Ecology

Author notesMikayla M. ClarkPresent address: University of Tennessee, Knoxville, TN, USAMichael W. SneddonPresent address: Predicine, Inc., Hayward, CA, USARoman SutorminPresent address: Google, Inc., San Francisco, CA, USAAuthors and AffiliationsLawrence Berkeley National Laboratory, Berkeley, CA, USADylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin & Adam P. ArkinOak Ridge National Laboratory, Oak Ridge, TN, USABenjamin H. Allen, Mikayla M. Clark, Miriam L. Land & Robert W. CottinghamArgonne National Laboratory, Lemont, IL, USATianhao Gu, Qizhi Zhang & Chris S. HenryAuthorsDylan ChivianSean P. JungbluthParamvir S. DehalElisha M. Wood-CharlsonRichard S. CanonBenjamin H. AllenMikayla M. ClarkTianhao GuMiriam L. LandGavin A. PriceWilliam J. RiehlMichael W. SneddonRoman SutorminQizhi ZhangRobert W. CottinghamChris S. HenryAdam P. ArkinCorresponding authorsCorrespondence to
Dylan Chivian or Adam P. Arkin. More

Department of Zoology, University of Cambridge, Cambridge, UKYucheng Wang, Bianca De Sanctis, Ruairidh Macleod, Daniel Money & Eske WillerslevLundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, DenmarkYucheng Wang, Ana Prohaska, Jialu Cao, Antonio Fernandez-Guerra, James Haile, Kurt H. Kjær, Thorfinn Sand Korneliussen, Nicolaj Krog Larsen, Ruairidh Macleod, Hugh McColl, Mikkel Winther Pedersen, Fernando Racimo, Alexandra Rouillard, Anthony H. Ruter, Lasse Vinner, David J. Meltzer & Eske WillerslevALPHA, State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS), Beijing, ChinaYucheng WangKey Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Science, Lanzhou University, Lanzhou, ChinaHaoran DongGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, FranceAdriana Alberti, France Denoeud & Patrick WinckerInstitute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, FranceAdriana AlbertiThe Arctic University Museum of Norway, UiT—The Arctic University of Norway, Tromsø, NorwayInger Greve Alsos, Eric Coissac, Galina Gusarova, Youri Lammers & Marie Kristine Føreid MerkelDepartment of Geography and Environment, University of Hawaii, Honolulu, HI, USADavid W. BeilmanDepartment of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, DenmarkAnders A. BjørkInstitute of Earth Sciences, St Petersburg State University, St Petersburg, RussiaAnna A. Cherezova & Grigory B. FedorovArctic and Antarctic Research Institute, St Petersburg, RussiaAnna A. Cherezova & Grigory B. FedorovUniversité Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, FranceEric CoissacDepartment of Genetics, University of Cambridge, Cambridge, UKBianca De Sanctis & Richard DurbinCarlsberg Research Laboratory, Copenhagen V, DenmarkChristoph Dockter & Birgitte SkadhaugeSchool of Geography and Environmental Science, University of Southampton, Southampton, UKMary E. EdwardsAlaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK, USAMary E. EdwardsSchool of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UKNeil R. Edwards & Philip B. HoldenCenter for the Environmental Management of Military Lands, Colorado State University, Fort Collins, CO, USAJulie EsdaleDepartment of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, CanadaDuane G. FroeseFaculty of Biology, St Petersburg State University, St Petersburg, RussiaGalina GusarovaDepartment of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen K, DenmarkKristian K. KjeldsenDepartment of Earth Science, University of Bergen, Bergen, NorwayJan Mangerud & John Inge SvendsenBjerknes Centre for Climate Research, Bergen, NorwayJan Mangerud & John Inge SvendsenDepartment of Geology, Quaternary Sciences, Lund University, Lund, SwedenPer MöllerCenter for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø, DenmarkDavid Nogués-Bravo, Hannah Lois Owens & Carsten RahbekCentre d’Anthropobiologie et de Génomique de Toulouse, Faculté de Médecine Purpane, Université Paul Sabatier, Toulouse, FranceLudovic OrlandoCenter for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, DenmarkHannah Lois Owens & Carsten RahbekGates of the Arctic National Park and Preserve, US National Park Service, Fairbanks, AK, USAJeffrey T. RasicDepartment of Geosciences, UiT—The Arctic University of Norway, Tromsø, NorwayAlexandra RouillardZoological Institute, Russian academy of sciences, St Petersburg, RussiaAlexei TikhonovResource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing, ChinaYingchun XingCollege of Plant Science, Jilin University, Changchun, Jilin, ChinaYubin ZhangDepartment of Anthropology, Southern Methodist University, Dallas, TX, USADavid J. MeltzerWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UKEske WillerslevMARUM, University of Bremen, Bremen, GermanyEske WillerslevAll authors contributed to the conception of the presented ideas. Y.W. and H.D. analysed the data. Y.W., D.J.M., A.P. and E.W. wrote the paper with inputs from all authors. More

Rearing O. biroi pupae in social isolation and collecting pupal fluidIn O. biroi colonies, larvae and pupae develop in discrete and synchronized cohorts26. Ten days after the first larvae had entered pupation in a large stock colony, the entire colony was anaesthetized using a CO2 pad, and white pupae were separated using a paintbrush. Pupae were individually placed in 0.2 ml PCR tubes with open lid. These tubes were then placed inside 1.5 ml Eppendorf tubes with 5 µl sterile water at the bottom to provide 100% relative humidity. The outer tubes were closed and kept in a climate room at 25 °C. The inner tube in this design prevents the pupa from drowning in the water reservoir. The outer tubes were kept closed throughout the experiment, except for once a day when the tubes were opened to remove pupal social fluid. Pulled glass capillaries were prepared as described elsewhere29, and used to remove and/or collect secretion droplets. We were careful to leave no remains of the secretion behind on the pupae or the inside of the tubes. To ensure that all secretion had been removed, pupae were taken out of the tube after fluid collection and briefly placed on a tissue paper to absorb any excess liquid. The inner tubes were replaced if needed—for example, if fluid traces were visible on the old tube after collection. Each pupa was checked daily for secretion (absent or present), onset of melanization and eclosion, and whether the pupa was alive (responding to touch). Control groups of 30 pupae and 30 adult ants from the same stock colony and cohort as the isolated pupae were placed in Petri dishes with a plaster of Paris floor, and the same parameters as for the isolated pupae were scored daily. Experiments ended when all pupae had either eclosed or died. Newly eclosed (callow) workers moved freely inside the tube and showed no abnormalities when put in a colony. A pupa was declared dead if it did not shed its pupal skin and did not respond to touch three days after all pupae in the control group had eclosed.To calculate the average secretion volume per secreting pupa (Fig. 1d), the total volume collected daily from a group of isolated pupae (142–166 pupae) was divided by the number of pupae from which fluid had been collected that day. The total volume was determined by multiplying the height of the fluid’s meniscus in the capillary by πr², where r is the inner radius of the capillary (0.29 mm). While pupae were secreting, pupal whole-body wash samples were collected daily. The pupae were removed from colonies with adults and washed promptly with 1500 µl LC–MS grade water. Whole-body wash samples were lyophilized and reconstituted in 15 µl LC–MS grade water.Collecting additional ant species and honeybees, rearing pupae in social isolation, and collecting pupal fluidsColonies of the ants N. flavipes, T. sessile, P. pennsylvanica and Lasius neoniger were collected in NY state, USA (Central Park, Manhattan; Pelham Bay Park, Bronx; Prospect Park, Brooklyn; and Woodstock). Solenopsis invicta colonies were collected in Athens, GA, USA. M. mexicanus colonies were collected in Piñon Hills, CA, USA. Colonies comprised of queens, workers and brood were maintained in the laboratory in airtight acrylic boxes with plaster of Paris floors. Colonies were fed a diet of insects (flies, crickets and mealworms). White pupae were socially isolated, cocoons were removed in the case of P. pennsylvanica, and secretion droplets were collected from melanized pupae as described for O. biroi. A. mellifera pupae of unknown age were socially isolated from hive fragments (A&Z Apiaries, USA) and reared as described for O biroi, except that the rearing temperature was set to 32 °C. Relative humidity was set to either 100% to replicate conditions used for the different ant species, or to 75% as recommended in the literature30.Injecting dye and tracking pupal fluidInjection needles were prepared as in previous studies31. Injections were performed using an Eppendorf Femtojet with a Narishige micromanipulator. The Femtojet was set to Pi 1000 hPa and Pc 60 hPa. Needles were broken by gently touching the capillary tip to the side of a glass slide. To inject, melanized pupae were placed on ‘Sticky note’ tape (Post-it), with the abdomen tip forward and the ventral side upward. Pupae were injected with blue food colouring (McCormick) into the exuvium for 1–2 s by gently piercing the pupal case at the abdominal tip with the needle. During successful injections, no fluid was discharged from the pupa when the needle was removed, and the moulting fluid inside the exuvium was immediately stained. Pupae were washed in water three times to remove any excess dye. Following injections, 10 pupae were reared in social isolation to confirm the secretion of dyed droplets. For experiments, injected pupae were transferred to colonies with adult ants (Figs. 1f and  4c) or to colonies with adult ants and larvae (Figs. 3b and  4c) to track the distribution of the pupal social fluid.After spending 24 h with dye-injected pupae, adults were taken out of the colony, briefly immersed in 95% ethanol, and transferred to PBS. Digestive systems were dissected in cold PBS and mounted in DAKO mounting medium. Crop and stomach images (Fig. 1f, inset and Fig. 4c, inset) were acquired with a Revolve microscope (Echo). Larvae are translucent, and the presence of dye in the digestive system can be assayed without dissection. Whole-body images of larvae were acquired with a Leica Z16 APO microscope equipped with a Leica DFC450 camera and Leica Application Suite version 4.12.0 (Leica Microsystems). In the experiment on larval growth (Fig. 3c), larval length was measured from images using ImageJ32.Occluding pupaeTen pupae were placed on double-sided tape on a glass coverslip with the ventral side up. The area between the pupae was covered with laser-cut filter paper to prevent adults from sticking to the tape. The pupae were then placed in a 5 cm diameter Petri dish with a moist plaster of Paris floor. To block pupal secretion, the tip of the gaster was occluded with a drop of oil-paint (Uni Paint Markers PX-20), which has no discernible toxic effect7. Secreting pupae received a drop of the same paint on their head to control for putative differences resulting from the paint. Pupae were left in isolation for one day before adults were added to the assay chamber.Behavioural tracking of adult preference assayVideos were recorded using BFS-U3-50S5C-C: 5.0 MP, 35 FPS, Sony IMX264, Colour cameras (FLIR) and the Motif Video Recording System (Loopbio). To assess adult preference (Fig. 1g), physical contact of adults with pupae was manually annotated for the first 10 min after the first adult had encountered (physically contacted) a pupa.Protein profilingWe extracted 30 µl of pupal social fluid and whole-body wash samples with 75:25:0.2 acetonitrile: methanol: formic acid. Extracts were vortexed for 10 min, centrifuged at 16,000g and 4 °C for 10 min, dried in a SpeedVac, and stored at −80 °C until they were analysed by LC–MS/MS.Protein pellets were dissolved in 8 M urea, 50 mM ammonium bicarbonate, and 10 mM dithiothreitol, and disulfide bonds were reduced for 1 h at room temperature. Alkylation was performed by adding iodoacetamide to a final concentration of 20 mM and incubating for 1 h at room temperature in the dark. Samples were diluted using 50 mM ammonium bicarbonate until the concentration of urea had reached 3.5 M, and proteins were digested with endopeptidase LysC overnight at room temperature. Samples were further diluted to bring the urea concentration to 1.5 M before sequencing-grade modified trypsin was added. Digestion proceeded for 6 h at room temperature before being halted by acidification with TFA and samples were purified using in-house constructed C18 micropurification tips.LC–MS/MS analysis was performed using a Dionex3000 nanoflow HPLC and a Q-Exactive HF mass spectrometer (both Thermo Scientific). Solvent A was 0.1% formic acid in water and solvent B was 80% acetonitrile, 0.1% formic acid in water. Peptides were separated on a 90-minute linear gradient at 300 nl min−1 across a 75 µm × 100 mm fused-silica column packed with 3 µm Reprosil C18 material (Dr. Maisch). The mass spectrometer operated in positive ion Top20 DDA mode at resolution 60 k/30 k (MS1/MS2) and AGC targets were 3 × 106/2 × 105 (MS1/MS2).Raw files were searched through Proteome Discoverer v.1.4 (Thermo Scientific) and spectra were queried against the O. biroi proteome using MASCOT with a 1% FDR applied. Oxidation of M and acetylation of protein N termini were applied as a variable modification and carbamidomethylation of C was applied as a static modification. The average area of the three most abundant peptides for a matched protein33 was used to gauge protein amounts within and between samples.Functional annotation and gene ontology enrichmentTo supplement the current functional annotation of the O. biroi genome34, the full proteome for canonical transcripts was retrieved from UniProtKB (UniProt release 2020_04) in FASTA format. We then applied the EggNog-Mapper tool35,36 (http://eggnog-mapper.embl.de, emapper version 1.0.3-35-g63c274b, EggNogDB version 2) using standard parameters (m diamond -d none –tax_scope auto –go_evidence non-electronic –target_orthologs all –seed_ortholog_evalue 0.001 –seed_ortholog_score 60 –query-cover 20 –subject-cover 0) to produce an expanded annotation for all GO trees (Molecular Function, Biological Process, Cellular Components). The list of proteins identified in the pupal fluid was evaluated for functional enrichment in these GO terms, P-values were adjusted with an FDR cut-off of 0.05, and the network plots were visualized using the clusterProfiler package37.Metabolite profilingFor bulk polar metabolite profiling, we used 10 µl aliquots of pupal social fluid and whole-body wash (pooled samples). For the time-series metabolite profiling, 1 µl of pupal social fluid and whole-body wash was used. Samples were extracted in 180 µl cold LC–MS grade methanol containing 1 μM of uniformly labelled 15N- and 13C-amino acid internal standards (MSK-A2-1.2, Cambridge Isotope Laboratories) and consecutive addition of 390 µl LC–MS grade chloroform followed by 120 µl of LC–MS grade water.The samples were vortexed vigorously for 10 min followed by centrifugation (10 min at 16,000g and 4 °C). The upper polar metabolite-containing layer was collected, flash frozen and SpeedVac-dried. Dried extracts were stored at −80 °C until LC–MS analysis.LC–MS was conducted on a Q-Exactive benchtop Orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe, which was coupled to a Vanquish UPLC system (Thermo Fisher Scientific). External mass calibration was performed using the standard calibration mixture every three days.Dried polar samples were resuspended in 60 µl 50% acetonitrile, and 5 µl were injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore). Chromatographic separation was achieved using the following conditions: buffer A was 20 mM ammonium carbonate, 0.1% (v/v) ammonium hydroxide (adjusted to pH 9.3); buffer B was acetonitrile. The column oven and autosampler tray were held at 40 °C and 4 °C, respectively. The chromatographic gradient was run at a flow rate of 0.150 ml min−1 as follows: 0–22 min: linear gradient from 90% to 40% B; 22–24 min: held at 40% B; 24–24.1 min: returned to 90% B; 24.1 −30 min: held at 90% B. The mass spectrometer was operated in full-scan, polarity switching mode with the spray voltage set to 3.0 kV, the heated capillary held at 275 °C, and the HESI probe held at 250 °C. The sheath gas flow was set to 40 units, the auxiliary gas flow was set to 15 units. The MS data acquisition was performed in a range of 55–825 m/z, with the resolution set at 70,000, the AGC target at 10 × 106, and the maximum injection time at 80 ms. Relative quantification of metabolite abundances was performed using Skyline Daily v 20.1 (MacCoss Lab) with a 2 ppm mass tolerance and a pooled library of metabolite standards to confirm metabolite identity (via data-dependent acquisition). Metabolite levels were normalized by the mean signal of 8 heavy 13C,15N-labelled amino acid internal standards (technical normalization).The raw data were searched for a targeted list of ~230 polar metabolites and the corresponding peaks were integrated manually using Skyline Daily software. We were able to assign peaks to 107 compounds based on high mass accuracy ( More

arising from Y. Wang et al. Nature https://doi.org/10.1038/s41586-021-04016-x (2021)A unique challenge for environmental DNA (eDNA)-based palaeoecological reconstructions and extinction estimates is that organisms can contribute DNA to sediments long after their death. Recently, Wang et al.1 discovered mammoth eDNA in sediments that are between approximately 4.6 and 7 thousand years (kyr) younger than the most recent mammoth fossils in North America and Eurasia, which they interpreted as mammoths surviving on both continents into the Middle Holocene epoch. Here we present an alternative explanation for these offsets: the slow decomposition of mammoth tissues on cold Arctic landscapes is responsible for the release of DNA into sediments for thousands of years after mammoths went extinct. eDNA records are important palaeobiological archives, but the mixing of undatable DNA from long-dead organisms into younger sediments complicates the interpretation of eDNA, particularly from cold and high-latitude systems.All animal tissues, including faeces, contribute DNA to eDNA records2, but the durations across which tissues can contribute genetic information must vary depending on tissue type and local rates of destruction and decomposition. On high-latitude landscapes, soft tissues and skeletal remains of large mammals may persist, unburied, for millennia3,4,5. For example, unburied antlers of caribou (Rangifer tarandus) from Svalbard (Norway) and Ellesmere Island (Canada) have been dated3,4 to between 1 and 2 cal kyr bp (calibrated kyr before present). Elephant seal (Mirounga leonina) remains near the Antarctic coastline5,6 can persist for more than 5,000 years. This is in contrast to bones in warmer settings, which persist for only centuries or decades7,8. Because bones are particularly resistant to decay, quantifying how their persistence changes across environments enables us to constrain the durations that dead individuals generally contribute to eDNA archives. To do this, we consolidated data on the oldest radiocarbon-dated surface-collected bones from different ecosystems. We included bones that we are reasonably confident persisted without being completely buried (‘never buried’), and bones for which exhumation cannot be confidently excluded (‘potentially never buried’). Pairing bone persistence with mean annual temperatures (MAT) from their sample localities, we find a strong link between the local temperature and the logged duration of bone persistence (Fig. 1, never buried bones: R2 = 0.94, P  More

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