Diversity Structure Research Articles

Exploring the genetic diversity and population structure of an ancient hexaploid wheat species Triticum sphaerococcum using SNP markers

BackgroundUnderstanding genetic diversity and population structure is crucial for strategizing and enhancing breeding efficiency. Wheat, a globally cultivated crop, is a significant source of daily calories for humans. To overcome challenges such as extreme climatic fluctuations, stagnant yields, and diminishing genetic variation, it is essential to develop diverse germplasms with new alleles. Triticum sphaerococcum, an underutilized ancient hexaploid wheat species, shows promise for contributing beneficial alleles. However, the genetic diversity of its germplasms remains unstudied. This is the first report where we have examined the genetic diversity and population structure of 116 T. sphaerococcum accessions using a 35 K SNP Array. The objective of this study is to apply these findings to improve wheat breeding programs.ResultsAnalysis of the population’s genetic structure identified four potential subpopulations, which was supported by principal coordinate analysis. Allele neutrality tests showed an abundance of intermediate genotypes, suggesting that many beneficial alleles are maintained through balancing selection. Among the three subgenomes, subgenome B exhibited the highest genetic diversity. AMOVA (Analysis of Molecular Variance) revealed significant variation both among (35%) and within (65%) the four subpopulations. The high genetic differentiation between subpopulations was corroborated by a moderate level of haploid migrant numbers (Nm = 1.286), indicating sufficient gene flow. SP4 emerged as the most diverse subpopulation, showing the highest values for allelic pattern indices due to its larger size and higher percentage of polymorphic loci. The D subgenome displayed a faster linkage disequilibrium (LD) decay rate compared to the A and B subgenomes. Haplotype block analysis identified 260 haplotype blocks of varying sizes distributed across the genome.ConclusionsThis research demonstrates that Indian dwarf wheat accessions, sourced from three distinct gene banks and local collections, possess considerable genetic diversity. These germplasm collections offer valuable opportunities to investigate their unexplored genetic potential. They can be utilized in wheat improvement initiatives to tackle both present and future breeding challenges. Furthermore, these accessions can introduce new alleles to broaden the genetic base of modern wheat varieties, enhancing their overall diversity.

Biodiversity and distribution of zoobenthos in the ecological water replenishment area of the Yellow River estuary coastal wetland revealed by eDNA metabarcoding.

The coastal wetland of the Yellow River Estuary, one of China's largest wetlands, is essential for biodiversity conservation and ecosystem services. Ecological water replenishment, a typical wetland restoration measure in the Yellow River Delta, has significantly impacted the habitat of zoobenthos, which are critical indicators of ecosystem health and water quality. However, the community characteristics of zoobenthos in this coastal wetland are poorly understood. This study utilized eDNA metabarcoding to assess the diversity and community structure of zoobenthos in the ecological water replenishment area of Yellow River Estuary Coastal Wetland. Zoobenthos from 174 families were identified, with 307 species recognized at the generic level, significantly more than those identified through traditional morpho-taxonomic approaches. Salinity emerged as a crucial factor in shaping these ecosystems. Contrary to expectations, in this study, brackish water exhibited the lowest species richness compared to freshwater and seawater, which may be attributed to local environmental stressors and fluctuating salinity conditions in the Yellow River Estuary. Environmental factors such as salinity, organic matter, and nutrient elements significantly influence the composition and distribution of zoobenthos. Specifically, cations, particularly Mg2⁺ and Ca2⁺, have a more substantial impact on zoobenthos than anions. Our results provide crucial information on zoobenthic biodiversity within ecological water replenishment areas, offering insights into the ecological dynamics and environmental factors shaping zoobenthos communities under ecological management.

Molecular identification, genetic diversity, and secondary structure predictions of Physalis species using ITS2 DNA barcoding

BackgroundThe genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.MethodologyPhysalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.ResultsThe success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.ConclusionsOur study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.

16S rRNA Sequencing Analysis Uncovers Dose-Dependent Cupric Chloride Effects on Silkworm Gut Microbiome Composition and Diversity

Copper-based pesticides are extensively used in agriculture, yet their impacts on beneficial insects remain poorly understood. Here, we investigate how cupric chloride exposure affects the gut microbiome of Bombyx mori, a model organism crucial for silk production. Using 16S rRNA sequencing, we analyzed the gut bacterial communities of fifth-instar silkworm larvae exposed to different concentrations of cupric chloride (0, 4, and 8 g/kg) in an artificial diet. The high-dose exposure dramatically altered the microbial diversity and community structure, where the Bacteroidota abundance decreased from 50.43% to 23.50%, while Firmicutes increased from 0.93% to 18.92%. A network analysis revealed complex interactions between the bacterial genera, with Proteobacteria and Firmicutes emerging as key players in the community response to copper stress. The functional prediction indicated significant shifts in metabolic pathways and genetic information processing in the high-dose group. Notably, the low-dose treatment induced minimal changes in both the taxonomic composition and predicted functions, suggesting a threshold effect in the microbiome response to copper exposure. Our findings provide novel insights into how agricultural chemicals influence insect gut microbiota and highlight potential implications for silkworm health and silk production. This work contributes to understanding the ecological impacts of copper-based pesticides and may inform evidence-based policies for their use in sericulture regions.

The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani.

Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes and Cyanobacteria, which could be attributed to pollution and eutriphication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.

Analyses of the Genetic Diversity and Population Structures of Sporothrix spp. Clinical Isolates from Paraíba, Brazil

Sporotrichosis is a subcutaneous mycosis of global distribution, capable of affecting both humans and animals, and caused by species of the genus Sporothrix spp. This study aimed to evaluate the genetic diversity and mating type distribution of clinical isolates of human sporotrichosis in Paraíba, Brazil, to better understand the population structure, epidemiology, and diversification of this pathogen, as well as to explore possible transmission routes. Methods: A total of 36 clinical isolates were morphologically identified, and clinical and demographic data were collected. Fungal DNA extraction was then performed, followed by species-specific PCR using markers targeting the calmodulin gene. The mating type idiomorph of the species was identified by PCR using primers targeting the MAT1-1 and MAT1-2 loci. Amplified Fragment Length Polymorphism (AFLP) was used to evaluate the genetic variability of Sporothrix spp. Results: The distribution of the disease identified that all cases occurred in João Pessoa and adjacent cities. From the 36 isolates, the majority (75%) being affected females, a prevalent occurrence of the lymphocutaneous form, and 98% zoonotic transmission were confirmed. Micro- and macromorphological structures were similar to each other, confirming Sporothrix spp. All isolates were confirmed as S. brasiliensis and the presence of a single sexual idiomorph, MAT1-2, was detected. The AFLP results indicate the possibility of the circulation of one or two genetic groups in João Pessoa and the metropolitan region. Conclusions: To our knowledge, this is the first time isolates in the Paraíba state are genetically characterised, all identified as Sporothrix brasiliensis. It is likely that this species in Paraiba originated from Rio de Janeiro, as all they possess the MAT1-2 idiomorph, indicating low intergenotypic variation.

Effects of Different Fertilization Treatments on Bacterial Community and Citrus Quality in Yellow Soils of the Yunnan-Guizhou Plateau

To investigate the intrinsic driving mechanism of citrus yield and quality enhancement under different fertilizer applications, a field experiment was conducted to study the effects of biochar （SW）, organic fertilizer （YJ）, farmyard manure （NJ）, chemical fertilizer （HF）, and no fertilizer as the control （CK） on soil physical and chemical properties, bacterial community characteristics, and citrus quality of citrus orchards in the yellow soil area of the Yunnan-Guizhou Plateau. The results showed that compared with those in the CK treatment, the yield, single fruit weight, edible rate, juice rate, vitamin C content, and soluble solids of citrus increased under the different fertilization treatments. In contrast, the titratable acid content of citrus decreased, resulting in an increase in the solid-acid ratio of citrus. Among the different fertilization treatments, the most significant effective treatment was SW. The SW and YJ treatments significantly increased the soil pH value, while the HF treatment decreased soil pH. Different fertilization treatments could increase the contents of soil organic matter, hydrolyzable nitrogen, available phosphorus, and available potassium. The SW treatment exhibited the most obvious effect on the contents of soil hydrolyzable nitrogen, available phosphorus, and available potassium. The YJ treatment exhibited the most obvious effect on the soil organic matter content. The different fertilization treatments significantly affected soil bacterial community diversity and community structure, among which the SW treatment significantly increased the soil Chao1 index, observed species index, and Shannon index； optimized soil bacterial community structure； and made the bacterial symbiotic network simple and stable. By contrast, the HF treatment significantly decreased the soil Chao1 index, observed species index, and Simpson index and had less effect on bacterial community structure. Redundancy analysis showed that soil available potassium （96.47%）, Chao1 index （73.80%）, and Chujaibacter （55.92%） were the key factors in improving citrus yield and quality. Variance decomposition analysis indicated that the soil bacterial community structure was the largest contributor （17.00%） to the improvement in citrus yield and quality. In conclusion, fertilization can effectively improve soil physical and chemical properties, increase soil nutrient supply level, optimize bacterial community structure, and improve citrus yield and quality. Of these, biochar can be used as a priority for the fertilization and improvement of the soil in citrus orchards in the yellow soil area of the Yunnan-Guizhou Plateau.

Assessment of genetic diversity and population structure analysis in Himalayan garlic genotypes from Sikkim using SSR markers.

Garlic (Allium sativum L.) is an important crop with significant medicinal and culinary uses. Understanding the genetic diversity and population structure of Himalayan garlic genotypes from Sikkim is crucial for effective breeding and conservation efforts. This study aims to analyze the genetic diversity among 60 Himalayan garlic genotypes collected from various altitudinal locations of Sikkim, India, using 27 Simple Sequence Repeats (SSR) markers. The genetic diversity was assessed using SSR markers, which revealed substantial variation among the genotypes. The number of alleles (Na) ranged from 1.13 to 2.00, while the major allele frequency (MAF) varied from 0.672 to 0.963. The observed heterozygosity (Ho) ranged from 0.0667 to 0.475, indicating moderate genetic diversity. Population structure analysis using STRUCTURE software grouped the genotypes into three distinct sub-populations, suggesting genetic differentiation not solely based on leaf morphology. Analysis of Molecular Variance (AMOVA) showed that genetic variation was more significant among individuals within populations (41%) than among populations (16%). UPGMA dendrogram and Principal Coordinates Analysis (PCoA) further confirmed the genetic relationships among the genotypes. This study reveals significant genetic diversity among Himalayan garlic genotypes from Sikkim, with clear genetic differentiation observed within and between populations. The results highlight the importance of both leaf morphology types and genetic structure in understanding the genetic basis of phenotypic variation in garlic. The finding provides valuable insights for future breeding programs and conservation strategies, emphasizing the need to consider morphological and genetic data for effective germplasm management and improvement of garlic cultivars.

Whole-genome resequencing to investigate the genetic diversity and mechanisms of plateau adaptation in Tibetan sheep

IntroductionTibetan sheep, economically important animals on the Qinghai–Tibet Plateau, have diversified into numerous local breeds with unique characteristics through prolonged environmental adaptation and selective breeding. However, most current research focuses on one or two breeds, and lacks a comprehensive representation of the genetic diversity across multiple Tibetan sheep breeds. This study aims to fill this gap by investigating the genetic structure, diversity and high-altitude adaptation of 6 Tibetan sheep breeds using whole-genome resequencing data.ResultsSix Tibetan sheep breeds were investigated in this study, and whole-genome resequencing data were used to investigate their genetic structure and population diversity. The results showed that the 6 Tibetan sheep breeds exhibited distinct separation in the phylogenetic tree; however, the levels of differentiation among the breeds were minimal, with extensive gene flow observed. Population structure analysis broadly categorized the 6 breeds into 3 distinct ecological types: plateau-type, valley-type and Euler-type. Analysis of unique single-nucleotide polymorphisms (SNPs) and selective sweeps between Argali and Tibetan sheep revealed that Tibetan sheep domestication was associated primarily with sensory and signal transduction, nutrient absorption and metabolism, and growth and reproductive characteristics. Finally, comprehensive analysis of selective sweep and transcriptome data suggested that Tibetan sheep breeds inhabiting different altitudes on the Qinghai–Tibet Plateau adapt by enhancing cardiopulmonary function, regulating body fluid balance through renal reabsorption, and modifying nutrient digestion and absorption pathways.ConclusionIn this study, we investigated the genetic diversity and population structure of 6 Tibetan sheep breeds in Qinghai Province, China. Additionally, we analyzed the domestication traits and investigated the unique adaptation mechanisms residing varying altitudes in the plateau region of Tibetan sheep. This study provides valuable insights into the evolutionary processes of Tibetan sheep in extreme environments. These findings will also contribute to the preservation of genetic diversity and offer a foundation for Tibetan sheep diversity preservation and plateau animal environmental adaptation mechanisms.

Variation in coral rubble cryptofauna is scale-dependent and driven by small-scale habitat characteristics

Motile cryptofauna living in dead coral rubble represent some of the greatest biodiversity and basal energetic resources on tropical coral reefs. Yet we know relatively little about how and why coral rubble cryptofauna communities change over space and time. As human impacts increase the degradation of living hard corals to dead coral rubble on many reefs worldwide, understanding the communities that will succeed in these degraded environments and the factors paramount to their success becomes increasingly central to coral reef ecology and conservation. Using a remote and uninhabited oceanic atoll in the Pacific Ocean, we quantified the natural spatial variability in motile cryptofauna diversity and community structure in coral rubble across scales (m to km) and tested whether variability at smaller scales could be explained by gradients in microhabitat. We show that coral rubble cryptofauna communities are most variable at intra-site scales (m) rather than inter-site scales (100s m) or between reef zones (km scales). We also show that a substantial amount of variation in cryptofauna density (55%) and phyla-level community structure (31%) is explained by small-scale habitat characteristics, specifically the substrate type below the rubble and the variability in macroalgal cover on individual rubble pieces. Our findings highlight the need to study small-scale processes that are relevant to motile cryptofauna and their community interactions if we are to elucidate the structuring forces of these diverse cryptic assemblages on coral reefs.

Piercing the Corporate Veil and Its Variations (On the Example of German, American, and English Legal Practices)

The capital form of a corporate entity is currently the most prevalent form of conducting business worldwide, driven by its diverse, profitable, convenient, and investor-oriented structure. Specifically, the privilege of limited liability encourages interested parties to boldly diversify their business portfolios without the risk of losing personal assets. However, this fundamental principle of corporate law also has exceptions, known as piercing the corporate veil. Most developed countries agree that in certain cases, it is unavoidable and necessary to invoke this exceptional measure to maintain or restore justice. This pertains to the personal liability of partners in cases of "abuse of rights" within the corporate structure. This paper examines the concept of piercing the corporate veil and the various approaches developed and established in different countries. Following the introduction, there is a brief historical overview of the formation of this doctrine, which thematically encompasses the essence of legal entities—legal fictions—and their independent, separate legal status, logically leading to the possibility of disregarding this separation through exceptional measures. It is crucial to highlight the legal foundations that legitimize the application of traditional piercing of the veil in the judicial practices of different countries, making the essence of the sub-types of this doctrine comprehensible to the reader. Additionally, the research aims to showcase the similarities and differences with variations such as reverse veil piercing in American law and the doctrine of lifting the veil in English law. Furthermore, the paper presents the latest approaches of German courts regarding the application or restraint from piercing the veil, where the aforementioned American/English terminology is not used, yet the approaches are fundamentally closely related. The conclusion summarizes the results of the research conducted around the topics discussed in the article.

Environmental concentrations of the fungicide tebuconazole alter microbial biodiversity and trigger biofilm-released transformation products

Freshwater microbial communities are integral components of riverine biodiversity. The ecological effects of toxic chemical pollutants, such as fungicides (e.g., tebuconazole), on microbial abundance and diversity are needed for risk assessment and regulation. The emergence of RNA metabarcoding approaches allow us to describe at unprecedented resolution the microbial diversity of the active part of a microbial community. Our study assesses the ecotoxicological impact of chronic and acute tebuconazole exposures on fungal, bacterial, and algal biomass and biodiversity of aquatic fungi and bacteria in stream biofilms using an RNA metabarcoding approach. In addition, the study uses HPLC-MS to evaluate the capability of biofilms to metabolize tebuconazole. Natural biofilm communities from a Swedish stream were exposed chronically (24 days) and acutely (96 h) to environmental concentrations of tebuconazole (10 and 100 μg/L) in microcosms conditions. The diversity and community structure of fungi and bacteria was assessed by ITS2 and 16S cDNA amplicon-sequencing, respectively. Biofilms chronically exposed to tebuconazole produced and released unidentified transformation products into the water column, suggesting a biotransformation capability following 24 days of uninterrupted exposure. The fungal biomass markedly decreased by a biomass loss of 40% when chronically exposed to 10 μg/L, and 60% when chronically exposed to 100 μg/L. Bacterial and algal biomass remained comparable with the controls in all tebuconazole treatments. Fungal and bacterial alpha diversity metrics were not significantly impacted, although a decreasing trend in fungal richness was observed with the treatments. However, beta diversity was significantly impacted in both fungal and bacterial compartments. Chronic exposures resulted in a shift in community composition, where taxa potentially more tolerant to tebuconazole (i.e. Lecanoromycetes) replaced more sensitive taxa (i.e. Malasseziomycetes). This study indicates that tebuconazole at environmental concentrations might pose a risk to freshwater systems, mainly due to its high toxicity to fungi.

Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.

Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties. To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups. The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers. This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.

Comparative analysis of community composition and network structure between phyllosphere endophytic and epiphytic fungal communities of Mussaenda pubescens.

The phyllosphere constitutes a critical habitat for microorganisms, exerting profound influences on host vitality, developmental dynamics, reproductive functions, and stress resilience. However, the diversity and network structure of endophytic and epiphytic fungal communities within this microecosystem have not been thoroughly explored. In this investigation, high-throughput sequencing technologies were employed to assess the diversity, community composition, and network structure of endophytic and epiphytic fungal communities associated with Mussaenda pubescens across six geographically distinct locations in Southeast China. The results revealed significant differences in community composition and diversity between endophytic and epiphytic fungi, with pronounced geographical variation observed within these phyllosphere fungal communities. Network analysis indicated that epiphytic fungal networks possess enhanced complexity compared with their endophytic counterparts, although the latter exhibit greater network stability. Moreover, stochastic processes were identified as pivotal in shaping the composition of these fungal communities. This research substantially enriches our comprehension of the diversity and organizational mechanisms of phyllosphere fungal communities, providing novel insights into the modalities of species coexistence and the stability of community equilibrium within ecosystems.IMPORTANCEThis study employs high-throughput sequencing technologies to explore the fungal communities within the phyllosphere of Mussaenda pubescens across Southeast China, offering significant insights into plant mycobiome. It demonstrates geographical variations in these fungal communities, with epiphytic fungi exhibiting more complex interaction networks compared with the endophytic fungi. Crucially, the research indicates that stochastic processes play a substantial role in the composition of fungal communities. These findings enhance our comprehension of plant-associated microecosystems and underscore the intricate interplay of randomness in maintaining ecosystem stability and diversity.

How does group availability affect distributional equity of outdoor physical activity facilities? Evidence from Nanjing, China

ABSTRACT Most studies have measured the distributional equity of outdoor physical activity facilities (OPAFs) considering the unified accessible quantity and ignored the disparity of group availability. This study adopts a multidimensional approach to measure the distributional equity of OPAFs from the levels of city and residential units. Considering the old city of Nanjing as a sample, we first categorised the existing OPAFs into equipped sites, multifunctional sites, and trails and quantified the size and composition of three age groups in each residential unit. Second, we modularised OPAFs’ services through which each service type corresponds to one physical activity (PA) module and identified each module’s available groups. Third, we adopted accessibility, diversity, and supply-demand structure consistency (SDSC) to measure the distributional equity of OPAFs at two levels. The results showed that at the city level, the gap in the diversity of the modules between Group C (60 years old and above) and Groups A (15–59 years old) and B (60 years old and above) was more significant than that of accessible quantity, while the mean SDSC for Group C was much higher than those for Groups A and B. At the unit level, the differences in OPAFs’ group availability generated more significant differences in distributing diversity and SDSC than in the distribution of accessibility. Compared to traditional assessments, this tool integrates the disparity of OPAFs’ availability among different groups into the equity measurement, which can enhance the analytical precision and granularity and provide tailored OPAF optimisation strategies.

Assessment of breeding nuclei contributions to the genetic diversity and population structure of the Cyprus Chios sheep

Cyprus, facing climate change and desertification, has Europe’s second highest population growth. Halloumi cheese’s Protected Designation of Origin status boosted goat and sheep milk demand. Optimizing primary sector production is key to balancing food production and environmental sustainability. The present study aims to explore the genetic diversity and population structure of Cyprus Chios sheep, as well as the impact of existing breeding nuclei on the breed’s gene pool. Two breeding nuclei aiming to preserve genetic diversity and boost local milk production and four private farms were sampled. Genome-wide data using Illumina 50 K arrays were generated, analyzing over 1000 animals from six farms. At least three distinct genetic groups were identified, two of which are represented by the nuclei’s distinct genetic profiles and a third was found in private farms. Calculated metrics indicate a negative correlation of gene flow with geographic distance in case of the Eastern nucleus. Presented results support recent, though limited inbreeding (mean FROH=0.046), compared to other commercial breeds. Estimated effective population size reveals a stabilizing trend to a relatively high number (Ne ~ 200) which indicates relatively high diversity that allows further genetic improvement. Revealed genomic diversity highlights the necessity of such exploration before effectively implementing genomic evaluation programs.

Genetic Diversity and Structure of the Darkfin hind (Cephalopholis urodeta) in the Spratly Islands, Vietnam

The darkfin hind, Cephalopholis urodeta, is a commercially valuable reef fish species inhabiting the ecologically important Spratly Islands. Understanding this species’ genetic diversity and population structure is crucial for developing effective conservation strategies, particularly given the increasing pressures on coral reef ecosystems. This study investigated the genetic diversity and population structure of C. urodeta within the Spratly archipelago using mitochondrial COI and Cyt b gene markers. We analyzed 30 individuals for COI and Cyt b, revealing high levels of haplotype diversity (Hd=0.9563±0.0226 for COI; Hd=0.9402±0.0229 for Cyt b). However, despite this high overall diversity, our analyses also revealed significant genetic structuring within the archipelago, suggesting restricted gene flow among some populations. This structuring is likely influenced by the complex oceanographic currents in the region and the spatial distance between reefs, which can limit larval dispersal. These findings highlight the need for spatially explicit conservation and management strategies for C. urodeta in the Spratly Islands. Recognizing the genetic differentiation within the archipelago and implementing management measures tailored to specific zones will be crucial for preserving genetic diversity, maintaining connectivity, and ensuring the long-term sustainability of this important resource.

Floristic Checklist and Conservation Status of Woody Species in Relation to Gradient in Osomba Hills of Cross River National Park, Nigeria

Extant floristic data checklist and conservation status of woody species were determined in relationship with elevation gradient in Osomba hills of the Cross River National Park, Oban division. A total of 78 species of woody plants in 31 families were identified. The family Fabaceae recorded the highest number of species (13) followed by Malvaceae with 8 species, Annonaceae and Euphorbiaceae had 6 species each, Apocynaceae had 5 species, Irvingiaceae, Ochnaceae, and Olacaceae had 3 species each, Buseraceae, Clusiaceae, Combretaceae, Ebenaceae, Moraceae, Myristicaceae, Rubiaceae and Sapotaceae had 2 species each, Anacardiaceae, Anisophylleaceae, Asteraceae, Bombacaceae, Cecropioaceae, Gentianaceae, Hyperiaceae, Lecythiddaceae, Meliaceae, Passifloraceae, Polygalaceae, Rhizophoraceae, Rutaceae, Simaroubaceae and Violaceae had 1 species each. The investigation of the conservation status of the species using the IUCN redlist data revealed that 1 species (Berlinia korupensis Mackinder& Burgt) is critically endangered (CR), 6 species are near threatened (NT), 7 species are vulnerable (VU), 7 species are not evaluated (NE) and 54 species are of least concerned (LC). Life forms identified included 14 shrubs and 64 tree species in the study area. In the dry season, a total of 29 species including 5 shrubs and 24 trees were identified, while in the rainy season, a total of 57 species including 10 shrubs and 47 trees were identified. Plant diversity along elevation gradient was generally heterogeneous and could be influenced by many factors such as climate, spatial heterogeneity, biotic processes, and evolutionary history. Overall species richness of both shrubs and trees decreased along the elevation gradient whereas the tree species increased with the elevation. Anthropogenic factors and accessibility to the mountainous terrain could also contribute to the patterns of the plant diversity and tree community structure in the study area. Common anthropogenic activities observed were timber harvesting, firewood collections, and harvesting of plants for food and medicinal uses.

The Elevational Distribution Patterns of Plant Diversity and Phylogenetic Structure Vary Geographically Across Eight Subtropical Mountains.

Mountains have been recognized as biodiversity hotspots and possess strong elevational gradients. Whether these gradients exhibit similar characteristics in the multidimensional diversity patterns across different mountain ranges is a subject of inquiry. Exploring the elevational patterns of the diversity and phylogenetic information of plant species in the different subtropical mountains is necessary. Here, we compiled the elevational patterns of plant diversity occurring in the eight subtropical mountains of China and focused on the assessment of the patterns and determinants of the multi-dimensional diversity and phylogenetic structure in different mountains. We also detected the elevational patterns and their relationship between different groups. The results indicate two main patterns of multi-dimensional diversity: monotonic decrease and hump-shaped, along with the area effect on the species diversity. There is a strong positive link between the non-native and native species of species richness, and significant differences in phylogenetic structure's elevational distribution. We did not find the same rule in the mountains that the plant species in the lowlands indicate phylogenetic overdispersion, and the species in the higher elevation regions indicate phylogenetic clustering. We found that the plants' diversity peak is related to the mountains size, and this result showed that we should pay more attention to the conservation of plant communities in the higher elevation regions for the higher mountains. This study suggested that we should take different protective measures for the subtropical mountains: the lowland regions should be paid more attention in Mt. Lushan (LS), Mt. Guanshan (GS), Mt. Huanggang (HG), and Mt. Fanjing (FJ), and the middle-altitude regions should be of concern for other mountains. This study helps to better understand the elevational gradients of species diversity on different scales and provides supporting scientific basis for biodiversity conservation in the subtropical mountain regions.

Recovery of intestinal microbial community in Penaeus vannamei after florfenicol perturbation

The concept and application of probiotic intervention for restoring intestinal microbial dysbiosis induced by antibiotics in aquaculture are still in early stages. This study aimed to investigate potential responses of various recovery strategies, including natural recovery and probiotic intervention, in restoring the growth and intestinal microbial community of Penaeus vannamei following florfenicol perturbation. The basal diet (control, CN) was supplemented with florfenicol (FC) or Lactobacillus plantarum W2 (LM) throughout the entire feeding trial. Meanwhile, the basal diet was supplemented with florfenicol for 7 days, followed by a period without florfenicol (natural recovery, FB), or with live strain W2 (probiotic recovery, FM), for a duration of 35 days. Results indicated that dietary supplementation of strain W2, whether continuous or following florfenicol perturbation, along with continuous florfenicol supplementation, significantly enhanced the growth performance of shrimp. Early natural recovery and probiotic intervention did not induce significant alterations in microbial diversity and community structure. Florfenicol perturbation resulted in a decrease in the abundance of potentially beneficial bacteria in intestinal microbial community of shrimp. However, both probiotic intervention and natural recovery strategies gradually reduced the abundance of potentially pathogenic bacteria while increasing the abundance of potentially beneficial ones. The robustness of microbial network decreased during florfenicol perturbation, showed gradual improvement during probiotic recovery, and remained relatively low during natural recovery and continuous florfenicol supplementation. Moreover, the microbial community composition in intestinal habitat significantly differed under various recovery strategies compared to the control. Notably, the microbial community composition of intestinal habitat following probiotic recovery exhibited greater similarity to that of continuous strain W2 supplementation without florfenicol perturbation. In summary, dietary supplementation of florfenicol perturbed intestinal microbial community stability of shrimp, whereas probiotic intervention and natural recovery facilitated the attainment of new stable states by altering keystone taxa. Considering intestinal microbial community stability of shrimp, the recovery of microbial community through probiotic intervention appears to be more effective than natural recovery.