Germonpré, M. et al. Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes. J. Archaeol. Sci. 36, 473–490 (2009).
Germonpré, M., Lázničková-Galetová, M. & Sablin, M. V. Palaeolithic dog skulls at the Gravettian Předmostí site, the Czech Republic. J. Archaeol. Sci. 39, 184–202 (2012).
Ovodov, N. D. et al. A 33,000-year-old incipient dog from the Altai Mountains of Siberia: evidence of the earliest domestication disrupted by the Last Glacial Maximum. PLoS ONE 6, e22821 (2011).
Camarós, E., Münzel, S. C., Cueto, M., Rivals, F. & Conard, N. J. The evolution of Paleolithic hominin–carnivore interaction written in teeth: stories from the Swabian Jura (Germany). J. Archaeol. Sci. Rep. 6, 798–809 (2016).
Sablin, M. V. & Khlopachev, G. A. The earliest ice age dogs: evidence from Eliseevichi 1. Curr. Anthropol. 43, 795–799 (2002).
Germonpré, M. et al. The Canis lupus ssp. (Mammalia, Carnivora) of the Baume Traucade (Issirac, Gard, France): a complete skeleton of a ‘dog-like’ individual from the post-LGM. Quat. Sci. Rev. 356, 109288 (2025).
Vilà, C. et al. Multiple and ancient origins of the domestic dog. Science 276, 1687–1689 (1997).
Feuerborn, T. R. et al. Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal. Proc. Natl Acad. Sci. USA 118, e2100338118 (2021).
Evin, A. et al. The emergence and diversification of dog morphology. Science 390, 741–744 (2025).
Baird, D. et al. Juniper smoke, skulls and wolves’ tails. The Epipalaeolithic of the Anatolian plateau in its South-west Asian context; insights from Pınarbaşı. Levant 45, 175–209 (2013).
Bello, S. M., Lewis, M. D. & Parfitt, S. A. 125 years of exploration and research at Gough’s Cave (Somerset, UK). J. R. Anthropol. Inst. https://doi.org/10.1111/1467-9655.70004 (2025).
Borić, D. et al. Late Mesolithic lifeways and deathways at Vlasac (Serbia). J. Field Archaeol. 39, 4–31 (2014).
Dimitrijević, V. & Vuković, S. Was the dog locally domesticated in the Danube gorges? Morphometric study of dog cranial remains from four Mesolithic-Early Neolithic archaeological sites by comparison with contemporary wolves: dog domestication in the Danube gorges Mesolithic. Int. J. Osteoarchaeol. 25, 1–30 (2015).
Posth, C. et al. Palaeogenomics of upper Palaeolithic to neolithic European hunter-gatherers. Nature 615, 117–126 (2023).
Bello, S. M., Saladié, P., Cáceres, I., Rodríguez-Hidalgo, A. & Parfitt, S. A. Upper Palaeolithic ritualistic cannibalism at Gough’s Cave (Somerset, UK): the human remains from head to toe. J. Hum. Evol. 82, 170–189 (2015).
Marsh, W. A. & Bello, S. Cannibalism and burial in the late Upper Palaeolithic: combining archaeological and genetic evidence. Quat. Sci. Rev. 319, 108309 (2023).
Janssens, L. A. A., Boudadi-Maligne, M., Lawler, D. F., O’Keefe, F. R. & van Dongen, S. Morphology-based diagnostics of ‘protodogs.’ A commentary to Galeta et al., 2021, Anatomical Record, 304, 42–62, doi: 10.1002/ar.24500. Anat. Rec. 304, 2673–2684 (2021).
Ameen, C. et al. A landmark-based approach for assessing the reliability of mandibular tooth crowding as a marker of dog domestication. J. Archaeol. Sci. 85, 41–50 (2017).
Boudadi-Maligne, M. & Escarguel, G. A biometric re-evaluation of recent claims for Early Upper Palaeolithic wolf domestication in Eurasia. J. Archaeol. Sci. 45, 80–89 (2014).
Baumann, C. et al. A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site. Sci. Rep. 11, 5137 (2021).
Ramos-Madrigal, J. et al. Genomes of Pleistocene Siberian wolves uncover multiple extinct wolf lineages. Curr. Biol. 31, 198–206.e8 (2021).
Bergström, A. et al. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 607, 313–320 (2022).
Janssens, L. et al. A new look at an old dog: Bonn-Oberkassel reconsidered. J. Archaeol. Sci. 92, 126–138 (2018).
Thalmann, O. et al. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342, 871–874 (2013).
Napierala, H. & Uerpmann, H.-P. A ‘new’ palaeolithic dog from central Europe. Int. J. Osteoarchaeol. 22, 127–137 (2012).
Hervella, M. et al. The domestic dog that lived ∼17,000 years ago in the Lower Magdalenian of Erralla site (Basque Country): a radiometric and genetic analysis. J. Archaeol. Sci. Rep. 46, 103706 (2022).
Boschin, F. et al. The first evidence for Late Pleistocene dogs in Italy. Sci. Rep. 10, 13313 (2020).
Boudadi-Maligne, M., Mallye, J.-B., Langlais, M. & Barshay-Szmidt, C. Magdalenian dog remains from Le Morin rock-shelter (Gironde, France). Socio-economic implications of a zootechnical innovation. Paléo 23, 39–54, (2012).
Jacobi, R. & Higham, T. in The Ancient Human Occupation of Britain (eds Ashton, N. et al.) 223–248 (Elsevier, 2011).
Currant, A. P. The Late Glacial mammal fauna of Gough’s Cave, Cheddar, Somerset. Proc. of the University of Bristol Spelaeological Society 17, 286–304 (1986).
Plassais, J. et al. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nat. Commun. 10, 1489 (2019).
Barton, L. et al. Agricultural origins and the isotopic identity of domestication in northern China. Proc. Natl Acad. Sci. USA 106, 5523–5528 (2009).
Mashkour, M. et al. Carnivores and their prey in the Wezmeh Cave (Kermanshah, Iran): a Late Pleistocene refuge in the Zagros. Int. J. Osteoarchaeol. 19, 678–694 (2009).
Scarsbrook, L. Canid identification (CanID) workflow. GitHub https://github.com/lachiescarsbrook/CanID (2024).
Ollivier, M. et al. Dogs accompanied humans during the Neolithic expansion into Europe. Biol. Lett. 14, 20180286 (2018).
Feldman, M. et al. Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Nat. Commun. 10, 1218 (2019).
Charlton, S. et al. Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain. Nat. Ecol. Evol. 6, 1658–1668 (2022).
Marginedas, F. et al. New insights of cultural cannibalism amongst Magdalenian groups at Maszycka Cave, Poland. Sci. Rep. 15, 2351 (2025).
Stevens, R. E., Reade, H., Tripp, J., Sayle, K. L. & Walker, E. A. in The Beef Behind All Possible Pasts: The Tandem-Festschrift in Honour of Elaine Turner and Martin Street (eds Gaudzinski-Windheuser, S. & Jöris, O.) 589–607 (Propylaeum, 2021).
Barton, R. N. E., Jacobi, R. M., Stapert, D. & Street, M. J. The Late-glacial reoccupation of the British Isles and the Creswellian. J. Quat. Sci. 18, 631–643 (2003).
Jacobi, R. & Higham, T. in Developments in Quaternary Sciences, Vol. 14 (eds Ashton, N., Lewis, S.G., & Stringer, C.) 223–247 (Elsevier, 2011).
Pedersen, J. B., Poulsen, M. E. & Riede, F. Jels 3, a new late Palaeolithic open-air site in Denmark, sheds light on the pioneer colonization of northern Europe. J. Field Archaeol. 47, 360–378 (2022).
Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).
Bortolini, E. et al. Early Alpine occupation backdates westward human migration in Late Glacial Europe. Curr. Biol. 31, 2484–2493.e7 (2021).
Bello, S. M., Wallduck, R., Parfitt, S. A. & Stringer, C. B. An Upper Palaeolithic engraved human bone associated with ritualistic cannibalism. PLoS ONE 12, e0182127 (2017).
Morey, D. F. & Jeger, R. When dogs and people were buried together. J. Anthropol. Archaeol. 67, 101434 (2022).
Losey, R. J. et al. Burying dogs in ancient Cis-Baikal, Siberia: temporal trends and relationships with human diet and subsistence practices. PLoS ONE 8, e63740 (2013).
Larsen, T., Fernandes, R., Wang, Y. V. & Roberts, P. Reconstructing hominin diets with stable isotope analysis of amino acids: new perspectives and future directions. Bioscience 72, 618–637 (2022).
O’Connell, T. C. ‘Trophic’ and ‘source’ amino acids in trophic estimation: a likely metabolic explanation. Oecologia 184, 317–326 (2017).
Chikaraishi, Y. et al. High-resolution food webs based on nitrogen isotopic composition of amino acids. Ecol. Evol. 4, 2423–2449 (2014).
Baumann, C. et al. Dietary niche partitioning among Magdalenian canids in southwestern Germany and Switzerland. Quat. Sci. Rev. 227, 106032 (2020).
Ollivier, M. et al. Amy2B copy number variation reveals starch diet adaptations in ancient European dogs. R. Soc. Open Sci. 3, 160449 (2016).
O’Connell, T. C. in Handbook of Archaeological Sciences (eds Pollard, A. M., Armitage, R. A. & Makarewicz, C. A.) 437–452 (Wiley, 2023).
Lübcker, N., Whiteman, J. P., Newsome, S. D., Millar, R. P. & de Bruyn, P. J. N. Can the carbon and nitrogen isotope values of offspring be used as a proxy for their mother’s diet? Using foetal physiology to interpret bulk tissue and amino acid δ15N values. Conserv. Physiol. 8, coaa060 (2020).
Lin, A. T. et al. The history of Coast Salish ‘woolly dogs’ revealed by ancient genomics and Indigenous Knowledge. Science 382, 1303–1308 (2023).
Frantz, L. A. F. et al. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352, 1228–1231 (2016).
Sinding, M.-H. S. et al. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 368, 1495–1499 (2020).
Bergström, A. et al. Origins and genetic legacy of prehistoric dogs. Science 370, 557–564 (2020).
Fan, Z. et al. Worldwide patterns of genomic variation and admixture in gray wolves. Genome Res. 26, 163–173 (2016).
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
Nielsen, S. V. et al. Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genet. 19, e1010410 (2023).
Botigué, L. R. et al. Ancient European dog genomes reveal continuity since the Early Neolithic. Nat. Commun. 8, 16082 (2017).
Zhang, S.-J. et al. Genomic evidence for the Holocene codispersal of dogs and humans across Eastern Eurasia. Science 390, 735–740 (2025).
Marchi, N. et al. The genomic origins of the world’s first farmers. Cell 185, 1842–1859.e18 (2022).
Frantz, L. A. F. et al. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proc. Natl Acad. Sci. USA 116, 17231–17238 (2019).
Park, S. D. E. et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 16, 234 (2015).
Scarsbrook, L., Frantz, L. A. F. & Larson, G. in Encyclopedia of Quaternary Science, 3rd edn (eds Woodroffe, S., Jones. A, & O’Rouke, D.) 709–718 (Elsevier, 2025).
Lin, A. T., Fairbanks, R. A., Barba-Montoya, J., Liu, H.-L. & Kistler, L. A legacy of genetic entanglement with wolves shapes modern dogs. Proc. Natl Acad. Sci. USA 122, e2421768122 (2025).
Reimer, P. J. et al. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).
Ramsey, C. B. Radiocarbon calibration and analysis of stratigraphy: the OxCal Program. Radiocarbon 37, 425–430 (1995).
Ramirez, M. D., Besser, A. C., Newsome, S. D. & McMahon, K. W. Meta-analysis of primary producer amino acid δ15N values and their influence on trophic position estimation. Methods Ecol. Evol. 12, 1750–1767 (2021).
Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241–242 (1971).
Styring, A. K. et al. Refining human palaeodietary reconstruction using amino acid δ15N values of plants, animals and humans. J. Archaeol. Sci. 53, 504–515 (2015).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, db.prot5448 (2010).
Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742–751 (2017).
Kemp, B. M. & Smith, D. G. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci. Int. 154, 53–61 (2005).
Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protoc. 13, 2447–2461 (2018).
Carøe, C. et al. Single-tube library preparation for degraded DNA. Methods Ecol. Evol. 9, 410–419 (2018).
Fellows Yates, J. A. et al. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9, e10947 (2021).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Bouckaert, R. et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
Meisner, J., Liu, S., Huang, M. & Albrechtsen, A. Large-scale inference of population structure in presence of missingness using PCA. Bioinformatics 37, 1868–1875 (2021).
Librado, P. & Orlando, L. Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics. Bioinformatics 38, 2070–2071 (2022).
Lichstein, J. W. Multiple regression on distance matrices: a multivariate spatial analysis tool. Plant Ecol. 188, 117–131 (2007).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Alaçamlı, E. et al. READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics. Genome Biol. 25, 216 (2024).
Monroy Kuhn, J. M., Jakobsson, M. & Günther, T. Estimating genetic kin relationships in prehistoric populations. PLoS ONE 13, e0195491 (2018).
Mallick, S. et al. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci. Data 11, 182 (2024).
Wright, S. Isolation by distance. Genetics 28, 114–138 (1943).
Quilodrán, C. S., Rio, J., Tsoupas, A. & Currat, M. Past human expansions shaped the spatial pattern of Neanderthal ancestry. Sci. Adv. 9, eadg9817 (2023).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
