Science Enabled by Specimen Data

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.

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.

Descôteaux, R., M. Huserbråten, L. Jørgensen, P. Renaud, R. Ingvaldsen, E. Ershova, and B. Bluhm. 2022. Origin of marine invertebrate larvae on an Arctic inflow shelf. Marine Ecology Progress Series.

Many benthic invertebrate taxa possess planktonic early life stages which drift with water currents and contribute to dispersal of the species, sometimes reaching areas beyond the current ranges of the adults. Until recently, it had been difficult to identify planktonic larvae to species level due to lack of distinguishing features, preventing detection of expatriate species. Here we used DNA metabarcoding of the COI gene to obtain species-level identification of early life stages of benthic invertebrates in zooplankton samples from the Barents Sea and around Svalbard, where, regionally, large volumes of warm Atlantic Water enter the Arctic from the south. We compared the larval community in the water column to the adult community on the seafloor to identify mismatches. In addition, we implemented particle tracking analysis to identify the possible areas of origin of larvae. Our results show that 30–45% of larval taxa—largely polychaetes and nudibranchs—were not local to the sampling area, though most were found nearby in the Barents Sea. In the particle tracking analysis, some larvae originating along the Norwegian coast were capable of reaching the northwest coast of Svalbard within 3 mo, but larvae found east of Svalbard had a more constrained possible area of origin which did not extend to the Norwegian coast. This study highlights largely regional-scale larval connectivity in the Barents Sea but demonstrates the potential for some long-lived larval taxa to travel to Svalbard and the Barents Sea from further south.

Ward, S. F., E. G. Brockerhoff, R. M. Turner, T. Yamanaka, L. Marini, S. Fei, and A. M. Liebhold. 2022. Prevalence and drivers of a tree-killing bark beetle, Ips typographus (Coleoptera, Scolytinae), in international invasion pathways into the USA. Journal of Pest Science.

The unintentional transport of insects beyond their native ranges has greatly increased with globalization over the past century, leading to higher propagule pressure in non-native ranges of many species. Knowledge about the prevalence of a species in international invasion pathways is important for predicting invasions and taking appropriate biosecurity measures. We investigated the spatiotemporal patterns and drivers of interceptions—detections of at least one individual with imported goods that potentially serve as a proxy for arrival rates—for a tree-killing bark beetle, the European spruce bark beetle ( Ips typographus L.; Coleoptera: Curculionidae: Scolytinae), in the USA from 1914 to 2008. Across the study period, there were 505 interceptions of I. typographus with shipments originating from > 25 countries at ports in 22 US states. Interceptions first occurred in 1938, peaked at 33 and 25 in 1984 and 1996, respectively, and declined after the mid-1990s. Interceptions of I. typographus did not have a statistically detectable relationship with outbreak levels in the native range, were inversely related to annual import volume (an artifact likely driven by changes in inspection policies), and were more frequent during the winter. Thus, while interceptions of I. typographus are challenging to predict, we found evidence that (i) biosecurity practices against this beetle could be increased during winter but not in response to outbreaks in source regions and (ii) the overall abundance of this beetle in invasion pathways has recently decreased, probably because strengthened phytosanitary protocols have reduced contamination levels and/or decreased the perceived need for inspections.

Testo, W. L., A. L. de Gasper, S. Molino, J. M. G. y Galán, A. Salino, V. A. de O. Dittrich, and E. B. Sessa. 2022. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. American Journal of Botany.

Premise Historical biogeography of ferns is typically expected to be dominated by long-distance dispersal, due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims are to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. Methods We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 out of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. Key results Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. Conclusions Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

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.

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 (; Lu et al., 2022).

Kopperud, B. T., S. Lidgard, and L. H. Liow. 2022. Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps. PeerJ 10: e13921.

We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.

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.

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.

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.

Bellingham, P. J., E. A. Arnst, B. D. Clarkson, T. R. Etherington, L. J. Forester, W. B. Shaw, R. Sprague, et al. 2022. The right tree in the right place? A major economic tree species poses major ecological threats. Biological Invasions.

Tree species in the Pinaceae are some of the most widely introduced non-native tree species globally, especially in the southern hemisphere. In New Zealand, plantations of radiata pine ( Pinus radiata D. Don) occupy c . 1.6 million ha and form 90% of planted forests. Although radiata pine has naturalized since 1904, there is a general view in New Zealand that this species has not invaded widely. We comprehensively review where radiata pine has invaded throughout New Zealand. We used a combination of observational data and climate niche modelling to reveal that invasion has occurred nationally. Climate niche modelling demonstrates that while current occurrences are patchy, up to 76% of the land area (i.e. 211,388 km 2 ) is climatically capable of supporting populations. Radiata pine has mainly invaded grasslands and shrublands, but also some forests. Notably, it has invaded lower-statured vegetation, including three classes of naturally uncommon ecosystems, primary successions and secondary successions. Overall, our findings demonstrate pervasive and ongoing invasion of radiata pine outside plantations. The relatively high growth rates and per individual effects of radiata pine may result in strong effects on naturally uncommon ecosystems and may alter successional trajectories. Local and central government currently manage radiata pine invasions while propagule pressure from existing and new plantations grows, hence greater emphasis is warranted both on managing current invasions and proactively preventing future radiata pine invasions. We therefore recommend a levy on new non-native conifer plantations to offset costs of managing invasions, and stricter regulations to protect vulnerable ecosystems. A levy on economic uses of invasive species to offset costs of managing invasions alongside stricter regulations to protect vulnerable ecosystems could be a widely adopted measure to avert future negative impacts.

Couvreur, T. L. P., X. Cornejo, J. N. Zapata, and A. Loor. 2022. Two new magnoliid (Annonaceae, Lauraceae) tree species from Manabí, western Ecuador. Blumea - Biodiversity, Evolution and Biogeography of Plants.

Western Ecuador harbours high plant diversity and endemism. The region of Manabí has known intense deforestation over the last decades, but lowland rain forests persist in a network of small forest fragment patches. Here, we describe two new magnoliid tree species from a small privately owned forest fragment known as La Esperanza reserve, in the El Carmen canton (Manabí): Aniba ecuadorica (Lauraceae) and Guatteria esperanzae (Annonaceae). For both species a detailed morphological description, a preliminary conservation status following IUCN criteria, distribution maps and high quality photographs are provided. This represents the second species of Aniba known to occur in western Ecuador, while there are 14 species of Guatteria documented for Ecuador west of the Andes. Aniba ecuadorica is only known from two localities and has a preliminary IUCN conservation status of Critically Endangered, while Guatteria esperanzae is known from six localities and is suggested to be Endangered. Finally, we provide a quick overview of Guatteria species in western Ecuador with a key to the species in the region. The description of these two new tree species underlines the important need of prospection and conservation of the remnant forests in the Manabí region of western Ecuador. We also stress the importance of privately owned forest fragments for biodiversity conservation.