Explore the vast range of titles available.

Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and taxonomic resolution. In particular, DNA metabarcoding (PCR-amplification and next generation sequencing of complex DNA mixtures) has seen a rapid growth in the field of wildlife ecology to assess species’ diets from faecal and gastric samples. Despite clear advantages, molecular approaches have not yet been established in routine human forensics to investigate the last meal components of deceased persons. In this pilot study we applied for the first time a DNA metabarcoding approach to assess both plant and vertebrate components of 48 human stomach content samples taken during medicolegal autopsies. We obtained a final dataset with 34 vertebrate and 124 vegetal unique sequences, that were clustered to 9 and 33 operational taxonomic units (OTUs), respectively. Our results suggest that this approach can provide crucial information about circumstances preceding death, and open promising perspectives for biomedical dietary surveys based on digested food items found in the gastrointestinal tract.

With increasing human domination of ecosystems, wildlife must either relocate or adapt its behaviour to anthropogenic impacts in order to survive. Vervet monkeys (Chlorocebus pygerythrus), whose natural habitats have been progressively encroached upon by urban expansion, have successfully adapted to urbanised environments because of their flexible and generalist feeding behaviour. Characterising diet composition of vervet monkeys can therefore reveal how they exploit anthropogenic resources and uncover opportunistic foraging behaviours. However, accurately determining complete diets through direct observations is challenging. In this study, we used an environmental DNA (eDNA) approach investigating the DNA mixtures present in faecal samples as a non‐invasive complementary method for assessing diet and foraging strategies. We identified the dietary components of vervet monkeys through DNA metabarcoding of 447 faecal samples collected from two monkey groups over 4 months in a semi‐urban neighbourhood in South Africa. We further compared the results with observational data on foraging to describe how vervet monkeys exploit anthropogenic resources. Subsequently, we evaluated whether dietary patterns can be distinguished between groups and within matrilineal levels. We found DNA metabarcoding data to be consistent with observational data, but the former revealed a broader diversity of consumed taxa. Additionally, we detected a difference in diet between the two investigated groups, and a tendency for similar dietary patterns among matrilineal pairs compared to other group members. Our results support the use of the DNA metabarcoding methodology, both to determine the complex diet of omnivorous species in urbanised ecosystems and to address interindividual foraging behaviours. We used eDNA metabarcoding of faecal samples to quantify the dietary composition of two vervet monkey populations in a semi‐urban environment in South Africa over a 4‐month period, and compared these results with visual observations. We found that both methods yielded similar results, but eDNA metabarcoding revealed a greater diversity of consumed taxa. We also detected dietary differences between the groups, as well as a similar pattern among matrilineal individuals compared to other group members.

Accurate detection and identification of vector-host-parasite systems are key to understanding their evolutionary dynamics and to design effective disease prevention strategies. Traditionally, microscopical and serological techniques were employed to analyse arthropod blood meals for host/parasite detection, but these were limited in taxonomic resolution and only to pre-selected taxa. In recent years, molecular techniques have emerged as a promising alternative, offering enhanced resolution and taxonomic range. While singleplex polymerase chain reaction (PCR) assays were used at first to identify host, vector and parasite components in separate reactions, today multiple primer pairs can be combined in a single reaction, i.e. , multiplex, offering substantial time and cost savings. Nonetheless, despite the potential benefits of multiplex PCR, studies quantifying its efficacy compared to singleplex reactions are scarce. In this study, we used partially digested mosquito blood meals within an avian malaria framework to jointly identify the host, vector and parasite using multiplex DNA metabarcoding, and to compare it with separate singleplex PCRs. We aimed to compare the detection probabilities and taxonomic assignments between both approaches. We found both to have similar performances in terms of detection for the host and the vector, but singleplex clearly outperformed multiplex for the parasite component. We suggest adjusting the relative concentrations of the PCR primers used in the multiplex assay could increase the efficiency of multiplex in detecting all the components of the studied multi-species system. Overall, the results show that multiplex DNA metabarcoding can be an effective approach that could be applied to any vector-borne interaction involving blood-feeding arthropods. Our insights from this proof-of-concept study will help improve laboratory procedures for accurate and cost-efficient medical diagnosis of vector-borne diseases, the spread of which is globally exacerbated by current climate change.

Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still required to highlight strengths and potential biases of different approaches. Therefore, this study compares environmental DNA and observational methods for the same study population and sampling duration. We employed DNA metabarcoding assays targeting plant and arthropod diet items in 823 fecal samples collected over 12 months in a wild population of an omnivorous primate, the vervet monkey (Chlorocebus pygerythrus). DNA metabarcoding data were subsequently compared to direct observations. We observed the same seasonal patterns of plant consumption with both methods; however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations, mostly due to the construction of a local plant DNA database. We found a strong effect of season on variation in plant consumption largely shaped by the dry and wet seasons. The seasonal effect on arthropod consumption was weaker, but feeding on arthropods was more frequent in spring and summer, showing overall that vervets adapt their diet according to available resources. The DNA metabarcoding assay outperformed also direct observations of arthropod consumption in both taxonomic coverage and resolution. Combining traditional techniques and DNA metabarcoding data can therefore not only provide enhanced assessments of complex diets and trophic interactions to the benefit of wildlife conservationists and managers but also opens new perspectives for behavioral ecologists studying whether diet variation in social species is induced by environmental differences or might reflect selective foraging behaviors. In this study, we compare observational and eDNA methodologies for studying plant and arthropod diet items of wild vervet monkeys (Chlorocebus pygerythrus). We observed the same seasonal patterns with both methods, however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations. The application of a DNA metabarcoding approach can be useful not only for conservation studies aimed at disentangling complex diets or reveal trophic interactions, but also opens new perspectives for behavioural ecologists studying social species in the wild.

[This corrects the article DOI: 10.1371/journal.pone.0279672.].

Understanding the relationship between a species feeding strategy and its environment (trophic ecology) is critical to assess environmental requirements and improve management policies. However, measuring trophic interactions remains challenging. Among the available methods, quantifying the plant composition of a species’ diet indicates how species use their environment and their associated niche overlap. Nevertheless, most studies focusing on herbivore trophic ecology ignore the influence that landscape variability may have. Here, we explored how landscape variability influences diet composition through niche overlap. We used eDNA metabarcoding to quantify the diet composition of two large herbivores of the Bialowieza Forest, red deer ( Cervus elaphus ) and European bison ( Bison bonasus ) to investigate how increasing habitat quality (i.e. higher abundance of deciduous forage species) and predation risk (i.e. density of wolf in the area) influence their diet composition and niche partitioning. Our findings indicate diet composition is non-homogeneous across the landscape, both within and between species. Red deer showed greater diet variability and lower niche overlap within species compared to bison. We detected a reduction of niche overlap for red deer with increasing predation risk, leading to more dissimilar diets, suggesting their feeding behaviour is affected by wolf presence. This correlation was not found for bison, which are rarely predated by wolf. Higher habitat quality was associated with higher niche overlap only within bison, probably due to their suboptimal feeding strategy as browsers. These results show the importance of integrating environment-induced diet variation in studies aimed at determining the landscape usage or niche overlap of a species.

The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of nonsynonymous (dN) versus synonymous (dS) substitution rates in birds versus mammals, however, has provided contradictory results, questioning the generality of the nearly neutral theory. Here we analyzed the impact of life history traits, taken as proxies of the effective population size, on molecular evolutionary and population genetic processes in amniotes, including the so far neglected reptiles. We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations—and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, short-lived species of birds. We show that this unexpected pattern is not due to a more narrow range of life history traits, a lack of correlation between traits and Ne, or a peculiar distribution of fitness effects of mutations in birds. Our analysis therefore highlights the bird dN/dS ratio as a molecular evolutionary paradox and a challenge for future research.

Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)‐based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non‐invasiveness and easiness of sampling, but remain challenging for terrestrial fauna. However, in remote desert areas where scattered water bodies attract terrestrial species, which release their DNA into the water, this method presents a unique opportunity for their detection. In order to identify the most efficient method for a given study system, comparative studies are needed. Here, we compare CT and DNA metabarcoding of water samples collected from two desert ecosystems, the Trans‐Altai Gobi in Mongolia and the Kalahari in Botswana. We recorded with CT the visiting patterns of wildlife and studied the correlation with the biodiversity captured with the eDNA approach. The aim of the present study was threefold: (a) to investigate how well waterborne eDNA captures signals of terrestrial fauna in remote desert environments, which have been so far neglected in terms of biomonitoring efforts; (b) to compare two distinct approaches for biomonitoring in such environments; and (c) to draw recommendations for future eDNA‐based biomonitoring. We found significant correlations between the two methodologies and describe a detectability score based on variables extracted from CT data and the visiting patterns of wildlife. This supports the use of eDNA‐based biomonitoring in these ecosystems and encourages further research to integrate the methodology in the planning and monitoring of conservation strategies. In this article, we compare camera trap and eDNA methodologies, with a focus on vertebrate terrestrial taxa in two extreme desert ecosystems, the Trans‐Altai Gobi in Mongolia and the Kalahari Desert in Botswana. Images and water samples were collected in some of the rare and scattered water bodies found in these areas, where animals must gather to drink. Based on camera trap data, we computed detectability scores and explored how combinations of different variables impact species' detection probabilities by eDNA metabarcoding, hence providing useful indications how best to use the potential of the eDNA methodology and to complement the two approaches.

Understanding the relationship between a species feeding strategy and its environment (trophic ecology) is critical to assess environmental requirements and improve management policies. However, measuring trophic interactions remains challenging. Among the available methods, quantifying the plant composition of a species' diet indicates how species use their environment and their associated niche overlap. Nevertheless, most studies focusing on herbivore trophic ecology ignore the influence that landscape variability may have. Here, we explored how landscape variability influences diet composition through niche overlap. We used eDNA metabarcoding to quantify the diet composition of two large herbivores of the Bialowieza Forest, Red deer (Cervus elaphus) and European bison (Bison bonasus) to investigate how increasing habitat quality (i.e. higher abundance of deciduous forage species) and predation risk (i.e. density of wolf in the area) influence their diet composition and niche partitioning. Our findings indicate diet composition is non-homogeneous across the landscape, both within and between species. Red deer showed greater diet variability and lower niche overlap within species compared to bison. We detected a reduction of niche overlap for red deer with increasing predation risk, leading to more dissimilar diets, suggesting their feeding behaviour is affected by wolf presence. This correlation was not found for bison, which are rarely predated by wolf. Higher habitat quality was associated with higher niche overlap only within bison, probably due to their suboptimal feeding strategy as browsers. These results show the importance of integrating environment-induced diet variation in studies aimed at determining the landscape usage or niche overlap of a species. Niche overlap can therefore be a powerful tool for inferring predation risk for red deer, and estimating predator abundance or its perception. This approach has enormous potential for wildlife management in areas where predator estimates are unknown or difficult to quantify.Competing Interest StatementThe authors have declared no competing interest.