Kuper, R. & Kröpelin, S. Climate-controlled Holocene occupation in the Sahara: motor of Africa’s evolution. Science 313, 803–807 (2006).
van de Loosdrecht, M. et al. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 360, 548–552 (2018).
COHMAP Members. Climatic changes of the last 18,000 years: observations and model simulations. Science 241, 1043–1052 (1988).
Ritchie, J. C., Eyles, C. H. & Haynes, C. V. Sediment and pollen evidence for an early to mid-Holocene humid period in the eastern Sahara. Nature 314, 352–355 (1985).
Tierney, J. E., Pausata, F. S. R. & deMenocal, P. B. Rainfall regimes of the Green Sahara. Sci. Adv. 3, e1601503 (2017).
Gasse, F. Hydrological changes in the African tropics since the Last Glacial Maximum. Quat. Sci. Rev. 19, 189–211 (2000).
Hoelzmann, P., Keding, B., Berke, H., Kröpelin, S. & Kruse, H.-J. Environmental change and archaeology: lake evolution and human occupation in the Eastern Sahara during the Holocene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 169, 193–217 (2001).
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).
Simões, L. G. et al. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature https://doi.org/10.1038/s41586-023-06166-6 (2023).
di Lernia, S. Earliest Herders of the Central Sahara (Tadrart Acacus Mountains, Libya): a punctuated model for the emergence of pastoralism in Africa. J. World Prehist. 34, 531–594 (2021).
Smith, A. Pastoralism in Africa. Oxford Research Encyclopedia of African History https://doi.org/10.1093/acrefore/9780190277734.013.1066 (2021).
McDonald, M. M. A. The pattern of Neolithization in Dakhleh Oasis in the Eastern Sahara. Quat. Int. 410, 181–197 (2016).
Vai, S. et al. Ancestral mitochondrial N lineage from the Neolithic ‘green’ Sahara. Sci. Rep. 9, 3530 (2019).
Manning, K. et al. Habitat fragmentation and the sporadic spread of pastoralism in the mid-Holocene Sahara. Quat. Sci. Rev. 309, 108070 (2023).
Cremaschi, M. et al. Takarkori rock shelter (SW Libya): an archive of Holocene climate and environmental changes in the central Sahara. Quat. Sci. Rev. 101, 36–60 (2014).
Biagetti, S. & di Lernia, S. Holocene deposits of saharan rock shelters: the case of Takarkori and other sites from the Tadrart Acacus Mountains (Southwest Libya). Afr. Archaeol. Rev. 30, 305–338 (2013).
di Lernia, S., Massamba N’siala, I. & Mercuri, A. M. Saharan prehistoric basketry. Archaeological and archaeobotanical analysis of the early-middle Holocene assemblage from Takarkori (Acacus Mts., SW Libya). J. Archaeol. Sci. 39, 1837–1853 (2012).
Dunne, J., Mercuri, A. M., Evershed, R. P., Bruni, S. & di Lernia, S. Earliest direct evidence of plant processing in prehistoric Saharan pottery. Nat. Plants 3, 16194 (2016).
Rotunno, R., Cavorsi, L. & di Lernia, S. A Holocene ceramic sequence in the Central Sahara: pottery traditions and social dynamics seen from the Takarkori Rockshelter (SW Libya). Afr. Archaeol. Rev. 40, 647–672 (2023).
Van Neer, W. et al. Aquatic fauna from the Takarkori rock shelter reveals the Holocene central Saharan climate and palaeohydrography. PLoS ONE 15, e0228588 (2020).
Cherkinsky, A. & di Lernia, S. Bayesian approach to 14C dates for estimation of long-term archaeological sequences in arid environments: the Holocene site of Takarkori rockshelter, southwest Libya. Radiocarbon 55, 771–782 (2013).
Lernia, S. di, di Lernia, S. & Tafuri, M. A. Persistent deathplaces and mobile landmarks: the Holocene mortuary and isotopic record from Wadi Takarkori (SW Libya). J. Anthropological Archaeol. https://doi.org/10.1016/j.jaa.2012.07.002 (2013).
Dunne, J. et al. First dairying in green Saharan Africa in the fifth millennium BC. Nature 486, 390–394 (2012).
Tafuri, M. A., Bentley, R. A., Manzi, G. & di Lernia, S. Mobility and kinship in the prehistoric Sahara: strontium isotope analysis of Holocene human skeletons from the Acacus Mts. (southwestern Libya). J. Anthropol. Archaeol. 25, 390–402 (2006).
Rohland, N. et al. Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs. Genome Res. 32, 2068–2078 (2022).
Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).
Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).
Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
Fan, S. et al. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 20, 82 (2019).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).
Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).
Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
Pickrell, J. K. et al. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).
Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71.e21 (2017).
Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).
Pickrell, J. K. et al. Ancient west Eurasian ancestry in southern and eastern Africa. Proc. Natl Acad. Sci. USA 111, 2632–2637 (2014).
D’Atanasio, E. et al. The genomic echoes of the last Green Sahara on the Fulani and Sahelian people. Curr. Biol. 33, 5495–5504 (2023).
Wang, K. et al. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa. Sci. Adv. 6, eaaz0183 (2020).
Lipson, M. et al. Ancient DNA and deep population structure in sub-Saharan African foragers. Nature 603, 290–296 (2022).
Llorente, M. G. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015).
Harney, É. et al. Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation. Nat. Commun. 9, 3336 (2018).
Prendergast, M. E. et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365, eaaw6275 (2019).
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).
Paris, F. in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics, and Ethnography (ed. MacDonald, K. B. R.) 111–126 (UCL Press, 2000).
Vernet, R. in Droughts, Food and Culture 47–63 (Kluwer Academic, 2006).
Prüfer, K. et al. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nat. Ecol. Evol. 5, 820–825 (2021).
Peter, B. M. 100,000 years of gene flow between Neandertals and Denisovans in the Altai mountains. Preprint at bioRxiv https://doi.org/10.1101/2020.03.13.990523 (2020).
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).
Maier, R. et al. On the limits of fitting complex models of population history to f-statistics. eLife 12, e85492 (2023).
Garcea, E. A. A. An alternative way towards food production: the perspective from the Libyan Sahara. J. World Prehist. 18, 107–154 (2004).
Mercuri, A. M., Fornaciari, R., Gallinaro, M., Vanin, S. & di Lernia, S. Plant behaviour from human imprints and the cultivation of wild cereals in Holocene Sahara. Nat. Plants 4, 71–81 (2018).
di Lernia, S. Dismantling dung: delayed use of food resources among Early Holocene foragers of the Libyan Sahara. J. Anthropol. Archaeol. 20, 408–441 (2001).
Rotunno, R., Mercuri, A. M., Florenzano, A., Zerboni, A. & di Lernia, S. Coprolites from rock shelters: hunter-gatherers ‘herding’ barbary sheep in the Early Holocene Sahara. J. Afr. Archaeol. 17, 76–94 (2019).
Kröpelin, S. et al. Climate-driven ecosystem succession in the Sahara: the past 6000 years. Science 320, 765–768 (2008).
Hoelzmann, P. et al. in Past Climate Variability through Europe and Africa (eds Battarbee, R. W. et al.) 219–256 (Springer, 2004).
Di Lernia, S. Saharan Hunter-Gatherers: Specialization and Diversification in Holocene Southwestern Libya (Routledge, 2022).
Drake, N. A., Blench, R. M., Armitage, S. J., Bristow, C. S. & White, K. H. Ancient watercourses and biogeography of the Sahara explain the peopling of the desert. Proc. Natl Acad. Sci. USA 108, 458–462 (2011).
Peter, B. M., Petkova, D. & Novembre, J. Genetic landscapes reveal how human genetic diversity aligns with geography. Mol. Biol. Evol. 37, 943–951 (2020).
Cheddadi, R. et al. Early Holocene greening of the Sahara requires Mediterranean winter rainfall. Proc. Natl Acad. Sci. USA 118, e2024898118 (2021).
Profico, A. et al. Medical imaging as a taphonomic tool: the naturally-mummified bodies from Takarkori rock shelter (Tadrart Acacus, SW Libya, 6100-5600 uncal BP). J. Cult. Herit. Manage. Sust. Dev. 10, 144–156 (2019).
Stloukal, M. & Hanáková, H. Die länge der längsknochen Altslawischer bevölkerungen unter besonderer berücksichtigung von wachstumsfragen. Homo 29, 53–69 (1978).
France, D. L. Lab Manual and Workbook for Physical Anthropology (West, 1988).
Ubelaker, D. H. Human Skeletal Remains. Excavation, Analysis, Interpretation (Taraxacum, 1989)
Buikstra, J. E. & Ubelaker, D. H. Standards for Data Collection from Human Skeletal Remains (Arkansas Archaeological Survey, 1994).
Todd, T. W. Age changes in the pubic bone. I. The male white pubis. Am. J. Phys. Anthropol. 3, 285–334 (1920).
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. Dental wear in the Libben population: its functional pattern and role in the determination of adult skeletal age at death. Am. J. Phys. Anthropol. 68, 47–56 (1985).
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).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Peyrégne, S. & Peter, B. M. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol. 21, 246 (2020).
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).
Neukamm, J., Peltzer, A. & Nieselt, K. DamageProfiler: fast damage pattern calculation for ancient DNA. Bioinformatics 37, 3652–3653 (2021).
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).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).
Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).
Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).
Mafessoni, F. et al. A high-coverage Neandertal genome from Chagyrskaya Cave. Proc. Natl Acad. Sci. USA 117, 15132–15136 (2020).
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Posth, C. et al. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nat. Commun. 8, 16046 (2017).
Pugach, I. et al. Ancient DNA from Guam and the peopling of the Pacific. Proc. Natl Acad. Sci. USA 118, e2022112118 (2021).
Prüfer, K. snpAD: an ancient DNA genotype caller. Bioinformatics 34, 4165–4171 (2018).
Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).
Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).
Bouckaert, R. R. & Drummond, A. J. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol. Biol. 17, 42 (2017).
Ringbauer, H., Novembre, J. & Steinrücken, M. Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat. Commun. 12, 5425 (2021).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).