Wild Species Research Articles

Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

Characterisation of wild and cultivated cucurbit species and their response to water deficit stress

Characterisation of wild and cultivated cucurbit species and their response to water deficit stress

Using Citizen Science Data to Investigate the Diet of the Mountain Caracara (Phalcoboenus megalopterus) and White-throated Caracara (Phalcoboenus albogularis)

ABSTRACT The Mountain Caracara (Phalcoboenus megalopterus) and White-throated Caracara (Phalcoboenus albogularis) are two sister species each with a limited distribution along the Andes from Ecuador to Tierra del Fuego. They occur in remote areas and are among the least known caracaras, and their diet has been little studied, particularly for the White-throated Caracara. We investigated the diet of these two caracaras by analyzing photographs provided by citizen scientists and obtained from the Macaulay Library (eBird) and iNaturalist platforms. We obtained 43 photographs for Mountain Caracara and 42 photographs for White-throated Caracara that could be used to identify food items. Photographs of the Mountain Caracara showed the species mainly feeding on carrion, often of domestic animals, followed by human foods and garbage. Photographs of the White-throated Caracara showed this species mainly feeding on carrion and garbage. However, we did find photographs of both caracaras feeding on wild species including camelids, rodents, birds, lizards, and some invertebrates. Further research should investigate possible effects of human-derived items in the diet of these caracaras, such as malnutrition due to consumption of inappropriate foods, and effects of ingestion of plastics and toxic substances.

A new exposure protocol adapted for wild bees reveals species-specific impacts of the sulfoximine insecticide sulfoxaflor.

Wild bees are crucial pollinators of flowering plants and concerns are rising about their decline associated with pesticide use. Interspecific variation in wild bee response to pesticide exposure is expected to be related to variation in their morphology, physiology, and ecology, though there are still important knowledge gaps in its understanding. Pesticide risk assessments have largely focussed on the Western honey bee sensitivity considering it protective enough for wild bees. Recently, guidelines for Bombus terrestris and Osmia bicornis testing have been developed but are not yet implemented at a global scale in pesticide risk assessments. Here, we developed and tested a new simplified method of pesticide exposure on wild bee species collected from the field in Belgium. Enough specimens of nine species survived in a laboratory setting and were exposed to oral and topical acute doses of a sulfoximine insecticide. Our results confirm significant variability among wild bee species. We show that Osmia cornuta is more sensitive to sulfoxaflor than B. terrestris, whereas Bombus hypnorum is less sensitive. We propose hypotheses on the mechanisms explaining interspecific variations in sensitivity to pesticides. Future pesticide risk assessments of wild bees will require further refinement of protocols for their controlled housing and exposure.

Climate change through the eyes of recreational hunters: impacts on wildlife and adaptive responses

ABSTRACT Climate change is increasingly recognized as a serious threat to wildlife globally. Environmentally unsustainable human activities do not only damage wildlife resources but also contribute to exacerbating the impacts of climate change. The objective of this research is to assess how local hunters in the Dana Biosphere Reserve perceive climate change and its impacts on wildlife resources, and to understand their adaptive responses to these impacts. Through semi-structured interviews with local hunters, it was revealed that the area faces multiple climate threats, including reduced rainfall, shifting rainy seasons, and more frequent and intense droughts. Climate change has resulted in several problems, including a decline in the rate of reproduction of many wild species, changes in geographical distribution, and substantial declines in wildlife abundance. Consequently, most hunters have changed their hunting practices, avoided overhunting, and engaged in alternative outdoor activities.

Comprehensive genomic characterization and expression analysis of calreticulin gene family in tomato.

Calreticulin (CRT) is a calcium-binding endoplasmic reticulum (ER) protein that has been identified for multiple cellular processes, including protein folding, regulation of gene expression, calcium (Ca2+) storage and signaling, regeneration, and stress responses. However, the lack of information about this protein family in tomato species highlights the importance of functional characterization. In the current study, 21 CRTs were identified in four tomato species using the most recent genomic data and performed comprehensive bioinformatics and SlCRT expression in various tissues and treatments. In the bioinformatics analysis, we described the physiochemical properties, phylogeny, subcellular positions, chromosomal location, promoter analysis, gene structure, motif distribution, protein structure and protein interaction. The phylogenetic analysis classified the CRTs into three groups, consensus with the gene architecture and conserved motif analyses. Protein structure analysis revealed that the calreticulin domain is highly conserved among different tomato species and phylogenetic groups. The cis-acting elements and protein interaction analysis indicate that CRTs are involved in various developmental and stress response mechanisms. The cultivated and wild tomato species exhibited similar gene mapping on chromosomes, and synteny analysis proposed that segmental duplication plays an important role in the evolution of the CRTs family with negative selection pressure. RNA-seq data analysis showed that SlCRTs were differentially expressed in different tissues, signifying the role of calreticulin genes in tomato growth and development. qRT-PCR expression profiling showed that all SlCRTs except SlCRT5 were upregulated under PEG (polyethylene glycol) induced drought stress and abscisic acid (ABA) treatment and SlCRT2 and SlCRT3 were upregulated under salt stress. Overall, the results of the study provide information for further investigation of the functional characterization of the CRT genes in tomato.

Habitat connectivity of threatened ungulate species in a native savanna landscape of northern South America

AbstractThe native savanna ecosystem of the Orinoquia region is the habitat of 50% of the wild ungulate species reported for Colombia. Over the last 20 years, this high species diversity has been strongly threatened by the human transformation of the natural land cover causing connectivity loss of the habitats. The Orinoquia region lacks a biological connectivity analysis with a multi-species approach involving species groups that are representative of the savanna ecosystem such as the ungulates. Understanding the spatial distributions of suitable areas and the main habitats that act as primary habitats for ungulate species in these landscapes is fundamental for the design of conservation strategies. We use an occurrence dataset for lowland tapir (Tapirus terrestris), white-tailed deer (Odocoileus virginianus), and white-lipped peccary (Tayassu pecari) in the development of species’ potential distribution models, binarization process, and morphological spatial pattern analysis. This information was used for the modeling of dispersal corridors connecting the core habitats of the ungulate focal species using the randomized shortest path algorithm and quantifying the weighted global connectivity metrics. Our results suggest an integral corridor with potential least-cost dispersal routes between the native savanna landscape on the middle basins of the savanna rivers and the Meta River. These areas associated with the fluvial dendritic systems are connected, while the core habitats in the eastern part of the savanna landscape are disconnected. We discuss how the application of such knowledge on the spatial ecology of ungulate focal species might improve the management of the metapopulations in the Orinoquia region.

Importance of Flora in the Economy of Local Inhabitants of Karnah in Jammu and Kashmir India

Present study, conducted in Karnah, Jammu and Kashmir, from February 2022 to August 2023, rigorously collected data through interviews, discussions, and observations. The Study investigated the economic significance of local flora, documenting 28 plant species across 20 families. Pinaceae (14%) stood out. Trees (n=18), herbs (n=10), and one shrub (n=1) were noted. Wild species (16) surpassed cultivated (12). Plant parts had varied economic uses; a significant difference (χ2=90.587, df=7, p<0.001) was observed. Notably, Juglans regia, Prunus cornuta, Celtis tetrandra, Ficus carica, Morus alba, and Cynodia oblang were highlighted for economic applications. "Whole plant" (51%), leaves (20%), fruits (17%), bulb and seeds (6% each) were the most used components. Six uses (Medicine, food, timber, fuel, aesthetic, and industrial) contributed to the local economy. This pioneering study sheds light on the economic role of plant taxa in the Karnah region of Jammu and Kashmir.

Species discrimination from hair using ATR-FTIR spectroscopy: Application in wildlife forensics

Hair is a commonly encountered trace evidence in wildlife crimes involving mammals and can be used for species identification which is essential for subsequent judicial proceedings. This proof of concept study aims, to distinguish the black guard hair of three wild cat species belonging to the genus Panthera i.e. Royal Bengal Tiger (Panthera tigris tigris), Indian Leopard (Panthera pardus fusca), and Snow Leopard (Panthera uncia) using a rapid and non-destructive ATR-FTIR spectroscopic technique in combination with chemometrics. A training dataset including 72 black guard hair samples of three species (24 samples from each species) was used to construct chemometric models. A PLS2-DA model successfully classified these three species into distinct classes with R-Square values of 0.9985 (calibration) and 0.8989 (validation). VIP score was also computed, and a new PLS2DA-V model was constructed using variables with a VIP score ≥ 1. External validation was performed using a validation dataset including 18 black guard hair samples (6 samples per species) to validate the constructed PLS2-DA model. It was observed that PLS2-DA model provides greater accuracy and precision compared to the PLS2DA-V model during cross-validation and external validation. The developed PLS2-DA model was also successful in differentiating human and non-human hair with R-Square values of 0.99 and 0.91 for calibration and validation, respectively. Apart from this, a blind test was also carried out using 10 unknown hair samples which were correctly classified into their respective classes providing 100 % accuracy. This study highlights the advantages of ATR-FTIR spectroscopy associated with PLS-DA for differentiation and identification of the Royal Bengal Tiger, Indian Leopard, and Snow Leopard hairs in a rapid, accurate, eco-friendly, and non-destructive way.

Non-destructive SPE-UPLC-based Quantification of Aflatoxins and Stilbenoid Phytoalexins in Single Peanut (Arachis spp.) Seeds.

Aflatoxins are highly carcinogenic secondary metabolites of some fungal species, particularly Aspergillus flavus. Aflatoxins often contaminate economically important agricultural commodities, including peanuts, posing a high risk to human and animal health. Due to the narrow genetic base, peanut cultivars demonstrate limited resistance to fungal pathogens. Therefore, numerous wild peanut species with tolerance to Aspergillus have received substantial consideration by scientists as sources of disease resistance. Exploring plant germplasm for resistance to aflatoxins is difficult since aflatoxin accumulation does not follow a normal distribution, which dictates the need for the analyses of thousands of single peanut seeds. Sufficiently hydrated peanut (Arachis spp.) seeds, when infected by Aspergillus species, are capable of producing biologically active stilbenes(stilbenoids) that are considered defensive phytoalexins. Peanut stilbenes inhibit fungal development and aflatoxin production. Therefore, it is crucial to analyze the same seeds for peanut stilbenoids to explain the nature of seed resistance/susceptibility to the Aspergillus invasion. None of the published methods offer single-seed analyses for aflatoxins and/or stilbene phytoalexins. We attempted to fulfill the demand for such a method that is environment-friendly, uses inexpensive consumables, and is sensitive and selective. In addition, the method is non-destructive since it uses only half of the seed and leaves the other half containing the embryonic axis intact. Such a technique allows germination and growth of the peanut plant to full maturity from the same seed used for the aflatoxin and stilbenoid analysis. The integrated part of this method, the manual challenging of the seeds with Aspergillus, is a limiting step that requires more time and labor compared to other steps in the method. The method has been used for the exploration of wild Arachis germplasm to identify species resistant to Aspergillus and to determine and characterize novel sources of genetic resistance to this fungal pathogen.

Widening the Arachis hypogaea seed chemical composition: the case of a recombinant inbred lines introgressed with genes from three different wild species

Widening the <i>Arachis hypogaea</i> seed chemical composition: the case of a recombinant inbred lines introgressed with genes from three different wild species

Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii

Key messageA new resistance locus acting against the potato cyst nematode Globodera pallida was mapped to chromosome VI in the diploid wild potato species Solanum spegazzinii CPC 7195.The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato.

Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season.

The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

Promoter variations of ClERF1 gene determines flesh firmness in watermelon

BackgroundFlesh firmness is a critical factor that influences fruit storability, shelf-life and consumer’s preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon.ResultsIn this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis.ConclusionsOur results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.

Surveillance of Sarcoptic Mange in Iberian Ibexes (Capra pyrenaica) and Domestic Goats (Capra hircus) in Southern Spain.

Sarcoptic mange is a highly contagious skin disease caused by Sarcoptes scabiei. Sera were collected from 411 Iberian ibexes, comprising 157 individuals with sarcoptic mange skin lesions and 254 clinically healthy animals, in 13 population nuclei across Andalusia (southern Spain) between 2015 and 2021. Skin samples from 88 of the 157 animals with mange-compatible lesions were also obtained. Moreover, 392 serum samples from domestic goats (Capra hircus) were collected in the same region and study period. Antibodies against S. scabiei were tested using an in-house indirect ELISA, while the presence of mites of S. scabiei was evaluated in the skin samples by potassium hydroxide digestion. Seropositivity was found in eight (3.1%) of the clinically healthy ibexes and in 104 (66.2%) of the animals with mange-compatible lesions. The presence of S. scabiei was confirmed in 57 (64.8%) out of the 88 skin samples analysed and anti-S. scabiei antibodies were found in 49 (86.0%) of these 57 mite-positive individuals. Seropositive animals were detected in population nuclei with previous records of sarcoptic mange, where S. scabiei mites were detected by potassium hydroxide digestion in individuals with sarcoptic mange-compatible external lesions. However, seropositivity was not observed in population nuclei that were historically free of this disease. None of the 392 domestic goats had antibodies against S. scabiei, suggesting an independent epidemiological cycle of sarcoptic mange in Iberian ibex populations in the study area, and a limited or null role of domestic goats in the transmission of the parasite to this wild species. Overall, our findings underscore the importance of maintaining and/or implementing integrated surveillance programs and control strategies in wildlife and livestock, to limit the risk of S. scabiei circulation in Iberian ibex populations.

Acclimation of Agave potatorum Zucc. micropropagated plants

Objective: Agave potatorum Zucc. is an intensively exploited wild plant species. We intend to evaluate how the concentration of mineral salts (MS), indole-butyric acid (IBA), and the incubation conditions affect in vitro-rooted A. potatorum during acclimation. Design/Methodology/Approach: We conducted 18 treatments that resulted from combining three factors: 1) MS concentrations (50%, 75%, and 100%); 2) IBA concentrations (without auxin, 0.5 mg L-1, and 1 mg L-1); and 3) incubation environments (fluorescent lighting in a laboratory or exposure to solar radiation in a greenhouse). Thirteen plants from each treatment were transplanted into individual pots containing a 1:1 mixture of peat moss and perlite. These were placed in the acclimation greenhouse for 150 days, exposed to changes in solar radiation, starting from 600 µmol m-2 s-1 and conditions of high relative humidity (80-90%), and reaching outdoor conditions with full solar radiation,1400 ±200 µmol m-2 s-1. All in vitro culture plants, both in greenhouse and laboratory, underwent the same environmental and management conditions. Results: After 150 days of acclimation, plants micropropagated in a culture medium with 0.5 to 1 mg L-1 of IBA, 100% MS, and incubated in a greenhouse showed better growth. Study limitations/Implications: The in vitro culture protocol was (successfully) modified by providing solar radiation in a greenhouse during the rooting of A. potatorum sprouts. Findings/Conclusions: Solar radiation during in vitro incubation of A. potatorum favors its acclimation.

Germination Kinetics of Ferula communis L. Seeds, a Potentially Multipurpose-Use Wild Species

Despite exhibiting intriguing features associated with its multipurpose applications and drought tolerance, Ferula communis remains a wild and uncultivated species, with limited experimental research on its biology, starting from seed germination and extending to its ecology. The purpose of this study was to investigate potential germination and kinetics in F. communis seeds in response to four cold stratification periods (0, 15, 45, and 90 days at a constant temperature of 5 °C) and four temperatures (5, 10, 15, and 20 °C) under continuous darkness. F. communis exhibited a pronounced germination potential exceeding 90%, with the optimal temperature for germination falling within the range of 5 °C to 15 °C, without necessitating cold stratification. A dramatic drop of the germination percentage was observed at 20 °C (&lt;10%), suggesting a form of conditional dormancy attributed to the higher temperature tested.

Perennial Baki™ Bean Safety for Human Consumption: Evidence from an Analysis of Heavy Metals, Folate, Canavanine, Mycotoxins, Microorganisms and Pesticides.

Global food production relies on annual grain crops. The reliability and productivity of these crops are threatened by adaptations to climate change and unsustainable rates of soil loss associated with their cultivation. Perennial grain crops, which do not require planting every year, have been proposed as a transformative solution to these challenges. Perennial grain crops typically rely on wild species as direct domesticates or as sources of perenniality in hybridization with annual grains. Onobrychis spp. (sainfoins) are a genus of perennial legumes domesticated as ancient forages. Baki™ bean is the tradename for pulses derived from sainfoins, with ongoing domestication underway to extend demonstrated benefits to sustainable agriculture. This study contributes to a growing body of evidence characterizing the nutritional quality of Baki™ bean. Through two studies, we investigated the safety of Baki™ bean for human consumption. We quantified heavy metals, folate, and canavanine for samples from commercial seed producers, and we quantified levels of mycotoxins, microorganisms, and pesticides in samples from a single year and seed producer, representing different varieties and production locations. The investigated analytes were not detectable or occurred at levels that do not pose a significant safety risk. Overall, this study supports the safety of Baki™ bean for human consumption as a novel pulse crop.

The virus is out of the barn: the emergence of HPAI as a pathogen of avian and mammalian wildlife around the globe.

Highly pathogenic avian influenza (HPAI) has persisted as a One Health threat whose current circulation and impact are addressed in the companion Currents in One Health by Puryear and Runstadler, JAVMA, March 2024. Highly pathogenic avian influenza emerged as a by-product of agricultural practices and adapted to endemic circulation in wild bird species. Over more than 20 years, continued evolution in a complex ecology involving multiple hosts has produced a lineage that expanded globally over the last 2 years. Understanding the continued evolution and movement of HPAI relies on understanding how the virus is infecting different hosts in different contexts. This includes understanding the environmental factors and the natural ecology of viral transmission that impact host exposure and ultimately evolutionary trajectories. Particularly with the rapid host expansion, increased spillover to mammalian hosts, and novel clinical phenotypes in infected hosts, despite progress in understanding the impact of specific mutations to HPAI viruses that are associated with spillover potential, the threat to public health is poorly understood. Active research is focusing on new approaches to understanding the relationship of viral genotype to phenotype and the implementation of research and surveillance pipelines to make sense of the enormous potential for diverse HPAI viruses to emerge from wild reservoirs amid global circulation.

Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats.

Plants grown under field conditions experience fluctuating light. Understanding the natural genetic variations for a similarly dynamic photosynthetic response among untapped germplasm resources, as well as the underlying mechanisms, may offer breeding strategies to improve production using molecular approaches. Here, we measured gas exchange under fluctuating light, along with stomatal density and size, in eight wild tomato species and two tomato cultivars. The photosynthetic induction response showed significant diversity, with some wild species having faster induction rates than the two cultivars. Species with faster photosynthetic induction rates had higher daily integrated photosynthesis, but lower average water use efficiency because of high stomatal conductance under natural fluctuating light. The variation in photosynthetic induction was closely associated with the speed of stomatal responses, highlighting its critical role in maximizing photosynthesis under fluctuating light conditions. Moreover, stomatal size was negatively correlated with stomatal density within a species, and plants with smaller stomata at a higher density had a quicker photosynthetic response than those with larger stomata at lower density. Our findings show that the response of stomatal conductance plays a pivotal role in photosynthetic induction, with smaller stomata at higher density proving advantageous for photosynthesis under fluctuating light in tomato species. The interspecific variation in the rate of stomatal responses could offer an untapped resource for optimizing dynamic photosynthetic responses under field conditions.