Jane Hallam

Prey depletion and human–wildlife conflict threaten the critically endangered West African populations of lion ( Panthera leo leo ), which occupy less than 1.1% of their historic range in West Africa. These threats may alter behaviour through prey selection and affect exposure to parasites to compromise their health. We extracted DNA from faecal samples collected in four national parks in Benin, Burkina Faso and Senegal to characterize haemoparasites, nemabiome and microbiome. We used microsatellite markers to differentiate individuals and five primer sets to complete molecular analyses. From 20 individuals (12 males and 8 females), we found significant differences in the species richness and composition for all parasite groups across host populations and individual lions. We detected haemoparasites, including Babesia and Sarcocystis species, along with Blechomonas , a kinetoplastid, all of which raise potential health concerns. The nemabiome was dominated by Ancylostoma species (hookworms) with additional detections of lungworms from the genera Oslerus and Troglostrongylus . Significant interactions were found between population-level microbiome richness and both nemabiome and haemoparasite diversity. Our study provides the first effort to determine the parasite diversity among West African lion populations using non-invasive metabarcoding. Our findings highlight metabarcoding as a powerful tool to assess spatial variation in health and parasite diversity metrics for an endangered apex predator.

Urban ecosystems are expanding rapidly, significantly altering natural landscapes and impacting biodiversity. Here we explore seasonal variation in mammal diversity using environmental DNA (eDNA) from soil samples collected during winter and summer across 21 urban parks in Detroit, Michigan. We estimated gamma (regional), alpha (local) and beta (compositional change) diversity to determine if seasonal shifts, reflecting winter scarcity and summer abundance in mammal community composition and human activity, could be detected using eDNA. We expected that larger parks would exhibit greater diversity and higher seasonal turnover, consistent with the species‐area relationship (SAR) and hypothesised that increased summer resource availability would lead to decreased network density as species disperse more broadly. We found that urban parks show subtle, park‐specific changes in community composition influenced by both ecological and anthropogenic factors, with species including striped skunk, brown rat and groundhog responsible for the observed seasonal variation. Consistent with the SAR, larger parks supported higher species richness and diversity. Ecological network analysis, focusing on metrics such as clustering coefficient and network density, revealed a decrease in the overall connectivity and cohesiveness of species interactions from winter to summer, supporting our hypothesis of broader species dispersal during resource‐rich periods. Notably, human DNA was prevalent in all parks, alongside detections of pig and cow eDNA, potentially reflecting human disturbance and anthropogenic food inputs. Our findings underscore the efficacy of eDNA analysis in capturing urban mammal community dynamics, the impact of human activities on biodiversity and its potential as a valuable tool for urban ecological research. Ultimately, enhancing monitoring capacity aids in conservation and urban planning efforts that will promote human‐wildlife coexistence and preserve the socio‐ecological benefits stemming from biodiversity across cityscapes.

Long‐term monitoring is critical to measure the response of biodiversity patterns and processes to human‐mediated environmental pressures. This is particularly pertinent in freshwaters, where recent estimates indicated a third of all fish species are threatened with extinction, making ongoing biomonitoring essential for conservation management. High frequency annual monitoring is critical for identifying temporal changes in fish community composition; however, traditional survey methods are typically less practical over such timeframes. While environmental (e)DNA measurement represents a potentially powerful tool for monitoring temporal community dynamics, studies are lacking. To address this deficit, we generated a high frequency time‐series dataset of entire fish communities using eDNA metabarcoding, to directly assess the repeatability and sensitivity of this method for detecting annual population trends. We targeted two differing environments (freshwater vs. intertidal) within the Thames catchment, UK, where detailed historical records from traditional monitoring were available for comparison. To test how robust eDNA data is for inferring the known community, we applied a hierarchical, nested design encompassing short and longer‐term variation in eDNA data. Our analyses showed that irrespective of environment, eDNA metabarcoding represented known seasonal shifts in fish communities, where increased relative read abundance of eDNA coincided with known migratory and spawning events, including those of the critically endangered native species Anguilla anguilla (European eel). eDNA species detections across a single year included over 75% of species recorded in a ca. 30‐year historical dataset, highlighting the power of eDNA for species detection. Our findings provide greater insight into the utility of eDNA metabarcoding for recovering temporal trends in fish communities from dynamic freshwater systems and insight into the potential best sampling strategy for future eDNA surveys.

Ongoing anthropogenic change is altering the planet at an unprecedented rate, threatening biodiversity, and ecosystem functioning. Species are responding to abiotic pressures at both individual and population levels, with changes affecting trophic interactions through consumptive pathways. Collectively, these impacts alter the goods and services that natural ecosystems will provide to society, as well as the persistence of all species. Here, we describe the physiological and behavioral responses of species to global changes on individual and population levels that result in detectable changes in diet across terrestrial and marine ecosystems. We illustrate shifts in the dynamics of food webs with implications for animal communities. Additionally, we highlight the myriad of tools available for researchers to investigate the dynamics of consumption patterns and trophic interactions, arguing that diet data are a crucial component of ecological studies on global change. We suggest that a holistic approach integrating the complexities of diet choice and trophic interactions with environmental drivers may be more robust at resolving trends in biodiversity, predicting food web responses, and potentially identifying early warning signs of diversity loss. Ultimately, despite the growing body of long‐term ecological datasets, there remains a dearth of diet ecology studies across temporal scales, a shortcoming that must be resolved to elucidate vulnerabilities to changing biophysical conditions.

While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer have considered riverine systems, particularly those spanning the environmental gradients present in large river basins. Such dynamic systems are challenging for eDNA biomonitoring due to differing eDNA transport distances in rivers and the effects of river chemistry. To address this challenge, we focused on the Thames River system, UK, which has exceptional historical fish records providing a baseline to test the accuracy of eDNA metabarcoding in recovering fish community structure across both fresh and tidal zones. Two primer sets targeting 12S and CO1 regions were used to capture fish communities across the Thames catchment, from the upper freshwaters to the mid estuary. eDNA was collected at 35 sites, 14 of which were simultaneously paired with traditional fish surveys for direct comparison. We demonstrated that eDNA metabarcoding consistently detected more freshwater species than traditional methods, despite extensive sampling effort using the latter. In contrast, metabarcoding did not perform as well as traditional approaches in estuarine waters, although results included the novel detection of the protected sea lamprey. We further demonstrated that minor variations in the recovery of all approaches would not impact on the assessment of simple ecological models of community structure and, thus, some variability between approaches should not be viewed as a serious hindrance to uptake. Rather, our findings support a growing consensus that eDNA can reliably detect fish communities across dynamic freshwater habitats.