Science Enabled by Specimen Data
Weiss, R. M., F. Zanetti, B. Alberghini, D. Puttick, M. A. Vankosky, A. Monti, and C. Eynck. 2024. Bioclimatic analysis of potential worldwide production of spring‐type camelina [Camelina sativa (L.) Crantz] seeded in the spring. GCB Bioenergy 16. https://doi.org/10.1111/gcbb.13126
Camelina [Camelina sativa (L.) Crantz] is a Brassicaceae oilseed that is gaining interest worldwide as low‐maintenance crop for diverse biobased applications. One of the most important factors determining its productivity is climate. We conducted a bioclimate analysis in order to analyze the relationship between climatic factors and the productivity of spring‐type camelina seeded in the spring, and to identify regions of the world with potential for camelina in this scenario. Using the modelling tool CLIMEX, a bioclimatic model was developed for spring‐seeded spring‐type camelina to match distribution, reported seed yields and phenology records in North America. Distribution, yield, and phenology data from outside of North America were used as independent datasets for model validation and demonstrated that model projections agreed with published distribution records, reported spring‐seeded camelina yields, and closely predicted crop phenology in Europe, South America, and Asia. Sensitivity analysis, used to quantify the response of camelina to changes in precipitation and temperature, indicated that crop performance was more sensitive to moisture than temperature index parameters, suggesting that the yield potential of spring‐seeded camelina may be more strongly impacted by water‐limited conditions than by high temperatures. Incremental climate scenarios also revealed that spring‐seeded camelina production will exhibit yield shifts at the continental scale as temperature and precipitation deviate from current conditions. Yield data were compared with indices of climatic suitability to provide estimates of potential worldwide camelina productivity. This information was used to identify new areas where spring‐seeded camelina could be grown and areas that may permit expanded production, including eastern Europe, China, eastern Russia, Australia and New Zealand. Our model is the first to have taken a systematic approach to determine suitable regions for potential worldwide production of spring‐seeded camelina.
Qin, F., T. Xue, X. Zhang, X. Yang, J. Yu, S. R. Gadagkar, and S. Yu. 2023. Past climate cooling and orogenesis of the Hengduan Mountains have influenced the evolution of Impatiens sect. Impatiens (Balsaminaceae) in the Northern Hemisphere. BMC Plant Biology 23. https://doi.org/10.1186/s12870-023-04625-w
Background Impatiens sect. Impatiens is distributed across the Northern Hemisphere and has diversified considerably, particularly within the Hengduan Mountains (HDM) in southwest China. Yet, the infra-sectional phylogenetic relationships are not well resolved, largely due to limited taxon sampling and an insufficient number of molecular markers. The evolutionary history of its diversification is also poorly understood. In this study, plastome data and the most complete sampling to date were used to reconstruct a robust phylogenetic framework for this section. The phylogeny was then used to investigate its biogeographical history and diversification patterns, specifically with the aim of understanding the role played by the HDM and past climatic changes in its diversification. Results A stable phylogeny was reconstructed that strongly supported both the monophyly of the section and its division into seven major clades (Clades I-VII). Molecular dating and ancestral area reconstruction suggest that sect. Impatiens originated in the HDM and Southeast China around 11.76 Ma, after which different lineages dispersed to Northwest China, temperate Eurasia, and North America, mainly during the Pliocene and Pleistocene. An intercontinental dispersal event from East Asia to western North America may have occurred via the Bering Land Bridge or Aleutian Islands. The diversification rate was high during its early history, especially with the HDM, but gradually decreased over time both within and outside the HDM. Multiple linear regression analysis showed that the distribution pattern of species richness was strongly associated with elevation range, elevation, and mean annual temperature. Finally, ancestral niche analysis indicated that sect. Impatiens originated in a relatively cool, middle-elevation area. Conclusions We inferred the evolutionary history of sect. Impatiens based on a solid phylogenetic framework. The HDM was the primary source or pump of its diversity in the Northern Hemisphere. Orogeny and climate change may have also shaped its diversification rates, as a steady decrease in the diversification rate coincided with the uplift of the HDM and climate cooling. These findings provide insights into the distribution pattern of sect. Impatiens and other plants in the Northern Hemisphere.
Metreveli, V., H. Kreft, I. Akobia, Z. Janiashvili, Z. Nonashvili, L. Dzadzamia, Z. Javakhishvili, and A. Gavashelishvili. 2023. Potential Distribution and Suitable Habitat for Chestnut (Castanea sativa). Forests 14: 2076. https://doi.org/10.3390/f14102076
Chestnut, Castanea sativa Miller (Fagales: Fagaceae), is an ecologically and economically important tree species of the forest ecosystem in Southern Europe, North-Western Europe, Western Asia, North Africa, and the Caucasus. The distributional range of chestnut in Europe has been highly modified by humans since ancient times. Biotic and abiotic factors have dramatically changed its distribution. Historic anthropogenic range expansion makes it difficult to identify habitat requirements for natural stands of chestnut. In the Caucasus, natural stands of chestnut survived in glacial forest refugia and landscapes that have been difficult for humans to colonize. To identify the species reliable habitat requirements, we estimated the relationship between climatic variables and 620 occurrence locations of natural chestnut stands from the Caucasus and validated the model using GBIF data from outside the Caucasus. We found that our best model is reasonably accurate and the data from the Caucasus characterize chestnut stands throughout the species range well.
Yim, C., E. S. Bellis, V. L. DeLeo, D. Gamba, R. Muscarella, and J. R. Lasky. 2023. Climate biogeography of Arabidopsis thaliana: Linking distribution models and individual variation. Journal of Biogeography. https://doi.org/10.1111/jbi.14737
Aim Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range‐wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity.LocationGlobal.TaxonArabidopsis thaliana (‘Arabidopsis’).MethodsWe fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current and future climates. We confronted model predictions with individual performance measured on 2194 herbarium specimens, and we asked whether predicted suitability was associated with life history and genomic variation measured on ~900 natural accessions.ResultsThe most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate‐associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late‐flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the centre of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well‐predicted by our native‐range model applied to certain regions but not others, suggesting it has colonized novel climates.Main ConclusionsIntegration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
Tippery, N. P., N. E. Harms, M. F. Purcell, S. H. Hong, P. Häfliger, K. Killoy, A. L. Wolfe, and R. A. Thum. 2023. Assessing the genetic diversity of Nymphoides peltata in the native and adventive range using microsatellite markers. Biological Invasions. https://doi.org/10.1007/s10530-023-03151-y
Nymphoides peltata (yellow floating-heart), native to Eurasia, is an invasive plant in the USA, where it grows in relatively isolated but widespread populations. The species is capable of sexual reproduction by seed and asexual reproduction through fragmentation. Although N. peltata is recognized as a noxious weed, little is known about its geographic region of origin or its dispersal mechanisms and relative amount of genetic variation in its adventive range. We conducted a genetic analysis of N. peltata by studying 68 localities across the native range and 47 localities in the adventive range, using microsatellite markers to determine genetic variability within and among populations, and to infer regions in the native range from which invasive plants originated. A large number of sites in the USA were genetically identical to one another, and there were two predominant multilocus allele phenotypes that were distributed in the northern and southern latitudes, respectively. Additional USA sites were similar to one of the predominant genetic profiles, with greater genetic diversity in southern populations. The genetically identical sites are consistent with asexual spread, potentially via anthropogenic mechanisms. Plants across the USA range were observed to produce viable seeds, and some genetic variation could be explained by sexual reproduction. All USA plants were more similar to plants in Europe than they were to plants in Asia, indicating that the plants likely were introduced originally from Europe. The existence of two genetic clusters and their similarity to plants in different parts of Europe constitute evidence for at least two N. peltata introductions into the USA.
Nikkel, E., D. R. Clements, D. Anderson, and J. L. Williams. 2023. Regional habitat suitability for aquatic and terrestrial invasive plant species may expand or contract with climate change. Biological Invasions. https://doi.org/10.1007/s10530-023-03139-8
The threat of invasive species to biodiversity and ecosystem structure is exacerbated by the increasingly concerning outlook of predicted climate change and other human influences. Developing preventative management strategies for invasive plant species before they establish is crucial for effective management. To examine how climate change may impact habitat suitability, we modeled the current and future habitat suitability of two terrestrial species, Geranium lucidum and Pilosella officinarum , and two aquatic species, Butomus umbellatus and Pontederia crassipes , that are relatively new invasive plant species regionally, and are currently spreading in the Pacific Northwest (PNW, North America), an area of unique natural areas, vibrant economic activity, and increasing human population. Using North American presence records, downscaled climate variables, and human influence data, we developed an ensemble model of six algorithms to predict the potential habitat suitability under current conditions and projected climate scenarios RCP 4.5, 7.0, and 8.5 for 2050 and 2080. One terrestrial species ( P. officinarum ) showed declining habitat suitability in future climate scenarios (contracted distribution), while the other terrestrial species ( G. lucidum ) showed increased suitability over much of the region (expanded distribution overall). The two aquatic species were predicted to have only moderately increased suitability, suggesting aquatic plant species may be less impacted by climate change. Our research provides a template for regional-scale modelling of invasive species of concern, thus assisting local land managers and practitioners to inform current and future management strategies and to prioritize limited available resources for species with expanding ranges.
Benson, C. W., M. R. Sheltra, P. J. Maughan, E. N. Jellen, M. D. Robbins, B. S. Bushman, E. L. Patterson, et al. 2023. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 24. https://doi.org/10.1186/s12864-023-09456-5
Background Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua’s diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua’s evolutionary novelty. Results We find that the diploids diverged from their common ancestor 5.5 – 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua’s B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. Conclusions The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding .
Gharde, Y., R. P. Dubey, P. K. Singh, and J. S. Mishra. 2023. Littleseed canarygrass (Phalaris minor Retz.) a major weed of rice-wheat system in India is predicted to experience range contraction under future climate. International Journal of Pest Management: 1–12. https://doi.org/10.1080/09670874.2023.2199258
Modelling was carried out using maximum entropy model (MaxEnt) to explore and predict the invasion potential of littleseed canarygrass (Phalaris minor Retz.) in India under current as well as future climatic conditions under Representative Concentration Pathways (RCPs) 4.5 and 8.5 for the years 2050 and 2070. Mutually least correlated 8 bioclimatic variables along with soil and elevation data were used for the modelling over 223 occurrence locations of the species. Jackknife test revealed the significance of temperature derived variables viz. temperature seasonality, annual mean temperature and minimum temperature of the coldest month in governing the potential distribution of P. minor. Currently, 21% of India’s area is either highly (9%) or moderately (12%) suitable as habitat for P. minor. Our model predicts approximately 90% contraction in the area considered to be highly or moderately suitable climatically between 2050 and 2070 under both moderate and high emissions scenarios. Thus, under future climate, a significant niche shift by the species and decreased suitability was observed compared to the current distribution. The present study is first of its kind in exploring the invasion potential of alien invasive weed P. minor under climate change scenarios which is a current threat to rice-wheat system in Indo-Gangetic plains of India.
Clemente, K. J. E., and M. S. Thomsen. 2023. High temperature frequently increases facilitation between aquatic foundation species: a global meta‐analysis of interaction experiments between angiosperms, seaweeds, and bivalves. Journal of Ecology. https://doi.org/10.1111/1365-2745.14101
Many studies have quantified ecological impacts of individual foundation species (FS). However, emerging data suggest that FS often co‐occur, potentially inhibiting or facilitating one another, thereby causing indirect, cascading effects on surrounding communities. Furthermore, global warming is accelerating, but little is known about how interactions between co‐occurring FS vary with temperature.Shallow aquatic sedimentary systems are often dominated by three types of FS: slower‐growing clonal angiosperms, faster‐growing solitary seaweeds, and shell‐forming filter‐ and deposit‐feeding bivalves. Here, we tested the impacts of one FS on another by analyzing manipulative interaction experiments from 148 papers with a global meta‐analysis.We calculated 1,942 (non‐independent) Hedges’ g effect sizes, from 11,652 extracted values over performance responses, such as abundances, growths or survival of FS, and their associated standard deviations and replication levels. Standard aggregation procedures generated 511 independent Hedges’ g that was classified into six types of reciprocal impacts between FS.We found that (i) seaweeds had consistent negative impacts on angiosperms across performance responses, organismal sizes, experimental approaches, and ecosystem types; (ii) angiosperms and bivalves generally had positive impacts on each other (e.g., positive effects of angiosperms on bivalves were consistent across organismal sizes and experimental approaches, but angiosperm effect on bivalve growth and bivalve effect on angiosperm abundance were not significant); (iii) bivalves positively affected seaweeds (particularly on growth responses); (iv) there were generally no net effects of seaweeds on bivalves (except for positive effect on growth) or angiosperms on seaweeds (except for positive effect on ‘other processes’); and (v) bivalve interactions with other FS were typically more positive at higher temperatures, but angiosperm‐seaweed interactions were not moderated by temperature.Synthesis: Despite variations in experimental and spatiotemporal conditions, the stronger positive interactions at higher temperatures suggest that facilitation, particularly involving bivalves, may become more important in a future warmer world. Importantly, addressing research gaps, such as the scarcity of FS interaction experiments from tropical and freshwater systems and for less studied species, as well as testing for density‐dependent effects, could better inform aquatic ecosystem conservation and restoration efforts and broaden our knowledge of FS interactions in the Anthropocene.
Wilson Brown, M. K., and E. B. Josephs. 2023. Evaluating niche changes during invasion with seasonal models in Capsella bursa‐pastoris. American Journal of Botany. https://doi.org/10.1002/ajb2.16140
Premise Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. Here, we assess compare ecological niche models generated from full-year averages to seasonal models Methods In this study, we generate full-year and monthly ecological niche models for Capsella bursa-pastoris in Europe and North America to see if we can detect changes in the seasonal niche of the species after long-distance dispersal. Key Results We find full-year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa-pastoris. Monthly models have greater predictive accuracy than full-year models in cooler seasons, but no monthly models are able to predict North American summer occurrences very well. Conclusions The relative predictive ability of European monthly models compared to North American monthly models suggests a change in the seasonal timing between the native range to the non-native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution.