Garstang, J. in The Burial Customs of Ancient Egypt (ed. Garstang, J.) 26–30 (Archibald Constable, 1907).
Lazaridis, I. et al. Ancient DNA from Mesopotamia suggests distinct pre-pottery and pottery Neolithic migrations into Anatolia. Science 377, 982–987 (2022).
Skourtanioti, E. et al. Genomic history of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus. Cell 181, 1158–1175.e28 (2020).
Haber, M. et al. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101, 274–282 (2017).
Agranat-Tamir, L. et al. The genomic history of the Bronze Age Southern Levant. Cell 181, 1146–1157.e11 (2020).
Salvatori, S. & Usai, D. The neolithic and ‘pastoralism’ along the Nile: a dissenting view. J. World Prehist. 32, 251–285 (2019).
Wengrow, D. The Archaeology of Early Egypt: Social Transformations in North-East Africa, 10,000 to 2,650 BC (Cambridge Univ. Press, 2006).
Bard, K. A. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 61–88 (Oxford Univ. Press, 2000).
Stevenson, A. in The Sumerian World (ed. Crawford, H.) 620–636 (Routledge, 2013).
Malek, J. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 89–117 (Oxford Univ. Press, 2000).
Doherty, S. K. The Origins and Use of the Potter’s Wheel in Ancient Egypt (Archaeopress, 2015).
Keita, S. O. Y. Further studies of crania from ancient northern Africa: an analysis of crania from First Dynasty Egyptian tombs. Am. J. Phys. Anthropol. 87, 245–254 (1992).
Prowse, T. L. & Lovell, N. C. Concordance of cranial and dental morphological traits and evidence for endogamy in ancient Egypt. Am. J. Phys. Anthropol. 101, 237–246 (1996).
Irish, J. D. Who were the ancient Egyptians? Dental affinities among Neolithic through postdynastic peoples. Am. J. Phys. Anthropol. 129, 529–543 (2006).
Zakrzewski, S. R. in Egyptian Bioarchaeology: Humans, Animals, and the Environment (eds Ikram, S. et al.) 157–167 (Sidestone, 2015).
Dicke-Toupin, C. R. Population Continuity or Replacement at Ancient Lachish? (Fairbanks, 2012).
Irish, J. D. Diachronic and synchronic dental trait affinities of late and post-Pleistocene peoples from North Africa. Homo 49, 138–155 (1998).
Maaranen, N., Zakrzewski, S. & Schutkowski, H. Who were the Hyksos? Curr. Anthropol. 63, 66–69 (2022).
Pääbo, S. Molecular cloning of ancient Egyptian mummy DNA. Nature 314, 644–645 (1985).
Schuenemann, V. J. et al. Ancient Egyptian mummy genomes suggest an increase of sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8, 15694 (2017).
Shaw, I. The Oxford History of Ancient Egypt (Oxford Univ. Press, 2000).
De Meyer, M. et al. in Under the Potter’s Tree: Studies on Ancient Egypt Presented to Janine Bourriau Vol. 204 (eds Aston, D. et al.) 679–702 (Peeters, 2011).
Power, R. K. & Tristant, Y. From refuse to rebirth: repositioning the pot burial in the Egyptian archaeological record. Antiquity 90, 1474–1488 (2016).
Lasisi, T. & Shriver, M. D. Focus on African diversity confirms complexity of skin pigmentation genetics. Genome Biol. 19, 13 (2018).
Buikstra, J. E. & Ubelaker, D. U. Standards for Data Collection from Human Skeletal Remains (Arkansas Archeological Survey, 1994).
Raxter, M. H. et al. Stature estimation in ancient Egyptians: a new technique based on anatomical reconstruction of stature. Am. J. Phys. Anthropol. 136, 147–155 (2008).
Işcan, M. Y., Loth, S. R. & Wright, R. K. Age estimation from the rib by phase analysis: white males. J. Forensic Sci. 29, 1094–1104 (1984).
Kennedy, K. A. R. in Reconstruction of Life from the Skeleton (eds Kennedy, K. A. R. & Işcan, M. Y.) 129–160 (Alan R. Liss, 1989).
Capasso, L., Kenney, K. A. R. & Wilczak, C. A. Atlas of Occupational Markers on Human Remains (Edigratifal, 1998).
Buzon, M. R. & Simonetti, A. Strontium isotope (87Sr/86Sr) variability in the Nile Valley: identifying residential mobility during ancient Egyptian and Nubian sociopolitical changes in the New Kingdom and Napatan periods. Am. J. Phys. Anthropol. 151, 1–9 (2013).
Stantis, C., Nowell, G. M., Prell, S. & Schutkowski, H. Animal proxies to characterize the strontium biosphere in the northeastern Nile Delta. Bioarchaeology of the Near East 13, 1–13 (2019).
Touzeau, A. et al. Egyptian mummies record increasing aridity in the Nile Valley from 5500 to 1500 yr before present. Earth Planet. Sci. Lett. 375, 92–100 (2013).
Richards, M. P. in Archaeological Science: An Introduction (eds Richards, M. P. & Britton, K.) 125–144 (Cambridge Univ. Press, 2019).
Touzeau, A. et al. Diet of ancient Egyptians inferred from stable isotope systematics. J. Archaeol. Sci. 46, 114–124 (2014).
Macko, S. A. et al. Documenting the diet in ancient human populations through stable isotope analysis of hair. Philos. Trans. R. Soc. London, B: Biol. Sci. 354, 65–76 (1999).
Thompson, A. H., Richards, M. P., Shortland, A. & Zakrzewski, S. R. Isotopic palaeodiet studies of ancient Egyptian fauna and humans. J. Archaeol. Sci. 32, 451–463 (2005).
Thompson, A. H., Chaix, L. & Richards, M. P. Stable isotopes and diet at ancient Kerma, Upper Nubia (Sudan). J. Archaeol. Sci. 35, 376–387 (2008).
Poulallion, E. et al. High δ15N values in Predynastic Egyptian archeological remains: a potential indicator for localised soil fertilisation practices in extreme conditions. Preprint at bioRxiv https://doi.org/10.1101/2024.11.18.624066 (2024).
Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Ringbauer, H., Novembre, J. & Steinrücken, M. Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat. Commun. 12, 5425 (2021).
Maier, R. et al. On the limits of fitting complex models of population history to f-statistics. eLife 12, e85492 (2023).
Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71.e21 (2017).
Yüncü, E. et al. False discovery rates of qpAdm-based screens for genetic admixture. Preprint at bioRxiv https://doi.org/10.1101/2023.04.25.538339 (2023).
Simões, L. G. et al. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature 618, 550–556 (2023).
Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).
Feldman, M. et al. Ancient DNA sheds light on the genetic origins of early Iron Age Philistines. Sci. Adv. 5, eaax0061 (2019).
Zvelebil, M. & Lillie, M. in Europe’s First Farmers (ed Price, T. D.) 57–92 (Cambridge Univ. Press, 2000).
Pinhasi, R. & Stock, J. T. Human Bioarchaeology of the Transition to Agriculture (Wiley, 2011).
Martin, N. et al. From hunter-gatherers to food producers: new dental insights into the Nile Valley population history (Late Paleolithic-Neolithic). Am. J. Biol. Anthropol. 184, e24948 (2024).
Stevenson, A. The Egyptian Predynastic and state formation. J. Archaeol. Res. 24, 421–468 (2016).
Redford, D. B. Egypt, Canaan, and Israel in Ancient Times (Princeton Univ. Press, 1992).
Llorente, M. G. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015).
Prendergast, M. E. et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365, eaaw6275 (2019).
Wang, K. et al. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa. Sci. Adv. 6, eaaz0183 (2020).
Bourriau, J. in The Oxford History of Ancient Egypt (ed. Shaw, I.) 172–206 (Oxford Univ. Press, 2000).
Ryholt, K. S. B. & Bülow-Jacobsen, A. The Political Situation in Egypt During the Second Intermediate Period, C. 1800-1550 B.C. (Museum Tusculanum, 1997).
Weiss, B. The decline of Late Bronze Age civilization as a possible response to climatic change. Clim. Change 4, 173–198 (1982).
Ward, W. A., Joukowsky, M. S. & Åström, P. The Crisis Years: The 12th Century B.C.: From Beyond the Danube to the Tigris (Kendall Hunt, 1992).
Harney, É. et al. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat. Commun. 9, 3336 (2018).
Salter-Townshend, M. & Myers, S. Fine-scale inference of ancestry segments without prior knowledge of admixing groups. Genetics 212, 869–889 (2019).
Elmonem, M. A. et al. The Egypt Genome Project. Nat. Genet. 56, 1035–1037 (2024).
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).
Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).
Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).
Dee, M. C14 data pottery coffin burial excavated by Garstang in Nuwayrat (World Museum, Liverpool, UK, 2016).
Vanthuyne, B. Early Old Kingdom Rock Circle Cemeteries in the 15th and 16th Nomes of Upper Egypt. A Socio-archaeological Investigation of the Cemeteries in Dayr al-Barshā, Dayr Abū Ḥinnis, Benī Ḥasan al-Shurūq and Nuwayrāt. PhD thesis, KU Leuven (2017).
Bronk Ramsey, C. Oxcal v.4.4.4 calibration program (2021); https://c14.arch.ox.ac.uk/oxcal.html.
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. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).
Bayliss, A. & Marshall, P. Radiocarbon Dating and Chronological Modelling: Guidelines and Best Practice (Historical Association, 2022).
Brown, T. A., Nelson, D. E., Vogel, J. S. & Southon, J. R. Improved collagen extraction by modified Longin method. Radiocarbon 30, 171–177 (1988).
Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241–242 (1971).
Scorrer, J. et al. Diversity aboard a Tudor warship: investigating the origins of the Mary Rose crew using multi-isotope analysis. R. Soc. Open Sci. 8, 202106 (2021).
Coplen, T. B. Normalization of oxygen and hydrogen isotope data. Chem. Geol. 72, 293–297 (1988).
Chenery, C. A., Pashley, V., Lamb, A. L., Sloane, H. J. & Evans, J. A. The oxygen isotope relationship between the phosphate and structural carbonate fractions of human bioapatite. Rapid Commun. Mass Spectrom. 26, 309–319 (2012).
Font, L., Nowell, G. M., Graham Pearson, D., Ottley, C. J. & Willis, S. G. Sr isotope analysis of bird feathers by TIMS: a tool to trace bird migration paths and breeding sites. J. Anal. At. Spectrom. 22, 513 (2007).
Nier, A. O. The isotopic constitution of strontium, barium, bismuth, thallium and mercury. Phys. Rev. 54, 275–278 (1938).
Avanzinelli, R., Conticelli, S. & Francalanci, L. High precision Sr, Nd, and Pb isotopic analyses using the new generation Thermal Ionisation Mass Spectrometer ThermoFinnigan Triton-Ti®. Periodico di Mineralogia 74, 147–166 (2015).
Işcan, M. Y., Loth, S. R. & Wright, R. K. Age estimation from the rib by phase analysis: white females. J. Forensic Sci. 30, 853–863 (1985).
Işcan, M. Y. & Loth, S. R. Determination of age from the sternal rib in white males: a test of the phase method. J. Forensic Sci. 31, 122–132 (1986).
Meindl, R. S. & Lovejoy, C. O. Ectocranial suture closure: a revised method for the determination of skeletal age at death based on the lateral-anterior sutures. Am. J. Phys. Anthropol. 68, 57–66 (1985).
Lovejoy, C. O., Meindl, R. S., Pryzbeck, T. R. & Mensforth, R. P. Chronological metamorphosis of the auricular surface of the ilium: a new method for the determination of adult skeletal age at death. Am. J. Phys. Anthropol. 68, 15–28 (1985).
Brooks, S. & Suchey, J. M. Skeletal age determination based on the os pubis: a comparison of the Acsádi-Nemeskéri and Suchey-Brooks methods. Hum. Evol. 5, 227–238 (1990).
Trotter, M. & Gleser, G. C. Estimation of stature from long bones of American whites and Negroes. Am. J. Phys. Anthropol. 10, 463–514 (1952).
Robins, G. & Shute, C. C. D. Predynastic Egyptian stature and physical proportions. Hum. Evol. 1, 313–324 (1986).
Bass, W. M. Human Osteology: A Laboratory and Field Manual (Missouri Archaeological Society, 2006).
Richard Scott, G. & Irish, J. D. Human Tooth Crown and Root Morphology (Cambridge Univ. Press, 2017).
Howells, W. W. Skull Shapes and the Map: Craniometric Analyses in the Dispersion of Modern Homo, Vol. 79 (Harvard Univ. Press, 1989) .
Scott, G. R. et al. rASUDAS: a new web-based application for estimating ancestry from tooth morphology. Forensic Anthropol. 1, 18–31 (2018).
Wright, R. Guide to Using the CRANID Programs Cr6bInd: For Linear and Nearest Neighbours Discriminant Analysis (2012); http://www.scribd.com/document/324417767/CRANID6b-ManuaL-1-pdf
Ortner, D. J. & Putschar, W. Identification of Paleopathological Conditions in Human Skeletal Remains (Smithsonian Institution, 1985).
Aufderheide, A. C. & Rodríguez-Martín, C. The Cambridge Encyclopedia of Human Paleopathology (Cambridge Univ. Press, 1998).
Hawkey, D. E. & Merbs, C. F. Activity‐induced musculoskeletal stress markers (MSM) and subsistence strategy changes among ancient Hudson Bay Eskimos. Int. J. Osteoarchaeol. 5, 324–338 (1995).
Alves-Cardoso, F. & Assis, S. Exploring ‘wear and tear’ of joints and ‘muscle function’ assumptions in skeletons with known occupation at death. Am. J. Phys. Anthropol. 175, 689–700 (2021).
Wallace, I. J. et al. Experimental evidence that physical activity inhibits osteoarthritis: implications for inferring activity patterns from osteoarthritis in archeological human skeletons. Am. J. Biol. Anthropol. 177, 223–231 (2022).
Wilkinson, C. M. & Mahoney, G. in Craniofacial Identification (eds Wilkinson, C. M. & Rynn, C.) 222–237 (Cambridge Univ. Press, 2012).
El-Mehallawi, I. H. & Soliman, E. M. Ultrasonic assessment of facial soft tissue thicknesses in adult Egyptians. Forensic Sci. Int. 117, 99–107 (2001).
Wilkinson, C. M. Facial reconstruction—anatomical art or artistic anatomy? J. Anat. 216, 235–250 (2010).
Rynn, C., Balueva, T. & Veselovskaya, E. in Craniofacial Identification (eds Wilkinson, C. M. & Rynn, C.) 193–202 (Cambridge Univ. Press, 2012).
Wilkinson, C. M. Cognitive bias and facial depiction from skeletal remains. Bioarchaeology Int. 4, 1–14 (2021).
Swali, P. et al. Yersinia pestis genomes reveal plague in Britain 4000 years ago. Nat. Commun. 14, 2930 (2023).
Fellows Yates, J. A. et al. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9, e10947 (2021).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531, 504–507 (2016).
Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014).
Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015).
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinf. 15, 356 (2014).
Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Schiffels, S. SequenceTool. https://github.com/stschiff/sequenceTools (2022).
Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87–e87 (2010).
Schönherr, S., Weissensteiner, H., Kronenberg, F. & Forer, L. Haplogrep3—an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 51, W263–W268 (2023).
Martiniano, R., De Sanctis, B., Hallast, P. & Durbin, R. Placing ancient DNA sequences into reference phylogenies. Mol. Biol. Evol. 39, msac017 (2022).
Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
Altınışık, N. E. et al. A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition. Sci. Adv. 8, eabo3609 (2022).
Antonio, M. L. et al. Ancient Rome: a genetic crossroads of Europe and the Mediterranean. Science 366, 708–714 (2019).
Broushaki, F. et al. Early Neolithic genomes from the eastern Fertile Crescent. Science 353, 499–503 (2016).
Clemente, F. et al. The genomic history of the Aegean palatial civilizations. Cell 184, 2565–2586.e21 (2021).
de Barros Damgaard, P. et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 360, eaar7711 (2018).
Damgaard, P. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (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).
Fregel, R. et al. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc. Natl Acad. Sci. USA 115, 6774–6779 (2018).
Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).
Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).
Gokhman, D. et al. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat. Commun. 11, 1189 (2020).
Haber, M. et al. A transient pulse of genetic admixture from the crusaders in the near east identified from ancient genome sequences. Am. J. Hum. Genet. 104, 977–984 (2019).
Haber, M. et al. A genetic history of the near east from an aDNA time course sampling eight points in the past 4,000 years. Am. J. Hum. Genet. 107, 149–157 (2020).
Hajdinjak, M. et al. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 592, 253–257 (2021).
Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015).
Kılınç, G. M. et al. The demographic development of the first farmers in Anatolia. Curr. Biol. 26, 2659–2666 (2016).
Lazaridis, I. et al. A genetic probe into the ancient and medieval history of Southern Europe and West Asia. Science 377, 940–951 (2022).
Lazaridis, I. et al. The genetic history of the Southern Arc: a bridge between West Asia and Europe. Science 377, eabm4247 (2022).
Lazaridis, I. et al. Genetic origins of the Minoans and Mycenaeans. Nature 548, 214–218 (2017).
Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).
Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017).
Lipson, M. et al. Ancient West African foragers in the context of African population history. Nature 577, 665–670 (2020).
Lipson, M. et al. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature 603, 290–296 (2022).
Mathieson, I. et al. The genomic history of southeastern Europe. Nature 555, 197–203 (2018).
McColl, H. et al. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018).
Omrak, A. et al. Genomic evidence establishes Anatolia as the source of the European Neolithic gene pool. Curr. Biol. 26, 270–275 (2016).
Patterson, N. et al. Large-scale migration into Britain during the Middle to Late Bronze Age. Nature 601, 588–594 (2022).
Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans. Nature 505, 87–91 (2014).
Rodríguez-Varela, R. et al. Genomic analyses of pre-European conquest human remains from the Canary Islands reveal close affinity to modern North Africans. Curr. Biol. 28, 1677–1679 (2018).
Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).
Seguin-Orlando, A. et al. Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113–1118 (2014).
Sirak, K. A. et al. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat. Commun. 12, 7283 (2021).
van de Loosdrecht, M. et al. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 360, 548–552 (2018).
Yaka, R. et al. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. Curr. Biol. 31, 2455–2468.e18 (2021).
Yang, M. A. et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27, 3202–3208.e9 (2017).
Wang, C.-C. et al. Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions. Nat. Commun. 10, 1–13 (2019).
Wang, C.-C. et al. Genomic insights into the formation of human populations in East Asia. Nature 591, 413–419 (2021).
Yang, M. A. et al. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science 369, 282–288 (2020).
Hofmanová, Z. et al. Early farmers from across Europe directly descended from Neolithic Aegeans.Proc. Natl Acad. Sci. USA 113, 6886–6891 (2016).
Flegontov, P. et al. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 570, 236–240 (2019).
Jeong, C. et al. The genetic history of admixture across inner Eurasia. Nat. Ecol. Evol. 3, 966–976 (2019).
Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).
Pagani, L. et al. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am. J. Hum. Genet. 96, 986–991 (2015).
Pickrell, J. K. et al. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).
Skoglund, P. et al. Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016).
Vyas, D. N., Al-Meeri, A. & Mulligan, C. J. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. Am. J. Phys. Anthropol. 164, 736–749 (2017).
Biagini, S. A. et al. People from Ibiza: an unexpected isolate in the Western Mediterranean. Eur. J. Hum. Genet. 27, 941–951 (2019).
Patterson, N., Moorjani, P., Luo, Y., Mallick, S. & Rohland, N. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Mallick, S. et al. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci. Data 11, 1–10 (2024).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Sousa da Mota, B. et al. Imputation of ancient human genomes. Nat. Commun. 14, 3660 (2023).
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120–126 (2021).
The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Chaitanya, L. et al. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: introduction and forensic developmental validation. Forensic Sci. Int. Genet. 35, 123–135 (2018).
Walsh, S. et al. Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage. Forensic Sci. Int. Genet. 9, 150–161 (2014).
Walsh, S. et al. Global skin colour prediction from DNA. Hum. Genet. 136, 847–863 (2017).