Background Keel flowers are bilaterally symmetrical, pentamerous flowers with three different petal types and reproductive organs enclosed by keel petals; generally there is also connation of floral parts such as stamens and keel petals. In this study, the evolution of keel flowers within the order Fabales is explored to investigate whether the establishment of this flower type within one of the species-rich families, the Fabaceae (Leguminosae), preceded and could have influenced the evolution of keel flowers in the Polygalaceae. We conducted molecular dating, and ancestral area and ancestral state analyses for a phylogeny constructed for 678 taxa using published matK , rbcL and trnL plastid gene regions. Results We reveal the temporal and spatial origins of keel flowers and traits associated with pollinators, specifically floral symmetry, the presence or absence of a pentamerous corolla and three distinct petal types, the presence or absence of enclosed reproductive organs, androecium types, inflorescence types, inflorescence size, flower size, plant height and habit. Ancestral area reconstructions show that at the time keel flowers appeared in the Polygaleae, subfamily Papilionoideae of the Fabaceae was already distributed almost globally; at least eight clades of the Papilionoideae had keel flowers with a functional morphology broadly similar to the morphology of the first evolving Polygaleae flowers. Conclusions The multiple origins of keel flowers within angiosperms likely represent convergence due to bee specialization, and therefore pollinator pressure. In the case of the Fabales, the first evolving keel flowers of Polygaleae have a functional morphology that corresponds with keel flowers of species of the Papilionoideae already present in the environment. These findings are consistent with the keel-flowered Polygaleae exploiting pollinators of keel-flowered Papilionoideae. The current study is the first to use ancestral reconstructions of traits associated with pollination to demonstrate that the multiple evolutionary origins of the keel flower pollinator syndrome in Fabales are consistent with, though do not prove, mimicry.
The past decade has seen the emergence of multidrug resistant pathogens as a leading cause of death worldwide, reigniting interest in the field of phage therapy. Modern advances in the genetic engineering of bacteriophages have enabled several useful results including host range alterations, constitutive lytic growth, and control over phage replication. However, the slow licensing process of genetically modified organisms clearly inhibits the rapid therapeutic application of novel engineered variants necessary to fight mutant pathogens that emerge throughout the course of a pandemic. As a solution to this problem, we propose the SpyPhage system where a “scaffold” bacteriophage is engineered to incorporate a SpyTag moiety on its capsid head to enable rapid postsynthetic modification of their surfaces with SpyCatcher-fused therapeutic proteins. As a proof of concept, through CRISPR/Cas-facilitated phage engineering and whole genome assembly, we targeted a SpyTag capsid fusion to K1F, a phage targeting the pathogenic strain Escherichia coli K1. We demonstrate for the first time the cell-free assembly and decoration of the phage surface with two alternative fusion proteins, SpyCatcher-mCherry-EGF and SpyCatcher-mCherry-Rck, both of which facilitate the endocytotic uptake of the phages by a urinary bladder epithelial cell line. Overall, our work presents a cell-free phage production pipeline for the generation of multiple phenotypically distinct phages with a single underlying “scaffold” genotype. These phages could become the basis of next-generation phage therapies where the knowledge-based engineering of numerous phage variants would be quickly achievable without the use of live bacteria or the need to repeatedly license novel genetic alterations.
Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes. Supplementary information: The online version contains supplementary material available at 10.1007/s10722-022-01389-4.
The tribe Sonerileae in tropical Africa and Madagascar is a morphologically diverse lineage that consists of 239 species in 10 genera. In this study, we present the first in‐depth phylogenetic analysis of African Sonerileae to test monophyly of the currently recognised genera. Phylogenetic analyses were performed using sequence data from two nuclear (nrITS and nrETS) and three plastid loci (accD‐psaI, ndhF and psbK‐psbL). Sampling consisted of 140 accessions including 64 African, 27 Malagasy, 46 Asian and three neotropical Sonerileae together with a broad outgroup sampling (105 spp.). Phylogenetic relationships were inferred using maximum likelihood and Bayesian inference approaches, and a careful reassessment of morphological characters was carried out. Our results neither support the monophyly of Old World nor African Sonerileae. The monospecific African genus Benna is partially supported as sister to Phainantha, one of the basal neotropical lineages, while African and Malagasy Medinilla are nested among the SE Asian genera. Gravesia (116 spp.), the most species‐rich and morphologically diverse genus in Madagascar, is recovered as monophyletic. The other African genera of Sonerileae (Calvoa, Dicellandra, and Preussiella) form well‐supported clades. In contrast, Amphiblemma (including Amphiblemma molle) and Cincinnobotrys s.l. (including Cincinnobotrys felicis) are not monophyletic. To accommodate the caulescent C. felicis we propose reinstatement of the monospecific genus Bourdaria. For the distinctive A. molle a new genus Mendelia is described. Calvoa hirsuta is designated here as the type of genus Calvoa, lectotypes are designated for Medinilla engleri and Veprecella lutea, and a neotype is designated for Preussiella kamerunensis. This article is protected by copyright. All rights reserved.
Ecological connectivity across landscapes is vital for the maintenance of biodiversity and the processes that enable life on earth. Despite this, environmental planning decisions are usually made at the scale of individual projects, failing to account for landscape-scale impacts. Incorporating habitat connectivity analysis in Environmental Impact Assessments (EIAs) could provide an opportunity to address this gap. We present a novel approach to model habitat connectivity in an EIA undertaken for the Heathrow Third Runway Expansion Project, a proposed development in southeast England. Drawing on field data, remote sensing, and species-specific literature reviews, a circuit theory approach was used to assess functional connectivity across the project landscape for grass snakes Natrix helvetica and soprano pipis-trelles Pipistrellus pygmaeus. Results indicated key areas for species movement and potential 'pinch-points' vulnerable to development impacts. We discuss lessons learnt, potential applications to inform impact assessment, mitigation design, and biodiversity net gain approaches, and further work required to mainstream connectivity analyses in EIA and decision-making. ARTICLE HISTORY
Over the course of history, humans have moved crops from their regions of origin to new locations across the world. The social, cultural and economic drivers of these movements have generated differences not only between current distributions of crops and their climatic origins, but also between crop distributions and climate suitability for their production. Although these mis-matches are particularly important to inform agricultural strategies on climate change adaptation, they have, to date, not been quantified consistently at the global level. Here, we show that the relationships between the distributions of 12 major food crops and climate suitability for their yields display strong variation globally. After investigating the role of biophysical, socioeconomic and historical factors, we report that high-income world regions display a better match between crop distribution and climate suitability. In addition, although crops are farmed predominantly in the same climatic range as their wild progenitors , climate suitability is not necessarily higher there, a pattern that reflects the legacy of domestication history on current crop distribution. Our results reveal how far the global distribution of major crops diverges from their climatic optima and call for greater consideration of the multiple dimensions of the crop socio-ecological niche in climate change adaptive strategies.
Protecting nature’s contributions to people requires accelerating extinction risk assessment and better integrating evolutionary, functional and used diversity with conservation planning. Here, we report machine learning extinction risk predictions for 1,381 palm species (Arecaceae), a plant family of high socio-economic and ecological importance. We integrate these predictions with published assessments for 508 species (covering 75% of all palm species) and we identify top-priority regions for palm conservation on the basis of their proportion of threatened evolutionarily distinct, functionally distinct and used species. Finally, we explore palm use resilience to identify non-threatened species that could potentially serve as substitutes for threatened used species by providing similar products. We estimate that over a thousand palms (56%) are probably threatened, including 185 species with documented uses. Some regions (New Guinea, Vanuatu and Vietnam) emerge as top ten priorities for conservation only after incorporating machine learning extinction risk predictions. Potential substitutes are identified for 91% of the threatened used species and regional use resilience increases with total palm richness. However, 16 threatened used species lack potential substitutes and 30 regions lack substitutes for at least one of their threatened used palm species. Overall, we show that hundreds of species of this keystone family face extinction, some of them probably irreplaceable, at least locally. This highlights the need for urgent actions to avoid major repercussions on palm-associated ecosystem processes and human livelihoods in the coming decades.
Introduction Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. Objectives To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. Methods Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barleys. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. Results Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. Conclusion Our findings reveal functional genes that have been selected across barley’s complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.
Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.
The food systems and territories of Indigenous Peoples sustain much of the world’s biodiversity, cultivated and wild, through agroecological practices rooted in Indigenous cosmovision and cultural and spiritual values. These food systems have a critical role to play in sustainability transformations but are widely threatened and have received limited research attention. This paper presents the results of four virtual workshops with Indigenous Peoples: a global workshop and local workshops with communities in coastal Kenya, northeast India and southwest China. Indigenous participants highlighted the role of their food systems in resilience to climate change, nutrition, sustainability and resilience to pandemics, and threats from agriculture, development and conservation policies. They called for research on the rapid loss of Indigenous knowledge; Indigenous Peoples’ land rights and food sovereignty; and the impacts of industrial agriculture on Indigenous food systems, stressing the need for decolonial approaches to revitalise Indigenous knowledge. The paper presents a decolonial and interdisciplinary framework for action-research on Indigenous food systems past and present, from farm to plate, drawing on the virtual workshops, Andean decolonising methods and historical approaches. It concludes that decolonising action-research, led by Indigenous Peoples, is urgently needed to reverse the rapid loss of food-related biocultural heritage.
The underlying mechanisms driving paternally-programmed metabolic disease in offspring remain poorly defined. We fed male C57BL/6 mice either a control normal protein diet (NPD; 18% protein) or an isocaloric low protein diet (LPD; 9% protein) for a minimum of 8 weeks. Using artificial insemination, in combination with vasectomised male mating, we generated offspring using either NPD or LPD sperm but in the presence of NPD or LPD seminal plasma. Offspring from either LPD sperm or seminal fluid display elevated body weight and tissue dyslipidaemia from just 3 weeks of age. These changes become more pronounced in adulthood, occurring in conjunction with altered hepatic metabolic and inflammatory pathway gene expression. Second generation offspring also display differential tissue lipid abundance, with profiles similar to those of first generation adults. These findings demonstrate that offspring metabolic homeostasis is perturbed in response to a suboptimal paternal diet with the effects still evident within a second generation.
Recent global warming affects species compositions at an unprecedented rate. To predict climate-induced changes in species assemblages, a better understanding of the link between species occurrence and climate is needed. Macrofungal fruit body assemblages are correlated with the thermal environment at the European scale. However, it is still unknown whether macrofungal communities are also phylogenetically structured by thermal environments. Thermal environments are characterized by annual temperature means but also by intra-annual temperature variability (hereafter termed temperature seasonality), which are both considered in this study. Here, we used distribution data of 2882 species based on fruit body records across Europe to address two main questions: 1) are mushroom assemblages at the extremes of the mean (warm and cold) and seasonal (high intra-annual variability, i.e. continental) climate gradient phyloge-netically more similar than expected (phylogenetic alpha diversity); 2) are mushroom assemblages, that are subject to different mean and seasonal temperature conditions, composed of different lineages (phylogenetic beta diversity). Our phylogenetic alpha diversity analysis shows that mushroom assemblages are phylogenetically structured by warm and cold environments, indicating that phylogenetically related species with similar traits thrive under more extreme conditions. In contrast, assemblages are phy-logenetically more dissimilar (overdispersed) in temperature seasonal environments, indicating limiting similarity. Phylogenetic beta diversity was significantly correlated with mean and seasonal temperature differences, a response mainly driven by a few genera. Our results show that macrofungal assemblages are phylogenetically structured by temperature across Europe, suggesting phylogenetically constrained specialization towards temperature extremes. Predicted anthropogenic warming is likely to affect species composition and phylogenetic diversity with additional consequences for the carbon-and nutrient cycles.
Fungal species are not immune to the threats facing animals and plants and are thus also prone to extinction. Yet, until 2015, fungi were nearly absent on the IUCN Red List. Recent efforts to identify fungal species under threat have significantly increased the number of published fungal assessments. The 597 species of fungi published in the 2022-1 IUCN Red List update (21 July 2022) are the basis for the first global review of the extinction risk of fungi and the threats they face. Nearly 50% of the assessed species are threatened, with 10% NT and 9% DD. For regions with a larger number of assessments (i.e., Europe, North America, and South America), subanalyses are provided. Data for lichenized and nonlichenized fungi are also summarized separately. Habitat loss/degradation followed by climate change, invasive species, and pollution are the primary identified threats. Bias in the data is discussed along with knowledge gaps. Suggested actions to address these gaps are provided along with a discussion of the use of assessments to facilitate on-the-ground conservation efforts. A research agenda for conservation mycology to assist in the assessment process and implementation of effective species/habitat management is presented.
In small seeds, light often promotes germination and longer-term exposure to darkness reduces light sensitivity. In cacti inhabiting harsh environments, a rapid response to light exposure is potentially advantageous for seedling establishment. We exposed dark-imbibed seeds of the cactus Cereus repandus to doses of red (RED) light and far-red (FR) light. The seeds exhibited positive photoblastism to RED light. Although the initial levels of germination varied between seed lots, the sensitivity to increasing the RED dose did not. As little as 5 min per day for 4 d was sufficient to saturate the light requirement for germination. The effects of RED light were reversed by FR exposure as long as the interval between RED and FR did not extend to 2 d, by which time the seeds had ‘committed’ to germinate. Dark incubation for 1–2 weeks prior to RED exposure reduced light sensitivity in two seed lots, such that RED only promoted around 20% germination. Phytochrome is assumed to mediate the reversibility of the RED:FR response. High sensitivity to light spectral quality suggests that seeds of C. repandus are able to germinate quickly in high-quality microsites, but seed burial or shading may commit the seeds to form a soil seed bank. The light characteristics of the germination trait in this species are typical of many small seeded species of the drylands.
Flow cytometry (FCM) is currently the most widely‐used method to establish nuclear DNA content in plants. Since simple, 1‐3‐parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
Species extinction risk status is critical to support conservation actions. However, full assessments published on the Red List are slow and resource intensive. To tackle assessments for mega-diverse groups, gains can be made through preliminary assessments that can help prioritize efforts toward full assessments. Here, we quantified how incomplete data collation and errors in the taxonomic, spatial, and temporal dimensions of species-occurrence data translate into misclassifications of extinction risk. Using a dataset of >30 million records of terrestrial plants occurring in Brazil compiled from nine databases we conducted preliminary risk assessments for ~94 % of the 6046 species assessed by the Brazilian Red List authority. We found that no unique database contained data sufficient to perform extinction risk assessment of all species; e.g., the risk of 78 % of species can be assessed using data from GBIF. The overall accuracy (66–75 %) and specificity (89–98 %, correct prediction of non-threatened species) were less affected by incomplete data collation and issues in species-occurrence records. Sensitivity rates (correct prediction of threatened species) were commonly low to moderate and strongly affected by incomplete data collation (13–47 %) and spatial issues (38 %). Our results demonstrate that species' preliminary risk assessments have high accuracy in identifying non-threatened species, even when data collection is low and in the presence of issues in species occurrence data highlighting that such an approach can be used to efficiently prioritize species for full Red List assessments. In addition, caution is needed before declaring a species as threatened without considering data collation intensity and quality.
Assessing species’ extinction risk is vital to setting conservation priorities. However, assessment endeavours like the IUCN Red List of Threatened Species have significant gaps in taxonomic coverage. Automated assessment (AA) methods are gaining popularity to fill these gaps. Choices made in developing, using, and reporting AA methods could hinder successful adoption or lead to poor allocation of conservation resources. We explored how choice of data‐cleaning, taxonomic group, training sample, and automation method affected performance of threat status predictions for plant species. We used occurrences from GBIF to generate assessments for species in three taxonomic groups using six different occurrence‐based AA methods. We measured each method's performance and coverage following increasingly stringent occurrence cleaning. Automatically‐cleaned data from GBIF yielded comparable performance to occurrence records cleaned manually by experts. However, all types of data‐cleaning limited the coverage of automated assessments. Overall, machine‐learning‐based methods performed well across taxa, even with minimal data‐cleaning. Results suggest a machine‐learning‐based method on minimally‐cleaned data offers the best compromise between performance and species coverage. However, optimal data‐cleaning, training sample, and automation methods depend on the study group, intended applications and expertise. Article impact statement: Evidence‐based guidelines for automated conservation methods will make their use easier and more reliable for conservation decisions. This article is protected by copyright. All rights reserved
Simple telomeric repeats composed of 6‐7 iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (1 newly sequenced) and 8 bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10,000‐fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non‐telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase‐sized blocks of telomeric repeats (i.e. billions of copies) were identified. Fluorescent in situ hybridization (FISH) experiments using variant‐specific probes revealed canonical Arabidopsis‐type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. Ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.
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