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.

Dimobe, K., K. Ouédraogo, P. Annighöfer, J. Kollmann, J. Bayala, C. Hof, M. Schmidt, et al. 2022. Climate change aggravates anthropogenic threats of the endangered savanna tree Pterocarpus erinaceus (Fabaceae) in Burkina Faso. Journal for Nature Conservation: 126299. https://doi.org/10.1016/j.jnc.2022.126299

Species distribution modelling is gaining popularity due to significant habitat shifts in many plant and animal species caused by climate change. This issue is particularly pressing for species that provide significant ecosystem goods and services. A prominent case is the valuable African rosewood tree (Pterocarpus erinaceus) that is threatened in sub-Saharan Africa, while its present distribution, habitat requirements and the impact of climate change are not fully understood. This native species naturally occurs in various savanna types, but anthropogenic interventions have considerably reduced its natural populations in the past decades. In this study, ensemble modelling was used to predict the current and future distribution potential of the species in Burkina Faso. Fifty-four environmental variables were selected to describe its distribution in the years 2050 and 2070 based on the greenhouse gas concentration trajectories RCP4.5 and 8.5, and the general circulation models CNRM-CM5 and HadGEM2-CC. A network of protected areas in Burkina Faso was also included to assess how many of the suitable habitats may contribute to the conservation of the species. The factors isothermality (31%), minimum temperature of coldest month (31%), pH in H2O at horizon 0–5 cm (11%), silt content at horizon 60–100 cm (9.2%) and precipitation of warmest quarter (8%) were the most influential distribution drivers for the species. Under current climate conditions, potentially highly suitable habitats cover an area of 129,695 km2, i.e. 47% of Burkina Faso. The projected distribution under RCP4.5 and 8.5 showed that this area will decrease, and that the decline of the species will be pronounced. The two models used in this study forecast a habitat loss of up to 61% for P. erinaceus. Hence, development and implementation of a conservation program are required to save the species in its native range. This study will help land managers prioritise areas for protection of the species and avoid introducing it to inappropriate areas unless suitable conditions are artificially created through the management options applied.

Yu, J., Y. Niu, Y. You, C. J. Cox, R. L. Barrett, A. Trias‐Blasi, J. Guo, et al. 2022. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan‐Hengduan Mountains. New Phytologist. https://doi.org/10.1111/nph.18580

Hybridization caused by frequent environmental changes can lead to both species diversification (speciation) and speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan‐Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence.We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focussed on reticulations in the trifoliolate lineage in the HHM region using a population‐level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation.Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal‐spatial framework. Around the HHM region, at least three hybridization hotspots were identified, one of which showed evidence of ongoing speciation reversal.We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.

Kroonen, G., A. Jakob, A. I. Palmér, P. van Sluis, and A. Wigman. 2022. Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages S. Wichmann [ed.],. PLOS ONE 17: e0275744. https://doi.org/10.1371/journal.pone.0275744

Questions on the timing and the center of the Indo-European language dispersal are central to debates on the formation of the European and Asian linguistic landscapes and are deeply intertwined with questions on the archaeology and population history of these continents. Recent palaeogenomic studies support scenarios in which the core Indo-European languages spread with the expansion of Early Bronze Age Yamnaya herders that originally inhabited the East European steppes. Questions on the Yamnaya and Pre-Yamnaya locations of the language community that ultimately gave rise to the Indo-European language family are heavily dependent on linguistic reconstruction of the subsistence of Proto-Indo-European speakers. A central question, therefore, is how important the role of agriculture was among the speakers of this protolanguage. In this study, we perform a qualitative etymological analysis of all previously postulated Proto-Indo-European terminology related to cereal cultivation and cereal processing. On the basis of the evolution of the subsistence strategies of consecutive stages of the protolanguage, we find that one or perhaps two cereal terms can be reconstructed for the basal Indo-European stage, also known as Indo-Anatolian, but that core Indo-European, here also including Tocharian, acquired a more elaborate set of terms. Thus, we linguistically document an important economic shift from a mostly non-agricultural to a mixed agro-pastoral economy between the basal and core Indo-European speech communities. It follows that the early, eastern Yamnaya of the Don-Volga steppe, with its lack of evidence for agricultural practices, does not offer a perfect archaeological proxy for the core Indo-European language community and that this stage of the language family more likely reflects a mixed subsistence as proposed for western Yamnaya groups around or to the west of the Dnieper River.

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.

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.

Shen, Y., Z. Tu, Y. Zhang, W. Zhong, H. Xia, Z. Hao, C. Zhang, and H. Li. 2022. Predicting the impact of climate change on the distribution of two relict Liriodendron species by coupling the MaxEnt model and actual physiological indicators in relation to stress tolerance. Journal of Environmental Management 322: 116024. https://doi.org/10.1016/j.jenvman.2022.116024

Climate change has a crucial impact on the distributions of plants, especially relict species. Hence, predicting the potential impact of climate change on the distributions of relict plants is critical for their future conservation. Liriodendron plants are relict trees, and only two natural species have survived: L. chinense and L. tulipifera. However, the extent of the impact of future climate change on the distributions of these two Liriodendron species remains unclear. Therefore, we predicted the suitable habitat distributions of two Liriodendron species under present and future climate scenarios using MaxEnt modeling. The results showed that the area of suitable habitats for two Liriodendron species would significantly decrease. However, the two relict species presented different habitat shift patterns, with a local contraction of suitable habitat for L. chinense and a northward shift in suitable habitat for L. tulipifera, indicating that changes in environmental factors will affect the distributions of these species. Among the environmental factors assessed, May precipitation induced the largest impact on the L. chinense distribution, while L. tulipifera was significantly affected by precipitation in the driest quarter. Furthermore, to explore the relationship between habitat suitability and Liriodendron stress tolerance, we analyzed six physiological indicators of stress tolerance by sampling twelve provenances of L. chinense and five provenances of L. tulipifera. The composite index of six physiological indicators was significantly negatively correlated with the habitat suitability of the species. The stress tolerance of Liriodendron plants in highly suitable areas was lower than that in areas with moderate or low suitability. Overall, these findings improve our understanding of the ecological impacts of climate change, informing future conservation efforts for Liriodendron species.

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.

Samal, P., J. Srivastava, S. R. Singarasubramanian, P. N. Saraf, and B. Charles. 2022. Ensemble modeling approach to predict the past and future climate suitability for two mangrove species along the coastal wetlands of peninsular India. Ecological Informatics 72: 101819. https://doi.org/10.1016/j.ecoinf.2022.101819

Mangroves support numerous ecosystem services and help in reducing coastal ecological risks, yet they are declining rapidly due to climate change, sea level fluctuations and human activities. It is important to understand their responses to climate and sea level changes and identify conservation target areas at spatio-temporal scales, specifically in regions of rich mangrove biodiversity. In this study, we predicted the potential impact of past (Middle Holocene, ~6000 years), current and future (2050s, 2070s); based on the extreme climate change scenarios (RCP 2.6 and RCP 8.5) on the two dominant species in the coastal mangrove forest wetlands of India, i.e., Rhizophora mucronata and Avicennia officinalis through an ensemble species distribution modeling approach. The ensemble modeling has been carried out by integrating eight single algorithm methods. Based on the receiver operating characteristics of area under the curve (AUC) and true skill statistics (TSS) values the ensemble modeling has yielded the highest predictive performance for SVM for both the species and lowest by cart for R. mucronata and BIOCLIM for A. officinalis. The internal evaluation metrics of the resulting Species distribution models (SDMs) tested its robustness with AUC-0.97 and TSS-0.89 for A. officinalis and AUC-0.99 and TSS-0.90 for R. mucronata. Precipitation of Wettest Month (Bio 13) and Mean Temperature of Warmest Quarter (Bio 10) was the most important variable (54–67%) for the distribution of A. officinalis and Precipitation Seasonality (Bio 15) and Precipitation of Warmest Quarter (Bio 18) for R. mucronata. High precipitation and sea-level highstand during middle Holocene led to the maximum range expansion of suitable habitat for the mangrove species which is also validated in the present study by the fossil pollen datasets. Total mangrove habitat in current and future climatic scenarios decreased in 2.6 and 8.5 Representative Concentration Pathways (RCPs) for 2050 and 2070 which indicates the vulnerability of the species to climate change impacts. Mangrove species are projected to shift their ranges more towards land in future experiencing a decrease in the amount of suitable coastal area available to them throughout the Indian coastline. The plausible cause for this range shift may be due to higher precipitation that is usually associated with longer period of soil inundation and because of the rise in sea level. Our findings will assist in formulating species-specific restoration plans for these keystone species in context of climate change in the Indian Subcontinent.