The early results that MHAAM has already produced may justly be called ground-breaking from a methodological as well as a historical perspective:
“A high-coverage yersinia pestis genome from a sixth-century Justinianic Plague victim.” Molecular Biology and Evolution, 33 (2016): 2911-23. doi: 10.1093/molbev/msw170.
M. Feldman, M. Harbeck, M. Keller, M.A. Spyrou, A. Rott, B. Trautmann, H.C. Scholz, B. Päffgen, J. Peters, M. McCormick, K. Bos, A. Herbig, J. Krause.
The Justinianic Plague (541-ca. 750 CE) is thought to be the first of three historically documented plague pandemics that caused massive casualties. Historical accounts and molecular data suggest the bacteriumYersinia pestisas its etiological agent. Here we presented a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestisgenome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.
“Genomic insights into the origin of farming in the ancient Near East.” Nature 536 (2016): 419-24.
I. Lazaridis, D. Nadel, G. Rollefson, D.C. Merrett, N. Rohland, S. Mallick, D. Fernandes, M. Novak, B. Gamarra, K. Sirak, S. Connell, K. Stewardson, E. Harney, Q. Fu, G. Gonzalez-Fortes, E.R. Jones, S.A. Roodenberg, G. Lengyel, F. Bocquentin, B. Gasparian, J.M. Monge, M. Gregg, V. Eshed, A. Mizrahi, C. Meiklejohn, F. Gerritsen, L. Bejenaru, M. Blüher, A. Campbell, G. Cavalleri, D. Comas, P. Froguel, E. Gilbert, S.M. Kerr, P. Kovacs, J. Krause, D. McGettigan, M. Merrigan, D.A. Merriwether, S. O'Reilly, M.B. Richards, O. Semino, M. Shamoon-Pour, G. Stefanescu, M. Stumvoll, A. Tönjes, A. Torroni, J.F. Wilson, L. Yengo, N.A. Hovhannisyan, N. Patterson, R. Pinhasi, D. Reich.
In this paper we reported genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 BCE, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
“Genetic origins of the Minoans and Mycenaeans.” Nature, 548: 23310 (2017), pp. 214-18. doi:10.1038/nature23310
I. Lazaridis, A. Mittnik, N. Patterson, S. Mallick, N. Rohland, S. Pfrengle, A. Furtwängler, A. Peltzer, C. Posth, A. Vasilakis, P.J.P. McGeorge, E. Konsolaki-Yannopoulou, G. Korres, H. Martlew, M. Michalodimitrakis, M. Özsait, N. Özsait, A. Papathanasiou, M. Richards, S.A. Roodenberg, Y. Tzedakis, R. Arnott, D.M. Fernandes, J.R. Hughey, D.M. Lotakis, P.A. Navas, Y. Maniatis, J.A. Stamatoyannopoulos, K. Stewardson, P.W. Stockhammer, R. Pinhasi, D. Reich, J. Krause, G. Stamatoyannopoulos.
This paper demonstrates that in spite of the close cultural relation between the Southern Greek mainland and Crete, this rich intercultural contact did not go hand in hand with a large-scale exchange of genetic material, since both southern Greek mainland as well as Cretan Late Bronze Age populations can clearly be distinguished genetically in the 2nd millennium BCE. Moreover, this paper has for the first time provided genetic evidence for a migration from the steppe that reached the Greek mainland, but not Crete. As this migration has hitherto been linked with the spread of the Indo-European languages (Haak et al. 2015), it could possibly be correlated with the existence of an Indo-European language on the Greek mainland in the 2nd millennium BCE (i.e., Linear B) and a non-Indo-European language at the same time on Crete (i.e., Linear A).
“Reconstructing prehistoric African population structure.” Cell 171 (2017): 59-71.
P. Skoglund, J.C. Thompson, M.E. Prendergast, A. Mittnik, K. Sirak, M. Hajdinjak, T. Salie, N. Rohland, S. Mallick, A. Peltzer, A. Heinze, I. Olalde, M. Ferry, E. Harney, M. Michel, K. Stewardson, J.I. Cerezo-Roman, C. Chiumia, A. Crowther, E. Gomani-Chindebvu, A.O. Gidna, K.M. Grillo, I.T. Helenius, G. Hellenthal, R. Helm, M. Horton, S. Lopez, A.Z.P. Mabulla, J. Parkington, C. Shipton, M.G. Thomas, R. Tibesasa, M. Welling, V.M. Hayes, D.J. Kennett, R. Ramesar, M. Meyer, S. Paabo, N. Patterson, A.G. Morris, N. Boivin, R. Pinhasi, J. Krause, D. Reich.
In this paper we assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we tracked the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We leveraged ancient genomes to document episodes of natural selection in southern African populations.
“Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods.” Nature Communications 8: 15694 (2017).
V.J. Schuenemann, A. Peltzer, B. Welte, W.P. van Pelt, M. Molak, C. Wang, A. Furtwängler, C. Urban, E. Reiter, K. Nieselt, B. Teßmann, M. Francken, K. Harvati, W. Haak, S. Schiffels, J. Krause.
In this study we presented the first genome-wide data of ancient Egyptian mummies. Our analysis suggests an increase of Sub-Saharan African ancestry in post-Roman periods. We furthermore find genetic continuity of Egyptians from the Late Bronze Age to the Roman period, despite multiple episodes of foreign domination. Post-Roman migrations from sub-Saharan Africa seem to have shifted the gene pool of Egyptians; as a result modern Egyptians share more genetic ancestry with Sub-Saharan Africans than ancient Egyptians.
“Parallel palaeogenomic transects reveal complex genetic history of early European farmers.” Nature 551 (2017): 368-72.
M. Lipson, A. Szécsényi-Nagy, S. Mallick, A. Pósa, B. Stégmár, V. Keerl, N. Rohland, K. Stewardson, M. Ferry, M. Michel, J. Oppenheimer, N. Broomandkhoshbacht, E. Harney, S. Nordenfelt, B. Llamas, G.B. Mende, K. Köhler, K. Oross, M. Bondár, T. Marton, A. Osztás, J. Jakucs, T. Paluch, F. Horváth, P. Csengeri, J. Koós, K. Sebők, A. Anders, P. Raczky, J. Regenye, J.P. Barna, S. Fábián, G. Serlegi, Z. Toldi, E.G. Nagy, J. Dani, E. Molnár, G. Pálfi, L. Márk,
B. Melegh, Z. Bánfai, L. Domboróczki, J. Fernández-Eraso, J. Antonio Mujika-Alustiza, C.A. Fernández, J.J. Echevarría, R. Bollongino, J. Orschiedt, K. Schierhold, H. Meller, A. Cooper, J. Burger, E. Bánffy, K.W. Alt, C. Lalueza-Fox, W. Haak, D. Reich.
In this paper we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42) and Spain (5500–2200 BCE, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.
“Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis.” Scientific Reports 8:13003 (2018). doi:10.1038/s41598-018-31123-z
S. Eisenmann, E. Banffy, P. van Dommelen, K.P. Hofmann, J. Maran, I. Lazaridis, A. Mittnik, M. McCormick, J. Krause, D. Reich, P.W. Stockhammer.
Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for investigating past populations and migrations. An important objective for the coming years is properly to integrate ancient genomics into archaeological research. Our article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analyzing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of “cultures” in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems along with their advantages and challenges.
“The genomic history of southeastern Europe.” Nature 555 (2018): 197-203.
I. Mathieson, S. Alpaslan-Roodenberg, C. Posth, A. Szécsényi-Nagy, N. Rohland, S. Mallick, I. Olalde, N. Broomandkhoshbacht, F. Candilio, O. Cheronet, D. Fernandes, M. Ferry, B. Gamarra, G.G. Fortes, W. Haak, E. Harney, E. Jones, D. Keating, B. Krause-Kyora, I. Kucukkalipci, M. Michel, A. Mittnik, K. Nägele, M. Novak, J. Oppenheimer, N. Patterson, S. Pfrengle, K. Sirak, K. Stewardson, S. Vai, S. Alexandrov, K.W. Alt, R. Andreescu, D. Antonovic, A. Ash, N. Atanassova, K. Bacvarov, M.B. Gusztáv, H. Bocherens, M. Bolus, A. Boroneant, Y. Boyadzhiev, A. Budnik, J. Burmaz, S. Chohadzhiev, N.J. Conard, R. Cottiaux, M. Cuka, C. Cupillard, D.G. Drucker, N. Elenski, M. Francken, B. Galabova, G. Ganetsovski, B. Gély, T. Hajdu, V. Handzhyiska, K. Harvati, T. Higham, S. Iliev, I. Jankovic, I. Karavanic, D.J. Kennett, D. Komšo, A. Kozak, D. Labuda, M. Lari, C. Lazar, M. Leppek, K. Leshtakov, D. Lo Vetro, D. Los, I. Lozanov, M. Malina, F. Martini, K. McSweeney, H. Meller, M. Mendušic, P. Mirea, V. Moiseyev, V. Petrova, T.D. Price, A. Simalcsik, L. Sineo, M. Šlaus, V. Slavchev, P. Stanev, A. Starovic, T. Szeniczey, S. Talamo, M. Teschler-Nicola, C. Thevenet, I. Valchev, F. Valentin, S. Vasilyev, F. Veljanovska, S. Venelinova, E. Veselovskaya, B. Viola, C. Virag, J. Zaninovic, S. Zäuner, P.W. Stockhammer, G. Catalano, R. Krauß, D. Caramelli, G. Zarina, B. Gaydarska, M. Lillie, A.G. Nikitin, I. Potekhina, A. Papathanasiou, D. Boric, C. Bonsall, J. Krause, R. Pinhasi, D. Reich.
In this article we document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
“The Beaker phenomenon and the genomic transformation of northwest Europe.” Nature 555 (2018): 190-6.
I. Olalde, S. Brace, M.E. Allentoft, I. Armit, K. Kristiansen, T. Booth, N. Rohland, S. Mallick, A. Szécsényi-Nagy, A. Mittnik, E. Altena, M. Lipson, I. Lazaridis, T.K. Harper, N. Patterson, N. Broomandkhoshbacht, Y. Diekmann, Z. Faltyskova, D. Fernandes, M. Ferry, E. Harney, P. de Knijff, M. Michel, J. Oppenheimer, K. Stewardson, A. Barclay, K.W. Alt, C. Liesau, P. Ríos, C. Blasco, J.V. Miguel, R.M. García, A.A. Fernández, E. Bánffy, M. Bernabò-Brea, D. Billoin, C. Bonsall, L. Bonsall, T. Allen, L. Büster, S. Carver, L.C. Navarro, O.E. Craig, G.T. Cook, B. Cunliffe, A. Denaire, K.E. Dinwiddy, N. Dodwell, M. Ernée, C. Evans, M. Kucharík, J.F. Farré, C. Fowler, M. Gazenbeek, R.G. Pena, M. Haber-Uriarte, E. Haduch, G. Hey, N. Jowett, T. Knowles, K. Massy, S. Pfrengle, P. Lefranc, O. Lemercier, A. Lefebvre, C.H. Martínez, V.G. Olmo, A.B. Ramírez, J.L. Maurandi, T. Majó, J.I. McKinley, K. McSweeney, B.G. Mende, A. Mod, G. Kulcsár, V. Kiss, A. Czene, R. Patay, A. Endrodi, K. Köhler, T. Hajdu, T. Szeniczey, J. Dani, Z. Bernert, M. Hoole, O. Cheronet, D. Keating, P. Velemínský, M. Dobeš, F. Candilio, F. Brown, R.F. Fernández, A.M. Herrero-Corral, S. Tusa, E. Carnieri, L. Lentini, A. Valenti, A. Zanini, C. Waddington, G. Delibes, E. Guerra-Doce, B. Neil, M. Brittain, M. Luke, R. Mortimer, J. Desideri, M. Besse, G. Brücken, M. Furmanek, A. Hałuszko, M. Mackiewicz, A. Rapinski, S. Leach, I. Soriano, K.T. Lillios, J.L. Cardoso, M.P. Pearson, P. Włodarczak, T.D. Price, P. Pilar Prieto, P.J. Rey, R. Risch, M.A. Rojo Guerra, A. Schmitt, J. Serralongue, A.M. Silva, V. Smrcka, L. Vergnaud, J. Zilhão, D. Caramelli, T. Higham, M.G. Thomas, D.J. Kennett, H. Fokkens, V. Heyd, A. Sheridan, K.G. Sjögren, P.W. Stockhammer, J. Krause, R. Pinhasi, W. Haak, I. Barnes, C. Lalueza-Fox, D. Reich.
In this paper we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
“Population turnover in remote Oceania shortly after initial settlement.” Current Biology 28 (2018): 1157-65.
M. Lipson, P. Skoglund, M. Spriggs, F. Valentin, S. Bedford, R. Shing, H. Buckley, I. Phillip, G.K. Ward, S. Mallick, N. Rohland, N. Broomandkhoshbacht, O. Cheronet, M. Ferry, T.K. Harper, M. Michel, J. Oppenheimer, K. Sirak, K. Stewardson, K. Auckland, A.V.S. Hill, K. Maitland, S.J. Oppenheimer, T. Parks, K. Robson, T.N. Williams, D.J. Kennett, A.J. Mentzer, R. Pinhasi, D. Reich.
In this paper we find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania. Papuan ancestry was subsequently diluted through admixture but remains at least 80–90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia—the most remote Pacific islands—derives from different sources, documenting a third stream of migration from Near to Remote Oceania.
“Indirect evidence for the social impact of the Justinianic Pandemic: episcopal burial and conciliar legislation in Visigothic Hispania.” Journal of Late Antiquity 11 (2018): 193-215.
The Justinianic Plague, the first documented pandemic outbreak of the bubonic plague, struck the Mediterranean region in the 540s CE. Despite some surviving narrative accounts, however, there is little direct written evidence for its impact in much of the Mediterranean world. This is especially true for Visigothic Hispania. However, certain texts that are not explicit accounts of the plague may hint at its impact. One such text is the fourth canon of the Council of Valencia, held in 546. This canon reflects episcopal concerns about what to do when a bishop dies “a sudden death.” According to it, the bishop should not be buried at once but “placed with great care in a coffin apart from the others.” Comparative philology, the archaeology of sixth-century Valencia, and recent paleogenetic investigation into the bacterium that causes the disease all combine to suggest that within the broader context of episcopal funerary displays, the “sudden death” referred to is the plague and that the canon is a response to changes in burial customs—especially the newfound prevalence of mass inhumation—caused by the first wave of the pandemic.
O. Loreille, S. Ratnayake, A.L. Bazinet, T.B. Stockwell, D.D. Sommer, N. Rohland, S. Mallick, P.L.F. Johnson, P. Skoglund, A.J. Onorato, N.H. Bergman, D. Reich, J.A. Irwin.
In this paper we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, (2018) Pantheon Books, New York.
David Reich describes how the revolution in the ability to sequence ancient DNA has changed our understanding of the deep human past. This book tells the emerging story of our often surprising ancestry - the extraordinary ancient migrations and mixtures of populations that have made us who we are.
“Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.” Nature Communications 9 (2018): 3336.
E. Harney, M. May, D. Shalem, N. Rohland, S. Mallick, I. Lazaridis, R. Sarig, K. Stewardson, S. Nordenfelt, N. Patterson, I. Hershkovitz, D. Reich.
The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. To test the hypothesis that the advent and decline of this culture was influenced by movements of people, in this article we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.
“Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.” Nature Communications 10 (2019): 1218. doi: 10.1038/s41467-019-09209-7.
M. Feldman, E. Fernández-Domínguez, L. Reynolds, D. Baird, J. Pearson, I. Hershkovitz, H. May, N. Goring-Morris, M. Benz, J. Gresky, R. A. Bianco, A. Fairbairn, G. Mustafaoğlu, P.W. Stockhammer, C. Posth, W. Haak, C. Jeong, J. Krause.
Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. In this study, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus-related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.
“Ancient Yersinia pestisgenomes from across Western Europe reveal early diversification during the First Pandemic (541–750).” Proceedings of the National Academy of Sciences 116 (25) (2019): 12363-72. doi: 10.1073/pnas.1820447116.
M. Keller, M.A. Spyrou, C.L. Scheib, G.U. Neumann, A. Kröpelin, B. Haas-Gebhard, B. Päffgen, J. Haberstroh, A. Ribera i Lacomba, C. Raynaud, C. Cessford, R. Durand, P. Stadler, K. Nägele, J.S. Bates, B. Trautmann, S.A. Inskip, J. Peters, J.E. Robb, T. Kivisild, D. Castex, M. McCormick, K.I. Bos, M. Harbeck, A. Herbig, J. Krause.
We identify bubonic plague (Yersinia pestis) in eight new sites from Britain, France, Germany, and Spain, demonstrating the geographic range of plague during the Justinianic Pandemic (541-750 CE), its microdiversity in the late Roman and early medieval period, and documenting the first Mediterranean victims in Spain and southern France. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. To elucidate the microevolution of the bacterium during this time period, we reconstructed eight genomes. Four of the reported strains form a polytomy similar to others seen across the Y. pestisphylogeny, associated with the Second and Third Pandemics; we also identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.
“Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.” Science Advances Vol. 5, no. 7, eaax0061 (2019). doi: 10.1126/sciadv.aax0061.
M. Feldman, D.M. Master, R.A. Bianco, M. Burri, P.W. Stockhammer, A. Mittnik, A.J. Aja, C. Jeong, J. Krause.
The ancient Mediterranean port city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a dramatic cultural change between the Late Bronze- and the early Iron- Age. It has long been debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples.” In this study, we report genome-wide data of Bronze- and Iron- Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. Interestingly, this genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze- to Iron- Age transition in Ashkelon but did not leave a long-lasting genetic signature.
“The genomic history of the Iberian Peninsula over the past 8000 years.” Science 363 (2019): 1230-4.
I. Olalde, S. Mallick, N. Patterson, N. Rohland, V. Villalba-Mouco, M. Silva, K. Dulias, C. Edwards, F. Gandini, M. Pala, P. Soares, M. Ferrando-Bernal, N. Adamski, N. Broomandkhoshbacht, O. Cheronet, B. Culleton, D. Fernandes, A.M. Lawson, M. Mah, J. Oppenheimer, K. Stewardson, Z. Zhang, J.M.J. Arenas, I.J.T. Moyano, D.C. Salazar-García, P. Castanyer, M. Santos, J. Tremoleda, M. Lozano, P.G. Borja, J. Fernández-Eraso, J.A. Mujika-Alustiza, C. Barroso, F.J. Bermúdez, E.V. Mínguez, J. Burch, N. Coromina, D. Vivó, A. Cebrià, J.M. Fullola, O. García-Puchol, J.I. Morales, F.X. Oms, T. Majó, J.M. Vergès, A. Díaz-Carvajal, I. Ollich-Castanyer, F.J. López-Cachero, A.M. Silva, C. Alonso-Fernández, G.D. de Castro, J.J. Echevarría, A. Moreno-Márquez, G.P. Berlanga, P. Ramos-García, J.R. Muñoz, E.V. Vila, G.A. Arzo, Á.E. Arroyo, K.T. Lillios, J. Mack, J. Velasco-Vázquez, A. Waterman, L.B. de Lugo Enrich, M.B. Sánchez, B. Agustí, F. Codina, G. de Prado, A. Estalrrich, Á.F. Flores, C. Finlayson, G. Finlayson, S. Finlayson, F. Giles-Guzmán, A. Rosas, V.B. González, G.G. Atiénzar, M.S.H. Pérez, A. Llanos, Y.C. Marco, I.C. Beneyto, D. López-Serrano, S.B. McClure, M.M. Pérez, A.O. Foix, M.S. Borràs, A.C. Sousa, J.M.V. Encinas, D.J. Kennett, M. Richards, K.W. Alt, W. Haak, R. Pinhasi, C. Lalueza-Fox, D. Reich.
In this article we assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
“The formation of human populations in South and Central Asia.” Science 365 (2019): 7487.
V. Narasimhan, N. Patterson, P. Moorjani, N. Rohland, R. Bernardos, S. Mallick, I. Lazaridis, N. Nakatsuka, I. Olalde, M. Lipson, A.M. Kim, L.M. Olivieri, A. Coppa, M. Vidale, J. Mallory, V. Moiseyev, E. Kitov, J. Monge, N. Adamski, N. Alex, N. Broomandkhoshbacht, F. Candilio, K. Callan, O. Cheronet, B.J. Culleton, M. Ferry, D. Fernandes, S. Freilich, B. Gamarra, D. Gaudio, M. Hajdinjak, E. Harney, T.K. Harper, D. Keating, A.M. Lawson, M. Mah, K. Mandl, M. Michel, M. Novak, J. Oppenheimer, N. Rai, K. Sirak, V. Slon, K. Stewardson, F. Zalzala, Z. Zhang, G. Akhatov, A.N. Bagashev, A. Bagnera, B. Baitanayev, J. Bendezu-Sarmiento, A.A. Bissembaev, G.L. Bonara, T.T. Chargynov, T. Chikisheva, P.K. Dashkovskiy, A. Derevianko, M. Dobes, K. Douka, N. Dubova, M.N. Duisengali, D. Enshin, A. Epimakhov, A.V. Fribus, D. Fuller, A. Goryachev, A. Gromov, S.P. Grushin, B. Hanks, M. Judd, E. Kazizov, A. Khokhlov, A.P. Krygin, E. Kupriyanova, P. Kuznetsov, D. Luiselli, F. Maksudov, A.M. Mamedov, T.B. Mamirov, C. Meiklejohn, D.C. Merrett, R. Micheli, O. Mochalov, S. Mustafokulov, A. Nayak, D. Pettener, R. Potts, D. Razhev, M. Rykun, S. Sarno, T.M. Savenkova, K. Sikhymbaeva, S.M. Slepchenko, O.A. Soltobaev, N. Stepanova, S. Svyatko, K. Tabaldiev, M. Teschler-Nicola, A.A. Tishkin, V.V. Tkachev, S. Vasilyev, P. Veleminsky, D. Voyakin, A. Yermolayeva, M. Zahir, V.S. Zubkov, A. Zubova, V.S. Shinde, C. Lalueza-Fox, M. Meyer, D. Anthony, N. Boivin, K. Thangaraj, D.J. Kennett, M. Frachetti, R. Pinhasi, D. Reich.
By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
“Kinship-based social inequality in Bronze Age Europe.” Science, 10 (2019).
A. Mittnik, K. Massy, C. Knipper, F. Wittenborn, S. Pfrengle, N. Carlichi-Witjes, H. Deeg, A. Furtwängler, M. Harbeck, K. von Heyking, C. Kociumaka, I. Kucukkalipci, S. Lindauer, S. Metz, A. Staskiewicz, A. Thiel, J. Wahl, W. Haak, E. Pernicka, S. Schiffels, P.W. Stockhammer, J. Krause.
Archaeology has used analysis of the artifacts and remains of people to uncover their past behaviors and to infer their cultural practices. However, establishing genetic relationships has only recently become possible. Mittnik et al. examined the kinship and inheritance of the remains of people from the German Lech River Valley over a time period spanning the Late Neolithic Corded Ware Culture, the Bell Beaker Complex, the Early Bronze Age, and the Middle Bronze Age (see the “Perspective” in the same issue by Feinman and Neitzel). From genetic and archaeological analyses, it was revealed that the Early Bronze Age household's burials over multiple generations consisted of a high-status core family and unrelated low-status individuals. Furthermore, women were not related to the men within the household, suggesting that men stayed within their birth communities in this society, but women did not, and potentially served as cultural transmitters between different regions.
“Ancient DNA’s impact on archaeology: what has been learned and how to build strong relationships.” The SAA Archaeological Record 19 (2019): 26-32.
This article discusses how ancient DNA (aDNA) has the potential to provide powerful new insights into humanity’s past. It may seem odd for such comments to come from someone who considers himself an American Southwest archaeologist; however, the author's role in the Reich Laboratory of Medical and Population Genetics as a liaison between geneticists and archaeologists has allowed him to critically examine the relationship between these two fields and to explore how they work together.
“An ancient Harappan genome lacks ancestry from Steppe Pastoralists or Iranian Farmers.” Cell 179 (2019): 729-35.
V. Shinde, V. Narasimhan, N. Rohland, S. Mallick, M. Mah, M. Lipson, N. Nakatsuka, N. Adamski, N. Broomandkhoshbacht, M. Ferry, A.M. Lawson, M. Michel, J. Oppenheimer, K. Stewardson, N. Jadhav, Y.J. Kim, M. Chatterjee, A. Munshi, A. Panyam, P. Waghmare, Y. Yadav, H. Patel, A. Kaushik, K. Thangaraj, M. Meyer, N. Patterson, N. Rai, D. Reich.
We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.
“Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.” Nature Communications, Advance online publication (2019).
E. Harney, A. Nayak, N. Patterson, P. Joglekar, V. Mushrif-Tripathy, S. Mallick, N. Rohland, J. Sedig, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, B.J. Culleton, M. Ferry, T.K. Harper, M. Michel, J. Oppenheimer, K. Stewardson, Z. Zhang, Harashawaradhana, M.S. Bartwal, S. Kumar, S.C. Diyundi, P. Roberts, N. Boivin, D.J. Kennett, K. Thangaraj, D. Reich, N. Rai.
Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.
“Plague before the pandemics: the Greek medical evidence for bubonic plague before the sixth century.” Bulletin of the History of Medicine 93.2 (2019): 151-79.
Recent biomolecular evidence has proven that Yersinia pestis, the pathogen that causes bubonic plague, was infecting human hosts in Eurasia as early as the Bronze Age, far earlier than previously believed. It remains an open question, however, whether bubonic plague was affecting Mediterranean populations of classical antiquity. This article evaluates the textual evidence for bubonic plague in classical antiquity from medical sources and discusses methodologies for “retrospective diagnosis” in light of new developments in microbiology. A close study of Greek medical texts using digital and traditional approaches suggests that bubonic plague was unfamiliar to medical writers until sometime before the second century CE, when sources cited by Rufus of Ephesus report a disease that resembles bubonic plague. Rufus of Ephesus describes this disease around CE 100, and Aretaeus (fl. ca. CE 50 or 150) appears to describe the same disease as well.
“Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.” Science, advance online publication (2019).
M.E. Prendergast, M. Lipson, E.A. Sawchuk, I. Olalde, C.A. Ogola, N. Rohland, K.A. Sirak, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, K. Callan, B.J. Culleton, L. Eccles, T.K. Harper, A.M. Lawson, M. Mah, J. Oppenheimer, K. Stewardson, F. Zalzala, S.H. Ambrose, G. Ayodo, H.L. Gates Jr., A.O. Gidna, M. Katongo, A. Kwekason, A.Z.P. Mabulla, G.S. Mudenda, E.K. Ndiema, C. Nelson, P. Robertshaw, D.J. Kennett, F.K. Manthi, D. Reich.
Cattle, sheep, and goats appeared in eastern Africa 5000 years ago, catalyzing the spread of herding throughout sub-Saharan Africa. Archaeologists have long debated the geographic origins of eastern Africa’s first herders, the extent to which people moved with livestock, and relationships among food-producing and foraging communities. In this work, we integrate ancient DNA with archaeological, linguistic, and genetic evidence to explore how pastoralism developed within this region, establishing the roots of one of Africa’s dominant economic strategies.
Travels of Our Genes: A Story about Us and Our Ancestors. (Die Reise unserer Gene. Eine Geschichte über uns und unsere Vorfahren). Berlin, Propyläen (2019).
J. Krause with T. Trappe.
Where do we come from? Who are we? How do we differ from others? These questions are more urgent than ever. Krause and Trappe reach back into Prehistory and use ancient DNA to explain how we became the Europeans that we are today.
“Emergence of human-adapted Salmonella enterica is linked to the Neolithization process.” Nature Ecology & Evolution 4 (2020): 324–33.
F.M. Key, C. Posth , L.R. Esquivel-Gomez, R. Hübler, M.A. Spyrou , G.U. Neumann, A. Furtwängler, S. Sabin , M. Burri, A. Wissgott, A.K. Lankapalli, Å.J. Vågene , M. Meyer, S. Nagel, R. Tukhbatova, A. Khokhlov, A. Chizhevsky, S. Hansen, A.B. Belinsky, A. Kalmykov, A.R. Kantorovich, V.E. Maslov, P.W. Stockhammer , S. Vai , M. Zavattaro, A. Riga , D. Caramelli , R. Skeates, J. Beckett, M.G. Gradoli, N. Steuri, A. Hafner , M. Ramstein, I. Siebke, S. Lösch , Y.S. Erdal, N. Alikhan, Z. Zhou, M. Achtman, K. Bos, S. Reinhold, W. Haak, D. Kühnert , A. Herbig, J. Krause.
It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists and agropastoralists in western Eurasia that were up to 6,500 yr old. Despite the high genetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of 5,000 yr. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human-adapted S. enterica is linked to human cultural transformations.
“Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.” Nature Communications 11, 939 (2020).
J.H. Marcus, C. Posth, H. Ringbauer, L. Lai, R. Skeates, C. Sidore, J. Beckett, A. Furtwängler, A. Olivieri, C.W.K. Chiang, H. Al-Asadi, K. Dey, T.A. Joseph, C. Liu, C. Der Sarkissian, R. Radzevičiūtė, M. Michel, M.G. Gradoli, P. Marongiu, S. Rubino, V. Mazzarello, D. Rovina, A. La Fragola, R.M. Serra, P. Bandiera, R. Bianucci, E. Pompianu, C. Murgia, M. Guirguis, R. Pla Orquin, N. Tuross, P. van Dommelen, W. Haak, D. Reich, D. Schlessinger, F. Cucca, J. Krause, J. Novembre.
The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia’s genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.