Search Results (605)

Elucidating the coexistence mechanisms of rapidly diverging species has long been a challenge in evolutionary biology. Genome-wide polymorphic loci are expected to provide insights into the speciation processes of these closely related species. This study focused on seven Chinese sclerophyllous oaks, represented by Quercus spinosa, Quercus aquifolioides, Quercus rehderiana, Quercus guyavifolia, Quercus monimotricha, Quercus semecarpifolia, and Quercus senescens, employing 27,592 single-nucleotide polymorphisms to examine their phylogenetic relationships at the genomic level. Combined with genetic structure analysis, phylogenetic trees revealed that the genetic clustering of individuals was influenced by both geographic distance and ancestral genetic components. Furthermore, this study confirmed the existence of reticulate evolutionary relationships among the species. Frequent gene flow and introgression within the seven species were primarily responsible for the ambiguous interspecies boundaries, with hybridization serving as a major driver of reticulate evolution. Additionally, the seven species exhibited distinct differences in niche occupancy. By reconstructing the climatic adaptability of ancestral taxonomic units, we found that the climatic tolerance of each species displayed differential responses to 19 climatic factors. Consequently, ecological niche differentiation and variations in habitat adaptation contributed to the preservation of species boundaries. This study provides a comprehensive understanding of the speciation processes in rapidly diverging genera and underscores the significance of both genetic and ecological factors in the formation and maintenance of species boundaries. Full article

In recent years, phylogenomic approaches have significantly deepened our understanding of moss diversity. These techniques have uncovered numerous previously overlooked species and provided greater clarity in resolving complex taxonomic relationships. In this context, the genus Rehubryum is particularly outstanding, because of its close morphological similarity to both Ulota and Atlantichella. The challenges posed by its segregation are addressed in this study, which integrates morphological and molecular data to reassess the circumscription of Rehubryum and its phylogenetic placement within the subtribe Lewinskyinae. Our results support the recognition of a new species, R. kiwi, and show that its inclusion within the genus further complicates the morphological delimitation of Rehubryum from Ulota, as both genera are distinguishable by only two consistent gametophytic characteristics: a submarginal leaf band of elongated cells, and the presence of geminate denticulations in the margins of the basal half of the leaf. Moreover, R. kiwi challenges the current morphological circumscription of Rehubryum itself, as it overlaps in key characteristics with its sister genus Atlantichella, rendering their morphological separation untenable. The striking interhemispheric disjunction between Rehubryum and Atlantichella raises new questions about long-distance dispersal and historical biogeography in mosses, despite these complexities at the generic level. Nevertheless, species-level distinctions remain well defined, especially in sporophytic traits and geographic distribution. These findings highlight the pervasive cryptic diversity within Orthotrichaceae, underscoring the need for integrative taxonomic frameworks that synthesize morphology, molecular phylogenetics, and biogeography to resolve evolutionary histories. Full article

Background: Lower phylogenetic species are known to rebuild cut-off caudal parts with regeneration of the central nervous system (CNS). In contrast, CNS regeneration in higher vertebrates is often attributed to immaturity, although this has never been conclusively demonstrated. The emergence of stem cells and their effective medical applications has intensified research into spinal cord regeneration. However, despite these advances, the impact of clinical trials involving spinal cord-injured (SCI) patients remains disappointingly low. Long-distance regeneration has yet to be proven. Methods: Our study involved a microsurgical dorsal myelotomy in fetal rats. The development of pioneering long primary afferent axons during early gestation was examined long after birth. Results: A single cut triggered the intrinsic ability of the dorsal root ganglion (DRG) neurons to reprogram. Susceptibility to hypoxia caused the axons to stop developing. However, the residual axonal outgrowth sheds light on the intriguing temporal and spatial events that reveal long-distance CNS regeneration. The altered phenotypes displayed axons of varying lengths and different features, which remained visible throughout life. The previously designed developmental blueprint was crucial for interpreting these enigmatic features. Conclusions: This research into immaturity enabled the exploration of the previously impenetrable domain of early life and the identification of a potential missing link in CNS regeneration research. Central axon regeneration appeared to occur much faster than is generally believed. The paradigm provides a challenging approach for exhaustive intrauterine reprogramming. When the results demonstrate pre-clinical effectiveness in CNS regeneration research, the transformational impact may ultimately lead to improved outcomes for patients with spinal cord injuries. Full article

Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples from naturally infected pigs in a commercial farm in Minas Gerais, Brazil. IAV RNA was detected in 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses from feces and effluent samples. Whole-genome sequencing revealed co-circulation of enzootic pH1N1 clade #2 (HA) and pN1 clade #4 (NA), alongside human-origin H3N2 sequences clustering within clade 3C.2a1b.2a.2a.1, and N2 segments related to pre-3C human lineages from 2001 to 2002. Phylogenetic and p-distance analyses support both recent reverse zoonosis and historical transmission events. Detection of complete HA/NA sequences from rectal swabs and treated effluent further emphasizes the surveillance value of non-respiratory matrices. The integration of respiratory and fecal/environmental sampling appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond. Full article

China’s southwestern karst landscapes support remarkable cavefish diversity, especially within Sinocyclocheilus, the world’s largest cavefish genus. Using integrative taxonomic methods, we describe Sinocyclocheilus wanlanensis sp. nov., found in a subterranean river in Guizhou Province. This species lacks horn-like cranial structures; its eyes are either reduced to a dark spot or absent. It possesses a pronounced nuchal hump and a forward-protruding, duckbill-shaped head. Morphometric analysis of 28 individuals from six species shows clear separation from related taxa. Nano-CT imaging reveals distinct vertebral and cranial features. Phylogenetic analyses of mitochondrial cytb and ND4 genes place S. wanlanensis within S. angularis group as sister to S. bicornutus, with p-distances of 1.7% (cytb) and 0.7% (ND4), consistent with sister-species patterns within the genus. Sinocyclocheilus wanlanensis is differentiated from S. bicornutus by its eyeless or degenerate-eye condition and lack of bifurcated horns. It differs from S. zhenfengensis, its morphologically closest species, in having degenerate or absent eyes, shorter maxillary barbels, and pelvic fins that reach the anus. The combination of morphological and molecular evidence supports its recognition as a distinct species. Accurate documentation of such endemic and narrowly distributed taxa is important for conservation and for understanding speciation in cave habitats. Full article

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances >0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges. Full article

Diaeretiella rapae (McIntosh, 1855) is a cosmopolitan koinobiont endoparasitoid of aphids, occurring mainly on crucifers and cereals. From description, it has changed several genera and has about 20 synonyms. The specimens for this study were collected between 1989 and 2023 from sites across Europe and the Middle East. For molecular analysis, the barcode mitochondrial gene COI was used, and morphological analysis was conducted with other Aphidius species. Morphologically, D. rapae falls within the determined variability of the same characters of the genus Aphidius. Dieretiella rapae comprised 23 haplotypes with a mean genetic distance between haplotypes of 0.8%. Phylogenetically, D. rapae is nested within Aphidius species with a genetic distance of 2.1% to 11.3%, which is within the range of other Aphidius species. Our results on morphological and molecular level confirm that D. rapae belongs to the genus Aphidius. Full article

Castor fiber birulai is a subspecies of the Eurasian beaver that has a relatively small population size compared to other Castor subspecies. There is limited genetic research on this subspecies. In this study, mitochondrial cytochrome b (Cytb) and D-loop sequences were analysed in genetic samples obtained from 19 individuals residing in the Buergen River Basin, Xinjiang, China. The Cytb region presented a single haplotype, whereas three haplotypes were identified in the D-loop region. The genetic diversity within the Chinese population was low (D-loop Hd = 0.444; Pi = 0.0043), markedly lower than that observed in other geographical populations of C. fiber. Phylogenetic reconstructions and haplotype network analyses revealed substantial genetic differentiation between C. f. birulai and other Eurasian lineages (Fst > 0.95), supporting the status of C. f. birulai as a distinct evolutionary lineage. Although the genetic distance between the Chinese and Mongolian populations was relatively small (distance = 0.00269), significant genetic differentiation was detected (Fst = 0.67055), indicating that anthropogenic disturbances—such as hydraulic infrastructure and fencing along the cross-border Bulgan River—may have impeded gene flow and dispersal. Demographic analyses provided no evidence of recent population expansion (Fu’s Fs = 0.19152), suggesting a demographically stable population. In subsequent studies, we recommend increasing nuclear gene data to verify whether the C. f. birulai population meets the criteria for Evolutionarily Significant Unit classification, and strengthening cross-border protection and cooperation between China and Mongolia. Full article

This study investigates the taxonomic status, phylogenetic relationships, and genetic diversity of Japanese chestnut (Castanea crenata Siebold & Zucc.) in Liaodong, China, and across East Asia. Additionally, it evaluates core germplasm resources through cluster and population structure analyses using simple sequence repeat (SSR) marker data from 13 Castanea henryi, 18 Castanea seguinii, and 27 Castanea mollissima, and 142 Japanese chestnut resources. The results show that the East Asian Castanea genus forms a monophyletic group with distinct interspecific boundaries. Japanese chestnut and two varieties/lines of C. seguinii (187 and 170) form a sister clade, indicating a close phylogenetic relationship. All Japanese chestnut resources are divided into two branches, with considerable admixture. The genetic diversity analysis revealed that the 142 Japanese chestnut varieties/lines collectively possessed 141 allelic loci, with genetic distances (GDs) ranging from 0.429 to 0.880 with an average of 0.740. Based on unique characteristics, seven resources with distinctive features were selected as mandatory. A total of 41 core germplasm resources were finally determined using the simulated annealing method. The comparative analysis revealed that, aside from a notable difference in polymorphic information loci, the core germplasm and original germplasm showed no significant differences in other genetic diversity parameters. This indicates that the 41 core germplasm resources effectively preserve the genetic diversity of the original germplasm and have been influenced by artificial selection. This study provides a scientific basis for conserving and using C. crenata germplasm resources. Full article

Background: Clinical features of asthma are associated with differences in the lower airway microbiome. However, knowledge is limited on whether airway microbiota composition differs between individuals residing in different geographic regions and if asthma-associated differences in lower airway microbiota are similar between distinct populations. Methods: Existing 16S rRNA gene sequence data, generated from sputum collected from adults with or without asthma (n = 74) from two single-center cohort studies in the U.S. and United Arab Emirates, were re-processed for merged computational analysis using standard available tools. Potential differences between study sites, asthma status and specific clinical factors (inhaled corticosteroid use, ICS; obesity) were examined. Results: Differences in sputum bacterial composition, assessed by alpha- and beta-diversity measures, were associated with study site. Despite this, asthma-related differences were discerned in both cohorts. Specifically, sputum microbiota of asthmatic patients on ICS treatment displayed reduced bacterial phylogenetic diversity, compared to those not on ICS treatment (p = 0.006). Sputum bacterial composition also differed by obesity status (unweighted Unifrac distance PERMANOVA, p = 0.004). Specific genera were identified in both cohorts that were differentially enriched between obese vs. non-obese subjects, including Rothia and Veillonella (obesity-associated) and Campylobacter (non-obesity-associated). Conclusions: Our findings suggest clinical factors associated with differences in the lower airway microbiome in asthma may transcend variation related to geographic area of residence. Full article

Crinum thaianum, commonly known as water onion, is an endangered species which is primarily threatened by flood-control-related habitat destruction and illegal harvesting for export, resulting in a sharp population decline; its genetic data still remains poorly studied. Retrotransposon-based markers have received significant attention due to their higher potential informativeness compared to conventional marker methods in genetic diversity studies. This study focused on the screening of Ty1-copia retrotransposons, which have been widely studied and are commonly used as molecular markers in various plant species. Ty1-copia reverse transcriptase (rt) fragments were amplified using degenerate primers targeting conserved regions, followed by cloning and sequencing. Sequences were screened for rt gene homology and translated into amino acid sequences. Lineages were assigned by alignment, and phylogenetic analysis was performed for each isolated sequence with a set of well-classified rt genes. The p-distance values were calculated between the isolated sequences and their closest homologous sequences. A total of 123 isolated sequences were analyzed, representing conserved domains in the rt gene of Ty1-copia elements from C. thaianum and four other Crinum species. The results revealed sequence homology to the Ale, TAR, or Angela lineages, which showed the closest resemblance to 9, 4, and 110 isolated rt sequences, respectively. The conserved rt domain SIYGLKQA was mostly found in Angela (87.27%), while SLY/HGLKQS/L and SLYG/ELKQF/S were mostly found in Ale (66.67%) and TAR (75.00%), respectively. The p-distance values obtained from comparisons with Ty1-copia elements in other plants suggest that the Angela and TAR lineages are more evolutionarily conserved than the Ale lineage. Whilst our study sheds light on the variety of Ty1-copia retrotransposons in C. thaianum and other Crinum species, further research on additional Crinum species and other plants is required to enhance our understanding and facilitate future retrotransposon-based marker development. Full article

Flavonoid synthases (FNSs) are key enzymes catalyzing the conversion of flavanones to flavonoids, yet their functions in citrus remain functionally uncharacterized. In this study, we identified three FNSII genes in the citrus genome. Phylogenetic analysis revealed that citrus FNSII genes share the closest evolutionary distance with apple FNSII genes. Chromosomal localization demonstrated that the three FNSII genes are distributed across two out of nine chromosomes. Gene structure analysis indicated that the majority of motifs within these three FNSII genes are highly conserved. We cloned a gene called CitFNSII-1 from citrus. Transient overexpression of CitFNSII-1 in citrus leaves significantly increased flavonoid content, while simultaneous virus-induced silencing of CitFNSII-1 led to synchronously and significantly reduced gene expression levels and flavonoid content in citrus seedlings. Through the Agrobacterium rhizogenes-mediated genetic transformation system, overexpression of CitFNSII-1 was found to markedly enhance flavonoid accumulation in hairy roots, whereas knockout of CitFNSII-1 resulted in a significant decrease in flavonoid content in hairy roots. Further experiments verified an interaction between CitFNSII-1 and the Chalcone isomerase-1 (CHI-1) protein. The results demonstrated that the flavonoid accumulation patterns of CHI-1 and CitFNSII-1 are highly similar. In conclusion, this study advances the understanding of the flavonoid biosynthesis pathway in citrus and provides a theoretical foundation for molecular breeding strategies in citrus. Full article

This study examined genetic diversity in the endangered medicinal plant Celastrus paniculatus using 62 individual samples from seven natural populations in northern and northeastern Thailand to inform conservation strategies. The analysis of the nuclear internal transcribed spacer (ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) markers revealed 17 haplotypes (CpI1–CpI17) across these populations, with 15 being population-specific. The genetic diversity varied significantly among populations: CMI showed the highest diversity (Hd = 0.944 ± 0.070), while LEI and LPN displayed complete homogeneity. The haplotype network identified a central shared haplotype (CpI4), suggesting a common ancestry, with the PLK population showing a distinct genetic divergence through unique haplotypes separated by multiple mutation steps. Genetic distance calculations revealed close relationships between LEI and NPM populations (distance = 0.0004), with greater differentiation between PLK and other populations (distances > 0.005). Phylogenetic analyses confirmed the species integrity while highlighting population clusters, especially PLK in ITS analyses and LPN in rbcL analyses. This genetic structure information provides a foundation for targeted conservation planning. Results suggest that conservation efforts should prioritize both genetically diverse populations (like CMI and MKM) and genetically distinct ones (like PLK) to preserve the maximum evolutionary potential. This study delivers crucial molecular data for developing evidence-based conservation strategies to protect this valuable medicinal species from further decline. Full article

Here, the biogeographic patterns of abundant and rare bacterial taxa in lemon farmlands with different cultivation modes were examined using the dataset obtained from high-throughput sequencing. The abundant sub-communities exhibited a lower richness, a similar abundance proportion, and lower compositional variations than rare taxa. With regard to different cultivation modes, a lower richness but higher beta-diversity distance was observed in abundant bacterial taxa from greenhouse soils compared to other open field farmlands. In addition, some potential indicators, including Proteobacteria, Chloroflexi, and Bacteroidota, were found to be enriched in the abundant sub-communities in greenhouse soils. Moreover, a stronger environmental-related distance–decay of similarity was observed in abundant taxa from greenhouse soils, but in hilly-converted farmlands for rare taxa. The abundant sub-communities were more sensitive to environmental changes and more tightly phylogenetically clustered. In contrast, homogeneous selection dominated the assembly of rare taxa, which was insensitive to dispersal limitations. Soil pH was identified as the key factor to driving the assembly of soil bacterial communities, with a more deterministic and stochastic assembly for abundant and rare taxa, respectively, at the neutral environments. Full article

The structural diversity of microbial communities plays a pivotal role in microbiological research and applications. However, the study of microbial transitions has remained challenging due to a lack of effective methods, limiting our understanding of microbial dynamics and their underlying mechanisms. To address this gap, we introduce MT-tracker (microbiome transition tracker), a novel algorithm designed to capture the transitional trajectories of microbial communities. Grounded in diversity and phylogenetic principles, MT-tracker reconstructs the virtual common ancestors of microbiomes at the community level. By calculating distances between microbiomes and their ancestors, MT-tracker deduces their transitional directions and probabilities, achieving a substantial speed advantage over conventional approaches. The accuracy and robustness of MT-tracker were first validated by a phylosymbiosis analysis using samples from 28 mammals and 24 nonmammal animals, describing the co-evolutionary pattern between hosts and their associated microbiomes. We then expanded the usage of MT-tracker to 456,702 microbiomes sampled world-wide, uncovering the global transitional directions among 21 ecosystems for the first time. This effort provides new insights into the macro-scale dynamic patterns of microbial communities. Additionally, MT-tracker revealed intricate longitudinal transition trends in human microbiomes over a sampling period exceeding 400 days, capturing temporal dynamics often overlooked by normal diversity analyses. In summary, MT-tracker offers robust support for the qualitative and quantitative analysis of microbial community diversity, offering significant potential for studying and utilizing the macrobiome variation. Full article