Marine protected areas (MPAs) are the main conservation tool for safeguarding biodiversity and ecological processes. However, their planning and effectiveness depend on a robust understanding of biodiversity patterns. We conducted a systematic review of the literature to investigate trends in biodiversity research within Brazilian MPAs. We evaluated the taxonomic groups, diversity facets (taxonomic, functional and phylogenetic), sampling approaches and geographic distribution of studies. Of the 191 articles reviewed, 71% investigated a single diversity facet and 29%% considered both taxonomic and functional facets. Despite an increase in research over recent decades, the literature remains taxonomically and geographically biased. Most studies focused on fishes (58%) and taxonomic diversity (52%), while 20% addressed functional diversity, and phylogenetic diversity was virtually absent. Vertebrates were overrepresented, and studies were concentrated in fully protected MPAs and in Southeastern, Eastern, and Northeastern ecoregions. Most articles (93%) generated primary data, mainly through diver-based and imaging surveys. The limited integration across diversity facets may hinder a comprehensive understanding of ecological processes and effective conservation planning. We identify knowledge gaps and recommend expanding research efforts to underrepresented regions, taxa, and diversity facets. We encourage basic diversity research through species inventories for poorly known taxa and MPAs. Incorporating diversity facets will contribute to improving the ecological representativeness and resilience of Brazilian MPAs.

Multidimensional riverine biodiversity reveals decadal and sub-decadal effects of hydrological and water-quality changes.

Phylogenetic diversity recovery along Atlantic Forest succession: The potential for conserving evolutionary history

Tropical forests are highly threatened habitats with the capacity to recover after disturbance. We studied the recovery of phylogenetic diversity (PD) and phylogenetic community structure in plants and animals along a chronosequence of regeneration. We tested expected phylogenetic patterns through succession, including a slower recovery of PD compared with species richness (SR), increasing phylogenetic overdispersion with regeneration time, and the role of environmental filtering and landscape in promoting phylogenetic clustering and overdispersion. PD recovery occurred after SR for only four out of eight groups. Frugivorous and invertivorous birds showed increasing phylogenetic overdispersion during succession, while frogs, bees and trees instead showed a tendency for increasing phylogenetic clustering. Phylogenetic clustering was mainly related to environmental factors during early and late regeneration. Phylogenetic overdispersion during late regeneration was driven by the distance to old-growth forests only in frugivorous birds. Our results show the complex nature of succession in tropical forests, reflecting idiosyncratic patterns of PD and phylogenetic community structure recovery after disturbance for plants and animals. However, they also show that PD can recover relatively rapidly under natural regeneration, suggesting that the studied communities are resilient to disturbance from an evolutionary perspective.

Bioregionalisation is a hierarchical system that categorises geographical areas according to their biotic composition and evolutionary history. While a global bioregionalisation has been proposed for angiosperms, this is lacking for plant families with global relevance, such as orchids. We used 732 359 orchid distribution records and a phylogeny of 19 123 species to define the global bioregionalisation of orchids based on phylogenetic beta diversity at 200 × 200 km resolution. Using the resulting bioregionalisation, we analysed the environmental drivers that determine the formation of realms. Additionally, we assessed the effect of sampling completeness, different metrics, and spatial resolutions. We identified six global orchid realms (Australian, Andean-Patagonian, Neotropical, Afrotropical, Indo-Malaysian, and Holarctic) and 10 bioregions; four main transition zones were also detected. Mean annual precipitation and temperature, and precipitation and temperature seasonality, had the strongest influence on the delimitation of realms. We present a global bioregionalisation for orchids, identifying the environmental factors that determine the realms. More generally, these results highlight the importance of bioregionalisation for understanding evolutionary patterns of taxonomic families. Using a comprehensive seven-step methodology, we emphasize the need to account for sampling completeness and spatial resolution in such analyses.

Background Pakistan experienced six COVID-19 waves with varying SARS-CoV-2 variants. Vaccination campaigns began in 2021, in an age-stratified manner starting with the older-aged individuals, yet the relationship between vaccination status and variant transmission remains unclear. We investigated SARS-CoV-2 phylogenetic diversity in relation to age and vaccination status, with a focus on children. Methods We analyzed 569 SARS-CoV-2 genome sequences collected across Pakistan from May 2021 to October 2022. Metadata including age, sex, and vaccination status were retrieved from GISAID. Additional data such as viral load was available for a set of 143 pediatric samples (< 18 years) sequenced at Aga Khan University Hospital (AKUH), Karachi, and was analyzed separately to gain further insights. Phylogenetic analyses were conducted using the Augur pipeline and visualized via Auspice. Viral loads were inferred from Ct values of SARS-CoV-2 PCR diagnostic assays. Results Among the 569 genomes, Delta (45.2%) dominated in 2021 and Omicron (45.9%) in 2022. Of these, 71% were from individuals <18 years; 29.3% were vaccinated. Variant distribution showed no significant difference between vaccinated and unvaccinated individuals (p=0.75), nor between age groups (<18 vs ≥18 years; p=0.60). Pediatric samples from AKUH Karachi mirrored national trends, with Delta predominating in 2021 and Omicron in 2022. Omicron variants were associated with higher viral loads (p<0.001). Conclusions SARS-CoV-2 variant distribution and genomic divergence were comparable across vaccination status and age groups. In a population with high subclinical transmission and delayed pediatric vaccination, our findings highlight the stability of variant spread irrespective of host immunity status, suggesting the role of widespread prior exposure in shaping transmission dynamics.

Global biodiversity is increasingly threatened, but still poorly known. Preserving higher taxa (e.g., genera, families, orders) is especially important because each higher taxon may represent more genetic, morphological, ecological, and functional diversity than a typical species within a genus. Given this, there has been considerable focus on the loss of clades and their phylogenetic diversity. However, we know little about whether there are also gains of new clades: new higher taxa that are based on newly discovered species. Here, we analyze these newly discovered branches across the Tree of Life. We estimate that >700 new genera, >20 new families, and >3 new orders are described every year, each associated with newly discovered species. The distribution of new genus-level clades largely reflects current species richness patterns among groups. Thus, they are dominated by terrestrial arthropods. At higher taxonomic ranks, the distribution of new clades among groups is increasingly unrelated to the current, known species richness of these groups, and fungi and bacteria predominate. New clades are increasingly microscopic at higher taxonomic ranks and are often marine or host associated. Overall, we suggest that the known Tree of Life is continuing to rapidly expand with many newly discovered clades, not merely contracting with recent extinctions. Discovering and describing these new clades before they disappear should be an urgent research priority. There is also a pressing need to better incorporate phylogenies into the discovery of these new higher taxa.

ABSTRACT Peziza echinospora (Ascomycota, Pezizomycetes) is a species of cup-forming fungi that bears spiny, ellipsoid ascospores and is typically found on burnt ground as a saprotrophic species. It has a cosmopolitan distribution and has been reported from Australia based on morphological studies, but this has not been confirmed with molecular data. To address this knowledge gap and explore the phylogenetic diversity within the group, we investigated the species delimitation of P. echinospora and related species from southern Australia, using multilocus phylogenetic analyses of nuclear rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS), partial 28S rRNA, and rpb2 (second largest subunit of RNA polymerase II) and morphological examination of fungarium specimens. Based on these analyses, we confirm the occurrence of P. echinospora in Australia and formally describe two new species, P. austroechinospora and P. meridionalis. Peziza austroechinospora is typically found on burnt ground and has spiny ascospores that are larger and proportionately longer than those of P. echinospora. Peziza meridionalis has smooth ascospores, similarly to the closely related species P. subvesiculosa from the Northern Hemisphere, but with smaller ascospores and an ecology not associated with burnt soil. The occurrence of Peziza meridionalis as an endophyte on orchid roots is also discussed.

Bacterial migration from the oral cavity to the upper gastrointestinal tract has been proposed as a contributor to pancreatic ductal adenocarcinoma (PDAC) onset and prognosis. Whether PDAC is associated with alterations of the oral-duodenal microbiome continuum remains unclear. In this prospective study, we profiled matched saliva and duodenal brushings from 24 treatment-naïve PDAC patients without ducts obstruction and 24 age- and sex-matched healthy controls (HC). Microbial composition was assessed by 16S rRNA gene sequencing. α-Diversity was evaluated using Faith's phylogenetic diversity (PD), observed ASVs, and Pielou's evenness; β-diversity using UniFrac, Bray-Curtis, and distance-based redundancy analysis (db-RDA). Associations with overall survival were examined using Cox models and ROC-derived cut-offs, with leave-one-out cross-validation for robustness. Duodenal Faith's PD was significantly lower in PDAC than HC (q=0.034), whereas richness and evenness did not differ; no α-diversity differences were observed in saliva. After adjustment for diabetes and periodontitis, lower duodenal Faith's PD (q=0.048) and ASV richness (q=0.030) in PDAC remained significant. β-Diversity was primarily driven by body site, but adjusted db-RDA revealed a small yet significant PDAC-HC difference in duodenal community composition (pseudo-F=2.16, p=0.002). Several genera showed differential abundance between groups. Higher salivary phylogenetic diversity predicted longer survival (aHR=0.19, p=0.001), along with specific genera associated with favourable prognosis. PDAC is associated with reduced duodenal phylogenetic diversity and subtle disease-related shifts in duodenal microbiota, independent of major confounders and in the absence of duct obstruction. Both α-diversity and selected genera may hold prognostic relevance, supporting further validation in larger, stage-stratified cohorts.

Ecosystems worldwide are undergoing unprecedented changes, and as a result amphibians are experiencing devastating population declines driven by subsequent habitat loss and emerging pathogens. The skin microbiota is an important first line of defence for amphibians against pathogens. Here, for the first time, we characterised the bacteria and fungi comprising the skin microbiota of 56 individual golden Alpine salamanders (Salamandra atra aurorae, Trevisan, 1982), a highly endemic and endangered amphibian subspecies. In addition, we investigated the impact of the 2018 Vaia windstorm on skin microbiota of salamanders in plots classified as impacted or non-impacted based on windthrows. Salamander sex, weather during sampling, and dominant tree species in plots were also investigated as influencers of microbiota. Beta diversity estimates revealed greater variation in bacterial microbiota composition among individuals from non-impacted plots compared to plots impacted by Vaia. Notably, we found differential abundances of five genera of bacteria and eight genera of fungi in the skin microbiota of salamanders from impacted compared with non-impacted plots. Further analyses revealed that median relative abundances of Aeromonas hydrophila, the causative agent of the potentially fatal red-leg syndrome, were significantly higher in microbiota of salamanders from impacted plots. Weather conditions during sampling significantly influenced both alpha and beta diversity of the skin microbiota, and explained up to 9% of bacterial and 6% of fungal variation. Bacterial richness and phylogenetic diversity were lower during rainfall, whereas fungal beta diversity increased, suggesting contrasting moisture preferences. These findings suggest that extreme weather events, as well as moderate daily weather fluctuations, may be associated with the microbial communities of amphibian skin, potentially affecting their resilience to pathogens. This study underscores the importance of considering both natural and human-mediated disturbances in conservation strategies for vulnerable species like the golden Alpine salamander.

Influence of Singular First Foods on the Infant Gut Microbiome: A Randomized Controlled Trial.

Protected areas with high species, phylogenetic, and functional diversity are complementary and occur in heavily modified Cerrado landscapes

Discovering functional and evolutionary interdependencies of hydraulic traits and crassulacean acid metabolism (CAM) is crucial to understand CAM phenotype diversity and convergence. In complex traits such as CAM, the co-option of associated traits strongly impacts the evolutionary outcome. Here we study Aeonium (Crassulaceae), a diverse Macaronesian genus that exhibits a broad array of CAM expression, focusing on two CAM-associated traits, minimum conductance (gmin) and succulence. At the heart of the study, there are two experiments: a comparative cultivation experiment to monitor nocturnal acidification (ΔH+) under drought and heat treatments and a leaf-drying curve experiment to quantify gmin. Our study group was comprehensively sampled to cover its phylogenetic and ecological diversity. We found a consistently negative correlation of gmin and ΔH+, indicating a critical role for the cuticle in the function of CAM. Although ΔH+ and succulence were overall not positively correlated, we found evidence that more succulent species remain in the CAM mode when stress is relaxed. We conclude that there is a tight evolutionary link between cuticular transpiration barrier properties and CAM performance. Thereby, the stronger CAM plants express diurnal stomatal closure typical of CAM, the more they may optimise water-use efficiency through reduced gmin.

Regional comparisons of phylogenetic diversity (PD) are difficult to interpret without a baseline for expected PD as a function of species richness (SR). We developed an SR-matched randomization method that preserves phylogenetic structure using mean pairwise distance (MPD). We partitioned the MPD into equal-width intervals and assigned bin quotas proportional to the observed frequencies. For each SR, we sampled species sets, computed the MPD, and accepted a set when its MPD fell within an MPD bin that still had a quota based on the observed frequencies. This bin-and-quota rule preserves the balance between clustering and overdispersion. Using the accepted sets, we estimated the expected PD as a function of the SR, and converted each region's PD at its SR to a standardized Z -score. We applied this to Korean vascular plants using 2.23 million records and presence–absence data for 162 administrative units. For the benchmarks, the MPD-constrained null model increased the proportion within the intervals from 79.6% to 92.6% in the observed units and from 85.9% to 97.1% in the evaluation units. MPD-constrained randomization tracked the observed PD–SR relationship more closely, conservatively maintained SR-specific uncertainty, and improved interpretability by excluding implausible draws. The southern and insular regions exceeded the expected PD, whereas high mountainous areas along the Baekdudaegan Mountains showed negative deviations. This framework is readily applicable to other taxa and regions to produce structure-aware, SR-specific expected PD baselines for fair mapping of PD hotspots and deficits, and support practical area prioritization alongside threats and connectivity. • New randomization approach preserves evolutionary relatedness among species. • Eliminates species richness bias for fair phylogenetic diversity comparisons. • Aligns randomized communities with the mean pairwise distance distribution. • Applied to Korean vascular plants, revealing distinct regional diversity patterns. • Outperforms existing null models in capturing phylogenetic diversity patterns.

Estuaries are ecologically vital yet highly impacted ecosystems that serve as transitional zones between land and sea. Monitoring their biodiversity is essential but challenging due to their dynamic nature and the transient presence of many species. Traditionally, actinopterygian monitoring in these systems still relies on conventional and intrusive methods such as gill nets and trawls. Environmental DNA (eDNA) metabarcoding offers a non-invasive, multi-taxa alternative that can complement these traditional approaches. Here, we applied an eDNA-based metabarcoding approach to characterize vertebrate diversity in the Rance Estuary, located in the Brittany Region of France. Water samples were collected from five stations spanning marine to freshwater environments. Special attention was given to two stations located upstream and downstream of the tidal power plant (TPP) dam to assess its potential impact on ecological continuity. We detected a total of 124 distinct vertebrate MOTUs, comprising actinopterygians, birds, mammals, and amphibians. Taxonomic composition followed the estuarine gradient, with Jaccard dissimilarity increasing with distance from the sea and largely driven by species turnover. While taxonomic and phylogenetic diversity remained relatively stable across the vertebrate community, functional diversity revealed an increasing terrestrial influence. For actinopterygians, taxonomic diversity decreased upstream, whereas phylogenetic and functional diversity indicated fine-scale structuring, even among nearby stations. This approach enabled the development of biodiversity metrics and facilitated comparisons with previous actinopterygian monitoring surveys in the same area based on conventional methods (scientific fishing using nets and dredges). Our results emphasize the potential of eDNA for holistic estuarine biomonitoring and establish a valuable baseline for future non-invasive assessments.

Assessment of microbial community changes in seawater of marine cage- culture large yellow croaker (Larimichthys crocea) farms.

Hospital environments host diverse microbial communities that may contribute to nosocomial infections. Moisture-retaining surfaces such as cleaning sponges and faucet edges represent high-contact, under-investigated hygiene hotspots, particularly in wards caring for immunocompromised patients. Environmental samples were collected from cleaning sponges (n = 14) and faucet edges (n = 4) across multiple hospital rooms of a paediatric haematology–oncology unit, with domestic physician sponges as controls (n = 3). DNA was extracted and sequenced targeting the V3–V4 and V7–V9 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. Taxonomic composition and alpha/beta diversity were assessed using QIIME 2 and R. Sponge samples were dominated by Moraxellaceae, particularly Acinetobacter and Enhydrobacter, and showed significantly lower alpha diversity than faucet samples (Shannon index: Kruskal–Wallis H = 8.4, p = 0.01; Faith’s phylogenetic diversity: H = 9.17, p = 0.01). Faucet samples were enriched in human-associated genera including Staphylococcus, Streptococcus, and Chryseobacterium. Statistically significant beta-diversity differences were detected between sponge and faucet communities by PERMANOVA based on Bray–Curtis dissimilarity (p = 0.01), whereas no significant clustering by room or floor location was observed (p = 0.29). Potentially pathogenic taxa including Aeromonas, Pseudomonas, and Enterobacteriaceae were identified across both surface types. Domestic control sponges showed distinct microbiome profiles from hospital samples. Microbial communities differ significantly between hospital sponges and faucets, with surface type rather than location as the primary determinant of community structure. The presence of opportunistic pathogens on both surface types highlights the importance of enhanced hygiene protocols, inclusion of faucet edges and sink drains in routine decontamination schedules, and regular microbiological surveillance in clinical settings caring for immunocompromised patients.

The increasing global burden of antimicrobial resistance (AMR) has been identified as a critical public health crisis, necessitating the development of robust, real-time surveillance frameworks to evaluate AMR dynamics. Sewage surveillance is emerging as a promising tool that utilizes sewage fingerprinting to provide comprehensive and unbiased information on antibiotic resistance genes (ARGs) within human populations. Here, we conducted a large-scale, year-long field surveillance of resistome in the community sewage using both short- and long-read metagenomic sequencing. We examined samples collected from 95 geographically distributed sites across Hong Kong, covering a population of 4.8 million residents, during summer and winter seasons. Our findings revealed distinct seasonal patterns through high-resolution resistome profiling. We found that the resistome structures shifted from the community sewage collected at sewer manholes to the influent of wastewater treatment plants (WWTPs), driven by taxonomic variation. Notably, community sewage exhibited a significantly higher similarity to the resistome of human feces than WWTP influent, which provides insights for selecting suitable sampling sites for epidemiological ARG surveillance. The application of long-read sequencing markedly enhanced our understanding of the phylogenetic diversity of ARG hosts and uncovered a broad spectrum of potentially mobile ARGs with varied genetic backgrounds. Furthermore, we observed multiple local ARG transmission patterns and subsequently evaluated their potential threats to public health based on the gene trees to inform future epidemiological control strategies. Overall, this work expands our current understanding of community sewage for population-level AMR monitoring and establishes a baseline for advancing sewage surveillance efforts to better combat AMR.

ABSTRACT The paleotropics of Euramerica provide nearly our entire picture of Permo–Carboniferous terrestrial tetrapod evolution. The geographic sampling bias inherent in this record obscures important events, such as the turnover between “pelycosaur”- and therapsid-dominated assemblages. The Cisuralian Pedra de Fogo Formation (PdF) of Brazil is a unique window into Gondwanan tropical to subtropical vertebrate assemblages of this time, including abundant chondrichthyans, actinopterygians, sarcopterygians, and temnospondyls, but the terrestrial tetrapod assemblage reported to date is limited to acleistorhinid stem reptiles and captorhinids. Here we describe the first two specimens of Synapsida from the PdF. One specimen is a natural mold of the cranial face of a posterior dorsal or anterior caudal vertebra. Its large size, amphicoelous centrum, and narrow neural arch with closely set, dorsolaterally angled anterior zygapophyses confirm that it is a synapsid. The second specimen is a natural mold of the medial surface of a partial maxilla. The large caniniform tooth, presence of a supracaniniform buttress lacking a dorsal process, and ventral convexity of the element permit its identification as a member of Sphenacodontia, but the straight, dagger-like caniniform is unusual within the clade. Phylogenetic analysis of the maxilla corroborates its sphenacodont affinities. Besides expanding the phylogenetic diversity of the PdF tetrapod assemblage, the specimens add a new size class (very large terrestrial amniote) and ecological guild (medium-size terrestrial faunivore) to the PdF terrestrial fauna. Together, these fossils hint at the presence of a complex terrestrial ecosystem between expansive, perennial water bodies of sufficient depth to support large aquatic predators.

The opportunistic pathogen Candida albicans is the leading cause of invasive Candida infections worldwide. Genomic variation between C. albicans clinical isolates complicates efforts to pinpoint novel genetic variants underlying antifungal drug resistance and tolerance. Studies of serial isolates from individual patients are uncommon, limiting our understanding of genomic and phenotypic diversity during invasive Candida infections. We performed comparative genomic analyses of 101 C. albicans bloodstream isolates from 55 patients in the Twin Cities region of Minnesota, including serial isolates from 19 patients. We analysed the phylogenetic relationships of these isolates relative to 199 globally collected public C. albicans genomes. This study's regional isolates span the phylogenetic diversity of C. albicans; six isolates represent novel outliers to known clades. While all serial isolates from the same patient clustered together phylogenetically, we observed extensive large-scale genomic variation between serial isolates including polyploidy, aneuploidy, copy number variation, loss of heterozygosity and chromosomal rearrangements. We demonstrated how a heterozygous ERG251 variant drives azole tolerance in a clinical isolate from a patient with a history of recurrent infections. Using serial isolates, we demonstrated that polyploidy provides an adaptive advantage in the presence of fluconazole despite the absence of overt antifungal drug resistance. Our analysis of closely matched serial isolates reveals the genomic plasticity of C. albicans during invasive infections and identifies variation driving antifungal drug tolerance. Our findings reveal limitations in current antifungal susceptibility testing and highlight the need to account for genomic and phenotypic variation during invasive Candida infections.