Distinct Habitats Research Articles

A review of migratory Alosidae marine ecology in the northwest Atlantic

AbstractMigratory animals play a crucial role in connecting distinct habitats by transferring matter and energy across ecosystem boundaries. In the North Atlantic, anadromous species exemplify this through their movement between freshwater and marine environments. Alosids, including species such as alewife (Alosa pseudoharengus), blueback herring (Alosa aestivalis), and American shad (Alosa sapidissima), exhibit this migratory behavior to maximize growth and fecundity and are, therefore, vital components of Atlantic coastal ecosystems. Despite their ecological importance, these species have experienced considerable population declines. Due to a research focus on dams and the freshwater phase of their ecology, the marine ecology of Alosids remains much less understood, potentially hindering effective management. This paper synthesizes current knowledge on the marine ecology of anadromous alewife, blueback herring, and American shad in the northwest Atlantic, focusing on life‐history aspects, migratory patterns, and foraging behavior at sea. The paper also outlines current fisheries management and the anthropogenic threats these species face during their marine phase. We identified knowledge gaps regarding marine distribution, migration routes, impacts of climate change on movement and behavior, population dynamics, and the identification of gaspereau. By identifying gaps in the literature, we highlight research needs, emphasizing the role of telemetry studies in tracking marine movements and the impact of climate change on habitat use. Addressing these gaps through targeted research on marine ecology and movement patterns is essential for developing informed management strategies aimed at increasing Alosid populations.

The Impact of Plant Diversity on Spider Populations in a Tropical Butterfly Conservatory, Tiruchirappalli, South India

Spiders, as crucial predators and biodiversity indicators, significantly influence ecosystem health. This study investigates the intricate relationship between plant diversity and spider communities within distinct habitats of the Tropical Butterfly Conservatory, Tiruchirappalli, India. By classifying spiders based on their hunting strategies, we aim to understand their ecological roles. This research establishes a baseline for the spider fauna within the conservatory, emphasizing the impact of plant life on spider diversity and distribution. Our findings contribute to a comprehensive evaluation of the ecological importance of spiders in this unique ecosystem, providing valuable insights for future conservation and management efforts. By unravelling the complex interplay between plants and spiders, this study underscores the necessity of preserving plant diversity to sustain a robust and balanced spider community.

Ectoparasite infection levels differ between fish from upwelling-exposed and sheltered rocky reefs areas in Brazil

Ubiquitous and abundant within marine ecosystems, parasites play essential ecological roles such as shaping host population dynamics, altering competition between species, and influencing energy flows through communities. Their diversity and population dynamics are demonstrably shaped by both seasonal and geographic variations. These variations have been often explored at broad spatial scale. However, parasite communities can exhibit significant disparities even at small spatial scales, driven by factors such as wave exposure, temperature fluctuations, and benthic habitat composition. We investigated how crustacean parasites of fish – caligids and gnathiids - differed between two distinct habitats, which are separated solely by a few kilometres, at Arraial do Cabo, Brazil. These two habitats were characterised by a sheltered embayment (hereinafter referred to as “inside”) or an exposed upwelling habitat (hereinafter referred to as “outside”). Individual fish from four species were examined in both habitats. We found that the infestation rate of caligids varied among fish species and, gnathiids varied between the two sampling sites. Gnathiids were absent from fish outside, while they were present on fish inside the embayment. This disparity suggests a critical role of local environmental factors in shaping gnathiid distribution. Potential drivers include temperature fluctuations, substrate composition, and wave exposure, which differed markedly between the two sites. Conversely, caligid parasites infected fish in both locations. While environmental factors may also influence caligid abundance, they appear to exhibit greater tolerance compared to gnathiids. These findings emphasize the importance of incorporating fine-scale environmental heterogeneity when investigating parasite distribution patterns.

Analysis of Heavy Metal Pollution in the Water of the Halda River: A Distinctive Breeding Habitat for Carp Fish in Bangladesh

ABSTRACTBackgroundThe present study aimed to assess the heavy metal concentrations in water from different sampling sites of the Halda River, the only natural breeding ground of Indian major carps.ObjectivesWe have analysed the contamination level and seasonal variations of heavy metals (viz. Fe, Cu, Zn, Cr, Cd and Pb). The favourability of the breeding environment was assessed by different contamination indices.MethodsSamples were collected from six sampling sites for four different seasons, and the metal concentrations were determined for water samples using Flame atomic absorption spectrophotometer.ResultsThe obtained order of mean concentrations of heavy metals for four seasons was winter > spring > monsoon > pre‐monsoon, and the assessed mean concentrations (mg/L) of heavy metals follow the trend: Fe (9.129) > Pb (0.033) > Zn (0.024) > Cr (0.017) > Cu (0.012) > Cd (0.002). The concentration of Fe was found above the permissible limit set by the World Health Organization (WHO) (Guidelines for Water Quality) and ECR (1997), and the concentrations for Pb were found above the USEPA (2006) limit in all four seasons. Contamination indices (heavy metal pollution Index [HPI] and metal index [MI]) indicate that during winter and monsoon, the river water metal condition is critical (HPI > 100) and the sites are moderately as well as slightly (1< MI <2) affected by the studied heavy metals. Contamination indices, such as contamination factors (Cf), degree of contamination (Cdeg) and the pollution load index (PLI), demonstrate the fact that Fe and Pb remarkably contaminated the studied sampling sites. The Pearson correlation matrix and the principal component analysis (PCA) revealed that the studied metals are connected by their sources, which can be geological or anthropogenic.ConclusionUrgent initiatives need to be taken, and effective strategies must be implemented to control the different sources responsible for the entry of heavy metals into the Halda River water.

Fine-scale habitat selection in tree-dwelling spiders: an experimental approach.

Habitat selection by spiders is strongly influenced by biotic factors such as the availability and diversity of prey and abiotic factors such as temperature, humidity, and the structural complexity of the habitat. Structural complexity is an aspect that intensely affects species persistence, population stability, and the coexistence of interacting species. Trees comprise a complex set of microhabitats due to their large biomass and heterogeneity of the architectural components of their trunk surface and branches. Spider species that live on trunks have diversified physiological or morphological adaptations that confer advantages in this environment. In this study, we experimentally examined the habitat choice by the tree-dwelling spiders Selenops cocheleti (Selenopidae), Corinna rubripes (Corinnidae), and Loxosceles gaucho (Sicariidae). We found that microhabitat specialization was restricted to trunk architectural characteristics rather than plant taxonomy. Selenops cocheleti and C. rubripes significantly preferred loose barks and holes in the trunks, respectively, showing that both spider species can evaluate the physical structure of the microhabitat on a fine scale. On the other hand, L. gaucho selected crevices and holes near the base of the trunk without giving much importance to the physical characteristics of the microhabitat per se (e.g., depth, height, length). Our findings indicate that for generalist predators like spiders, coexistence relies heavily on spatial segregation driven by distinct habitat preferences, irrespective of their method for capturing prey.

The Adaptive Mechanism of Ginseng Rhizomes in Response to Habitat Changes

Panax ginseng, a perennial medicinal plant, utilizes its dried roots and rhizomes for medicinal purposes. Currently, in China, ginseng cultivation employs two methods: under-forest and farmland planting. These methods create distinct habitats, significantly influencing the ginseng’s rhizome morphology and, consequently, its economic value. In this study, two-year-old ginsengs were transplanted into farmland (TCG), a larch forest (TLCG) and a Quercus mongolica forest (TQCG) to analyze the differences in rhizome phenotypes caused by habitat changes. The results showed that there were significant differences in light intensity and the soil’s available phosphorus and potassium contents between farmland and forest environments. The differences in habitats led to different adaptability of the ginseng’s rhizome morphology. Compared with TCG, the rhizomes of TLCG and TQCG were significantly elongated by 48.36% and 67.34%, respectively. After the rhizomes’ elongation in TLCG and TQCG, there was an increase in indole-3-acetic acid (IAA) contents and a decrease in lignin contents. By analyzing the expression of key genes, we found that, compared with TCG, the expression of key enzymes of lignin biosynthesis genes such as PgCOMT and PgCCR4 were down-regulated. The difference in ginseng’s rhizome length is related to the signal transduction pathway of auxin and gibberellin. In addition, we preliminarily screened out transcription factors PgWRKY75, PgDIV, and PgbHLH93.1, which can actively respond to habitat changes and play important roles in the elongation of ginseng rhizomes. In summary, this study elucidates the phenotypic plasticity strategy of ginseng rhizomes in response to habitat changes and delineates the regulatory mechanism behind phenotypic adaptation, offering novel insights into ginseng’s morphogenesis.

The Influence of Habitat Diversity on Bat Species Richness and Feeding Behavior in Chilean Vineyards: Implications for Agroecological Practices

Agriculture is a leading cause of biodiversity loss, making the transition to sustainable agroecological practices crucial. Insectivorous bats play a crucial role as biological controllers in regard to agricultural crops, serving as important insect predators. The purpose of this study is to assess bat communities in three distinct habitats, namely the interior of a vineyard, native vegetation, and the transitional edge between them, by analyzing the echolocation patterns of different species. Generalized linear mixed models were used to evaluate the influence of landscape characteristics on bat communities and at the species level, allowing the incorporation of variables at different scales (at 10 m, 100 m, and 1000 m radius) from each sampling site. Our results show that edges enhance bat richness, their general activity, and feeding patterns, and are of particular benefit to certain species: Tadarida brasiliensis, Myotis chiloensis, and Lasiurus varius. Implementing agroecological practices, such as the maintenance of tree hedgerows at the landscape scale, along with native vegetation at the landscape scale, can amplify feeding activity in vineyards, thereby enhancing the provision of ecosystem services in agroecosystems. The edges of vineyards and natural vegetation are crucial for providing habitats for bats and increasing their foraging activity, as well as providing a way to enhance agroecological practices in vineyards to bolster ecosystem services.

Nanostructural Influence on Optical and Thermal Properties of Butterfly Wing Scales Across Forest Vertical Strata.

Butterfly wing scales feature complex nanostructures that influence wing coloration and various mechanical and optical properties. This configuration plays a key role in ecological interactions, flight conditions, and thermoregulation, facilitated by interactions with environmental electromagnetic energy. In tropical forests, butterflies occupy distinct vertical habitats, experiencing significant light and temperature variations. While wing nanostructures have been widely studied, their variation across different vertical flight preferences remains underexplored. This study investigates the wing nanostructures of 12 tropical butterfly species from the Nymphalidae family, focusing on their optical, morphological, and thermal properties across different forest strata. We analyzed the optical response through diffuse reflectance in the UV, Vis, and NIR ranges, correlating these findings with nanostructural configuration and thermal stability using thermogravimetric analysis (TGA). Our results reveal a significant correlation between flight stratification and wing optical responses, alongside distinct nanostructural features within each stratum. This study demonstrates the variability in butterfly wing nanostructures along the vertical stratification of the forest to cope with environmental conditions, raising new questions for future research on eco-evolutionary flight and thermal adaptations. Additionally, this underscores the importance of understanding how these structural adaptations influence butterfly interactions with their environment and their evolutionary success across different forest strata.

Montane willow scrub restoration in Scotland: reviewing 30 years of progress to reestablish the altitudinal treeline

Many mountain woodlands across the globe have undergone anthropogenic degradation with negative implications for the ecological and socioeconomic systems dependent on them. Montane willows are arctic‐alpine species of high nature conservation concern within the altitudinal treeline. Scotland has been pioneering the restoration of montane willow scrub for three decades following widespread loss linked particularly to overgrazing by sheep and deer since the eighteenth century. In the 1990s, the total area of montane willows throughout the country was less than 10 ha, with most remaining populations highly fragmented, in rapid decline, and restricted to inaccessible cliffs. Subsequently, montane willow scrub restoration has been part of an overall 2659 ha area managed for the recovery of mountain woodlands in Scotland. By May 2023, 396,868 montane willows were planted in projects encompassing large‐scale habitat creation, relict population reinforcement by genetic rescue, fencing, and landscape‐scale management for low‐density deer populations. This review summarizes restoration methods and outcomes with case study examples to promote conservation evidence and research on plant growth and survival, planting sites, associated biodiversity, molecular ecology, genomics, and long‐term population sustainability. With the potential for montane scrub restoration to be widely expanded, improved connectivity to revive a treeline mosaic shaped by regeneration will tackle biodiversity loss and help mitigate climate change impacts on a national scale. However, caution must be applied to creating definitions of distinct habitats for restoration that are based on non‐natural or ecologically degraded systems. These experiences are particularly relevant to montane and circumpolar regions with strongly modified landscape histories.

A highly variable habitat selection in moose across diel and seasonal scales

PurposeHabitat selection in animals is a hierarchal process that operates across multiple temporal and spatial scales, adapting to changes in environmental conditions, human disturbances, and predation risks. Despite its significance, previous research often oversimplifies temporal dynamics by categorizing them into broad seasonal and diel patterns, overlooking the continuous nature of temporal variability and habitat specificity.MethodsWe investigated the temporal patterns in habitat selection of moose (Alces alces) in highly heterogenous landscapes at the southwestern edge of their European range using step-selection functions. Utilizing over 700,000 GPS locations from 34 adult moose, we aimed to assess seasonal and diel patterns in their selectivity for both natural and human-related habitats.ResultsOur findings revealed significant overall temporal variation in moose habitat selection at both seasonal and diel scales. Moose selectivity toward different habitats showed low repeatability over time, with 35% of cases displaying negative correlation between selectivity in different time windows. Diel changes were more pronounced, showing 5.6-fold difference in cumulative selectivity, compared to 1.4-fold difference in seasonal dynamics. Notably, moose exhibited lower selectivity during nighttime hours throughout the year compared to daytime hours. The study also highlighted distinct habitat selection patterns across different habitat types: natural habitats (deciduous forests, coniferous forests, wetlands) exhibited pronounced seasonal variation, while anthropogenic habitats (grasslands, arable land, roads and settlements) showed more diel variability. Moose generally avoided human-related habitats during daytime hours, but their preferences during nighttime varied depending on the habitat type and time of year.ConclusionThis research advances our understanding of the complex temporal patterns in habitat selection by large herbivores and underscores the importance of considering temporal dynamics in habitat selection modelling.

Historical insights, current challenges: tracking marine biodiversity in an urban harbor ecosystem in the face of climate change

The Boston Harbor Islands is the only coastal drumlin archipelago in the USA, featuring a distinctive and uncommon geological intertidal habitat known as mixed coarse substrate, which supports a range of coastal species and ecological processes. Recently designated as one of America’s 11 most endangered historic places due to climate change impacts, coastal adaptation and restoration efforts are crucial to their preservation. Such efforts can benefit from historic and current knowledge of endemic and emergent biodiversity. To investigate broad trends in coastal biodiversity, we compiled an inventory of marine coastal macroalgae, macroinvertebrates, fish, mammals, and shorebirds observed in the harbor since 1861. Records span 159 years, consisting of 451 unique taxa from 19 phyla. Analysis of average taxonomic distinctness (AvTD) revealed increases in diversity towards the end of the twentieth and early twenty-first century, likely associated with improved water quality (dissolved oxygen; AvTD > 85, p = 0.01) due to harbor restoration in the 1980s. Macroinvertebrates comprised 50% of the records, making this the most diverse taxonomic group in the time series. A significant increase of non-indigenous species, primarily macroinvertebrates and macroalgae, was observed over the last 20 years near human infrastructure and across multiple islands, a consequence of global change and characteristic of most urban harbors. The mixed coarse intertidal habitat, which makes up > 70% of Boston Harbor’s inner islands and supports high macroinvertebrate and macroalgal diversity (47% of species records), is not routinely monitored; our findings serve as a foundational resource for climate adaptation projects and decision-making.

Temperature-Induced Seasonal Dynamics of Brain Gangliosides in Rainbow Trout (Oncorhynchus mykiss Walbaum) and Common Carp (Cyprinus carpio L.).

This study aimed to determine the expression and distribution of gangliosides in specific regions of the brains of rainbow trout (Oncorhynchus mykiss Walbaum) and common carp (Cyprinus carpio L.) with regard to seasonal temperature changes. Seasonal changes in ganglioside expression and distribution within the species were expected. The natural ecosystems of these fishes differ significantly due to their distinct habitat preferences, geographic distributions, and environmental requirements. Based on the fact that the common carp is eurythermic and adapts to a wide range of temperatures, while the rainbow trout is stenothermic and thrives in a narrower temperature range, it was expected that these species would exhibit distinct patterns of ganglioside modification as part of their adaptive response to temperature fluctuations. Immunohistochemistry using specific antibodies for the major brain gangliosides (GM1, GD1a, GD1b, GT1b), along with the Svennerholm method for quantifying sialic acid bound to gangliosides, revealed that cold acclimatization led to an increase in polysialylated gangliosides in the common carp brain and an increase in trisialogangliosides in the rainbow trout brain. Immunohistochemical analysis also identified region-specific changes in ganglioside expression, suggesting specific functional roles in neuronal adaptation. These results supported the hypothesis that the composition and distribution of brain gangliosides change in response to seasonal thermal shifts as part of the adaptive response. The results underscore the importance of gangliosides in neuronal function and adaptation to environmental stimuli, with implications for understanding fish resilience to temperature changes. This study offers valuable insights into species' temperature adaptation, with implications for physiological and ecological management and improved aquaculture practices. Future research could expand the species scale, study molecular mechanisms and regulatory pathways in ganglioside metabolism, and examine ganglioside interactions with membrane proteins and lipids for a deeper understanding of thermal adaptation.

Enrichment and characterization of thermophilic anaerobic ammonium oxidizing bacteria from hot spring

Anaerobic ammonium oxidization (Anammox) process plays a crucial role in the global nitrogen cycle and sustainable biological nitrogen removal from wastewater. Although Anammox bacteria have been detected across mesophilic and thermophilic conditions, the direct cultivation of Anammox bacteria from thermal environments has remained elusive. This impedes limiting our understanding of their physiology and ecology in high-temperature habitats. Here, we successfully enriched Anammox bacteria from hot spring sediments at 45 °C, achieving an ammonium oxidation rate of 158.0 mg NH4+-N l-1d-1, with the genus ‘Candidatus Brocadia’ presenting 22.9 % of the total microbial community after about 500 days of operation. Metagenomic analysis recovered two high-quality genomes of novel Anammox bacteria, which we designed as ‘Candidatus Brocadia thermophilus’ and ‘Candidatus Brocadia thermoanammoxidans’. Both of them encoded and actively expressed key metabolic genes involved in Anammox process and several genes associated with thermotolerance, demonstrating their remarkable ability to perform Anammox reaction in thermophilic environments. Notably, phylotypes related to ‘Candidatus Brocadia thermoanammoxidans’ have frequently been retrieved from geographically distinct natural habitats. These findings expand our understanding of thermophilic Anammox bacteria and underscore their potential in the nitrogen cycle of thermal natural and engineering ecosystems.

Habitat-mediated direct and indirect interactions in a marine sedimentary system from Atlantic Canada

Trophic cascades focusing on direct (consumptive) effects have been well studied in marine ecosystems. However, less attention has been given to cascades involving indirect interactions embedded in distinct habitats. We focused on the interactions between a non-indigenous predator (the green crab Carcinus maenas), a consumer (the mud crab Panopeus herbstii), and a prey species (juvenile eastern oysters Crassostrea virginica). These interactions were studied in 3 small yet distinct habitats of increasing complexity: bare sediments, patches of blue mussels Mytilus edulis (BM), and a unique habitat consisting of giant Irish moss Chondrus crispus and mussels combined (IMBM). In the field, green crab predation rates on mud crabs were estimated in each of the abovementioned habitats using tethering experiments. The results showed that green crab foraging was most effective in bare sediments and least effective in IMBM, i.e. the least and most complex habitats, respectively. Trials conducted in the laboratory with mud crabs foraging over oysters showed a similar outcome: oyster mortality rates declined with increased habitat complexity. However, when trials were conducted in the presence of a green crab, this pattern reversed, and oyster mortality was lowest in bare sediments. Mud crab behavior was consistent with these results: in the presence of a green crab, mud crabs were less active and spent more time sheltering, whereas in its absence, the opposite pattern was observed, especially in bare sediments. These behaviorally driven indirect interactions are dependent on the presence of a non-indigenous predator and mediated by the type of habitat.

Ski slopes as an unrecognized source of human impact on vegetation

AbstractVarious anthropogenic activities, e.g. construction, soil disturbance, and introducing artificial plant mixtures on newly-created ski slopes after forest clearing are significant interventions in ecosystems. These drastic acts influence the species composition of vegetation cover in the landscape. Although synanthropic species are typically infrequent in mountainous areas, they tend to flourish in disturbed environments; ski slopes are no exception to this pattern. Here we assessed the composition of vascular plants in three distinct ski slope habitats across 30 Slovak ski resorts: the ski lift entrance areas, the ski lift exit areas, and the central areas of the ski slopes. To gain insights into the dynamics of the spreading of synanthropic species on ski slopes, we used selected species traits, synanthropization indices for both flora and vegetation, and considered specific disturbance criteria. The outcomes of our study confirmed that the highest richness of synanthropic species was observed in plots located at the ski lift entrance areas, while the lowest in the central areas of the ski slopes. This difference could be attributed to the proximity of anthropogenically-disturbed zones, which act as propagule sources for synanthropic species into these mountainous habitats. At the same time, elevation also plays an important role in limiting spread of synanthropic plants on ski slopes. The study of synanthropic plant species distribution on ski slopes provides valuable insights into the complex interactions between human activities and the environment.

Acidic proteomes are linked to microbial alkaline preference in African lakes

Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.

Spatiotemporal patterns of greenhouse gas fluxes in the subtropical wetland ecosystem of Indian Himalayan foothill.

The study characterized the temporal and spatial variability in greenhouse gas (GHG) fluxes (CO2, CH4, and N2O) between December 2020 and November 2021 and their regulating drivers in the subtropical wetland of the Indian Himalayan foothill. Five distinct habitats (M1-sloppy surface at swamp forest, M2-plain surface at swamp forest, M3-swamp surface with small grasses, M4-marshy land with dense macrophytes, and M5-marshy land with sparse macrophytes) were studied. We conducted in situ measurements of GHG fluxes, microclimate (AT, ST, and SMC(v/v)), and soil properties (pH, EC, N, P, K, and SOC) in triplicates in all the habitat types. Across the habitats, CO2, CH4, and N2O fluxes ranged from 125 to 536mgm-2h-1, 0.32 to 28.4mgm-2h-1, and 0.16 to 3.14mgm-2h-1, respectively. The habitats (M3 and M5) exhibited higher GHG fluxes than the others. The CH4 flux followed the summer > autumn > spring > winter hierarchy. However, CO2 and N2O fluxes followed the summer > spring > autumn > winter. CO2 fluxes were primarily governed by ST and SOC. However, CH4 and N2O fluxes were mainly regulated by ST and SMC(v/v) across the habitats. In the case of N2O fluxes, soil P and EC also played a crucial role across the habitats. AT was a universal driver controlling all GHG fluxes across the habitats. The results emphasize that long-term GHG flux monitoring in sub-tropical Himalayan Wetlands has become imperative to accurately predict the near-future GHG fluxes and their changing nature with the ongoing climate change.

Adaptive radiation of the Callicarpa genus in the Bonin Islands revealed through double-digest restriction site-associated DNA sequencing analysis.

The Bonin Islands, comprised of the Mukojima, Chichijima, and Hahajima Islands, are known for their isolated and distinctive habitats, hosting a diverse array of endemic flora and fauna. In these islands, adaptive radiation has played a remarkable role in speciation, particularly evident in the Callicarpa genus that is represented by three species: Callicarpa parvifolia and C. glabra exclusive to the Chichijima Islands, and Callicarpa subpubescens, distributed across the entire Bonin Islands. Notably, C. subpubescens exhibits multiple ecotypes, differing in leaf hair density, flowering time, and tree size. In this study, we aimed to investigate species and ecotype diversification patterns, estimate divergence times, and explore cryptic species within Callicarpa in the Bonin Islands using phenotypic and genetic data (double-digest restriction site-associated DNA sequencing). Genetic analysis revealed that C. parvifolia and C. glabra both formed single, distinct genetic groups. Conversely, C. subpubescens consisted of six genetic groups corresponding to different ecotypes and regions, and a hybrid group resulting from the hybridization between two of these genetic groups. Population demography analysis focusing on six Chichijima and Hahajima Islands-based species/ecotypes indicated that all species and ecotypes except one ecotype diverged simultaneously around 73-77 kya. The star-shaped neighbor-net tree also suggests the simultaneous divergence of species and ecotypes. The species and ecotypes that simultaneously diverged adapted to dry environments and understory forests, suggesting that aridification may have contributed to this process of adaptive radiation. Moreover, leaf morphology, flowering time, and genetic analyses suggested the presence of two cryptic species and one hybrid species within C. subpubescens.

A catalog of small proteins from the global microbiome

Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.

Identification and application of quality elements, indicators, and criteria for assessment of impact on habitats in marine Natura 2000 areas

The EU Habitat Directive adopted in 1992, requires member states of the European Union to protect species and habitats considered to be of ‘Community Interest’ and listed in annexes to the directive. The appropriate environmental assessment of “plans and projects” is an important part of the conservation process. Despite several amendments and guidelines supporting the implementation of the Habitat Directive, science based operational procedures, indicators, and impact criteria for assessing potential negative impacts on marine Natura 2000 areas are still lacking. The lack of a generic and operational methodology complicates the management of plans and projects with potential impact on marine Natura 2000 areas. In this study, generic methods for the assessment of marine aquaculture in the inner Danish waters in relation to Natura 2000 areas was developed and applied for assessment of nine existing marine fin fish farms, in accordance with the latest methodological guidance on the provisions of Article 6(3) and (4) of the Habitat Directive. The applied methodology is based on high resolution 3D hydrodynamic- and ecosystem modelling (MIKE by DHI), that describes the dynamical physical, chemical, and biogeochemical processes and changes of marine ecosystems in time and space. To our knowledge, this is the first study that formulates operational biological quality elements, key indicators, concrete and generic impact criteria, and assessment procedures for operational assessment across several distinct marine habitat types. The method represents a generic, operational, transparent, and science-based assessment tool, that simplifies management, and is widely applicable for quantification of environmental impacts from various marine activities and eutrophication related pressures across geographical zones and different marine habitat types in marine Natura 2000 areas.