Search Results (57)

Sin Nombre virus (SNV) is the main causative agent of hantavirus cardiopulmonary syndrome (HCPS) in North America. SNV is transmitted via environmental biological aerosols (bioaerosols) produced by infected deer mice (Peromyscus maniculatus). It is similar to other viruses that have environmental transmission routes rather than a person-to-person transmission route, such as avian influenza (e.g., H5N1) and Lassa fever. Despite the lack of person-to-person transmission, these viruses cause a significant public health and economic burden. However, due to the lack of targeted pharmaceutical preventatives and therapeutics, the recommended approach to prevent SNV infections is to avoid locations that have a combination of low foot traffic, receive minimal natural sunlight, and where P. maniculatus may be found nesting. Consequently, gaining insight into the SNV bioaerosol decay profile is fundamental to the prevention of SNV infections. The Biological Aerosol Reaction Chamber (Bio-ARC) is a flow-through system designed to rapidly expose bioaerosols to environmental conditions (ozone, simulated solar radiation (SSR), humidity, and other gas phase species at stable temperatures) and determine the sensitivity of those particles to simulated ambient conditions. Using this system, we examined the bioaerosol stability of SNV. The virus was found to be susceptible to both simulated solar radiation and ozone under the tested conditions. Comparisons of decay between the virus aerosolized in residual media and in a mouse bedding matrix showed similar results. This study indicates that SNV aerosol particles are susceptible to inactivation by solar radiation and ozone, both of which could be implemented as effective control measures to prevent disease in locations where SNV is endemic. Full article

The genus Rhododendron presents significant challenges for systematic classification due to extensive hybridization and adaptive radiation. Here, we employed double-digest restriction site-associated DNA sequencing (ddRAD-seq) to resolve phylogenetic relationships among nine ecologically significant Rhododendron species (34 accessions) endemic to Zhejiang Province, China, a biodiversity hotspot for this genus. Using R. simsii as the reference genome, we generated 39.40 Gb of high-quality sequencing data with a Q30 score of 96.65% and a GC content of 39.63%, achieving an average alignment rate of 92.79%. Through stringent filtering (QD ≥ 2, MQ ≥ 40), we identified 14,048,702 genome-wide single nucleotide polymorphism (SNP), predominantly characterized by the mutation types T:A>C:G and C:G>T:A. The widespread R. simsii and R. simsii var. putuoense exhibited significant genetic diversity, whereas the low-altitude widespread R. molle and the endemic R. simiarum exhibited lower genetic diversity. Moderate genetic differentiation (F_st = 0.097) was observed between R. simsii and R. simsii var. putuoense, while substantial genetic differentiation was detected among the other Rhododendron species. Principal component analysis (PCA), combined with phylogenomic reconstruction, demonstrated that the Rhododendron genus can be stratified into six well-supported genetic clades. Furthermore, this study provides the first genomic validation of the sibling relationship between R. simsii and its variety, R. simsii var. putuoense, and clarifies the systematic position of R. huadingense, suggesting that it should be classified as a new subgenus. This study establishes ddRAD-seq as a cost-effective tool, providing both a theoretical framework for SNP-based phylogenetics and critical insights for conserving China’s azalea biodiversity. Full article

The genus Cyprinus encompasses economically vital freshwater fish species; yet the phylogenetic relationships and evolutionary history of many taxa within this genus remain unresolved. To address this knowledge gap, we reconstructed the molecular phylogenetic and estimated divergence times using complete mitochondrial cytochrome b (CYTB) sequences of 76 Cyprinidae specimens, within Cyprinidae, including 4 outgroup species. Phylogenetic trees were reconstructed using maximum likelihood (ML) and Bayesian inference (BI) methods, while divergence times were estimated using a Bayesian relaxed molecular clock approach. The results confirmed the monophyly of the genus Cyprinus. The relationships among C. (Cyprinus) multitaeniata, C. (C.) pellegrini, C. (C.) acutidorsalis, and three Erhai Lake species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) were resolved with strong support. Cyprinus (C.) multitaeniata is basal. The species in Erhai Lake form a monophyletic group, and C. (C.) acutidorsalis is at the top of the phylogenetic tree. The taxonomic delineation within the genus Cyprinus remains controversial, particularly regarding the proposed division into two subgenera (Cyprinus and Mesocyprinus), which has been historically constrained by limited specimen availability for Mesocyprinus. Our comprehensive phylogenetic analysis reveals significant evolutionary divergence patterns: The genus Cyprinus diverged from Carassius during the 56.9 Mya. Notably, the Erhai Lake radiation species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) originated during 2.03 Mya, while the Lake Biwa endemic C. (C.) haematopterus demonstrates 8.7 Mya. We identified a late Pleistocene speciation event (0.75 Mya) in C. (C.) acutidorsalis, coinciding with its adaptation to brackish water ecosystems. The native C. (C.) pellegrini of Xingyun Lake and Chilu Lake may have originated 4.8 Mya, when the ancient lake that its ancestral population inhabited became isolated. These findings provide robust molecular evidence supporting the recognition of two evolutionary distinct subgenera within Cyprinus. Full article

Yunnan Province, a global biodiversity hotspot, hosts a diverse array of Acrididae grasshoppers essential for ecosystem dynamics and agriculture. To elucidate the phylogenetic relationships and evolutionary history of this group, we sequenced and analyzed complete mitochondrial genomes from 17 Acrididae species endemic to Yunnan, with genome lengths ranging from 15,403 to 15,943 base pairs. These data were integrated with mitochondrial sequences from 46 additional species to construct comprehensive phylogenetic trees. The maximum-likelihood tree identified four major clades with robust support (bootstrap values > 90%), revealing significant lineage diversification during the Early Eocene (51.94 million years ago, Mya) and subsequent radiations in the Miocene (~20 Mya) and Pliocene (~5 Mya). These divergence times correlate with major geological events and climatic shifts in the region, such as the uplift of the Tibetan Plateau and the intensification of the Asian monsoon. Notably, several species within the Coptacrinae and Oxyinae subfamilies, particularly Pseudodotraulia cornuata and Spathosternum prasiniferum, were found to be polyphyletic, indicating the necessity for taxonomic revisions. Further cluster analyses of codon usage bias and genetic distance support these taxonomic revisions within Acrididae. This robust phylogenetic framework underpins conservation strategies aimed at preserving Yunnan’s rich grasshopper biodiversity and informs updates to their phylogeny. Full article

Quillay (Quillaja saponaria Molina) and peumo (Cryptocarya alba [Molina] Looser) are two tree species endemic to Chile that grow in Mediterranean climate zones, characterized by a summer season with high temperatures, high solar radiation, and low soil water availability. A study was conducted with 2-year-old Q. saponaria and C. alba plants and two substrate water conditions: well-watered and controlled water restriction. At the end of the study, anatomical leaf modifications were analyzed. The tissues were anatomically described in transverse sections of juvenile and adult leaves, measuring leaf thickness, cuticle thickness, and cell density of the mesophyll parenchymal tissues. In the young leaves of Q. saponaria plants undergoing water restriction treatment, an increase in cuticle and leaf thickness and a decrease in the density of the palisade and spongy parenchyma were observed. In contrast, a significant reduction in leaf thickness was observed in adult leaves of both species with water restriction treatment. The anatomical changes in the leaves of Q. saponaria and C. alba suggest an adaptation to adverse environmental conditions, such as water restriction. Full article

This study offers an in-depth analysis of the mitochondrial genome of Selene dorsalis (Gill 1863), a species native to the Eastern Atlantic Ocean. The circular mitochondrial DNA molecule measures 16,541 base pairs and comprises 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a control region (CR). The nucleotide composition exhibits a notable adenine-thymine (AT) bias, accounting for 53.13%, which aligns with other species in the Carangidae family. Most PCGs initiate with the ATG codon, with the exception of Cytochrome C oxidase subunit I, which starts with GTG. Analysis of relative synonymous codon usage reveals that leucine and serine are the most prevalent amino acids in the mitochondrial genome of S. dorsalis and its congeners (S. vomer and S. setapinnis). All tRNAs display the typical cloverleaf structure, though tRNA Serine (S1) lacks a dihydrouracil arm. Pairwise comparisons of synonymous and nonsynonymous substitutions for all PCGs yielded values below ‘1’, indicating strong purifying selection. The CR spans 847 bp, representing 5.12% of the mitochondrial genome, and is characterized by high AT content (62.81%). It is situated between tRNA-Pro (TGG) and tRNA-Phe (GAA). The CR contains conserved sequence blocks, with CSB-1 being the longest at 22 bp and CSB-D the shortest at 18 bp. Phylogenetic analysis, using Bayesian and Maximum-likelihood trees constructed from concatenated PCGs across 72 species, successfully differentiates S. dorsalis from other carangids. This study also explores how ocean currents and gyres might influence lineage diversification and parapatric speciation of Selene species between the Atlantic and Pacific Oceans. These results highlight the importance of the mitochondrial genome in elucidating the structural organization and evolutionary dynamics of S. dorsalis and its relatives within marine ecosystems. Full article

Hieracium is one of the largest flowering plant genera that has recently experienced a rapid evolutionary radiation. Due to the massive morphological variation among species, frequent hybridization, and polyploidization events, combined with apomictic reproduction in polyploids, the concept of species in Hieracium is widely debated, and species identification is incredibly challenging. Taxonomic investigation can lead to changes in conservation status or, in some cases, to de-extinctions of species. Taxa with doubtful classification are particularly sensitive to this kind of problem. Hieracium tolstoii was a narrow Italian endemic species that is nowadays considered extinct. Described as a morphological intermediate form between two other species, no further investigations were conducted after its first description. To clarify H. tolstoii’s origin and ensure the validity of its current conservation status, we conducted a taxonomic investigation on herbaria specimens of the early XX century. Specimens were studied using a morphometric analysis that compared H. tolstoii with other closely related taxa. Moreover, we performed phylogenetic investigations using three plastid intergenic spacers to evaluate the relationship between species. Plastid markers revealed the presence of indels and SNPs in H. tolstoii sequences that differ from sequences of the supposed parental species. Morphometry revealed differences among species that led us to confirm the validity of H. tolstoii as an independent apomictic species and, therefore, unfortunately, its extinction. Full article

In Chile, honey is produced from several native species with interesting biological properties. Accordingly, those attributes are present in Chilean honeys owing to the presence of phenolic compounds inherited from specific floral sources. In recent years, the exported volume of Chilean honeys has been increased, reaching new markets with demanding regulations directed toward the fulfilment of consumers’ expectations. Accordingly, there are countries with special requirements referring to Paenibacillus larvae spore-free honeys. This microorganism is the pathogen responsible for American foulbrood disease in beehives; however, antibiotics are not allowed when an apiary tests positive for P. larvae. On the other hand, it is mandatory to have an accurate method to remove the potential presence of spores in bee products intended for export. Exposure to ionizing radiation can be an efficient way to achieve this goal. In this work, 54 honey samples harvested from northern, central and southern Chile were analyzed for physicochemical patterns, total phenols, antioxidant activity and antiradical activity. Honeys with and without spores were exposed to ionizing radiation at three levels of intensity. Afterwards, the presence of spores and the effect on phenol bioavailability, antiradical activity and antioxidant activity were measured again. This research presents results showing a positive correlation between the percentage of prevalence of native endemic species in the set of honeys analyzed and the capacity to resist this process, without altering their natural attributes determined before irradiation treatments. Full article

Phellinotus (Polyporales) is a common genus of wood-decay fungi in tropical and subtropical areas, endemic to the Seasonally Dry Tropical Forest (SDTF) biome. However, Phellinotus diversity remains unexplored, despite being a major threat to living trees. Therefore, this study is aimed at confirming and characterizing through morphological and molecular data the first isolates of Phellinotus teixeirae in Pithecellobium dulce (Fabaceae) trees (locally referred to as ‘Chiminango’) from the endangered Colombian SDTF biome. Fifteen fungal specimens were recovered from living P. dulce trees, in the urban area and at the Universidad del Valle campus, and classified as P. teixeirae based on taxonomical descriptors. Phylogenetic relationships were inferred from a four-loci dataset (ribosomal and gene-coding regions), including 82 taxa covering 3991 nucleotide positions. The analysis recovered seven highly supported (>90% bootstrapping) monophyletic taxa of the ‘Phellinotus Clade’, and confirmed the new distribution range of P. teixeirae (100% bootstrap support), which extends approx. 1000 km north in the Neotropics. Hierarchical stratified Analysis of MOlecular VAriance (AMOVA) provided a clear genetic distinction between species (70% of variation, p-value = 0.001) and low differentiation among country of origin within species (11%, p-value = 0.044). Discriminant Analysis for Principal Components (DAPC) indicated complex clustering including closely related species, probably a signal of recent radiation and weak species boundaries. Median-joining haplotype network analysis identified unique haplotypes, which may correlate with new host colonization and population expansion (Tajima’s D ≤ −0.5). In conclusion, this study provides the first assessment of the genetic diversity of P. teixeirae in a novel geography (SDTP) and host tree (P. dulce). However, increasing the number of isolates remains critical to understand further the genus’ distribution patterns and drivers of genetic diversity. Full article

With the depletion of the ozone layer, the intensity of ultraviolet B (UV-B) radiation reaching the Earth’s surface increases, which in turn causes significant stress to plants and affects all aspects of plant growth and development. The aim of this study was to investigate the mechanism of response to UV-B radiation in the endemic species of Rhododendron chrysanthum Pall. (R. chrysanthum) in the Changbai Mountains and to study how exogenous ABA regulates the response of R. chrysanthum to UV-B stress. The results of chlorophyll fluorescence images and OJIP kinetic curves showed that UV-B radiation damaged the PSII photosystem of R. chrysanthum, and exogenous ABA could alleviate this damage to some extent. A total of 2148 metabolites were detected by metabolomics, of which flavonoids accounted for the highest number (487, or 22.67%). KEGG enrichment analysis of flavonoids that showed differential accumulation by UV-B radiation and exogenous ABA revealed that flavonoid biosynthesis and flavone and flavonol biosynthesis were significantly altered. GO analysis showed that most of the DEGs produced after UV-B radiation and exogenous ABA were distributed in the cellular process, cellular anatomical entity, and catalytic activity. Network analysis of key DFs and DEGs associated with flavonoid synthesis identified key flavonoids (isorhamnetin-3-O-gallate and dihydromyricetin) and genes (TRINITY_DN2213_c0_g1_i4-A1) that promote the resistance of R. chrysanthum to UV-B stress. In addition, multiple transcription factor families were found to be involved in the regulation of the flavonoid synthesis pathway under UV-B stress. Overall, R. chrysanthum actively responded to UV-B stress by regulating changes in flavonoids, especially flavones and flavonols, while exogenous ABA further enhanced its resistance to UV-B stress. The experimental results not only provide a new perspective for understanding the molecular mechanism of the response to UV-B stress in the R. chrysanthum, but also provide a valuable theoretical basis for future research and application in improving plant adversity tolerance. Full article

Erigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola–E. luteoviridis and E. fernandezia–E. ingae–E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex. Full article

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae. Full article

Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota’s diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán’s water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet. Full article

The Midlands region of KwaZulu-Natal (KZN) Province in South Africa was hitherto a putative centre of floristic endemism (CFE) based on conjecture. The aim of this study was to empirically explore this concept by delineating unambiguous boundaries for this CFE and documenting the endemic spermatophytes within a conservation framework. The Greater Midlands Centre of Floristic Endemism (GMCFE), a more expanded study area than the parochial Midlands region of KZN, is formally described as southern Africa’s 20th CFE. It is a mid-elevation region occupying the greater Midlands of KZN, with extensions of contiguous grasslands extending northwards into southern Mpumalanga and southwards into north-eastern Eastern Cape. This “foothills” CFE covers ca. 77,000 km² of predominantly mesic C₄ grassland, ranging in elevation from ca. 700–2200 m a.s.l. It is congruent with the “sub-escarpment ecoregion,” essentially a composite of the Sub-escarpment Grassland and Savanna Bioregions and the sub-escarpment grasslands of southern Mpumalanga and northern KZN. The GMCFE hosts at least 220 endemic spermatophytes, of which almost a fifth belong to the family Apocynaceae. Families Asteraceae, Asphodelaceae, Fabaceae, and Iridaceae also contribute significantly. Genera Ceropegia, Aloe, Dierama, Kniphofia, Helichrysum, and Streptocarpus contribute the most endemics. More than half are forbs, and almost three-quarters are confined to the Grassland Biome. Endemic radiations are attributed to geodiversity and geological complexity (especially the strong lithological influence of dolerite); physiographic heterogeneity (particularly elevation gradients and variable terrain units); strategic proximity to hyper-diverse temperate and subtropical “border floras”; and localized pollinator-driven adaptive radiations. Of alarming concern is the high number of threatened plant taxa, with ca. 60% of the endemic flora Red Listed in threat categories (CE, E, and VU) or considered “rare”. Extremely low levels of formal protection and poor ecological connectivity, coupled with high levels of land transformation and intensive utilization, render the GMCFE one of the most imperilled CFE in South Africa. Urgent conservation action is required to safeguard this unique and highly threatened “rangeland flora” and stem the biodiversity crisis gripping the region. Full article

The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation. Full article