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Acknowledgements: Acknowledgements: We acknowledge support from the Carlsberg Foundation for logistics to carry out two expeditions to Kap København in 2006 and 2012 (S. Funder, principal investigator for Carlsberg foundation grant to LongTerm and Kap København—the age). The fieldwork in 2016 was supported by a grant to N.K.L. from the Villum Foundation. We highly appreciate the collaborative support by Illumina Inc. that was crucial for the success of the project. E.W. and K.H.K. thank the Danish National Research Foundation (DNRF) and the Lundbeck Foundation (R302-2018-2155) for providing long-term funds to develop the necessary DNA technology that eventually made it possible to retrieve environmental DNA from these ancient deposits in the Kap København Formation. E.W. also acknowledges the Wellcome Trust (UNS69906), the Carlsberg Foundation (CF18-0024), Novo Foundation (NNF18SA0035006), Leverhume (RPG-2016-235) and GRF EXC CRS Chair - Cluster of Excellence (44113220) for their support. M.W.P. acknowledges support from the Carlsberg Foundation (CF17-0275). K.K.S. and S.J. acknowledge support from VILLUM FONDEN (00025352). I.G.A. and E.C. have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 819192). B.D.S. acknowledges support from the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023). J.Å.K. was supported by the Carlsberg Foundation (CF20-0238). C.B. acknowledges ERC Advanced Award Diatomic (grant agreement no. 835067). J.C.G. was supported by Natural Science and Engineering Research Council of Canada–Discovery Grant 06785 and Canada Foundation for Innovation grant 21305. M.J.C. acknowledges support from the Danish National Research Foundation DNRF128. We thank G. Yang for cosmogenic isotope AMS target chemistry; S. Funder for introducing us to the Kap København Formation and generating much of the platform that enabled us to conduct our research; T. O. Delmont for providing data and guidance on the SMAGs analysis; Minik Rosing for providing talc minerals; T. B. Zunic for providing tremolite, orthoclase and chlorite; Z. Vardanyan for help with the DNA extractions and library build; and L. B. Levy and D. Skov for their help collecting samples in 2016. This work was prepared in part by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344; LLNL-JRNL-830653. E.W. thanks St Johns College, Cambridge for providing him with a stimulating environment for scientific thoughts and discussion., Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

1. Differences in botanical diet compositions among a large number of moose faecal samples collected during winter correlated with the nutritional differences identified in the same samples (Mantel r = 0.89, p = 0.001), but the nutritional differences were significantly smaller (p 0).3. Available protein (AP) and total non-structural carbohydrates (TNC) were significantly correlated in observed diets but not in hypothetical diets based on food availability.4. The level of Acetoacetate in moose serum (i.e. "starvation') was weakly negatively associated with digestibility of diets (p = 0.08) and unrelated to increasing AP:TNC and AP:NDF ratios in diets (p > 0.1).5. Our study is the first to demonstrate complementary feeding in free-ranging moose to attain a nutritional target that has previously been suggested in a feeding trial with captive moose. Our results add support to the hypothesis of nutritional balancing as a driver in the nutritional strategy of moose with implications for both the management of moose and food resources.

International audience; Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.