Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years

Article https://doi.org/10.1038/s41467-026-72977-6 Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years Received: 17 October 2025 2 , & Check for updates 1234567890():,; 1234567890():,; Accepted: 24 April 2026 Tyler J. Murchie 1,2 , Scott L. Cocker3,4, Sina Baleka2, Nicola Alexandra Vogel2,5, Libby Natola1, Emil Karpinski2,6, Diana Tirlea 7, McIntyre A. Barrera 1, Danielle M. Grant 1, Evan Morien1, George S. Long Linda Y. Rutledge1,8, Grant D. Zazula9,10, Britta J. Jensen3, Duane G. Froese 3 Hendrik N. Poinar 2,11 Permafrost-preserved ground squirrel (Urocitellus) burrows in Yukon, Canada contain coprolites (palaeofaeces) that span from the Holocene to at least the Middle Pleistocene (~700 kya). Using shotgun metagenomics and targeted enrichment, we recover a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including: plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. These coprolites consistently preserve an abundance of eukaryotic DNA, enabling the assembly of >18 mitochondrial genomes (ground squirrel, snowshoe hare, steppe bison, horse, and mammoth), and revealing previously unrecognized diversity within Arctic Urocitellus, including a ~700 kya lineage that predates divergence among several extant clades. Characteristic damage patterns, positive/negative controls, and in silico taxon validations strongly support aDNA authenticity, and comparisons with regional permafrost datasets indicate minimal postdepositional leaching. These results show that permafrost coprolites can yield high-resolution records of Quaternary ecosystems and multi-organism population histories, providing a powerful complement to sedimentary and skeletal ancient DNA. Coprolites (ancient faeces) can serve as a time-restricted biological snapshot of the past, preserving a variety of biomolecules1,2 and even ancient DNA (aDNA)3–12. This includes the aDNA of the defecator, their diet13, their gut microbiome, and the aDNA of other organisms in their local environment. When preserved in permafrost over immense timescales, faecal pellets can retain ancient environmental DNA (aeDNA) that helps reconstruct past communities and track ecological change across glacial–interglacial cycles. In unglaciated regions of eastern Beringia (Yukon and Alaska) (Fig. 1), ground squirrels construct burrows that can remain frozen and sealed for tens to hundreds of 1 Biodiversity Genomics, Hakai Institute, Heriot Bay, BC, Canada. 2McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada. 3Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada. 4Department of Geological Sciences and Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden. 5Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark. 6Harvard Medical School, Harvard University, Cambridge, MA, USA. 7Quaternary Environments, Royal Alberta Museum, Edmonton, AB, Canada. 8Forestry and Conservation, University of British Columbia, Vancouver, BC, Canada. 9Department of Tourism and Culture, Yukon Government, Palaeontology Program, Whitehorse, YT, Canada. 10Collections and Research, Canadian Museum of Nature, Ottawa, ON, Canada. 11McMaster e-mail: ; Ancient DNA Centre, Departments of Biochemistry and Biology, McMaster University, Hamilton, ON, Canada. ; Nature Communications | (2026)17:4868 1 Article https://doi.org/10.1038/s41467-026-72977-6 1000 800 0 0 63°40' N Gold Run 0 12 0 800 1000 800 LGM ice extent SI 0 10 110 0 12 0 800 0 80 Arctic Ocean 700 1000 0 80 120 0 Quartz Creek 63°50'N 800 1000 800 0 60 Quartz Creek Paradise Hill Dom in Cre ion ek 0 600 100 0 r Rive 60 0 Canyon Creek 600 Yuko n 0 10 0 100 0 0 Little Blanche 63°50' N 800 600 10 0 0 800 90 0 800 Klondike River 600 0 10 800 0 80 80 0 0 60 64°0'N 60 0 Hunker Creek (Upper/Lower) Hun ker Cre ek 0 60 0 70 80 0 400 138°0' W 800 10 0 1000 800 Dawson 0 60 0 100 138°30' W 600 700 800 64°10'N 139°0' W 800 139°30' W 80 0 140°0' W 800 A Eureka Creek 63°30'N n D a w so 10 0 60 0 0 B 0 Pacific Ocean 1:40,000,000 10 30 km 20 C 139°30 W aDNA ID Site Core ID Age Shotgun Enriched (cal. yr BP) (total reads) (total reads) SC-2 SC-3 SC-5 SC-6 SC-8 SC-9 SC-10 SC-11 SC-12 Hunker Creek Hunker Creek Lower Hunker Quartz Creek Quartz Creek Canyon Creek Eureka Creek Eureka Creek Lile Blanche DF09-HC-30 DF09-HC-29a SLC21-KL-1D SC-AGS-01 SC-AGS-04 SC-AGS-12 SC-AGS-15 SC-AGS-18 SC-AGS-21 17,175 15,920,534 8,619,666 17,175 1,867,770 10,531,629 30,000DT 2,571,597 80,000SCT 2,131,519 80,000SCT 19,883,053 80,000SCT 31,035 16,287,382 19,659,670 28,660 1,875,061 682 2,777,265 SC-13 Quartz Creek SC-AGS-22 Nest latrine Gold Run Tephra (732-644 kya) SC-14 aDNA subsampling 12,734,374 15,852,759 Gold Run Site Holocene 4.0 4 2 LGM 13a 11d/e 9a 50,000 15a 6d 8b 6b Age ranges 6c associated with tephras 6a 100,000 200,000 10b 8a 8c 15d 12b 10c Glacial 10a maxima 300,000 13b 400,000 15b 16a 12a 500,000 17d 18b/d 17b 600,000 c 19a/b 16b 14a/b/c 12c Calibrated years before present (BP) Fig. 1 | Coprolites processed for ancient environmental DNA with their midden locations. A Nest midden sites in the Klondike region of Yukon, Canada. Base map data from GeoYukon (Government of Yukon); contours in metres above sea level. Inset: Beringia during the last glacial maximum (LGM, 26.5–19 thousand years before present [ka BP])67. Ice sheet data from Dyke193. Sea level during LGM set to 126 m below sea level based on Clark and Mix194. Beringian palaeo-drainage data Nature Communications | (2026)17:4868 17a 11b 9b 7b 6e 13c 19c 17c 15e 15c 11a 9d 5b 5d Marine Isotope Stages (MIS) 9c 5a 5c 4.5 0 Interglacial 7c 7a 3 5.0 11c 9e 5e Pleistocene Benthic δ18 O LR04 3.5 1 63°20' N 138°30' W Tephrochronology ages: GRTGold Run Tephra; SCTSheep Creek Klondike Tephra, DT Dawson Tephra. Other ages based on 14C (median calibrated years BP). 3.0 0 1:600,000 139°0' W SC-14 Gold Run GZ.07.07 700,000GRT 242,855,809 290,600,543 SC-15 Lower Hunker SLC21-KL-4A 30,000DT 12,678,828 1,956,241 SC-16 Treadstone Mine SLC21-TM-1C 30,000DT 2,208,612 SC-17 Lower Hunker SLC21-KL-8 30,000DT Negave controls (air, extracon, library) x11 975,495 4,675,363 •Arcc ground squirrel (Urocitellus sp.) • Posive Holocene control D 40 1 140°0' W 35,850 5 0 10 Ste Ground squirrel coprolite/midden site 63°30'N 800 0 Holocene coprolite r Population centres BC 0 60 0 ive 10 0 0 10 u 0 0 80 Ju n ea 0 12 Roads or se wa W hi t eh rt R YK r ag e An ch o 0 80 on Yu k r e R i v Fa ir ba nk s 63°40'N 800 c cti Ar cle C i r NWT AK SC-14 18a 18e 16c age range 700,000 20a 800 kya from Bond195. B Sample metadata and summary of (...truncated)