Giemsch, L. & Hansen, S. (eds) The Caucasus: Bridge Between the City Centres in Mesopotamia and the Pontic Steppes within the 4th and threeth millennium BC. Proceedings of the Caucasus Convention Frankfurt 2018 (Schnell & Steiner, 2021).
Scott, A. et al. Emergence and intensification of dairying within the Caucasus and Eurasian steppes. Nat. Ecol. Evol. 6, 813–822 (2022).
Allentoft, M. E. et al. Inhabitants genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
Haak, W. et al. Large migration from the steppe was a supply for Indo-European languages in Europe. Nature 522, 207–211 (2015).
Wang, C.-C. et al. Historic human genome-wide information from a 3000-year interval within the Caucasus corresponds with eco-geographic areas. Nat. Commun. 10, 590 (2019).
Posth, C. et al. Palaeogenomics of Higher Palaeolithic to Neolithic European hunter-gatherers. Nature 615, 117–126 (2023).
Jones, E. R. et al. Higher Palaeolithic genomes reveal deep roots of contemporary Eurasians. Nat. Commun. 6, 8912 (2015).
Hansen, S. in Western Anatolia earlier than Troy: Proto-urbanisation within the 4th Millennium BC? (eds Horejs, B. & Mehofer, M.) 243–260 (Austrian Academy of Sciences Press, 2014).
Dinerstein, E. et al. An ecoregion-based strategy to defending half the terrestrial realm. Bioscience 67, 534–545 (2017).
Kohl, P. L. The Making of Bronze Age Eurasia (Cambridge Univ. Press, 2007).
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).
Balanovsky, O. et al. Parallel evolution of genes and languages within the Caucasus area. Mol. Biol. Evol. 28, 2905–2920 (2011).
Yunusbayev, B. et al. The Caucasus as an uneven semipermeable barrier to historic human migrations. Mol. Biol. Evol. 29, 359–365 (2012).
Yaka, R. et al. Variable kinship patterns in Neolithic Anatolia revealed by historic genomes. Curr. Biol. 31, 2455–2468 (2021).
Lazaridis, I. et al. Historic DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia. Science 377, 982–987 (2022).
Skourtanioti, E. et al. Genomic historical past of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus. Cell 181, 1158–1175 (2020).
Anthony, D. W. et al. The Eneolithic cemetery at Khvalynsk on the Volga River. Praehist. Zeitschr. 97, 22–67 (2022).
Mathieson, I. et al. Genome-wide patterns of choice in 230 historic Eurasians. Nature 528, 499–503 (2015).
Chintalapati, M., Patterson, N. & Moorjani, P. The spatiotemporal patterns of main human admixture occasions in the course of the European Holocene. Elife 11, e77625 (2022).
Lazaridis, I. et al. The genetic historical past of the Southern Arc: a bridge between West Asia and Europe. Science 377, eabm4247 (2022).
Penske, S. et al. Early contact between late farming and pastoralist societies in southeastern Europe. Nature 620, 358–365 (2023).
Mimokhod, R. A., Gak, E. I., Khomutova, T. E., Ryabogina, N. E. & Borisov, A. E. Paleoekologiya – kul’tura – metalloproizvodstvo: printsipy i mekhanizmy epokhi v kul’turnom nasledii Vostochnoy Yevropy v sredniye veka – pervyye pozdney bronzy. Ross. Arkheol. 24–38 (2022).
Reinhold, S., Belinskiy, A. B. & Atabiev, B. C. in Der Kaukasus zwischen Osteuropa und Vorderem Orient in der Bronze- und Eisenzeit (eds Kašuba, M. T. et al.) 405–456 (Dietrich Reimer, 2020).
Lazaridis, I. et al. Genomic insights into the origin of farming within the historic Close to East. Nature 536, 419–424 (2016).
Shishlina, N. Reconstruction of the Bronze Age of the Caspian Steppes: Life Types and Life Methods of Pastoral Nomads Vol. 1876 (Archaeopress, 2008).
Andreeva, M. V. Vostochnomanychskaya Kata-Kombnaya Kul’tura: Analiz Materialov Pogrebal’nykh Pamyatnikov (TAUS, 2014).
Ringbauer, H. et al. Correct detection of identity-by-descent segments in human historic DNA. Nat. Genet. 56, 143–151 (2023).
Ringbauer, H., Novembre, J. & Steinrücken, M. Parental relatedness by way of time revealed by runs of homozygosity in historic DNA. Nat. Commun. 12, 5425 (2021).
Golovanova, L. V. et al. The Epipaleolithic of the Caucasus after the Final Glacial Most. Quat. Int. 337, 189–224 (2014).
Manko, V. O. & Chkhatarashvili, G. L. in Aere Perennius. Extra Lasting than Bronze. Essays in Honour of Valentin Dergachev on the Event of his eightieth Birthday (ed. Dergacheva, L. V.) 101–118 (Stratum Library, 2023).
Helwing, B. et al. The Kura Initiatives: New Analysis on the Later Prehistory of the Southern Caucasus Vol. 16 (Dietrich Reimer, 2017).
Baudouin, E. L’structure de Mésopotamie et Du Caucase de La Fin Du 7e á La Fin Du 5e Millénaire Vol. 2 (Brepols, 2021).
Guarino-Vignon, P. et al. Genome-wide evaluation of a collective grave from Mentesh Tepe offers perception into the inhabitants construction of early neolithic inhabitants within the South Caucasus. Commun. Biol. 6, 309 (2023).
Korenevskiy, S. N. Rozhdenie Kurgana: (pogrebalnye Pamyatniki Eneoliticheskogo Vremeni Predkavkazya I Volgo-Donskogo Mezhdurechia) (TAUS, 2012).
Gorelik, A., Tsybryi, A. V. & Tsybryi, V. V. ‘Neolithisation’ within the NE Sea of Azov area: one step ahead, two steps again? Doc. Praehist. 43, 139–160 (2016).
Hollund, H. I., Higham, T., Belinskij, A. & Korenevskij, S. Investigation of palaeodiet within the North Caucasus (South Russia) Bronze Age utilizing steady isotope evaluation and AMS courting of human and animal bones. J. Archaeol. Sci. 37, 2971–2983 (2010).
Shishlina, N., Zazovskaya, E., van der Plicht, J. & Sevastyanov, V. Isotopes, crops, and reservoir results: case examine from the Caspian steppe Bronze Age. Radiocarbon 54, 749–760 (2012).
Reinhold, S. Der Kaukasus und die Eurasische Steppe – Konjunkturen einer kulturellen Kontaktzone während der Bronze- und frühen Eisenzeit. in You Solely See What You Know. You Solely Know What You See. World Historic Views on Intercultural Phenomena of Mobility. Festschrift Für Hermann Parzinger zum 65. Geburtstag (eds Schneeweiss, J. et al.) 437–460 (Marie Leidorf, 2024).
Hermes, T. R. et al. Early integration of pastoralism and millet cultivation in Bronze Age Eurasia. Proc. Biol. Sci. 286, 20191273 (2019).
Honeychurch, W. et al. The earliest herders of East Asia: inspecting Afanasievo entry to Central Mongolia. Archaeol. Res. Asia 26, 100264 (2021).
Korenevskiy, S. N. & Berezin, Y. B. Eneolithic Kurgan Burials from the Cemetery of Konstantinovsky-6. Strat. Plus 2/17, 385–396 (2017).
Knipper, C. et al. Eating regimen and subsistence in Bronze Age pastoral communities from the southern Russian steppes and the North Caucasus. PLoS ONE 15, e0239861 (2020).
Reinhold, S. et al. in Appropriating Improvements (eds Stockhammer, P. W. & Maran, J.) 78–97 (Oxbow, 2017).
Librado, P. et al. The origins and unfold of home horses from the Western Eurasian steppes. Nature 598, 634–640 (2021).
de Barros Damgaard, P. et al. The primary horse herders and the affect of early Bronze Age steppe expansions into Asia. Science 360, eaar7711 (2018).
Burmeister, S. in Appropriating Improvements (eds Stockhammer, P. W. & Maran, J.) 69–77 (Oxbow, 2017).
Shishlina, N., Ankusheva, P., Orfinskaya, O. & Kiseleva, D. in The Indo-European Puzzle Revisited. Integrating Archaeology, Genetics, and Linguistics (eds Kristian, Okay., Kroonen, G. & Willerslev, E.) 275–281 (Cambridge Univ. Press, 2023).
Hansen, S. in The Caucasus (eds Giemsch, L. & Hansen, S.) 31–86 (Schnell & Steiner, 2021).
Jeong, C. et al. Bronze Age inhabitants dynamics and the rise of dairy pastoralism on the japanese Eurasian steppe. Proc. Natl Acad. Sci. USA 115, E11248–E11255 (2018).
Wilkin, S. et al. Dairying enabled Early Bronze Age Yamnaya steppe expansions. Nature 598, 629–633 (2021).
Kaiser, E. Das dritte Jahrtausend im osteuropäischen Steppenraum: Kulturhistorische Studien zu prähistorischer Subsistenzwirtschaft und Interaktion mit benachbarten Räumen (Freie Universität Berlin, 2019).
Batiuk, S. D. The fruits of migration: understanding the ‘longue durée’ and the socio-economic relations of the Early Transcaucasian Tradition. J. Anthropol. Archaeol. 32, 449–477 (2013).
Perşoiu, A., Ionita, M. & Weiss, H. Atmospheric blocking induced by the strengthened Siberian Excessive led to drying in west Asia in the course of the 4.2 ka BP occasion – a speculation. Clim. Previous 15, 781–793 (2019).
Reinhold, S. et al. On the onset of settled pastoralism – implications of archaeozoological and isotope analyses from Bronze Age websites within the North Caucasus. Quat. Int. https://doi.org/10.1016/j.quaint.2023.05.008 (2023).
Reinhold, S., Korobov, D. S. & Belinskiy, A. B. Landschaftsarchäologie im Nordkaukasus: Studien zu einer neu entdeckten bronzezeitlichen Kulturlandschaft im Hochgebirge des Nordkaukasus Vol. 38 (Habelt, 2017).
Dabney, J. et al. Full mitochondrial genome sequence of a Center 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 extremely multiplexed goal seize and sequencing. Chilly Spring Harb. Protoc. 2010, db.prot5448 (2010).
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase remedy for screening of historic DNA. Philos. Trans. R. Soc. B 370, 20130624 (2015).
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. & Meyer, M. Single-stranded DNA library preparation for the sequencing of historic or broken DNA. Nat. Protoc. 8, 737–748 (2013).
Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Guide and automatic preparation of single-stranded DNA libraries for the sequencing of DNA from historic organic stays and different sources of extremely degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).
Kapp, J. D., Inexperienced, R. E. & Shapiro, B. A quick and environment friendly single-stranded genomic library preparation methodology optimized for historic DNA. J. Hered. 112, 241–249 (2021).
Peltzer, A. et al. EAGER: environment friendly historic genome reconstruction. Genome Biol. 17, 60 (2016).
Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence seize of mitochondrial genomes utilizing PCR merchandise. PLoS ONE 5, e14004 (2010).
Rohrlach, A. B. et al. Utilizing Y-chromosome seize enrichment to resolve haplogroup H2 exhibits new proof for a two-path Neolithic enlargement to Western Europe. Sci. Rep. 11, 15005 (2021).
Jun, G., Wing, M. Okay., Abecasis, G. R. & Kang, H. M. An environment friendly and scalable evaluation framework for variant extraction and refinement from population-scale DNA sequence information. Genome Res. 25, 918–925 (2015).
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Evaluation of Subsequent Era Sequencing Knowledge. BMC Bioinform. 15, 356 (2014).
Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for historic DNA. Genome Biol. 16, 224 (2015).
Fu, Q. et al. A revised timescale for human evolution based mostly on historic mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).
Furtwängler, A. et al. Ratio of mitochondrial to nuclear DNA impacts contamination estimates in historic DNA evaluation. Sci. Rep. 8, 1–8 (2018).
Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification within the period of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).
Rohrlach, A. B., Tuke, J., Popli, D. & Haak, W. BREADR: An R package deal for the Bayesian estimation of genetic relatedness from low-coverage genotype information. Preprint at bioRxiv https://doi.org/10.1101/2023.04.17.537144 (2023).
Alaçamlı, E. et al. READv2: superior and user-friendly detection of organic relatedness in archaeogenomics. Genome Biol. 25, 216 (2024).
Chao, F., Gerland, P., Cook dinner, A. R. & Alkema, L. Systematic evaluation of the intercourse ratio at start for all international locations and estimation of nationwide imbalances and regional reference ranges. Proc. Natl Acad. Sci. USA 116, 9303–9311 (2019).
Sedgwick, P. A number of significance assessments: the Bonferroni correction. BMJ 344, e509 (2012).
Champely, S. Pwr: Primary Capabilities for Energy Evaluation. https://CRAN.R-project.org/package deal=pwr (2020).
Cohen, J. Statistical Energy Evaluation for the Behavioral Sciences (Routledge, 2013).
Lazaridis, I. et al. Historic human genomes recommend three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
Patterson, N. et al. Historic admixture in human historical past. Genetics 192, 1065–1093 (2012).
Rasmussen, M. et al. Historic human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial website in western Montana. Nature 506, 225–229 (2014).
Seguin-Orlando, A. et al. Genomic construction in Europeans courting again at the least 36,200 years. Science 346, 1113–1118 (2014).
Raghavan, M. et al. Higher Palaeolithic Siberian genome reveals twin ancestry of Native Individuals. Nature 505, 87–91 (2014).
Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015).
Kılınç, G. M. et al. The Demographic improvement of the primary farmers in Anatolia. Curr. Biol. 26, 2659–2666 (2016).
Broushaki, F. et al. Early Neolithic genomes from the japanese Fertile Crescent. Science 353, 499–503 (2016).
Fu, Q. et al. The genetic historical past of Ice Age Europe. Nature 534, 200–205 (2016).
van den Brink, E. C. M. et al. A Late Bronze Age II clay coffin from Tel Shaddud within the Central Jezreel Valley, Israel: context and historic implications. Levantina 49, 105–135 (2017).
Mittnik, A. et al. The genetic prehistory of the Baltic Sea area. Nat. Commun. 9, 442 (2018).
Harney, É. et al. Historic DNA from Chalcolithic Israel reveals the function of inhabitants combination in cultural transformation. Nat. Commun. 9, 3336 (2018).
Mathieson, I. et al. The genomic historical past of southeastern Europe. Nature 555, 197–203 (2018).
Krzewińska, M. et al. Historic genomes recommend the japanese Pontic-Caspian steppe because the supply of western Iron Age nomads. Sci. Adv. 4, eaat4457 (2018).
de Damgaard, P. B. et al. 137 historic human genomes from throughout the Eurasian steppes. Nature 557, 369–374 (2018).
Feldman, M. et al. Late Pleistocene human genome suggests a neighborhood origin for the primary farmers of central Anatolia. Nat. Commun. 10, 1218 (2019).
Sikora, M. et al. The inhabitants historical past of northeastern Siberia for the reason that Pleistocene. Nature 570, 182–188 (2019).
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 historical past of admixture throughout interior Eurasia. Nat. Ecol. Evol. 3, 966–976 (2019).
Rivollat, M. et al. Historic genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers. Sci. Adv. 6, eaaz5344 (2020).
Yu, H. et al. Paleolithic to Bronze Age Siberians reveal connections with First Individuals and throughout Eurasia. Cell 181, 1232–1245 (2020).
Agranat-Tamir, L. et al. The genomic historical past of the Bronze Age Southern Levant. Cell 181, 1146–1157 (2020).
Jeong, C. et al. A dynamic 6,000-year genetic historical past of Eurasia’s Japanese Steppe. Cell 183, 890–904 (2020).
Kılınç, G. M. et al. Human inhabitants dynamics and Yersinia pestis in historic northeast Asia. Sci. Adv. 7, eabc4587 (2021).
Saag, L. et al. Genetic ancestry modifications in Stone to Bronze Age transition within the East European plain. Sci. Adv. 7, eabd6535 (2021).
Zhang, F. et al. The genomic origins of the Bronze Age Tarim Basin mummies. Nature 599, 256–261 (2021).
Altınışık, N. E. et al. A genomic snapshot of demographic and cultural dynamism in Higher Mesopotamia in the course of the Neolithic Transition. Sci. Adv. 8, eabo3609 (2022).
Koptekin, D. et al. Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean. Curr. Biol. 33, 41–57 (2023).
Wang, X. et al. Isotopic and DNA analyses reveal multiscale PPNB mobility and migration throughout Southeastern Anatolia and the Southern Levant. Proc. Natl Acad. Sci. USA 120, e2210611120 (2023).
Mallick, S. et al. The Allen Historic DNA Useful resource (AADR): a curated compendium of historic human genomes. Sci. Knowledge 11:182 (2024).
Schmid, C. et al. Poseidon – a framework for archaeogenetic human genotype information administration. eLife https://doi.org/10.7554/elife.98317.1 (2024).
Patterson, N., Worth, A. L. & Reich, D. Inhabitants construction and eigenanalysis. PLoS Genet. 2, e190 (2006).
Alexander, D. H., Novembre, J. & Lange, Okay. Quick model-based estimation of ancestry in unrelated people. Genome Res. 19, 1655–1664 (2009).
Petr, M., Vernot, B. & Kelso, J. admixr—R package deal for reproducible analyses utilizing ADMIXTOOLS. Bioinformatics 35, 3194–3195 (2019).
Harney, É., Patterson, N., Reich, D. & Wakeley, J. Assessing the efficiency of qpAdm: a statistical instrument for finding out inhabitants admixture. Genetics 217, iyaa045 (2021).
Delaneau, O. GLIMPSE: Low Protection Calling of Genotypes https://github.com/odelaneau/GLIMPSE (2020).
Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Environment friendly phasing and imputation of low-coverage sequencing information utilizing giant reference panels. Nat. Genet. 53, 120–126 (2021).
Rohrlach, B. BenRohrlach/CaucasusIIAncientDNAStudy: v1.0.0. Zenodo https://doi.org/10.5281/zenodo.13709775 (2024).
