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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.

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. It would help assessing the relative role of historical contingencies versus determinism in evolution. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability and determinism.

With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.

Made available in DSpace on 2021-06-25T11:00:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Leaf litter habitats shelter a great variety of organisms, which play an important role in ecosystem dynamics. However, monitoring species in leaf litter is challenging, especially in highly diverse environments such as tropical forests, because individuals may easily camouflage themselves or hide in the litter layer. Identifying species based on environmental DNA (eDNA) would allow us to assess biodiversity in this microhabitat, without the need for direct observation of individuals. We applied eDNA metabarcoding to analyze large amounts of leaf litter (1 kg per sample) collected in the Brazilian Atlantic forest. We compared two DNA extraction methods, one total and one extracellular, and amplified a fragment of the mitochondrial 18S rRNA gene common to all eukaryotes, to assess the performance of eDNA from leaf litter samples in identifying different eukaryotic taxonomic groups. We also amplified two fragments of the mitochondrial 12S rRNA gene to specifically test the power of this approach for monitoring vertebrate species, with a focus on anurans. Most of the eukaryote sequence reads obtained were classified as Fungi, followed by Metazoa, and Viridiplantae. Most vertebrate sequences were assigned to Homo sapiens; only two sequences assigned to the genus Phyllomedusa and the species Euparkerella brasiliensis can be considered true detections of anurans in our eDNA samples. The detection of taxa varied depending on the DNA extraction method applied. Our results demonstrate that the analysis of eDNA from leaf litter samples has low power for monitoring vertebrate species and should be preferentially applied to describe active and abundant taxa in terrestrial communities, such as Fungi and invertebrates. Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP) Environmental Futures Research Institute Griffith University Laboratorio de Genética Departamento de Ciencias Naturales (FHUC - UNL) CONICET Department of Ecology and Evolutionary Biology Cornell University Laboratoire d’Ecologie Alpine Université Grenoble Alpes Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista (UNESP)

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.

Les inventaires d’espèces dulçaquicoles par analyse de l’ADN environnemental (ADNe) se sont développés depuis une dizaine d’années. Nous présentons ici l’application de cette méthode à l’inventaire des Bivalves d’eau douce de France. De 2015 à 2018, nous avons réalisé plusieurs tests de terrain en France, en choisissant différentes conditions environnementales. Nous avons comparé les résultats des analyses ADNe avec les connaissances sur la répartition des Bivalves à l’échelle de la France métropolitaine, à l’échelle des bassins-versants de la Meuse et du Rhône, et avec des sites ayant fait l’objet d’inventaires poussés, impliquant plusieurs malacologues utilisant les méthodes traditionnelles (observations au bathyscope, plongée hyperbare, tri de sédiment). Nos résultats montrent l’efficacité des analyses d’ADNe pour la détection et la distinction de presque tous les taxons de Bivalves dulçaquicoles de France (à l’exception des différentes espèces de Corbicules et des sous-espèces de la Mulette méridionale Unio mancus Lamarck, 1819). La méthode est commercialisée depuis 2018 et notre base de données comporte fin 2020 plus de 300 sites inventoriés par analyse de l’ADNe. L’analyse de ces résultats montre que certaines espèces peu étudiées, en particulier des espèces des écosystèmes de l’aval, souffrent d’extinctions locales en France. Ils plaident en faveur de la mise en œuvre d’actions de conservation en particulier pour la Cyclade des fleuves Sphaerium solidum (Normand, 1844), la Grande Cyclade Sphaerium rivicola (Lamarck, 1818) et l’Anodonte comprimée Pseudanodonta complanata (Rossmässler, 1835).

The increase in plant species richness in the Alps over the last century has been described as a direct response to climate warming. Alpine ecosystems are expected to have an upward displacement of vegetation, resulting in shifts of species ranges, high replacement rates, and species loss. To apply proper management measures, it is necessary to understand how drivers of change affect species and ecosystem tipping points. Palaeoecological studies allow us to understand how species responded to similar situations in the past. However, such studies are often challenged by proxy preservation and taxonomic resolution. Metabarcoding approaches based on sedimentary ancient DNA (sedaDNA) can overcome these caveats. Here we use plant sedaDNA and the new PhyloAlps taxonomic reference database, which covers 4500 plant taxa from the Alps, to explore alpine floral diversity of Sulseewlii, a subalpine lake in the Central Alps (Switzerland). We present a 12,000 year record of vegetational composition and structural changes in a subalpine ecosystem. To disentangle the relationship between climate and vegetation, we used a novel local temperature reconstruction inferred from chironomids of the same lake. We also used coprophilous fungal spores and charcoal, together with pastoral and arable indicators, to infer human pressure. With 377 identified taxa, including 140 at species level, Sulseewlii has yielded the richest dataset of plant sedaDNA to date and emphasizes the Alps as an important biodiversity hotspot in Europe. Out of the identified taxa, 91 are indicators that allowed us to reconstruct the vegetation stages and altitudinal shifts of the main vegetation groups. Total taxonomic richness increases from the onset of the Holocene and has a similar pattern to subalpine-montane DNA taxa, with three marked drops at 8200, 3200, and ~500 cal yr BP. Plant sedaDNA registered a marked transition from alpine to subalpine communities at the onset of the Holocene. The highest proportions of montane taxa occurred during the Holocene climatic optimum (9,000-6,000 cal yr BP). Finally, a shift back to subalpine-montane species with some lowland influence occurs as we approach the present.

International audience; The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

We analyzed the effect of forest management and wolf (Canis lupus) space-use on diet composition of red deer (Cervus elaphus) and European bison (Bison bonasus) in Bialowieza Primeval Forest (BPF), Poland. The red deer is the main prey species for the wolf, whereas the European bison is rarely preyed upon. As both species behave as intermediate feeders in BPF, we expected a large overlap in their diet composition. The red deer perceives the risk of wolf predation; thus, we hypothesized that its diet would change in relation to the intensity of wolf space-use, whereas bison’s would not. We compared diet composition between two contrasting management regimes: a national park managed as a protected area (no hunting, no forestry activities, restricted tourism), and an adjacent production forest managed for timber growth and extraction, where hunting on ungulates (but not wolves) does occur. We collected dung pellets of bison and red deer along transects in low and high wolf-use areas (with distance to settlements as proxy for wolf space-use) in both management types and analyzed diet composition using DNA-metabarcoding. In the national park both the bison and red deer had higher proportions of broadleaved tree species in their diet (bison 39%, red deer 42%) than in the managed forest (bison 26%, red deer 28%). The bison diet contained a higher proportion of shrubs, and specifically Rubus in the managed forest (shrubs 29%, Rubus 31%), compared to the national park (shrubs 21%, Rubus 8%). Only in the national park, red deer ate relatively more broadleaved tree species (51%) and fewer forbs (23%) in the high wolf-use area than in the low wolf-use area (33% broadleaved trees versus 37% forbs). Bison showed a qualitatively similar shift in diet composition as red deer, but the shift was not significant and also much smaller in extent. Our results indicate that forest management shapes the diet composition of both ungulate species. In addition, red deer showed larger shifts in diet composition than bison in high versus low wolf-use areas. This suggests that in addition to habitat differences, predation risk also plays a role in shaping the red deer diet. While earlier studies in BPF illustrated that wolves affect fine-scale deer foraging behavior, this study suggests this could potentially lead to changes in diet composition. We present alternative explanations for these diet shifts and urge others to look further into predation risk as a possible driver of dietary shifts in red deer.

Primary Biogenic Organic Aerosols (PBOA) were recently shown to be produced by only a few types of microorganisms, emitted by the surrounding vegetation in the case of a regionally homogeneous field site. This study presents the first comprehensive description of the structure and main sources of airborne microbial communities associated with temporal trends in Sugar Compounds (SC) concentrations of PM10 in 3 sites under a climatic gradient in France. By combining sugar chemistry and DNA Metabarcoding approaches, we intended to identify PM10-associated microbial communities and their main sources at three sampling-sites in France, under different climates, during the summer of 2018. This study accounted also for the interannual variability in summer airborne microbial community structure (bacteria and fungi only) associated with PM10-SC concentrations during a 2 consecutive years’ survey at one site. Our results showed that temporal changes in PM10-SC in the three sites are associated with the abundance of only a few specific taxa of airborne fungi and bacterial. These taxa differ significantly between the 3 climatic regions studied. The microbial communities structure associated with SC concentrations of PM10 during a consecutive 2-year study remained stable in the rural area. Atmospheric concentration levels of PM10-SC species varied significantly between the 3 study sites, but with no clear difference according to site typology (rural vs. urban), suggesting that SC emissions are related to regional rather than local climatic characteristics. The overall microbial beta diversity in PM10 samples is significantly different from that of the main vegetation around the urban sites studied. This indicates that the airborne microorganisms at these urban sites are not solely from the immediate surrounding vegetation, which contrasts with observations at the scale of a regionally homogeneous rural site in 2017. These results improve our understanding of the spatial behavior of tracers of PBOA emission sources, which need to be better characterized to further implement this important mass fraction of Organic Matter (OM) in Chemical Transport models (CTM).

Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time-consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular-based alternative to the morphology-based monitoring of streams using macroinvertebrates. We compared results achieved with the standard morphological identification of organisms sampled in 18 sites located on 15 French wadeable streams to results obtained with the DNA metabarcoding identification of sorted bulk material of the same macroinvertebrate samples, using read numbers (expressed as relative frequencies) as a proxy for abundances. In particular, we evaluated how combining and filtering metabarcoding data obtained from three different markers (COI: BF1-BR2, 18S: Euka02 and 16S: Inse01) could improve the efficiency of bioassessment. In total, 140 taxa were identified based on morphological criteria, and 127 were identified based on DNA metabarcoding using the three markers, with an overlap of 99 taxa. The threshold values used for sequence filtering based on the "best identity" criterion and the number of reads had an effect on the assessment efficiency of data obtained with each marker. Compared to single marker results, combining data from different markers allowed us to improve the match between biotic index values obtained with the bulk DNA versus morphology-based approaches. Both approaches assigned the same ecological quality class to a majority (86%) of the site sampling events, highlighting both the efficiency of metabarcoding as a biomonitoring tool but also the need for further research to improve this efficiency.

The most remarkable feature of our planet is the diversity of its life forms, ranging from viruses and nanobacteria to blue whales and giant sequoias to satanic leaf‐tailed geckos and leafy seadragons (look them up!). Life is found in essentially all environments on earth, and the number of species living on our planet is many times greater than we could have imagined a century ago. A well‐regarded estimate pegs the number of eukaryotic species on earth at 8.7 million (±1.3 million), of which fewer than 15% are currently described (Mora et al., 2011). The diversity of prokaryotes is less clear (and highly controversial), but an analysis of 1.6 billion 16S ribosomal RNA sequences estimated that 0.8–1.6 million prokaryotic operational taxonomic units exist globally (Louca et al., 2019). While we do not know how many species are currently extant, or have existed in the past, we do know that this biodiversity is valuable, providing food, fibre and medicine, furnishing ecosystem services such as water and air purification, nutrient cycling, pollination and carbon uptake, and contributing to technological innovations ranging from biotechnology to robotics to material science. Moreover, biodiversity underlies the cultural identity of human populations and is important to human health and well‐being. Geographically, species richness increases from the Polar Regions to the tropics in terrestrial and surface marine ecosystems. Thus, some countries, especially those in tropical and subtropical regions, are endowed with much greater biodiversity than others. Unfortunately, benefits arising from the access and utilization of this biodiversity have been unequally shared, with (paradoxically) biodiversity‐poor countries often accruing the lion's share of economic gains. There can be imbalances within countries as well, wherein some segments of the population obtain greater economic benefits from biodiversity and associated traditional knowledge than indigenous peoples. The “Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization,” which came into force in 2014, is an international agreement designed to ensure that the benefits arising from biodiversity are shared equitably (https://www.cbd.int/abs/). However, few scientific journals require compliance with the Nagoya Protocol or the reporting of benefits from biodiversity research. In this editorial, we (the editors of Molecular Ecology and Molecular Ecology Resources) express support for the Nagoya Protocol and the principle of benefit sharing. We believe that scientific journals publishing research on biodiversity can play an important role in implementing the Nagoya Protocol and in reporting on benefits generated from such research. Below, we provide background on the Nagoya Protocol, discuss the kinds of benefits that may arise from biodiversity research, describe the rationale for reporting on these benefits and introduce changes to the journals’ Data Accessibility Statements to incorporate the requirements and goals of the Nagoya Protocol.

Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.

The sociopolitical acceptance necessary for the conservation of controversial species requires scientific knowledge that disentangles empirical facts from myth and misinformation. An epitome of such, the gray wolf (Canis lupus) had been eradicated from most of Western Europe by the early twentieth century. However, a few mysteriously re-appeared in the Alps throughout the twentieth century, leading to systematic hunts encouraged by popular folklore and massive waves of panic. These historical events are reminiscent of the hostile context now surrounding the recolonization of the wolf across former ranges. Through historical DNA sequencing of five rare museum specimens shot post-WWII, we tell the true story of these mystery beasts. The oldest ones (1947–1954) were just the very last survivors of an endemic, extremely resilient wolf population, thought to be extinct decades earlier, while recent ones (1978–1990) most likely originated from captivity. This parable reminds that today more than ever, scientific evidence is necessary to conduct an objective societal debate over the management and conservation of controversial species.

The analysis of environmental DNA (eDNA) allows efficient surveys of freshwater species and is being increasingly used. However, most studies generally have a limited sampling plan. Because different methods are used by different authors, all the data produced with eDNA cannot be easily pooled together for a global overview. Nevertheless, one of the promising perspectives is the standardization of the methods and protocols, for long-term monitoring, early detection of invasive species, and rare species detection. We here present the biggest dataset using eDNA metabarcoding with standardized methods for freshwater bivalves. Sampling was performed mainly in France, with over 350 localities spread over all major basins. Metabarcoding was performed using two new sets of primers, one for the Unionida and one for the Venerida. The species distributions inferred from eDNA sampling are then compared with those currently known. Results give an insight into the valuable data that eDNA analysis can provide if used at a large scale. Some species were found outside of their known range, especially invasive species but also species of conservation interest. Others were found in a surprisingly low number of localities, although currently considered widespread and of no conservation interest. This can be explained by the databases currently used to establish conservation status, which are often biased by including ancient data, shell-only data, and potentially misidentified species. The present study shows that our eDNA metabarcoding approach will be an essential tool to unveil the true species distributions, to better evaluate their status and improve conservation policymaking.

In the last decade, eDNA and metabarcoding have opened new avenues to biodiversity studies; amphibians and reptiles are animals for which these new approaches have allowed great leaps forward. Here we review different approaches through which eDNA can be used to study amphibians, reptiles and many more organisms. eDNA is often used to evaluate the presence of target species in freshwaters; it has been particularly useful to detect invasive alien amphibians and secretive or rare species, but the metabarcoding approach is increasingly used as a cost-effective approach to assess entire communities. There is growing evidence that eDNA can be also useful to study terrestrial organisms, to evaluate the relative abundance of species, and to detect reptiles. Metabarcoding has also revolutionized studies on the microbiome associated to skin and gut, clarifying the complex relationships between pathogens, microbial diversity and environmental variation. We also identify additional aspects that have received limited attention so far, but can greatly benefit from innovative applications of eDNA, such as the study of past biodiversity, diet analysis and the reconstruction of trophic interactions. Despite impressive potential, eDNA and metabarcoding also bear substantial technical and analytical complexity; we identify laboratory and analytical strategies that can improve the robustness of results. Collaboration among field biologists, ecologist, molecular biologists, and bioinformaticians is allowing fast technical and conceptual advances; multidisciplinary studies involving eDNA analyses will greatly improve our understanding of the complex relationships between organisms, and our effectiveness in assessing and preventing the impact of human activities.

Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.

Environmental DNA retrieved from modern soils (eDNA) and late-Quaternary palaeosols and sediments (aDNA and sedaDNA) promises insight into the composition of present and past terrestrial biotic communities, but few studies address the spatial relationship between recovered eDNA and contributing organisms. Svalbard’s vascular plant flora is well known, and a cold climate enhances preservation of eDNA in soils. Thus, Svalbard plant communities are excellent systems for addressing the representation of plant eDNA in soil samples. In two valleys in the inner fjord region of Spitsbergen, we carried out detailed vegetation surveys of circular plots up to a 4-m radius. One or three near-surface soil samples from each plot were used for extraction and metabarcoding of soil-derived eDNA. Use of PCR replicates and appropriate filtering, plus a relevant reference metabarcode catalogue, provided taxon lists that reflected the local flora. There was high concordance between taxa recorded in plot vegetation and those in the eDNA, but floristic diversity was under-sampled, even at the scale of a 1-m radius plot. Most detected taxa grew within < 0.5–1.0 m of the sampling point. Taxa present in vegetation but not in eDNA tended to occur further from the sampling point, and most had above-ground cover of < 5%. Soil-derived eDNA provides a highly local floristic signal, and this spatial constraint should be considered in sampling designs. For palaeoecological or archaeological studies, multiple samples from a given soil horizon that are spatially distributed across the area of interest are likely to provide the most complete picture of species presence.

Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published accounts of larval dung sources. C. bacchus is traditionally considered to specialise on the dung of large herbivores for both larval and adult feeding. We successfully extracted mammal DNA from 151 adult C. bacchus fecal samples, representing 16 mammal species (ranging from elephants to small rodents), many of which are hitherto undescribed in the diet. Adult C. bacchus showed clear dung source preferences, especially for large herbivores inhabiting dense-cover vegetation. Our approach also confirmed the presence of cryptic taxa in the study area, and we propose that this may be used for biodiversity survey and monitoring purposes. Murid rodent feces were the most commonly fed-upon dung source (77.5%) for adult C. bacchus, differing markedly from the large and megaherbivore dung sources used for larval rearing. These findings support the hypothesis of life history-specific shifts in resource use in dung beetles, and reveal a hitherto unsuspected, but ecologically important, role of these dung beetles in consuming rodent feces. The differences in feeding abilities of the larval and adult life history stages have profound consequences for their resource use and foraging strategies, and hence the ecological role of dung beetles. This principle and its ecological consequences should be explored in other scarabaeids.

High rates of gene duplication and the highest levels of functional allelic diversity in vertebrate genomes are the main hallmarks of the major histocompatibility complex (MHC), a multigene family with a primordial role in pathogen recognition. The usual tight linkage among MHC gene duplicates may provide an opportunity for the evolution of haplotypes that associate functionally divergent alleles and thus grant the transmission of optimal levels of diversity to coming generations. Even though such associations may be a crucial component of disease resistance, this hypothesis has been given little attention in wild populations. Here, we leveraged pedigree data from a barn owl (Tyto alba) population to characterize MHC haplotype structure across two MHC class I (MHC-I) and two MHC class IIB (MHC-IIB) duplicates, in order to test the hypothesis that haplotypes’ genetic diversity is higher than expected from randomly associated alleles. After showing that MHC loci are tightly linked within classes, we found limited evidence for shifts towards MHC haplotypes combining high diversity. Neither amino acid nor functional within-haplotype diversity were significantly higher than in random sets of haplotypes, regardless of MHC class. Our results therefore provide no evidence for selection towards high-diversity MHC haplotypes in barn owls. Rather, high rates of concerted evolution may constrain the evolution of high-diversity haplotypes at MHC-I, while, in contrast, for MHC-IIB, fixed differences among loci may provide barn owls with already optimized functional diversity. This suggests that at the MHC-I and MHC-IIB respectively, different evolutionary dynamics may govern the evolution of within-haplotype diversity.

Diet studies are essential to understand animal ecology and ecosystem dynamics, especially in the case of large omnivores. These studies are particularly relevant in areas where human disturbance is intense and, thus, species dietary patterns might change due to the easy accessibility of food resources of human origin, which may hinder the ecosystem services these species provide. We assessed the diet of brown bears (Ursus arctos) by DNA metabarcoding in Tatra National Park (southern Poland), a highly touristic protected area. Brown bears' diet showed a marked seasonality, a characteristic feature of brown bear populations relying on natural foods. Graminoids represented the main food during spring, while fleshy-fruited plants became more important from mid-summer. Fleshy-fruited plants were present in 56% of faeces and during the entire activity period of bears, revealing that fruits play a pivotal role in the feeding ecology of Tatra brown bears. Two berry species, Vaccinium myrtillus and Rubus idaeus, were the most frequently detected (in 42% and 20% of faeces, respectively). The large consumption of fleshy-fruited plants, and particularly of berries, suggests that, despite high levels of human disturbance in the area, brown bears still play a key role as seed dispersers. Management strategies focused on an effective waste management, control of berry picking, strict regulations about human activities in specific areas during sensitive periods in the feeding ecology of bears, and the lack of artificial food provisioning are crucial to ensure the seed dispersal processes and associated ecosystem services that bears and other frugivores provide.

Summary 1.In forest ecosystems, the influence of landscape history on contemporary biodiversity patterns has been shown to provide a convenient framework to explain shifts in plant assemblages. However, very few studies have controlled for present human-induced activities when analyzing the effect of forest continuity on community structures. By cutting and removing trees, foresters substantially change stand ecological conditions, with consequences on biodiversity patterns. Disentangling the effect of past and present human activities on biodiversity is thus crucial for ecosystem management and conservation. 2.We explored the response of plant and springtail species richness and composition to forest continuity (ancient vs recent) in montane forests, while controlling for stand maturity (mature vs overmature). We established 70 sites in landscapes dominated by unfragmented ancient forests where we surveyed plants and assessed springtails by analyzing environmental DNA. 3.Neither plant nor springtail species richness was influenced by forest continuity or by stand maturity. Instead, site-specific characteristics, especially soil properties and canopy openness, were of major importance in shaping above- and below-ground richness. 4.For plant and springtail species composition, the effect of forest continuity was mediated by stand maturity. Thus, both plants and springtails showed a convergence in assemblage patterns with the increasing availability of overmature stand attributes. Moreover, soil and stand-scale factors were evidently more important than landscape-scale factors in shaping above- and below-ground species composition. 5.sSynthesis. We clearly demonstrated that biodiversity patterns are more strongly influenced by present human-induced activities than by past human-induced activities. In the Northern Alps where our study sites were located, the colonization credit of most species has been paid off and the transient biodiversity deficit usually related to forest continuity has moved toward equilibrium. These findings emphasize the necessity to better control for local-scale factors when analyzing the response of biodiversity to forest continuity; we call for more research into the effects of forest continuity in unfragmented mountain forests. This article is protected by copyright. All rights reserved.

Over the past decade, an increasing number of studies has used environmental DNA from lake sediments to trace past lake ecosystem and landscape changes, agricultural activities or human presence and more broadly the biodiversity. In the environment, DNA can be found as intracellular and extracellular DNA (iDNA and exDNA). The contribution of each of these pools varies according to the environments, but exDNA often represents a high proportion of the total DNA (e.g. Vuillemin et al. 2017 and reference therein). Focusing the analyses on these different pools will lead to different community composition and structure of communities (e.g. Vuillemin et al. 2017). For plants, we propose to focus on the exDNA fraction to avoid the extraction of DNA from plant macro-remains, which might lead to an overrepresentation of these taxa and limit the detection of the other, “rarer” taxa. The manipulation of ancient DNA is delicate, and the biases brought during the experiments can be multiple. Therefore, it is essential to work carefully, under strict laboratory conditions, with multiple controls and several replicates of samples or extraction or PCR (e.g. Fulton 2012). This protocol details a sampling and extraction method of exDNA from sediments. This method was firstly developed for soils by Taberlet et al. 2012. It uses a phosphate buffer to desorb the DNA fragments from particles such as clays and then, the binding, wash and elution buffers from the NucleoSpin® Soil kit (Macherey-Nagel). Here we present a modified protocol from Taberlet et al. 2012. One modification consists in the addition of a concentration step (by using the amicon ultra centrigugal filter system) after the mixing of sediments with the saturated phosphate buffer. This step allow to increase the DNA yield. The quantity of phosphate buffer is usually based on the quantity of wet sediments (e.g. for 15g of wet sediment/soil, we add 15 ml of phosphate buffer). However, because lake sediments can have very different water content (depending on the composition and compaction) and because the exDNA is adsorbed onto particles, we now propose to base the phosphate buffer quantity on the dry weight of sediments. Fulton T., 2012. Setting Up an Ancient DNA Laboratory. Book Chapter, Ancient DNA in Methods in Molecular Biology edited by Shapiro B. and Hofreiter M., 1-11. Taberlet, P., Prud’Homme, S.M., Campione, E., Roy, J., Miquel, C., Shehzad, W., Gielly, L., Rioux, D., Choler, P., Clément, J.‐C., Melodelima, C., Pompanon, F. and Coissac, E, 2012. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology, 21: 1816-1820. Vuillemin A., Horn F., Alawi M., Henny C., Wagner D., Crowe S. A., Kallmeyer J., 2017. Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia. Frontiers in Microbiology 8, 1440.

Primary biogenic organic aerosols (PBOA) represent a major fraction of coarse organic matter (OM) in air. Despite their implication in many atmospheric processes and human health problems, we surprisingly know little about PBOA characteristics (i.e., composition, dominant sources, and contribution to airborne-particles). In addition, specific primary sugar compounds (SCs) are generally used as markers of PBOA associated with Bacteria and Fungi but our knowledge of microbial communities associated with atmospheric particulate matter (PM) remains incomplete. This work aimed at providing a comprehensive understanding of the microbial fingerprints associated with SCs in PM10 (particles smaller than 10 µm) and their main sources in the surrounding environment (soils and vegetation). An intensive study was conducted on PM10 collected at rural background site located in an agricultural area in France. We combined high-throughput sequencing of Bacteria and Fungi with detailed physicochemical characterization of PM10, soils and plant samples, and monitored meteorology and agricultural activities throughout the sampling period. Results shows that in summer SCs in PM10 are a major contributor of OM in air, representing 0.8 to 13.5 % of OM mass. SCs concentrations are clearly determined by the abundance of only a few specific airborne Fungi and Bacteria Taxa. These microbial are significantly enhanced in leaf over soil samples. Interestingly, the overall community structure of Bacteria and Fungi are similar within PM10 and leaf samples and significantly distinct between PM10 and soil samples, indicating that surrounding vegetation are the major source of SC-associated microbial taxa in PM10 in rural area.

The moose (Alces alces) is a dominant large mammalian herbivore in the world’s boreal zones. Moose exert significant browsing impacts on forest vegetation and are therefore often at the centre of wildlife-forestry conflicts. Consequently, understanding the drivers of their foraging behaviour is crucial for mitigating such conflicts. Management of moose in large parts of its range currently largely ignores the fact that moose foraging is influenced by increasing populations of sympatric deer species. In such multispecies systems, resource partitioning may be driven by foraging height and bite size. Feeding competition with smaller species might replace larger species from the field layer and drive them towards higher foraging strata offering larger bites. This bite size hypothesis has been well documented for African ungulate communities. Based on a large diet DNA metabarcoding dataset we suggest that feeding competition from three smaller deer species (red deer Cervus elaphus, fallow deer Dama dama, and roe deer Capreolus capreolus) over Vaccinium shrubs in the forest field layer might drive moose towards increasing consumption of Scots pine (Pinus sylvestris) in Sweden. We found that in areas of high deer density, moose diets consistently contained less Vaccinium and higher proportions of pine over three spring periods. Utilization of these food items by the smaller deer species was either unaffected by deer density or, for Vaccinium showed the opposite pattern to moose, i.e., increases of proportions in the diet of roe and red deer with increasing deer density. Availability of pine and Vaccinium, measured as proportion of available bites, did not explain the observed patterns. Our results suggest that managing key food items like Vaccinium and the populations of smaller deer may play an important role in controlling browsing impacts of moose on pine.

DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be thoroughly quantified before it can be mainstreamed into biomonitoring programmes. Here, we used 80 unsorted macroinvertebrate samples collected in Portugal under a Water Framework Directive monitoring programme, to compare community diversity and taxonomic composition metrics estimated through morphotaxonomy versus metabarcoding from storage ethanol using three markers (COI-M19BR2, 16S-Inse01 and 18S-Euka02) and a multimarker approach. A preliminary in silico analysis showed that the three markers were adequate for the target taxa, with detection failures related primarily to the lack of adequate barcodes in public databases. Metabarcoding of ethanol samples retrieved far less taxa per site (alpha diversity) than morphotaxonomy, albeit with smaller differences for COI-M19BR2 and the multimarker approach, while estimates of taxa turnover (beta diversity) among sites were similar across methods. Using generalized linear mixed models, we found that after controlling for differences in read coverage across samples, the probability of detection of a taxon was positively related to its proportional abundance, and negatively so to the presence of heavily sclerotized exoskeleton (e.g., Coleoptera). Overall, using our experimental protocol with different template dilutions, the COI marker showed the best performance, but we recommend the use of a multimarker approach to detect a wider range of taxa in freshwater macroinvertebrate samples. Further methodological development and optimization efforts are needed to reduce biases associated with body armouring and rarity in some macroinvertebrate taxa info:eu-repo/semantics/publishedVersion

International audience; The rainforests of the Neotropics shelter a vast diversity of plant, animal and microscopic species that provide critical ecosystem goods and services for both local and worldwide populations. These environments face a major crisis due to increased deforestation, pollution, and climate change, emphasizing the need for more effective conservation efforts. The adequate monitoring of these ecosystems has proven a complex and time consuming endeavour, which depends on ever dwindling taxonomic expertise. To date, many species remain undiscovered, let alone described, with otherwise limited information regarding known species population distributions and densities. Overcoming these knowledge shortfalls and practical limitations is becoming increasingly possible through techniques based on environmental DNA (eDNA), i.e., DNA that can be obtained from environmental samples (e.g. tissues, soil, sediment, water, etc.). When coupled with high-throughput sequencing, these techniques now enable realistic, cost-effective, and standardisable biodiversity assessments. This opens up enormous opportunities for advancing our understanding of complex and species-rich tropical communities, but also in facilitating large-scale biomonitoring programs in the neotropics. In this review, we provide a brief introduction to eDNA methods, and an overview of their current and potential uses in both terrestrial and aquatic ecosystems of neotropical rainforests. We also discuss the limits and challenges of these methods for our understanding and monitoring of biodiversity, as well as future research and applied perspectives of these techniques in neotropical rainforests, and beyond.

Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.

[This corrects the article DOI: 10.1371/journal.pone.0225698.].

International audience; High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retriev-ing and interpreting the structure of such data sets requires efficient methods for di-mensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical for-est and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, con-firming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiver-sity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity.

The origin of modern disjunct plant distributions in the Brazilian Highlands with strong floristic affinities to distant montane rainforests of isolated mountaintops in the northeast and northern Amazonia and the Guyana Shield remains unknown. We tested the hypothesis that these unexplained biogeographical patterns reflect former ecosystem rearrangements sustained by widespread plant migrations possibly due to climatic patterns that are very dissimilar from present-day conditions. To address this issue, we mapped the presence of the montane arboreal taxa Araucaria, Podocarpus, Drimys, Hedyosmum, Ilex, Myrsine, Symplocos, and Weinmannia, and cool-adapted plants in the families Myrtaceae, Ericaceae, and Arecaceae (palms) in 29 palynological records during Heinrich Stadial 1 Event, encompassing a latitudinal range of 30°S to 0°S. In addition, Principal Component Analysis and Species Distribution Modelling were used to represent past and modern habitat suitability for Podocarpus and Araucaria. The data reveals two long-distance patterns of plant migration connecting south/southeast to northeastern Brazil and Amazonia with a third short route extending from one of them. Their paleofloristic compositions suggest a climatic scenario of abundant rainfall and relative lower continental surface temperatures, possibly intensified by the effects of polar air incursions forming cold fronts into the Brazilian Highlands. Although these taxa are sensitive to changes in temperature, the combined pollen and speleothems proxy data indicate that this montane rainforest expansion during Heinrich Stadial 1 Event was triggered mainly by a less seasonal rainfall regime from the subtropics to the equatorial region., This work was funded by FAPESP research grant 2015/50683-2 to P.E. De Oliveira, VULPES Project, Belmount Forum.

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure. ISSN:0906-7590 ISSN:1600-0587

Made available in DSpace on 2020-12-10T17:38:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-07-30 Fundacao de Amparo a Pesquisa do Estado do Rio Grande do Sul Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Agence Nationale de la Recherche Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genusCtenomysdistributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition. Univ Grenoble Alpes, Univ Savoie Mt Blanc, Lab Ecol Alpine, CNRS,UMR 5553, Grenoble, France Univ Fed Rio Grande do Sul, Dept Genet, Lab Citogenet & Evolucao, Porto Alegre, RS, Brazil Univ Fed Rio Grande do Sul, Dept Bot, Porto Alegre, RS, Brazil CNPq: 201262/20118 FAPESP: 2016/14054-3

Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

International audience

Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies.

DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and plant diversity from tropical soil samples of ca. 10 g. The total DNA extraction protocol yielded more high-quality DNA. Yet, the extracellular DNA protocol provided similar diversity assessments although it presented some differences in clades relative abundance and undersampling biases. We argue that extracellular DNA is a good compromise between cost, labor, and accuracy for high-throughput DNA metabarcoding studies of soil biodiversity.

Environmental DNA (eDNA) and metabarcoding are boosting our ability to acquire data on species distribution in a variety of ecosystems. Nevertheless, as most of sampling approaches, eDNA is not perfect. It can fail to detect species that are actually present, and even false positives are possible: a species may be apparently detected in areas where it is actually absent. Controlling false positives remains a main challenge for eDNA analyses: in this issue of Molecular Ecology Resources, Lahoz-Monfort et al. () test the performance of multiple statistical modelling approaches to estimate the rate of detection and false positives from eDNA data. Here, we discuss the importance of controlling for false detection from early steps of eDNA analyses (laboratory, bioinformatics), to improve the quality of results and allow an efficient use of the site occupancy-detection modelling (SODM) framework for limiting false presences in eDNA analysis.

International audience; Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic-distance-dependent neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12-ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs. K E Y W O R D S DNA metabarcoding, eDNA, French Guiana, multitaxa, neutral assembly, niche determinism, propagule size, soil diversity

Cow genes dictate environmentally friendly microbiomes: a step towards reducing greenhouse gas emissions., A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.

Pellet counts are widely used to monitor ungulates but rely on the assumption that pellets of different species are correctly identified in the field. Recent studies question this assumption using DNA barcoding techniques to check field identification rates. For Europe, which is undergoing a rapid shift towards more diverse ungulate assemblages, such an assessment is still missing. Using DNA barcoding on 3889 fecal samples from nine ungulate species in four European countries, we found average field misidentification rates varied from 0.6% for horse (Equus ferus) to 41.1% for roe deer (Capreolus capreolus). Most identification errors occurred between similar-sized species from the same taxonomic family. For a subset of samples from Sweden, we looked at the effect of dung morphometry, observer experience, and season on species identification success. Dung morphometry clearly distinguished moose (Alces alces) but not red (Cervus elaphus), roe, and fallow deer (Dama dama). Experienced observers performed better than novices for red and fallow deer although still making significant identification errors (26% and 17% incorrectly identified). Identification success was higher during spring and winter ( $$ \overline{x} $$ = 86%) than summer and autumn ( $$ \overline{x} $$ = 74%). We question pellet counts as an accurate monitoring tool where similar-sized species coexist and monitoring relates to the whole community. For this increasingly common situation across Europe, DNA testing or camera traps may be a better alternative. Pellet counts remain useful where only few species with clearly different dung morphology coexist (e.g., moose and roe deer) or when focused on species with distinctive dung morphology (e.g., moose).

Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf ( Canis lupus ) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.

Rabbits have had a stronger impact on the landscape and plant communities of a remote island than one century of climate change., What are the long-term consequences of invasive species? After invasion, how long do ecosystems require to reach a new equilibrium? Answering these questions requires long-term, high-resolution data that are vanishingly rare. We combined the analysis of environmental DNA extracted from a lake sediment core, coprophilous fungi, and sedimentological analyses to reconstruct 600 years of ecosystem dynamics on a sub-Antarctic island and to identify the impact of invasive rabbits. Plant communities remained stable from AD 1400 until the 1940s, when the DNA of invasive rabbits was detected in sediments. Rabbit detection corresponded to abrupt changes of plant communities, with a continuous decline of a dominant plant species. Furthermore, erosion rate abruptly increased with rabbit abundance. Rabbit impacts were very fast and were stronger than the effects of climate change during the 20th century. Lake sediments can allow an integrated temporal analysis of ecosystems, revealing the impact of invasive species over time and improving our understanding of underlying mechanisms.

International audience