database of I. capensis localities was compiled based on the public database – the Global Biodiversity Information Facility (GBIF), herbarium specimens, and a field survey in Poland. The initial dataset was verified, and each record was assigned to one of two groups – native (3664 records from North America) or non-native (750 records from Europe and the western part of North America). The analyses involved bioclimatic variables in 2.5 arc-minutes of interpolated climate surface downloaded from WorldClim v. 2.1. MaxEnt version 3.3.2 was used to conduct the ecological niche modeling based on presence-only observations of I. capensis. Forecasts of the future distribution of the climatic niches of the studied species in 2080–2100 were made based on climate projections developed by the CNRM/CERFACS modeling and Model for Interdisciplinary Research on Climate (MIROC-6).Main conclusionsDistribution models created for “present time” showed slightly broader potential geographical ranges of both native and invasive populations of orange balsam. On the other hand, some areas (e.g. NW Poland, SW Finland), settled by the species, are far outside the modeled climate niche, which indicates a much greater adaptation potential of I. capensis. In addition, the models have shown that climate change will shift the native range of orange balsam to the north and the range of its European populations to the northwest. Moreover, while the coverage of niches suitable for I. capensis in America will extend due to climate change, the European populations will face 31–95 % habitat loss.