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Monitoring biodiversity is essential to protect, preserve and restore ecosystems, particularly in the context of current challenges such as climate change, habitat destruction and globalization (Baird & Hajibabaei, 2012). Biomonitoring is needed for developing biotic indices for assessing ecological status, measuring impacts of anthropogenic activities in natural ecosystems, evaluating biodiversity loss, surveying nonindigenous species, conservation, and identifying cryptic species (Balvanera et al., 2006; Fišer et al., 2018). Thus, spatially and temporally structured biomonitoring activities provide a powerful tool for the implementation of regional, national and international regulations, directives and policies for nature conservation. However substantial impediments exist including access to remote locations, limited specialist taxonomic knowledge, cost, slow pace of human-driven data analyses, and typically low sensitivity for detection of rare and elusive species (Zinger et al., 2020). These drawbacks are often translated into expensive monitoring activities with limited spatial, temporal and taxonomic coverage. In this context, new approaches for biomonitoring are being explored, among which advanced DNA-based technologies are emerging (Kissling et al., 2018). The field of biodiversity monitoring through the analysis of the pool of DNA isolated from environmental samples, referred to as environmental DNA or eDNA (Pawlowski et al., 2020; Taberlet et al., 2012), is rapidly growing. This growth is being driven through improved approaches for sampling, data generation and analyses, and with recent advances on how eDNA should be interpreted for biodiversity assessments (Bohmann et al., 2014). The success of eDNA-based biomonitoring is reflected in exponential growth of publications within this area and increasing submissions to Molecular Ecology Resources in particular (Figure 1). Molecular Ecology Resources aims to publish high quality eDNA studies that serve as broad resources, including innovative methodologies for DNA sampling, enhanced laboratory protocols for data generation, or new computer programs and statistical advances for data analyses. Thus, the aim of this editorial is to contribute to producing good quality DNA data-derived essential biodiversity variables (EBVs) (Kissling et al., 2018) by providing guidance to the community submitting articles on the subject. For that purpose, we have summarized best practices established in published literature related to the different phases involved in the process, namely sampling, laboratory work, bioinformatic analyses and data interpretation (Figure 2).

Species diversity may be underestimated even in well-explored mountain regions due to the lack of in-depth research in taxonomically intricate groups. Filling such knowledge gap is necessary to optimize conservation management, specially for species occurring in vulnerable ecosystems such as Southern European mountains. Campanula sect. Heterophylla is a complex group with a high proportion of endemic taxa in European mountain ranges, and whose species delineation is often controversial due to extensive morphological variation. We investigated the phylogenetic relationships and evolutionary entity of its taxa occurring in the Pyrenees, with a special focus on the Pyrenean endemic C. jaubertiana (which is sometimes included as a subspecies of or merged with C. cochleariifolia); and C. andorrana, a taxon allegedly endemic to Andorra (Eastern Pyrenees) and of uncertain taxonomic value. We obtained chloroplast genome and nuclear ribosomal DNA sequences, including several individuals of the three focus taxa, and conducted morphometric analyses. Phylogenetic analyses show that C. jaubertiana sensu lato (s. l.; i.e. including C. andorrana) constitutes a clearly distinct lineage that is not even closely related to C. cochleariifolia; consistent differences in floral morphology were detected between them. Our results support two main evolutionary lineages within C. jaubertiana s. l., one corresponding to populations in Central Pyrenees, and another one in Eastern Pyrenees plus Catalan Pre-Pyrenees. Given the degree of genetic and morphological differentiation, we propose the species rank for each lineage (C. jaubertiana and C. andorrana, respectively) and provide a taxonomic treatment. These two Pyrenean endemics likely diverged through transverse allopatric speciation.

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.

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.

Alpine areas are well known biodiversity hotspots, but their future may be threatened by expanding forest and changing human land use. Here, we reconstructed past vegetation, climate, and livestock over the past ~ 12,000 years from Lake Sulsseewli (European Alps), based on sedimentary ancient DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3,923 plant species), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. The vegetation mainly responded to temperature during the first half of the Holocene, while human activity drove changes from 6 ka onwards. Land-use shifted from episodic grazing (Neolithic, Bronze Age) to agropastoral intensification (Medieval Age). This prompted a coexistence of species typically found at different elevational belts, thereby increasing plant richness to levels that characterise present-day alpine diversity. Our results indicate that traditional agropastoral activities should be maintained to prevent reforestation and preserve alpine plant biodiversity.

BackgroundRecently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study.ResultsWe assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For thein silicosimulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors.ConclusionsGenome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.

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.

The Alps contain highly biodiverse ecosystems including a large number endemic flora. As a result of climate change and anthropogenic activities, such ecosystems are at risk from upward vegetation displacement and species loss. Extensive archaeological research in the Eastern Alps has documented human settlement from ~5500 years ago driven by salt and copper mining; which has caused significant impact on the ecosystems through mining, deforestation, and pastoral farming. To elucidate the effects of climate change and anthropogenic activities on plant biodiversity, multi-proxy reconstructions have been carried out throughout the Western Alps . Despite this research, the palaeoecological history of the Eastern Alps is relatively understudied. Consequently, we are limited in our understanding of how climate change and human impact have affected past biodiversity and the formation of the contemporary vegetation in this region. Here, we focus on the Austrian sub-alpine lake, Großer Winterleitensee located at the Easternmost margin of the Alps; only locally glaciated during the Pleistocene. We applied sedimentary ancient DNA (sedaDNA) metabarcoding to reconstruct Holocene plant community dynamics within the lake catchment. These data, in conjunction with local temperature reconstructions, sediment elemental composition, magnetic susceptibility, and loss-on-ignition analyses, allowed us to identify key intervals of plant diversity change. Two such intervals begin at samples dated ~5500 cal. yr BP and ~2200 cal. yr BP, coinciding with Neolithic and Iron Age settlement phases in the area. Palaeoecological reconstructions of plant biodiversity and their responses to climate change and anthropogenic pressures may be able to provide essential information for future conservation purposes.

Acknowledgements: Acknowledgements: We thank D. H. Mann for his detailed and constructive comments; and T. Ager, J. Austin, T. B. Brand, A. Cooper, S. Funder, M. T. P. Gilbert, T. Jørgensen, N. J. Korsgaard, S. Liu, M. Meldgaard, P. V. S. Olsen, M. L. Siggaard-Andersen, J. Stenderup, S. A. Woodroffe and staff at the GeoGenetics Sequencing Core and National Park Service-Western Arctic National Parklands for help and support. E.W. and D.J.M. thank the staff at St. John’s College, Cambridge, for providing a stimulating environment for scientific discussion of the project. E.W. thanks Illumina for collaboration. The Lundbeck Foundation GeoGenetics Centre is supported by the Carlsberg Foundation (CF18-0024), the Lundbeck Foundation (R302-2018-2155), the Novo Nordisk Foundation (NNF18SA0035006), the Wellcome Trust (UNS69906) and GRF EXC CRS Chair (44113220)—Cluster of Excellence. The PhyloNorway plant genome database is part of the Norwegian Barcode of Life Network (https://www.norbol.org) funded by the Research Council of Norway (226134/F50), the Norwegian Biodiversity Information Centre (14-14, 70184209) and The Arctic University Museum of Norway. Metabarcoding sequencing was funded by the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2017B001 and 2020A001). B.D.S. is supported by the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023); F.R. by a Villum Fonden Young Investigator award (no. 00025300); D.J.M. by the Quest Archaeological Research Fund; P.M. by the Swedish Research Council (VR); R.D. by the Wellcome Trust (WT207492); and A.R. by a Marie Skłodowska-Curie Actions Individual Fellowship (MSCA-IF, 703542) and the Research Council of Norway (KLIMAFORSK, 294929). L.O. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (no. 681605); I.G.A. and Y.L. from the ERC under the European Union’s Horizon 2020 research and innovation programme (no. 819192). J.I.S. and J.M. are supported by the Research Council of Norway. P.B.H. and N.R.E. acknowledge NERC funding (grant NE/P015093/1). D.W.B. was supported by a Marie Skłodowska-Curie Actions Incoming International Fellowship (MCIIF-40974). T.S.K. is funded by a Carlsberg Foundation Young Researcher Fellowship (CF19-0712)., During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

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.

Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

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.

Climate change has already started to rapidly transform ecosystems. Predicted scenarios of future ecosystem changes inferred from contemporary ecological data may be uncertain, as these records do not provide the temporal depth needed to understand how ecosystems have responded to past periods of climatic changes and human pressure. However, palaeoecological approaches allow for the reconstruction of past ecosystem changes, including the composition of plant communities, thereby enabling researchers to improve models of future climatic change impacts.Lakes located in high-mountain ranges, such as the Alps, are suitable ecosystems for studying long-term species turnover and environmental shifts driven by past climate changes, as they preserve a wealth of palaeoecological information in its sediment archives. The Alpine ecosystems are expected to be affected by ongoing climate warming, prompting an upward displacement of vegetation, elevated replacement rates and species losses, with projected increased intensity of impacts in the future.Previous studies of the Alps have used pollen and macrofossil evidence to infer past vegetation dynamics. However, microscopic morphological determinations are time-consuming and some inferences have been limited by low taxonomic resolution and the biased preservation of identifiable remains. Ancient DNA from organisms is also often preserved in the sediment (sedaDNA), which can rapidly be detected and analysed using metabarcoding approaches. Together with a novel, region-specific barcode reference database for the flora of the Alps (PhyloAlps; 4500 taxa), we can bypass the morphological limitations of previous palaeobotanical studies and refine taxonomic resolution, often to the species level.To investigate the origin and impact of past environmental changes in alpine ecosystems throughout the Holocene, we performed a multi-proxy reconstruction of 9 lake sediment cores from the Western Alps (France, Italy and Switzerland). Using metabarcoding, we reconstructed the plant community composition and used XRF, magnetic susceptibility, and loss-on-ignition data to understand lacustrine dynamics during the Holocene for each lake. We will present the major findings from these analysed records, the general ecosystem shifts inferred, and the impacts of perturbations caused by human pressure and climatic changes.

The Eastern Alps in Europe have a rich alpine biodiversity and a long archaeological history. However, the palaeoecological record of this region has been relatively understudied, which has limited our understanding of the formation of the contemporary vegetation since the end of the last Ice Age, including the likely impacts of changes in climate and human pressures through pasturing and agriculture. To fill this knowledge gap, we are using plant and mammal sedaDNA taken from five sub-alpine to alpine Holocene lake cores in the Austrian and Italian Eastern Alps: Grosser Winterleitensee, Krummschnabelsee, Mittlerer Kaltenbachsee and Sulzkarsee (Austria), and Laghetti Colbricon (Italy). We will outline our first results on full plant community reconstructions from some lakes and on the mammal presence. Findings from the plant record will allow us for uncovering the Holocene dynamics of plant communities, and for identifying key intervals where biodiversity may have been strongly affected by anthropogenic factors and climate change. The mammal sedaDNA data will also be used to track the presence of domestic livestock through time and therefore provide insight into past human pastoral practices in the region.

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.

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was &gt, 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

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

MotivationMolecular biology and ecology studies can produce high dimension data. Estimating correlations and shared variation between such data sets are an important step in disentangling the relationships between different elements of a biological system. Unfortunately, classical approaches are susceptible to producing falsely inferred correlations.ResultsHere we propose a corrected version of the Procrustean correlation coefficient that is robust to high dimensional data. This allows for a correct estimation of the shared variation between two data sets and the partial correlation coefficients between a set of matrix data.AvailabilityThe proposed corrected coefficients are implemented in the ProcMod R package available on CRAN. The git repository is hosted at https://git.metabarcoding.org/lecasofts/ProcModContacteric.coissac@metabarcoding.org

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

International audience

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.