Globally, biodiversity is at risk of extinction, and megadiverse countries become key targets for conservation. South Africa, the only country hosting three biodiversity hotspots, harbours tremendous diversity of at-risk species deserving to be protected. However, the lengthy risk assessment process and the lack of required data to complete assessments is a serious limitation to conservation since several species may slide into extinction while awaiting risk assessment. Here, we employed deep neural network model integrating species climatic and geographic features to predict the conservation status of 116 unassessed plant species. Our analysis involved in total 1072 plant species and 112 066 occurrence points. The best-performing model exhibits high accuracy, reaching up to 83.6% at the binary classification and 56.8% at the detailed classification. Our best-performing model predicts that 32% and 8% of Data Deficient and Not-Evaluated species are likely threatened, respectively, amounting to a proportion of 24.1% of unassessed species facing a risk of extinction. Interestingly, all unassessed species predicted to be threatened are in protected areas, revealing the effectiveness of the South Africa’s network of protected areas in conservation, although these likely threatened species are more abundant outside protected areas. Considering the limitation in assessing only species with available data, there remains a possibility of a higher proportion of unassessed species being imperiled.

The oceanographic conditions of the Southern California Bight (SCB) dictate the distribution and abundance of prey resources and therefore the presence of mobile predators, such as Cuvier’s beaked whales (Ziphius cavirostris). Cuvier’s beaked whales are deep-diving odontocetes that spend a majority of their time foraging at depth. Due to their cryptic behavior, little is known about how they respond to seasonal and interannual changes in their environment. This study utilizes passive acoustic data recorded from two sites within the SCB to explore the oceanographic conditions that Cuvier’s beaked whales appear to favor. Utilizing optimum multiparameter analysis, modeled temperature and salinity data are used to identify and quantify these source waters: Pacific Subarctic Upper Water (PSUW), Pacific Equatorial Water (PEW), and Eastern North Pacific Central Water (ENPCW). The interannual and seasonal variability in Cuvier’s beaked whale presence was related to the variability in El Niño Southern Oscillation events and the fraction and vertical distribution of the three source waters. Cuvier’s beaked whale acoustic presence was highest during the winter and spring and decreased during the late summer and early fall. These seasonal increases occurred at times of increased fractions of PEW in the California Undercurrent and decreased fractions of ENPCW in surface waters. Interannual increases in Cuvier’s beaked whale presence occurred during El Niño events. These results establish a baseline understanding of the oceanographic characteristics that correlate with Cuvier’s beaked whale presence in the SCB. Furthering our knowledge of this elusive species is key to understanding how anthropogenic activities impact Cuvier’s beaked whales.

Invasive omnivores may have profound impacts on ecological communities through diet selection, particularly when their functional roles differ from those in their native range. While the threat of feral pigs (Sus scrofa) to native plant communities in Hawai‘i are well known, their trophic dynamics and the drivers of variation in their diet remain understudied. We investigated the feral pig dietary niche on Hawai‘i Island using stable isotopes (13C and 15N) and Bayesian mixing models to identify drivers of variation in resource use. We also chronologically reconstructed diets for six subsampled individuals to understand temporal variation in resource use and individual diet specialization. Our results revealed feral pigs on Hawai‘i Island exhibit a broad dietary niche characterized by diverse diets, with substantial overlap in resource use across districts and habitats. Differences in dietary composition in the transition from forest to open habitat were driven primarily by an increasing reliance on human food subsidies in conjunction with a decreasing reliance on invertebrates, which may be partially driven by protein constraints on dietary composition. Pigs in forested areas largely displayed generalist feeding strategies, while those in open habitat tended to specialize, particularly on human food resources. Diets for chronologically subsampled individuals varied little, suggesting feral pig resource-use strategies in Hawai‘i tend to be stable through time. Individual niche-width was relatively narrow compared to that of feral pigs in Hawai‘i at large, indicating the relatively wide feral pig dietary niche is characterized by substantial intraspecific diet specialization, likely as a result of strong intraspecific competition. Understanding the drivers of feral pig resource use is crucial for informing management strategies aimed at mitigating their ecological impacts in imperiled systems like Hawai‘i.

Many social insect species build nests, which strongly differ from the surrounding environment and are often occupied by specific organismal communities. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create such distinct, highly developed nests, which consist of large, above-ground mounds. Those structures are built primarily out of plant matter collected from the forest litter. Common fungal dwellers of forest litter are representatives of Mucoromycota, engaged in the decomposition process of this substrate. However, data on co-occurrence or interactions between these ants and fungi remains unknown. In order to elucidate these interactions we characterized Mucoromycota communities of Formica polyctena nests and the surrounding forest litter. We sampled four sites, twice in a season and used: a culturomics approach, complemented with DNA barcoding to describe fungal communities; PERMANOVA test and non-metric multidimensional scaling ordinations to compare those communities; and multilevel pattern analysis to indicate taxa associated with the mounds. Our results show that the Mucoromycota community of Formica polyctena’s mound is specific and more stable than the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants’ nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in close proximity to ants.

Past forest use often has a long-term negative impact on the recovery of the original plant composition of semi-natural grasslands, which are known as a legacy effect. This study investigates the impact of seed dispersal limitations on the restoration of grassland plant diversity on ski slopes with past forest use, highlighting the negative legacy effect on biodiversity recovery. Focusing on ski areas, our research contrasts the vegetation on ski slopes originally created on semi-natural grasslands such as pasture (pasture slopes) and constructed by clearing secondary forests or conifer plantations (forest slopes). We examined species richness and abundance, considering seed dispersal mechanisms, grassland management history and seed source proximity. We reveal that the proximity to species-rich grassland sources and sustained management for more than 50 years are pivotal for the restoration of native grassland vegetation. Particularly, wind-dispersed species show significant recovery on slopes with a history of extensive grassland management, suggesting that both the duration of management and the proximity to seed sources are critical for overcoming the legacy effects of past forest use. Our findings emphasize the importance of considering seed dispersal dynamics and management history in the restoration and conservation of grasslands and their biodiversity, particularly in landscapes experiencing past human intervention.

1. Rivers are crucial ecosystems supporting biodiversity and human well-being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. 2. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain. 3. DNA metabarcoding of homogenised bulk samples and water eDNA revealed a mean of 100 and 87 macrozoobenthos species per sample respectively. However, it was a significantly different specific composition with only 27.3% of the total species shared. It was not possible to identify all the OTUs to species level, only 17.43% and 49.4% of the OTUs generated could be identified to species level In the Bulk and eDNA samples respectively. However, a total of 11 exotic species (2 first records for the Iberian Peninsula and another 3 first records for Asturias region) and 1 endangered species were detected by molecular tools. Molecular methods showed significant correlations with morphological identification for EQR values (Ecological quality ratio) of IBMWP index, yet differences in inferred river ecological status were noted, with bulk samples tending to indicate higher status. 4. Overall, DNA metabarcoding offers a promising approach for river biomonitoring, providing insights into biodiversity, invasive species, and ecological status within a single analysis. Further optimization and intercalibration are needed for its implementation in routine biomonitoring programs, but its scalability and multi-tasking capabilities position it as a valuable tool for integrated monitoring of river ecosystems.

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (He = 0.55) was lower than reported in the mainland (He = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador’s northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands’ local flora and fauna.

1. This study introduces a novel approach for quantitatively assessing sea-surface paleotemperatures exemplified in the study of the Upper Paleozoic of Siberia. 2. The method relies on the evaluation of the taxonomic composition of biota. It utilizes a comprehensive dataset encompassing the geographic distribution and ecology of various biotic groups in Siberia and adjacent regions, leveraging the newly developed PaleoSib database. Fossils collected from individual locations often exhibit a wide spectrum of paleotemperatures. 3. To address this variability, we developed an algorithm for calculating average biotic paleotemperatures in each locality/time slice. Utilizing the PaleoSib database, our computations have unveiled a coherent pattern of paleoclimate dynamics, particularly Sea Surface Temperature, across Siberian basins during the Late Paleozoic era. 4. These findings significantly contribute to a refined comprehension of paleoclimate and paleotectonic dynamics in the region during that specific time. To enhance paleotemperature analyses, we have integrated lithological indices with biotic ones, fortifying the overall methodology and furnishing a more robust framework for interpreting paleoclimate data. We aim to incorporate this method into the Paleobiology Database, enhancing its accessibility and fostering its adoption by the broader scientific community.

Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri-urban forests. A notable case are fir(Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 pollution since the 1970s. Interestingly, some young individuals exhibiting minimal O3—related damage have been observed within a zone of significant O3 exposure. Using this setting as a natural experiment, we compared asymptomatic and symptomatic individuals of similar age (≤15 years old; n = 10) using histological, metabolomic and transcriptomic approaches. Plants were sampled during days of high (170 ppb) and moderate (87 ppb) O3 concentration. Given that there have been reforestation efforts in the region, with plants from different source populations, we first confirmed that all analysed individuals clustered within the local genetic group when compared to a species-wide panel (Admixture analysis with ~1.5K SNPs). We observed thicker epidermis and more collapsed cells in the palisade parenchyma of needles from symptomatic individuals than from their asymptomatic counterparts, with differences increasing with needle age. Furthermore, symptomatic individuals exhibited lower concentrations of various terpenes (ß-pinene, ß-caryophylene oxide, α-caryophylene and ß-α-cubebene) than asymptomatic trees, as evidenced through GC-MS. Finally, transcriptomic analyses revealed differential expression for thirteen genes related to carbohydrate metabolism, plant defense, and gene regulation. Our results indicate a rapid and contrasting phenotypic response among trees, likely influenced by standing genetic variation and/or plastic mechanisms. They open the door to future evolutionary studies for understanding how O3 tolerance develops in urban environments, and how this knowledge could contribute to forest restoration.

Secondary forests represent significant proportions of global forest cover, with over 65% of forests in Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of sub-tropical forest succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity subcomponents of Turnover and Nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigated plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary sub-tropical forests in Hong Kong. Plant survey data for 28 plots were analysed, generating additive Simpsons and Nestedness beta diversity metrics as subcomponents of Sorenson Beta Diversity. Dissimilarity matrices were generated and modelled as a function of transformed environmental matrices of forest plant community age (years following onset of secondary succession), elevation (metres), inter-community distance (metres), soil moisture saturation (%) and soil organic carbon (g kg-1). Generalized dissimilarity models were generated for plant species Turnover and Nestedness. Nonmetric Multidimensional Scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Our findings indicate that elevation was the primary driver of plant species Turnover, while age and inter-community distance played less prominent roles. Models of Nestedness found that plot age and soil moisture saturation were the sole drivers of Nestedness patterns in plant communities. While models of Turnover were robust, the low explanatory power of Nestedness models suggest additional unobserved factors driving patterns of plant community Nestedness during secondary succession. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between Lowland and Montaine forest types, as well as between successional age classes.

Although the postdispersal function of fruit appendages has been reported, little is known about their protective/defensive functions. In this context, diaspores with appendages (persistent inner tepals and/or fruit wings) that experienced predispersal herbivory by insects in natural populations of Rheum nanum were investigated. The seed abortion percentage, seed and embryo masses, and germination of seeds from diaspores with different categories of insect herbivory were measured and compared. Predispersal insect herbivory of R. nanum diaspores was prevalent in the four natural populations, but the percentage of diaspores with appendages (persistent inner tepals and and/or fruit wings) damaged by insects was significantly higher than that of diaspores with the pericarp damaged by insects. Seeds from diaspores with gnawed appendages experienced significantly less damage than those with gnawed pericarps. Importantly, we conclude that fruit appendages of Rheum nanum help to mechanically protect developing seeds from predispersal insect herbivory.

Gene flow is important for maintaining the genetic diversity required for adaptation to environmental disturbances, though gene flow may be limited by site fidelity in small coastal sharks. Bonnethead sharks (Sphyrna tiburo) - a small coastal hammerhead species - demonstrate site fidelity, as females are philopatric while males migrate to mediate gene flow. Consequently, bonnetheads demonstrate population divergence with distance and Atlantic populations are genetically distinct from those of the Gulf of Mexico. Indeed, Florida forms a vicariant zone between these two bodies of water for many marine species, including some sharks. However, while bonnetheads are expected to have limited dispersal, the extent and rate of bonnethead migration remains uncertain. Thus, we aimed to determine their dispersal capacity by evaluating connectivity between disparate populations from the Gulf of Mexico and Atlantic Ocean. Using 10,733 SNPs derived from 2bRAD sequences, we evaluated genetic connectivity between Tampa Bay on the Gulf Coast of Florida and Biscayne Bay on the Atlantic coast of Florida. While standard analyses of genetic structure revealed little differentiation between Tampa Bay and Biscayne Bay populations, demographic history inference based on the site frequency spectrum favored the model with divergence between 2000 - 6000 years ago, with continuous unidirectional gene flow from Tampa Bay to Biscayne Bay. Combined with prior findings of small-scale genetic divergence in bonnethead mitochondrial (female-transmitted) loci, our findings support the hypothesis that female bonnetheads are highly philopatric while male bonnetheads often migrate over relatively large distances (>300 miles) to find mates. Together, these results provide optimism that under proper management, a small-bodied globally Endangered shark can undergo long migrations to sustain genetic diversity.

1. Organisms have evolved diverse strategies to manage parasite infections. Broadly, hosts may avoid infection by altering behaviour, resist infection by targeting parasites, or tolerate infection by repairing associated damage. Effectiveness of a strategy depends on interactions between, e.g., resource availability, parasite traits (virulence, life-history) and the host itself (nutritional status, immunopathology). 2. To understand how these factors shape host parasite-mitigation strategies, we developed a mathematical model of within-host, parasite-immune dynamics in the context of helminth infections. The model incorporated host nutrition and resource allocation to different mechanisms of immune response: larval parasite prevention; adult parasite clearance; damage repair (tolerance). We also considered a non-immune strategy: avoidance via anorexia, reducing intake of infective stages. Resources not allocated to immune processes promoted host condition, whereas harm due to parasites and immunopathology diminished it. Maximising condition (a proxy for fitness), we determined optimal host investment for each parasite-mitigation strategy, singly and combined, across different environmental resource levels and parasite trait values. 3. Which strategy was optimal varied with scenario. Tolerance generally performed well, especially with high resources. Success of the different resistance strategies (larval prevention or adult clearance) tracked relative virulence of larval and adult parasites: slowly maturing, highly damaging larvae favoured prevention; rapidly maturing, less harmful larvae favoured clearance. Anorexia was viable only in the short-term, due to reduced host nutrition. Combined strategies always outperformed any lone strategy: these were dominated by tolerance, with some investment in resistance. 4. Choice of parasite mitigation strategy has profound consequences for hosts, impacting their condition, survival and reproductive success. We show the efficacy of different strategies is highly dependent on timescale, parasite traits and resource availability. Models that integrate such factors can inform the collection and interpretation of empirical data, to understand how those drivers interact to shape host immune responses in natural systems.

The Deep Reef Refugia Hypothesis suggests that disturbances decrease with increasing depth, thus, reefs at the mesophotic zone potentially serve as refuges for communities found in shallower areas. This study aimed to evaluate fish diversity at shallow and mesophotic reefs at Parque Nacional Espíritu Santo (PNZMAES) and compare them to determine if deep reefs indeed serve as refuges for shallow communities. During 2021-2022 we conducted five-minute video-transects using remotely operated vehicles to document species richness and abundance at shallow and mesophotic habitats. For the recorded species, six biological traits were compiled (length, mobility, position, gregariousness, diet, and activity period) to estimate four functional indices (number of entities, richness, originality, and divergence) as well as Hill’s numbers for taxonomic and functional indices. Furthermore, monthly water turbidity (Kd490) satellite data products were transformed into a light attenuation coefficient (KdPAR) to locate the mesophotic zone (area between 10 and 0.1% of light penetration). At PNZMAES, the mesophotic zone was identified to extend to 21 m under optimal conditions (high stratification and low primary production), which is shallower compared to what is typically observed in oligotrophic regions. The PERMANOVA revealed significant variations in reef fish composition across spatial (site and zone) and temporal (season and year) dimensions. Additionally, univariate tests of functional richness, originality, and taxonomic Hill’s numbers exhibited significantly higher values in the shallow zone. However, functional divergence and functional Hill’s numbers indicated similarities in fish assemblages. Despite differences in fish taxonomic diversity among zones that could be related to less habitat complexity, environmental variation, and resource availability at deep strata, mesophotic reef fish assemblages presented similar functions. This maintenance of functions at mesophotic reefs suggests connectivity between zones and their potential role as a partial refugia in the face of current and near-future disturbances that could affect shallow zones.

Deep lakes are critical for freshwater storage, although they are struggling against major ecological issues from climate change and nutrient pollution. A comprehensive understanding of internal feedback mechanisms would be helpful for nutrient regulation within such lakes. A five-year consecutive study of the diatom community and its abiotic environment was conducted in Lake Fuxian, which is the largest deep freshwater lake in China and is currently heading toward a eutrophic state. The results indicate a shift in the diatom community from a stable state dominated by a single species to a rapid seasonal fluctuation, along with a significant increase in diatom biomass. Specifically, stable stratification and low nutrient concentrations are limiting the growth of diatom biomass and maintaining the dominance of Cyclotella. Nutrients in the hypolimnion were replenished in the epilimnion during the extreme cold of winter, triggering a shift in the diatom community. This shift may imply that future climate change will exacerbate the positive feedback of hypoxia-nutrient release of algal blooms, potentially triggering a regime shift in the ecosystem of the entire lake. This study underscores the fact that climate change alters the internal feedback mechanisms of deep lakes and reduces the stability of their ecosystems, and provides a scientific basis for further clarification of protection measures for deep lakes.

Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacteria in wild non-primate mammals. Here we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate, and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. Civetta, while in Genetta spp. we observed an opposite pattern. We further found that individuals with similar diets have similar gut bacterial communities in both species. This association tended to be driven by specific associations of dietary items to specific gut bacterial taxa, rather than entire communities, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of wild mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat change.

Aim: The genus Stasimopus is endemic to South Africa but has never undergone a phylogeographic review. This study aims to unravel the phylogeographic patterns and history of the many Stasimopus species which occur in the greater Karoo region. Location: The Karoo region, South Africa Time period: 2017-2018 Major taxa studied: Cork-lid trapdoor spider, Stasimopus (15 species). Methods: A fossil-calibrated phylogeny was produced based on three gene regions (CO1, 16S and EF-1ɣ) for Stasimopus specimens collected in the Karoo region, to infer dates of origin and diversification. Demographic analyses were performed on species with sufficient sample sizes (>4). Haplotype networks were constructed for each gene region and plotted on a map to infer phylogeographic patterns. Lastly, Mantel tests were performed to test for isolation by distance. Results: It was found that 15 species occur in the Karoo and that the genus radiation in the area is in the early Paleocene. Most diversification occurred between the late Eocene and the Miocene. Several species show signals of demographic expansions. Isolation by distance was detected, but only with a slight correlation. Main conclusions: It is apparent that aridification has played a vital role in the diversification of the genus in the Karoo region. This is a shared biogeographic influence between the mygalomorph fauna of the Karoo and arid region of western Australia. Stasimopus has radiated from the late Eocene and through the Miocene resulting in 15 extant species in the region. The Tankwa Karoo has been identified as a possible Pleistocene glacial cycle refugia for the species S. leipoldti. Many of the species in the Karoo are short range endemics, making them of high conservation concern. This study provided vital information as the Karoo is undergoing further desertification due to factors such as climate change, which may affect the future of short-range endemic spiders.

Livestock grazing can strongly determine how grasslands function and their role in carbon cycle. However, how ecosystem carbon exchange responds to grazing and the underlying mechanisms remain unclear. We measured ecosystem carbon fluxes to explore the changes in carbon exchange and their driving mechanisms in a 16-year long term experiment with different grazing intensities in a desert steppe grassland. We found that grazing intensity influenced above- and belowground biomass during the peak growing season, primarily by decreasing shrubs and semi-shrubs and perennial forbs. Furthermore, alter patterns of net ecosystem exchange primarily via their negative influence on the biomass of shrub and semi-shrub. In addition, grazing-induced reduction belowground biomass, as well as in total plant nitrogen and soil ammonium nitrogen, can strongly influence ecosystem carbon exchange and soil respiration. When nitrogen is lost from the soil due to grazing, plants reallocate resources belowground to maintain growth and development, thus promoting photosynthesis and respiration. Our study indicates that soil available nitrogen and shrubs and semi-shrubs are important factors in regulating ecosystem carbon exchange under grazing disturbance in the desert steppe, which provide a basis for grazing management.