Search Results (235)

Climate change is jeopardizing global food security, with at least 713 million people facing hunger. To face this challenge, legumes as common beans could offer a nature-based solution, sourcing nutrients and dietary fiber, especially for rural communities in Latin America and Africa. However, since common beans are generally heat and drought susceptible, it is imperative to speed up their molecular introgressive adaptive breeding so that they can be cultivated in regions affected by extreme weather. Therefore, this study aimed to couple an advanced panel of common bean (Phaseolus vulgaris L.) × tolerant Tepary bean (P. acutifolius A. Gray) interspecific lines with Bayesian regression algorithms to forecast adaptation to the humid and dry sub-regions at the Caribbean coast of Colombia, where the common bean typically exhibits maladaptation to extreme heat waves. A total of 87 advanced lines with hybrid ancestries were successfully bred, surpassing the interspecific incompatibilities. This hybrid panel was genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Three yield components (yield per plant, and number of seeds and pods) and two biomass variables (vegetative and seed biomass) were recorded for each genotype and inputted in several Bayesian regression models to identify the top genotypes with the best genetic breeding values across three localities on the Colombian coast. We comparatively analyzed several regression approaches, and the model with the best performance for all traits and localities was BayesC. Also, we compared the utilization of all markers and only those determined as associated by a priori genome-wide association studies (GWAS) models. Better prediction ability with the complete SNP set was indicative of missing heritability as part of GWAS reconstructions. Furthermore, optimal SNP sets per trait and locality were determined as per the top 500 most explicative markers according to their β regression effects. These 500 SNPs, on average, overlapped in 5.24% across localities, which reinforced the locality-dependent nature of polygenic adaptation. Finally, we retrieved the genomic estimated breeding values (GEBVs) and selected the top 10 genotypes for each trait and locality as part of a recommendation scheme targeting narrow adaption in the Caribbean. After validation in field conditions and for screening stability, candidate genotypes and SNPs may be used in further introgressive breeding cycles for adaptation. Full article

The advent of alignment-free k-mer barcoding has revolutionized taxonomic analysis, enabling bacterial identification at phylogroup resolution within natural communities. We applied this approach to characterize Escherichia coli intraspecific diversity in human gut microbiomes using publicly available datasets representing diverse human physiological states. By estimating the relative abundance of eight E. coli phylogroups defined by their 18-mer markers in 558 fecal samples, we compared their distribution between gut microbiomes of healthy individuals, patients with chronic bowel diseases and volunteers subjected to various external interventions. Across all datasets, phylogroups exhibited bidirectional abundance shifts in response to host physiological changes, indicating an inherent bimodality in their adaptive strategies. Correlation analysis of phylogroup persistence revealed positive intraspecific connectivity networks and dependence of their patterns on both acute interventions like antibiotic or probiotic treatment and chronic bowel disorders. Along with predominantly negative correlations with Bacteroides, we observed a transition from positive to negative associations with Prevotella in Prevotella-rich microbiomes. Several interspecific correlations individually established by E. coli phylogroups with dominant taxa suggest their potential role in shaping intraspecific networks. Machine learning techniques statistically confirmed an ability of phylogroup patterns to discriminate the physiological state of the host and virtual diagnostic assays opened a way to optimize intraspecific phylotyping for medical applications. Full article

Exploring host preference and resource partitioning among seed predator species is essential for understanding the coexistence mechanisms and guiding effective forest pest management. This study aimed to elucidate how seed traits influence infestation dynamics and species interactions, focusing on acorn weevils infesting Quercus mongolica. Species identification and clarification of their evolutionary relationships within the Curculio genus were performed through phylogenetic analyses of the mitochondrial cytochrome c oxidase subunit I gene sequences. The seed infestation patterns were assessed by comparing the infestation rates across various seed size classes. Furthermore, the correlations between the seed morphological traits (length, width, aspect ratio, and weight) and weevil abundance were analyzed. The phylogenetic results revealed well-supported monophyletic clades corresponding to Curculio arakawai and Curculio sikkimensis. This confirmed the clear genetic separation between these two distinct weevil species, thereby substantiating the divergence observed in weevil populations correlated with different seed hosts. The infestation patterns revealed the association of weevil species-specific preferences with seed size: C. arakawai predominantly infested larger acorn seeds, whereas C. sikkimensis predominantly infested smaller acorn seeds. C. sikkimensis favored smaller ones. Both species exhibited positive correlations between abundance and seed length and width in larger seeds; however, the seed weight displayed no significant effect. These results indicate niche differentiation mediated by seed size and morphology, which likely reduced interspecific competition and facilitated coexistence. This study elucidates species-specific host selection patterns in acorn weevils and highlights acorn traits as crucial factors shaping seed predator assemblages. The findings provide valuable insights for developing targeted pest management strategies and supporting sustainable oak forest regeneration. Full article

Meiotic recombination is essential for chromosomal segregation and facilitates the exchange between homologs, which leads to the transmission of new combinations of linked alleles to the progeny. The eukaryotic meiotic machinery is generally highly conserved, but the frequency of crossover occurrence can vary dramatically across species and populations, between individuals, and across sexes. The chicken and the guinea fowl exhibit interspecific variation in the distribution of crossovers along their largest chromosomes. In many organisms, an association has been observed between the preferred crossover location and certain sequence parameters, such as high GC content, CpG islands, or gene promoters. Here, we compared the distribution of these genomic parameters with the recombination landscape, represented by MLH1 focus frequencies, in the two birds. We found an association between GC content density and recombination in the chicken, but the remaining parameters showed weak or no association with recombination, especially in the guinea fowl. We conclude that despite the different broad-scale crossover distribution, the investigated genomic parameters remained remarkably similar in these two species. We suggest that the density of these genomic features is more likely related to microscale variations in recombination rates, such as those determined by open chromatin configurations. Full article

Litchi chinensis, a crucial tropical and subtropical fruit tree in southern China, is widely appreciated for its distinctive flavor, high nutritional value, and significant economic impact. The bZIP (basic leucine zipper) gene family plays an essential role in regulating key biological functions during plant growth and development. In this study, we performed a comprehensive bioinformatics analysis of the bZIP gene family in litchi to systematically elucidate its molecular characteristics and functional properties. A total of 55 bZIP gene family members were identified, with the encoded proteins containing between 129 and 845 amino acid residues and theoretical isoelectric points (pI) ranging from 4.85 to 10.23. Protein–protein interaction network analysis revealed that 46 proteins exhibited interaction relationships. Phylogenetic analysis classified these genes into 13 distinct subgroups (A–K, M, and S). Chromosomal localization analysis indicated that bZIP gene family members were successfully mapped to 15 chromosomes. Intraspecific collinearity analysis identified 39 segmental duplication events, while interspecific and single-gene collinearity analyses suggested evolutionary conservation, with only a few genes exhibiting duplication or loss events. Cis-acting element analysis revealed a total of 213 elements associated with growth and development, which may play an important role in fruit development regulation. The results of differential gene expression, related to fruit development across different litchi cultivars, tissues, and flowering stages, combined with qRT-PCR validation, suggest that LITCHI017015.m1 and LITCHI004463.m1 may be involved in the early regulation of fruit development, while LITCHI018843.m1 may play a regulatory role during the later stages of fruit development. These findings provide a strong theoretical foundation for understanding the roles of bZIP genes in litchi fruit growth and development, and lay the groundwork for further functional studies. This study has potential application value in litchi fruit development and genetic improvement. Full article

Studying spatial distribution patterns and intraspecific and interspecific associations of tree species is crucial for understanding the maintenance of biodiversity and offering insights into community dynamics and stability. The Shennongjia National Park, located in the transition zone between the (sub)tropics and the temperate climate, holds great significance for understanding how species interact with each other and coexist within forest communities. We used data from a fully mapped 25 ha montane deciduous broad-leaved forest dynamic plot at Shennongjia (SNJ) National Park, central China, to conduct a community-level evaluation of spatial distribution patterns and intraspecific and interspecific associations. We analyzed the spatial distribution patterns of 20 dominant species with univariate and bivariate g(r) functions, as well as intraspecific and interspecific associations across different life-history stages. We assessed the relative contributions of underlying processes in community assembly with three models: complete spatial randomness (CSR), heterogeneous Poisson (HP), and antecedent condition (AC). The results showed that all 20 tree species exhibited aggregated distribution patterns within a 100 m scale. After excluding the influence of environmental heterogeneity, the degree of aggregation decreased, and with the increasing spatial scale from 0 to 100 m, the distribution gradually shifted from aggregated to random or uniform appearance. Positive associations were common in different life-history stages. Negative associations were common across different species, while most of the intraspecific and interspecific associations turned out to be irrelevant when environmental heterogeneity was excluded. We concluded that habitat heterogeneity and dispersal limitation may primarily determine the spatial distribution of species in subtropical montane deciduous broad-leaved forests. This indicates that species distribution may align with environmental patterns, and interspecific correlations may exist. However, the exact responses of these species to environmental changes remain uncertain. Upcoming management approaches ought to concentrate on ongoing observation, which is crucial for mitigating how climate change might affect species distribution and community interactions, thus guaranteeing enduring stability and the conservation of biodiversity. Full article

To investigate the structure of phytoplankton communities and the ecological niches of dominant species in the middle and upper reaches of the Yarlung Zangbo River, we collected samples at 14 sites in April (spring) and September (autumn) 2023. A total of 198 phytoplankton species were identified belonging to 6 classes, 13 orders, 24 families, and 53 genera. The community structure was dominated by diatoms, green algae, and cyanobacteria. In April, 163 species of phytoplankton from four phyla were identified, with abundance ranging from 2.94 × 10⁵ to 2.32 × 10⁶ cells/m³ and an average of 1.28 × 10⁶ cells/m³. In September, the abundance of phytoplankton ranged from 1.52 × 10⁵ to 1.58 × 10⁶ cells/m³, with an average value of 6.76 × 10⁵ cells/m³. Sixteen species were classified as dominant (Y > 0.02), among which four showed dominance in both sampling periods, with their dominance level and niche width differing with the season. Water temperature increased with decreasing altitude. At <3500 m in September, Ankistrodesmus falcatus and Oocystis borgei became dominant. Cymbella cistula, Amphora ovalis, and Navicula cryptocephala occupy broad ecological niches and can represent indicator species for water quality. Water temperature, pH, and salinity were identified as primary factors influencing the ecological niche differentiation of dominant phytoplankton species. The interspecific niche overlap was higher in September than in April and greater at >4500 m compared to other elevation ranges (>4500 m; 4000–4500 m; 3500–<4000 m; <3500 m). The effect of elevation on the community structure was greater than that of season. This is the first study to characterize the association of ecological niches of phytoplankton in the upper reaches of the Yarlung Zangbo River with physicochemical environmental parameters. This provides baseline information for the conservation of biodiversity and management of aquatic ecosystems in the rivers of the Tibetan Plateau. Full article

Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal swab samples collected from 56 bird species. We identified 74 AIVs of H3N6, H3N8, H4N6, H5N3, H7N7, H10N3, and H11N9 subtypes in Anseriformes order. Phylogenetic analysis showed that the isolates belong to the Eurasian lineage and have genetic similarities with strains from East Asia, Europe, and North America. Cluster analysis has demonstrated the circulation of stable AIV genotypes for several years. We assume that Yakutia is an important territory for viral exchange on the migratory routes of migrating birds. In addition, several amino acid substitutions have been found to be associated with increased virulence and adaptation to mammalian hosts, highlighting the potential risk of interspecific transmission. These results provide a critical insight into the ecology of the AIV and highlight the importance of continued monitoring in this geographically significant region. Full article

Mesopredator suppression has implications for community structure, biodiversity, and ecosystem function, but mesopredators with physical defenses may not avoid apex predators. We investigated nine-banded armadillos (Dasypus novemcinctus) in southwestern Oklahoma (USA) to evaluate if a species with physical defenses was influenced by a dominant predator, the coyote (Canis latrans). We sampled nine-banded armadillos and coyotes with motion-activated cameras. We used single-species and conditional two-species occupancy models to assess the influences of environmental factors and coyotes on nine-banded armadillo occurrence and site-use intensity (i.e., detection). We used camera-based detections to characterize the diel activity of each species and their overlap. Nine-banded armadillo occupancy was greater at sites closer to cover, with lower slopes, and further from water, whereas coyote space use was greater at higher elevations; both species were positively associated with recent burns. Nine-banded armadillo occurrence was not influenced by coyotes, but site-use intensity was suppressed by the presence of coyotes. Nine-banded armadillos (strictly nocturnal) and coyotes (predominantly nocturnal) had a high overlap in summer diel activity. Nine-banded armadillos are ecosystem engineers but are often considered a threat to species of concern and/or a nuisance. Thus, understanding the role of interspecific interactions on nine-banded armadillos has important implications for conservation and management. Full article

This paper presents a pilot project conducted by ISPRA and ARPA Campania to develop a monitoring protocol to detect the presence of genetically modified (GM) oilseed rape (Brassica napus) plants resulting from accidental seed dispersal during transportation from entry points to storage and processing facilities; the project has been implemented in Italy’s Campania region. The unintentional dispersal of GM oilseed rape seeds and the potential establishment of feral populations have been identified as environmental concerns in various countries, even when GM oilseed rape is imported solely for processing and not for cultivation. The project activities were designed, taking into account the characteristics of the Italian environment and infrastructures. Multiple sampling campaigns were conducted in autumn 2018, spring 2019, and autumn 2019 to validate the selected transects and assess the presence of Brassicaceae species, with a particular focus on oilseed rape. These efforts involved direct monitoring and sample collection along transport routes from the port of Salerno to seed companies in the provinces of Benevento and Caserta. Field observations and import data revealed a decrease in oilseed rape movement at the port of Salerno in the years preceding the survey, while seed companies near Benevento remained active sites for white mustard (Sinapis alba). The presence of S. alba and the simultaneous occurrence of oilseed rape and Raphanus raphanistrum—a species with high hybridization potential—support the hypothesis that seed companies may act as hotspots for accidental seed dispersal and that potential interspecific gene flow can occur. The study also validated the adopted sampling and molecular analysis methods, including DNA extraction and PCR, for the detection of the Cruciferin A (CruA) gene in all Brassica species collected. These findings highlight the need to strengthen post-marketing monitoring plans, even when GM rapeseed is imported solely for processing, to mitigate the potential risks associated with unintended gene flow. Full article

Nanchuan Dachashu (Camellia nanchuanica), an arboreal tea species from Chongqing, China, exhibits valuable germplasm characteristics and tea production quality. However, the morphological diversity and genetic basis of key traits, such as tree architecture, leaf anatomy, and ovary trichomes, within this natural population remain to be elucidated. In this study, we conducted a survey on 90 wild individuals from this population, with a special focus on ovary trichomes—an important taxonomic trait. Considerable variations were observed in tree architecture, leaf size and shape, and anatomical structures. Through association analysis, we identified the SNP locus Chr9_89939207 to be associated with the glabrous/hairy ovary trait. A KASP marker was subsequently developed based on this locus, which could accurately distinguish between glabrous and hairy ovary individuals of Nanchuan Dachashu, as well as differentiate this species from C. sinensis or other hairy ovary species. The SNP locus Chr9_89939207 resides in the exon of a predicted protein phosphatase 2C (PP2C) gene, CSS0003297, which potentially regulates ovary trichome development in tea plants. These results reveal extensive morphological variation within the Nanchuan Dachashu population, establish a molecular tool for the identification of valuable interspecific hybrids, and provide insights into the breeding and industrial applications of this germplasm. Full article

Oaks in the genus Quercus L. are keystone species in the forest ecosystem and are considered ideal models for the study of plant evolution. In this research, we applied population genetics, ecological niche analysis and phenotypic traits to explore patterns of species differentiation and demographic history of two Chinese montane oak species (Quercus baronii Skan and Quercus dolicholepis A. Camus) from Quercus section Ilex across species distribution ranges. Analyses of population genetics with ten nuclear microsatellite loci on 33 populations of the two oak species indicated great interspecific genetic variations with distinct genetic backgrounds for the two oaks. Simulations on species demography suggested a speciation-without-migration model as the best to explain species divergence, while an approximate Bayesian computation analysis indicated that the two studied oak species probably split at about 17.80–28.48 Ma. A comparison of two core bioclimatic factors and ecological niche tests revealed strong niche differentiation between the two oak species, and association analysis also found a significantly positive correlation between interspecific genetic variations and bioclimatic distances. Additionally, analyses of the leaf morphology of 117 specimens with five quantitative characteristics showed clear species discrepancy between Q. baronii and Q. dolicholepis. Based on this evidence from genetic, ecological and phenotypic analyses, our research indicated clear species differentiation between Q. baronii and Q. dolicholepis, possibly in relation to an early species divergence and varying adaptative features of the two oaks shaped by heterogeneous environments within Qinling-Daba Mountains and surroundings. This study provides an example for future investigation of species differentiation and evolution among related oak species with integrated analyses and highlights the importance of ecological conditions on adaptive evolution and genetic conservation of endemic tree species in montane regions. Full article

Forests are complex systems in which subtle variations in terrain can reveal much about plant community structure and interspecific interactions. Despite a wealth of studies focusing on broad-scale environmental gradients, the role of fine-scale topographic nuances often remains underappreciated, particularly in subtropical settings. In our study, we explore how minute differences in microtopography—encompassing local elevation, slope, aspect, terrain position index (TPI), terrain ruggedness index (TRI), and flow direction—affect neighborhood-scale interactions among plants. We established an 11.56-hectare dynamic plot in a subtropical forest at the northern margin of China’s subtropical zone, where both microtopographic factors and neighborhood indices (density, competition, diversity) were systematically measured using 5 m × 5 m quadrats. Parameter estimation and mixed-effects models were employed to examine how microtopography influences plant spatial patterns, growth, and competitive dynamics across various life stages. Our findings demonstrate that aspect and TPI act as key drivers, redistributing light and moisture to shape conspecific clustering, heterospecific competition, and tree growth. Remarkably, sun-facing slopes promoted sapling aggregation yet intensified competitive interactions, while shaded slopes maintained stable moisture conditions that benefited mature tree survival. Moreover, in contrast to broader-scale observations, fine-scale TRI was associated with reduced species richness, highlighting scale-dependent heterogeneity effects. The intensification of plant responses with life stage indicates shifting resource demands, where light is critical during early growth, and water becomes increasingly important for later survival. This study thus advances our multiscale understanding of forest dynamics and underscores the need to integrate fine-scale abiotic and biotic interactions into conservation strategies under global change conditions. Full article

Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.) forests are a vital forest type in subtropical China. This study investigates the diversity, floristic composition, and phylogenetic structure of understory vegetation in these bamboo forests within evergreen broad-leaved forests of eastern subtropical China. Using grid-based sampling, we calculated species diversity and phylogenetic indices, and employed correlation analysis, redundancy analysis, and structural equation modeling to assess the effects of canopy closure, soil properties, and topography. The understory exhibited high species richness, with shrub layer demonstrating phytogeographic characteristics predominantly associated with tropical distribution types, while the herbaceous layer is characterized by temperate distribution types. Canopy closure and environmental factors significantly influenced shrub diversity, showing a clustered phylogenetic structure (NTI > 0, NRI > 0) and a negative correlation with species diversity. In contrast, the herb layer displayed a divergent phylogenetic structure (NTI < 0, NRI < 0), shaped by neutral stochastic processes, reflecting endemic taxa and interspecific interactions. These findings emphasize the need for targeted management practices to conserve understory biodiversity, focusing on enhancing floristic and phylogenetic diversity while protecting endemic species and their ecological interactions. Full article

Nightlily (Hemerocallis citrina Baroni) is an important vegetable with edible floral organs. It possesses considerable economic value due to its edibility, ornamental, and medicinal properties. However, the genetic linkage map construction and quantitative trait locus (QTL) mapping of nightlily have not been performed. This study used two varieties ‘Dongzhuanghuanghua’ and ‘Chonglihua’ of nightlily as cross parents to establish an intraspecific hybridization population of 120 F₁ progenies. The ‘Datonghuanghua’ (female) variety of nightlily and ‘Lullaby Baby’ (male) variety of daylily were selected to construct an interspecific hybridization population of 55 F₁ progenies. A total of 965 expressed sequence tag–simple sequence repeats (EST-SSRs), along with 20 SSR markers from various sources, were used for genetic mapping. Among these markers, CT/TC (9.24%) of the dinucleotide and GGA/GAG/AGG (4.67%) of the trinucleotide repeat motifs were most abundant. In the intraspecific hybridization genetic map, a total of 124 markers were resolved into 11 linkage groups, with a total map length of 1535.07 cM and an average interval of 12.38 cM. Similarly, the interspecific hybridization map contained 11 linkage groups but with 164 markers, a total map length of 2517.06 cM, and an average interval of 15.35 cM. The two constructed maps had 48 identical markers and demonstrated good collinearity. The collinearity analysis showed that 161 markers hit the genomic sequence of the published H. citrina genome, indicating that the two constructed genetic maps had high accuracy. Phenotypic data were investigated over two consecutive years (2018 and 2019) for flower bud fresh weight, dry weight, and bud length in two hybridization populations. A total of nine QTLs associated with flower bud-related traits were identified, among which those located on linkage group 8 of the intraspecific genetic map and linkage group 4 of the interspecific genetic map showed good stability. All nine QTLs had LOD values of not less than 4 and PVE values of not less than 15% over two years. This is the first report about the intra- and interspecific genetic map construction and QTL mapping of the flower bud-related traits in nightlily based on a genetic map. The results promote marker-assisted breeding and offer insights into the mechanisms underlying important traits of the genus Hemerocallis. Full article