Science Enabled by Specimen Data

Campbell, L. C. E., E. T. Kiers, and G. Chomicki. 2022. The evolution of plant cultivation by ants. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.09.005

Outside humans, true agriculture was previously thought to be restricted to social insects farming fungus. However, obligate farming of plants by ants was recently discovered in Fiji, prompting a re-examination of plant cultivation by ants. Here, we generate a database of plant cultivation by ants, identify three main types, and show that these interactions evolved primarily for shelter rather than food. We find that plant cultivation evolved at least 65 times independently for crops (~200 plant species), and 15 times in farmer lineages (~37 ant taxa) in the Neotropics and Asia/Australasia. Because of their high evolutionary replication, and variation in partner dependence, these systems are powerful models to unveil the steps in the evolution and ecology of insect agriculture.

Hinojosa-Espinosa, O., D. Potter, M. Ishiki, E. Ortiz, and J. L. Villaseñor. 2021. Dichrocephala integrifolia (Astereae, Asteraceae), a new exotic genus and species for Mexico and second record for the New World. Botanical Sciences 99: 708–716. https://doi.org/10.17129/botsci.2754

Background: Dichrocephala is an Old-World genus of the tribe Astereae within the family Asteraceae. One species, D . integrifolia , has been recently reported as introduced in the New World from a pair of collections from Guatemala. During field work in the state of Chiapas in southern Mexico, the species was found and collected. This is the first record of both the genus and species in Mexico and the second record for these taxa in the Americas.
 Question: Can D . integrifolia occur in more areas in the New World besides those known from Guatemala and Chiapas?
 Studied species: Dichrocephala integrifolia 
 Study site and dates: Mexico, Central America, and the Caribbean.
 Methods: An ecological niche model was made and it was projected into the New World.
 Results: The ecological niche model predicts the records of D. integrifolia in the New World in addition to other ecologically suitable areas, mostly in pine-oak forests in Mexico and Central America and zones with humid mountain and pine forest in the Caribbean. Moreover, a morphological description and illustrations of the species are provided to help with its identification.
 Conclusions: It is desirable to avoid the further spreading of D . integrifolia in the New World. Although this species is not considered as invasive, it seems to have a high dispersal potential and the ecological niche modelling indicates larger regions in the Americas that might be affected.

García, L., J. Veneros, S. Chavez, M. Oliva, and N. B. Rojas Briceño. 2022. World historical mapping and potential distribution of Cinchona spp. in Peru as a contribution for its restoration and conservation. Journal for Nature Conservation: 126290. https://doi.org/10.1016/j.jnc.2022.126290

Peru is a megadiverse country in neotropical flora and is home to an important genus of plants called Cinchona and commonly all its individual species are called Cinchona Tree (Cinchona spp.), which represents the national tree for this nation. This country has 18 species, a group of these species are listed as vulnerable, endangered, and their population trend is currently unknown. This genus is at risk of extinction due to overexploitation for its medicinal, constructive and food uses. The IUCN also mentions that increased species assessments and records will help make the IUCN Red List a “barometer of life”. Based on the fact that understanding the effects of environmental change on ecosystems requires the identification of historical and current baselines, which can act as reference conditions, this research generated georeferenced global historical maps of Cinchona spp. and then determined the appropriate sites based on environmental variables using the Maxent software and established the probabilities of occurrence of this genus in Peru to establish priority areas for its conservation and restoration. Four maps were obtained, one for each centennial, from 1737 to the present, with 10,860 occurrences of Cinchona. In the MaxEnt modeling, 10.30 % (13 3172.56 km2) and 19.20 % (24 7371.32 km2) of Peru's surface area had high (> 0.6) and moderate (0.4 - 0.6) probabilities, respectively, of hosting Cinchona. Only 7.6 % (17 305.32 km2) and 22.0 % (50 153.73 km2) of the areas with high and moderate distribution potential, respectively, were covered by natural protected areas. Likewise, 11.90 % (21 738.75 km2) and 33.20 % (60 789.17 km2) of the high and moderate probability lands, respectively, correspond to degraded areas (DAs) and, therefore, are considered a priority for restoration with Cinchona spp. The results may stimulate the rethinking of decision making for the National Action Plan for Reforestation with Species of the Genus Cinchona and other plans or tools for Cinchona conservation in Peru.

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.

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. https://doi.org/10.1002/ajb2.16062

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. 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).

Luo, W., J. S. Strijk, M. Barstow, and A. K. S. Wee. 2022. The role of protected areas in tropical tree conservation post-2020: A case study using threatened Dipterocarpaceae. Biological Conservation 272: 109634. https://doi.org/10.1016/j.biocon.2022.109634

Protected areas (PAs) are key tools to prevent extinction and preserve ecosystem functions. As countries reiterated their commitment to expand the reach of PAs by up to 30 % by 2030, stronger purpose and pertinence in the establishment of PAs is needed to ensure effective conservation. In this study, we used Dipterocarpaceae as a proxy for threatened and ecologically important trees to determine the role of PAs in tree conservation and the potential shortfalls at a global scale. We quantified the overlap between the geo-referenced occurrence data of 433 Dipterocarpaceae species and the distribution of global PAs, followed by a conservation gap analysis on Borneo, the center of diversity of the family. We found that while Southeast Asia is the hotspot for species diversity and threat to Dipterocarpaceae, a high proportion of threatened species were found at the range edges of Dipterocarpaceae. Half of all the countries with Dipterocarpaceae met the Aichi Target 11 of designating at least 17 % of their land area as PAs, and most had <10 % of their total number of PAs being relevant to Dipterocarpaceae conservation. Our conservation gap analysis demonstrated that only 5.02 % of the total area of habitat (AOH) of endemic and Critically Endangered dipterocarps was formally protected, while 18.6 % of the total AOH was included in the Heart of Borneo complex. Our data highlights the need for a more effective global conservation gap analysis for threatened trees that could inform area-based conservation post-2020.

Escolástico-Ortiz, D. A., L. Hedenäs, D. Quandt, D. Harpke, J. Larraín, M. Stech, and J. C. Villarreal A. 2022. Cryptic speciation shapes the biogeographic history of a northern distributed moss. Botanical Journal of the Linnean Society. https://doi.org/10.1093/botlinnean/boac027

Abstract Increasing evidence indicates that wide distributed bryophyte taxa with homogeneous morphology may represent separate evolutionary lineages. The evolutionary histories of these cryptic lineages may be related to historical factors, such as the climatic oscillations in the Quaternary. Thus, the post-glacial demographic signatures paired with cryptic speciation may result in complex phylogeographic patterns. This research has two aims: to determine whether the widespread moss Racomitrium lanuginosum represents cryptic molecular taxa across the Northern Hemisphere and to infer the effects of Quaternary glaciations on spatial genetic diversity. We used the internal transcribed spacer (ITS) marker to resolve the phylogeographic history of the species and single nucleotide polymorphisms (genotyping-by-sequencing) to infer the genetic structure and demographic history. Finally, we assessed the historical changes in the distribution range using species distribution models. Racomitrium lanuginosum comprises distinct molecular lineages sympatrically distributed in the Northern Hemisphere. We also uncovered long-distance dispersal from eastern North America to Scandinavia and potential in situ survival in northern Scandinavia. Due to the genetic signatures, the Alaska Peninsula could be considered a glacial refugium. The species experienced post-glacial expansion northwards in the Northern Hemisphere, mainly from the Alaska Peninsula. Our results exemplify the complex phylogeographic history in cold environments and contribute to recognizing evolutionary patterns in the Northern Hemisphere.

Zhao, J., X. Yu, W. J. Kress, Y. Wang, Y. Xia, and Q. Li. 2022. Historical biogeography of the gingers and its implications for shifts in tropical rain forest habitats. Journal of Biogeography 49: 1339–1351. https://doi.org/10.1111/jbi.14386

Aim The relationships between biome shifts and global environmental changes in temperate zone habitats have been extensively explored; yet, the historical dynamics of taxa found in the tropical rain forest (TRF) remain poorly known. This study aims to reconstruct the relationships between tropical rain forest shifts and global environmental changes through the patterns of historical biogeography of a pantropical family of monocots, the Zingiberaceae. Location Global. Taxon Zingiberaceae. Methods We sampled DNA sequences (nrITS, trnK, trnL-trnF and psbA-trnH) from GenBank for 77% of the genera, including 30% of species, in the Zingiberaceae. Global fossil records of the Zingiberaceae were collected from literatures. Rates of speciation, extinction and diversification were estimated based on phylogenetic data and fossil records through methods implemented in BAMM. Ancestral ranges were estimated using single-tree BioGeoBEARS and multiple-trees BioGeoBEARS in RASP. Dispersal rate through time and dispersal rate among regions were calculated in R based on the result of ancestral estimation. Results The common ancestor of the Zingiberaceae likely originated in northern Africa during the mid-Cretaceous, with later dispersal to the Asian tropics. Indo-Burma, rather than Malesia, was likely a provenance of the common ancestor of Alpinioideae–Zingiberoideae. Several abrupt shifts of evolutionary rates from the Palaeocene were synchronized with sudden global environmental changes. Main conclusions Integrating phylogenetic patterns with fossil records suggests that the Zingiberaceae dispersed to Asia through drift of the Indian Plate from Africa in the late Palaeocene. Formation of island chains, land corridors and warming temperatures facilitated the emigration of the Zingiberaceae to a broad distribution across the tropics. Moreover, dramatic fluctuations of the speciation rate of Zingiberoideae appear to have been synchronized with global climate fluctuations. In general, the evolutionary history of the Zingiberaceae broadens our understanding of the association between TRF shifts in distribution and past global environmental changes, especially the origin of TRF in Southeast Asia.

Ramirez-Villegas, J., C. K. Khoury, H. A. Achicanoy, M. V. Diaz, A. C. Mendez, C. C. Sosa, Z. Kehel, et al. 2022. State of ex situ conservation of landrace groups of 25 major crops. Nature Plants 8: 491–499. https://doi.org/10.1038/s41477-022-01144-8

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation. By analysing the state of representation of traditional varieties of 25 major crops in ex situ repositories, this study demonstrates conservation progress made over more than a half-century and identifies the gaps remaining to be filled.