Wild Species Research Articles

Identification of Capsicum species from Colombia by DNA barcoding and high resolution melting (HRM) analysis

AbstractDNA barcoding allows the use of molecular markers to differentiate the species of an interest group. This is especially useful when morphological characters are insufficient due to high similarity between species. The genus Capsicum contains some species that are difficult to determine by taxonomic means, in particular the annuum complex. Thus, the objective of this study was to investigate the discriminatory ability of two molecular markers in Colombian Capsicum accessions, including three wild species belonging to the Andean clade of the genus. A total of 95 Capsicum accessions, representing eight species, were genotyped by high resolution melting analysis (HRM) using the Waxy and C2_At5g04590 markers. Waxy could discriminate the Andean clade species (C. rhomboideum, C. dimorphum and C. lycianthoides), C. baccatum, C. pubescens and C. chinense, while C2_At5g04590 could discriminate C. frutescens, C. annuum var. annuum and C. annuum var. glabriusculum. Hence, a combination of the two markers could be used for discrimination of the eight species including the wild variety of C. annuum: C. annuum var. glabriusculum. Most nucleotide substitutions and indels were found in the sequences of the three Andean species, indicating that the Andean clade has a high genetic diversity compared to the other species. The incorporation of more wild species and varieties in this study allowed to correct the power of both markers to discriminate Capsicum species, besides the registration of new haplotypes.

A Draft Genome Resource for ‘Candidatus Phytoplasma prunorum’, the Agent Associated with European Stone Fruit Yellows Disease

‘Candidatus Phytoplasma prunorum’ is associated with European stone fruit yellows disease, affecting wild and cultivated species of Prunus at different degrees of susceptibility, so far being mainly restricted to Europe. Here, we report draft genome sequences for ‘Ca. Phytoplasma prunorum’ strains ESFY1 and LNS1, which represent the first available for this species. Strain ESFY1 is the causal agent of the European stone fruit yellows disease of Prunus persica in Germany and LNS1, leptonecrosis disease of Prunus salicina in Italy. Their draft genomes consist of 480,123 and 490,930 bases, assembled into 28 and 16 contigs, respectively, with an average GC content of 21.1% and 20.7%, respectively. Analysis of average nucleotide identity values between genomes further supported the delineation of ‘Ca. Phytoplasma prunorum’ as a species distinct from ‘Ca. Phytoplasma mali’, in agreement with previous phylogenetic data.

QTL Mapping of Fiber- and Seed-Related Traits in Chromosome Segment Substitution Lines Derived from Gossypium hirsutum × Gossypium darwinii.

A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using G. darwinii accession 5-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC1 population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including GH_A01G1096 (ARF5) and GH_A10G0141 (PDF2) for lint percentage, and GH_D01G0047 (KCS4) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton.

Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages

The cultivated tomato, Solanum lycopersicum, is highly sensitive to cold stress (CS), resulting in significant losses during cultivation and postharvest fruit storage. Previously, we demonstrated the presence of substantial genetic variation in fruit chilling tolerance in a tomato recombinant inbred line (RIL) population derived from a cross between a chilling-sensitive tomato line and a chilling-tolerant accession of the wild species S. pimpinellifolium. Here, we investigated molecular and biochemical components associated with chilling tolerance in fruit and leaves, using contrasting groups of “chilling tolerant” and “chilling sensitive” RI lines. Transcriptomic analyses were conducted on fruit exposed to CS, and gene expressions and biochemical components were measured in fruit and leaves. The analyses revealed core responding genes specific to either the cold-tolerant or cold-sensitive RI lines, which were differentially regulated in similar fashion in both leaves and fruit within each group. These genes may be used as markers to determine tomato germplasm cold tolerance or sensitivity. This study demonstrated that tomato response to CS in different developmental stages, including seedling and postharvest fruit, might be mediated by common biological/genetic factors. Therefore, genetic selection for cold tolerance during early stages of plant development may lead to lines with greater postharvest fruit chilling tolerance.

Plant cultivation and diversity at the Early Neolithic settlement in Biskupice in Poland

The emergence of the Linear Pottery Culture (LBK) during the Neolithic period within Polish territory 5400–4900 BC, introduced plant cultivation, yet the definitive list of cultivated species remains debated. This study examines plant assemblages (fruits, seeds, pollen, and spores) from the LBK settlement in Biskupice, southern Poland, aiming to identify cultivated and wild species used during the development of the first stable settlements in the Carpathian Foothills. Due to extensive sampling, Biskupice yielded over 11,000 macroscopic plant specimens, enabling detailed analysis of plant diversity, distribution, and implications for agrarian and dietary practices. The analysis revealed a focus on emmer and einkorn wheat cultivation, with barley playing a minor role, alongside evidence of flax and pulses. Radiocarbon dating supported the settlement’s existence in the 6th millennium BCE, and confirmed the use of barley. However, a younger date excluded bread wheat cultivation at this site. The plant assemblage included a diverse array of herbaceous wild plants like black bindweed, fat hen and brome species, suggesting their economic use. Additionally, the presence of cockspur grass, linked with Southeast Asia, indicates alternative migration routes of weeds in Europe, as supported by radiocarbon dating. Palynological analysis suggests existence of nearby cereal plots or the processing of cereals at the settlement, supporting archaeological evidence.

Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii.

Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

Structural interspecies variability of mammals' hairs.

Hairs are fundamental structures for mammals, serving crucial functions such as thermal insulation and hydrophobicity. In domestic animals, hair is also a valuable source of high-performance fibers for the textile industry, which has led to intensive study. However, there is limited comparative knowledge about the physical properties of hair across different wild mammalian species. In our lab, we are investigating the physical properties of hairs from a diverse range of wild mammalian species, laying the groundwork for an in-depth comparative study. These physical properties can be linked to the internal structures of the hairs. Using polarized light microscopy, we can visualize the internal structure of hairs, which are composed of a hollow channel (medulla) surrounded by a cortex and a keratin cuticle(1). By examining the brown hairs of three distinct mammals-the Patagonian mara, the brown bear, and the Amur tiger-we observe striking differences in their internal structures. We speculate that these structural differences correspond to varying physical properties, which we are currently investigating.

DNA Methylation Carries Signatures of Sublethal Effects Under Thermal Stress in Loggerhead Sea Turtles.

To date, studies of the impacts of climate warming on individuals and populations have mostly focused on mortality and thermal tolerance. In contrast, much less is known about the consequences of sublethal effects, which are more challenging to detect, particularly in wild species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch field experiment, we relocated clutches of wild, nesting loggerhead sea turtles (Caretta caretta) to an insitu hatchery. Eggs were then split into two sub-clutches and incubated under shallow or deep conditions, with those in the shallow treatment experiencing significantly higher temperatures in otherwise natural conditions. Although no difference in hatching success was observed between treatments, hatchlings from the shallow, warmer treatment had different length-mass relationships and were weaker at locomotion tests than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. We identified 287 differentially methylated sites between hatchlings from different treatments, including on genes with neurodevelopmental, cytoskeletal, and lipid metabolism functions. Taken together, our results show that higher incubation temperatures induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. These sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming reduces hatchling fitness, which has implications for dispersal capacity and ultimately a population's adaptive potential. Conservation efforts for these endangered species and similar climate-threatened taxa will therefore benefit from strategies for monitoring and mitigating exposure to temperatures that induce sublethal effects.

Utilizing citizen science data to rapidly assess changing associations between wild birds and avian influenza outbreaks in poultry.

High pathogenicity avian influenza virus (HPAIV) is a rapidly evolving virus causing significant economic and environmental harm. Wild birds are a key viral reservoir and an important source of viral incursions into animal populations, including poultry. However, we lack a thorough understanding of which species drive incursions and whether this changes over time. We explored associations between the abundances of 152 avian species and outbreaks of highly pathogenic avian influenza (HPAI) in poultry premises across Great Britain between October 2021 and January 2023. Spatial generalized additive models were used, with species abundance distributions sourced from eBird. Associations were investigated at the species-specific level and across species aggregations. During autumn/winter, associations were generally strongest with waterbirds such as ducks and geese; however, we also found significant associations in groups such as non-native gamebirds and rapid change in species-specific associations over time. Our results demonstrate the value of citizen science to rapidly explore wild species as potential facilitators of disease incursions into well-monitored populations, especially in regions where viral surveillance in wild species is limited. This can be a critical step towards prioritizing targeted surveillance that could inform species-specific biosecurity measures; particularly for HPAIV, which has undergone sudden shifts in host range and continues to rapidly evolve.

Differential effects of increasing temperature on the germination of five wild species with varying range sizes in a Carrara marble quarry

Assessing the performance of spontaneous plants in abandoned quarries under future environmental scenarios is important for successful restoration practises. Air warming is one of the most relevant ongoing climatic changes in the Mediterranean. We tested the effects of increasing temperature on the germination of five species spontaneously colonising the abandoned sectors of a Carrara marble quarry (Tuscany, central Italy). We selected five plant species with different widths of their distribution range, from local endemic to invasive alien: Santolina pinnata, Globularia incanescens, Hypericum coris, Helichrysum italicum, and Buddleja davidii. Seeds were collected in situ and their germination was tested in laboratory conditions at 10, 15, 20, 25, and 30 °C. The effects of temperature and species on germination percentage (GP) and mean germination time (MGT) were tested through two-way ANOVA. Increasing temperatures negatively affected the GP of S. pinnata and H. coris. G. incanescens performed better at intermediate temperatures, whilst H. italicum benefited from increasing temperatures. B. davidii showed a similar high GP under all the treatments. MGT decreased with increasing temperature for all the species, except for S. pinnata, which showed an increase of MGT with increasing temperature. We highlighted that, under future warmer climatic conditions, the two endemic species will be disadvantaged with respect to the species with a wider distribution range and the non-native species in the studied quarry. This evidence is relevant for restoration planning since seeding the two endemic species could be unsuccessful under future environmental scenarios, when H. italicum and B. davidii will be more competitive in the colonisation of the quarry.

Long-term memory in wild falcons

Long-term memory - information retention over long timescales - can allow animals to retain foraging skills and efficiently respond to seasonally available resources and changing environments1. Most long-term memory research is with captive species, focusing on spatial, individual or object recognition, with less known about wild species and the retention of motor task abilities, as in the case of complex foraging skills2,3. We have examined whether wild striated caracaras (Phalcoboenus australis), recently shown to rapidly and flexibly innovate with an eight-task puzzle box4, retain task memories one year later. We found that, despite no reinforcement, caracaras repeated motor techniques that led to their most recent success on tasks the year prior, solving nearly twice as fast as a naïve control group and four times faster than when naïve. Our results suggest long-term memory may be important for non-migratory opportunistic generalists, particularly in remote island environments with seasonally available resources, and further highlight how striated caracaras are promising candidates for avian cognitive studies.

Plant Growth Regulator-based Tissue Culture System Optimization for Cymbidium faberi Rolfe

Cymbidium faberi, a member of the Cymbidium genus known for its fragrant blooms and graceful foliage, has recently become endangered in the wild due to reproductive challenges. This study aimed to establish systematically a tissue culture system for Cymbidium faberi Rolfe (wild species) by evaluating the effects of various plant growth regulators its propagation stages, including rhizome proliferation, differentiation, shoot strengthening, and rooting. The results showed that 0.5 mg·L−1 thidiazuron significantly promoted rhizome proliferation, achieving a proliferation coefficient of 6.08 after 60 days of culture. For adventitious bud induction, 1.92 mg·L−1 brassinolide was most effective, inducing 6.43 buds per rhizome with an average bud height of 5.25 mm after 90 days of culture. The optimal strategy for shoot growth was using 3.0 mg·L−1 1-naphthaleneacetic acid, resulting in an average shoot height of 6.47 cm after 60 days. The highest rooting rate of 87.5% was achieved with 0.5 mg·L−1 zeatin, producing an average of 3.5 roots per shoot with an average root length of 3.06 cm. This study successfully developed a propagation system for C. faberi and highlighted the significant role of BL in promoting rhizome differentiation. In conclusion, this study provides a robust propagation method to support the conservation and industrial development of C. faberi.

Mechanism of betterment towards growth and induction of defense in rice (Oryza sativa L.) by biopriming with bacterial endophytes isolated from wild rice

Utilizing beneficial microorganisms associated with plants, particularly endophytes, is becoming more and more prevalent since it supports the physiological health and evolutionary adaption of the host. The range of enhanced endophytic bacteria found in wild rice makes it a promising resource for sustainable agriculture. Current study focused on bacterial endophytes the tissues of wild rice plants' roots, stems, and leaves for managing the health and development of rice (Oryza sativa L.) plants. Bacterial endophytes were characterized using 16S rRNA. Treatments with Priestia megaterium (NRRI EB 1) and Priestia aryabhattai (NRRI EB 2) outperformed the other isolates in rice growth enhancement activities significantly. The biocontrol efficacy of bacterial endophytes was tested against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani and percentage of inhibition was the higher in NRRI EB 1 by 79.32-80.83% and in NRRI EB 2 by 79.69-80.45%. Bio-priming the seeds with specific endophytic bacterial strains led to a decrease in average germination time, an increase in seedling vigor, and total chlorophyll content. Additionally, they generated greater amounts of soluble phosphate (40.91-83.70 μg/mL) and indole acetic acid (28.10-60.18 μg/mL), which are in the midst of encouraging more plant development. Higher expressions of defense enzymes in comparison to the control, including catalase (>220% in root and shoot), peroxidase (>200% in shoot and root), and superoxide dismutase (> 150% in shoot and root) illustrates the rice crop's resilience to withstand stress. The activity of the mentioned enzymes was further validated through the activation of corresponding defense genes such as DEFENSIN (>2-fold), PAL (>3-fold), PR-3 (>2-fold), POX (>2-fold) and LOX (>1-fold) relative to the control's untreated plants. The possibility exists to extract advantageous endophytic bacteria from wild rice species, potentially rewilding the microbiome of farmed rice cultivators and fostering their development.

Structure, function and formation of the amniote skin pattern

From feather and hair dotted arrays to pigmented stripes and spots, the spatial distribution of skin appendages and colouration often forms visible ornaments crucial for fitness in the coat of birds and mammals. These geometrical motifs are extremely diverse in nature. Yet, phenotypic surveys evidenced common themes in variation: the orientation, appendage-specificity or pigmentation of a given region may be conserved across groups or species. Here, we review naturalist observations of natural variation in the anatomy and ecological function of the skin pattern in amniotes. We then describe several decades of genetics, mathematical modelling and experimental embryology work aiming at understanding the molecular and morphogenetic mechanisms responsible for pattern formation. We discuss how these studies provided evidence that the morphological trends and differences representative of the phenotypic landscape of skin patterns in wild amniote species is rooted in the mechanisms controlling the production of distinct compartments in the embryonic skin.

Histochemical studies of aroma components in fruits of wild tomato species native to the Peruvian Andes and the Galapagos Islands

Histochemical studies of aroma components in fruits of wild tomato species native to the Peruvian Andes and the Galapagos Islands

Landscape heterogeneity correlates with bee and pollen diversity while size and specialization degree explain species-specific responses of wild bees to the environment

Access to adequate pollen sources in agricultural landscapes is critical for the nutrition and development of bees. The type and quantity of pollen available to bees and may be determined by local plant diversity, land-use intensity and landscape structure but different bee species likely respond differently to these parameters. Identifying community and specific responses is therefore imperative to understand pollinator population dynamics in agricultural landscapes. We sampled bees in 36 plots along a land-use gradient at 4 sites in Belgium and Germany over two years. We collected 1821 bees from 100 bee species and constructed a pollen foraging network with 36 common wild bee species based on pollen metabarcoding. We investigated differences in community responses and species-specific responses to environmental variables.Landscape heterogeneity positively correlated with bee species richness, diversity and functional richness, and significantly explained bee community composition per plot. Bee collected pollen diversity correlated with bee species diversity. Furthermore, landscape heterogeneity positively correlated with bee collected pollen diversity when pooling abundant bee species, while it did not correlate with pollen diversity of the most abundant generalists. Land-use intensity and local plant diversity had no significant effect on bee diversity. Larger bees showed negative responses to increasing land-use intensity and bees with more specialized diets showed positive correlations with landscape heterogeneity. Our study goes beyond mere floral diversity and provides new insight into the responses of wild bee communities to landscape structure and regional pollen availability, as well as the interplay between bee abundance and pollen foraging traits. Our results highlight the importance of determining species-specific nutritional needs and considering landscape level structure in pollinator conservation programs.

Expression analysis of flowering gene in diploid wild strawberry species

Expression analysis of flowering gene in diploid wild strawberry species

A Functional Analysis of Inflorescence Architecture in Musa L. (Musaceae)

ABSTRACTInflorescence architecture underpins sexual reproduction in wild Musa species and productivity in edible banana cultivars. In a functional analysis, we identified the apical inflorescence and lateral ‘cushion’ meristems and the change in flower type as the three primary components that generate inflorescence architecture. Five genotypes of two clone sets of edible plantains (Musa AAB) were grown for four generations along an elevation gradient (1100–2200 m, 16°C–24°C) straddling the equator in the humid highlands of East Africa. The data consisted of reproductive peduncle length at harvest (Pr), fruit per hand (Fh) and hands per bunch (Hb). The activity of the apical inflorescence meristem drives peduncle length and generates lateral ‘cushion’ meristems which determine Fh. However, Hb is determined by a change in flower type—from fruit forming to non‐fruit forming. Site temperature affected Hb more than Fh, while the development of the genet (rhizome) changed the allocation of resources between Hb and Fh, independently of the effect of site temperature. Clone sets differed in their response to genet development. Cooler temperatures reduced the number of fruit‐forming flowers in an inflorescence and changed the balance away from female towards male flowers. In banana breeding schemes, manipulating inflorescence components independently raises options for producing genotypes better suited to markets, environments and cultural practices.

Biochemical analysis of wild and cultivated Momordica species

Biochemical analysis of wild and cultivated Momordica species

Cryptosporidium spp. in German wildlife: Detection, regional occurrence and diversity in wild boar, roe, red and fallow deer

Cryptosporidium is a cause of diarrheal infections responsible for a loss of human and animal welfare worldwide. The impact of the parasite is underestimated and the reported sources of infection are diverse, as it occurs in a wide variety of hosts. Wildlife has been reported as a notifiable source, but few studies are available on its occurrence in European wild boar and cervid species. To determine the occurrence of Cryptosporidium in game in Brandenburg, Germany, a molecular survey was conducted during the 2017 to 2020 hunting seasons. A total of 562 fecal samples from wild boar (Sus scrofa, n = 262), roe deer (Capreolus capreolus, n = 174), red deer (Cervus elaphus, n = 62), fallow deer (Dama dama, n = 51) and 13 samples of unspecified species were analyzed for both 18S ribosomal RNA (18S rRNA) and Cryptosporidium oocyst wall protein (COWP) gene sequence regions. PCR results showed that 21.2 % of the samples (n = 119/562) were positive for at least one target gene (18S rRNA: n = 114; COWP: n = 14), but differences in Cryptosporidium occurrence were observed within species and hunting seasons, with variations ranging from 1.8 % to 41.7 % (roe deer), respectively. Analysis of Sanger sequences of the 18S rRNA and COWP PCR products indicated that the C. sp. deer genotype was predominant in deer (roe deer: 86.7 %, red deer: 66.7 %, fallow deer: 58.8 %), while C. suis and C. scrofarum were mainly detected in wild boar (88.5 %). The human pathogenic species C. parvum was detected in only 1.2 % (n = 7) of the samples analyzed, but without a clear indication of a specific wild animal host. The highest Cryptosporidium diversity was found in wild boar and roe deer with five and four different species, respectively. Comparison of the 18S rRNA sequences with the designated reference revealed minor variations at several nucleotide positions in some isolates, possibly indicating evolutionary adaptations and the development of new subtypes. In conclusion, wildlife represents a reservoir for a diverse spectrum of Cryptosporidium species and may thus contribute to their environmental spread and the transmission to humans.