Ancient DNA (Anthropology)

New genetic technologies are allowing for innovative applications in archaeology and anthropology, providing new insights into past populations’ origins and interactions, and even identifying close genetic links between ancient peoples and their living biological relatives. Yet for Indigenous peoples, these technological advances raise many questions around their very identity as founding populations and their histories, their ancestries, and connections between past and present groups. Scientific pronouncements about identity and related concepts may have profound social, cultural, political and economic consequences for Indigenous peoples. In particular, DNA is increasingly perceived as being able to provide objective evidence to support or refute land claims and other identity-based rights, to provide genetic criteria for tribal enrollment and to adjudicate the repatriation of ancestral remains to descendant communities. There is also concern that the lure and mystique of genetic information has the potential to reduce the complexities of identity to biological categories.
  These pressing issues were at the heart of a public symposium and workshop held in Vancouver, British Columbia, in October 2015. The event, “DNA and Indigeneity: The Changing Role of Genetics in Indigenous Rights, Tribal Belonging, and Repatriation,”  examined the ethical, legal, and scientific prospects and perils surrounding the use of genetic information to inform or substantiate claims of identity and cultural affiliation; and 2) discussed the real-world implications of genetic analysis in relation to Indigenous rights, tribal enrollment, and the repatriation of human remains. This volume shares the proceedings of the public symposium portion of the event.

By: Nick Patterson, Michael Isakov, Thomas Booth, Lindsey Büster, Claire-Elise Fischer, Iñigo Olalde, Harald Ringbauer, Ali Akbari, Olivia Cheronet, Madeleine Bleasdale, Nicole Adamski, Eveline Altena, Rebecca Bernardos, Selina Brace, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Brendan Culleton, Elizabeth Curtis, Lea Demetz, Kellie Sara Duffett Carlson, Daniel M. Fernandes, M. George B. Foody, Suzanne Freilich, Helen Goodchild, Aisling Kearns, Ann Marie Lawson, Iosif Lazaridis, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Megan Michel, Guillermo Bravo Morante, Jonas Oppenheimer, Kadir Toykan Özdoğan, Lijun Qiu, Constanze Schattke, Kristin Stewardson, J. Noah Workman, Fatma Zalzala, Zhao Zhang, Bibiana Agustí, Tim Allen, Katalin Almássy, Luc Amkreutz, Abigail Ash, Christèle Baillif-Ducros, Alistair Barclay, László Bartosiewicz, Katherine Baxter, Zsolt Bernert, Jan Blažek, Mario Bodružić, Philippe Boissinot, Clive Bonsall, Pippa Bradley, Marcus Brittain, Alison Brookes, Fraser Brown, Lisa Brown, Richard Brunning, Chelsea Budd, Josip Burmaz, Sylvain Canet, Silvia Carnicero-Cáceres, Morana Čaušević-Bully, Andrew Chamberlain, Sébastien Chauvin, Sharon Clough, Natalija Čondić, Alfredo Coppa, Oliver Craig, Matija Črešnar, Vicki Cummings, Szabolcs Czifra, Alžběta Danielisová, Robin Daniels, Alex Davies, Philip de Jersey, Jody Deacon, Csilla Deminger, Peter W. Ditchfield, Marko Dizdar, Miroslav Dobeš, Miluše Dobisíková, László Domboróczki, Gail Drinkall, Ana Đukić, Ceiridwen J. Edwards, Michal Ernée, Christopher Evans, Jane Evans, Manuel Fernández-Götz, Slavica Filipović, Andrew Fitzpatrick, Harry Fokkens, Chris Fowler, Allison Fox, Zsolt Gallina, Michelle Gamble, Manuel R. González Morales, Borja González-Rabanal, Adrian Green, Katalin Gyenesei, Diederick Habermehl, Tamás Hajdu, Derek Hamilton, James Harris, Chris Hayden, Joep Hendriks, Bénédicte Hernu, Gill Hey, Milan Horňák, Gábor Ilon, Eszter Istvánovits, Andy M. Jones, Martina Blečić Kavur, Kevin Kazek, Robert A. Kenyon, Amal Khreisheh, Viktória Kiss, Jos Kleijne, Mark Knight, Lisette M. Kootker, Péter F. Kovács, Anita Kozubová, Gabriella Kulcsár, Valéria Kulcsár, Christophe Le Pennec, Michael Legge, Matt Leivers, Louise Loe, Olalla López-Costas, Tom Lord, Dženi Los, James Lyall, Ana B. Marín-Arroyo, Philip Mason, Damir Matošević, Andy Maxted, Lauren McIntyre, Jacqueline McKinley, Kathleen McSweeney, Bernard Meijlink, Balázs G. Mende, Marko Menđušić, Milan Metlička, Sophie Meyer, Kristina Mihovilić, Lidija Milasinovic, Steve Minnitt, Joanna Moore, Geoff Morley, Graham Mullan, Margaréta Musilová, Benjamin Neil, Rebecca Nicholls, Mario Novak, Maria Pala, Martin Papworth, Cécile Paresys, Ricky Patten, Domagoj Perkić, Krisztina Pesti, Alba Petit, Katarína Petriščáková, Coline Pichon, Catriona Pickard, Zoltán Pilling, T. Douglas Price, Siniša Radović, Rebecca Redfern, Branislav Resutík, Daniel T. Rhodes, Martin B. Richards, Amy Roberts, Jean Roefstra, Pavel Sankot, Alena Šefčáková, Alison Sheridan, Sabine Skae, Miroslava Šmolíková, Krisztina Somogyi, Ágnes Somogyvári, Mark Stephens, Géza Szabó, Anna Szécsényi-Nagy, Tamás Szeniczey, Jonathan Tabor, Károly Tankó, Clenis Tavarez Maria, Rachel Terry, Biba Teržan, Maria Teschler-Nicola, Jesús F. Torres-Martínez, Julien Trapp, Ross Turle, Ferenc Ujvári, Menno van der Heiden, Petr Veleminsky, Barbara Veselka, Zdeněk Vytlačil, Clive Waddington, Paula Ware, Paul Wilkinson, Linda Wilson, Rob Wiseman, Eilidh Young, Joško Zaninović, Andrej Žitňan, Carles Lalueza-Fox, Peter de Knijff, Ian Barnes, Peter Halkon, Mark G. Thomas, Douglas J. Kennett, Barry Cunliffe, Malcolm Lillie, Nadin Rohland, Ron Pinhasi, Ian Armit & David Reich


Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2–6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain’s independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.

While Phoenician culture and trade networks had a significant impact on Western civilizations , we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6 th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.

Archaeogenetic research over the last decade has demonstrated that european neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early neolithic central european Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had a mixture of WHG-related and ANF-related ancestry, one of them with approximately 50% of each, while the third individual had approximately all ANF-related ancestry. Stable carbon and nitrogen isotope ratios for all three individuals were within the range of variation reflecting diets of other Neolithic agrarian populations. Strontium isotope analysis revealed that the ~50% WHG-ANF individual was non-local to the Brunn 2 area. Overall, our data indicate interbreeding between incoming farmers, whose ancestors ultimately came from western Anatolia, and local HGs, starting within the first few generations of the arrival of the former in central Europe, as well as highlighting the integrative nature and composition of the early LBK communities. The Linearbandkeramik or Linear Pottery culture (LBK) played a key role in the Neolithization of central Europe. Culturally, economically, and genetically, the LBK had its ultimate roots in western Anatolia, but it also displayed distinct features of autochthonous European Mesolithic hunter-gatherer societies. Several models for the origins of the LBK culture have been proposed over the years 1. The Indigenist model suggests the LBK was founded through the adaptation of elements of the West Asian Neolithic Package by indigenous Mesolithic populations exclusively through frontier contact and cultural diffusion. The Integrationist model views the formation of LBK as the integration of Mesolithic hunter-gatherers into an agro-pastoral lifeway through mechanisms such as leapfrog colonization, frontier mobility and contact. According to this model, small groups associated with the Starčevo-Körös-Criş (SKC) culture, the likely LBK predecessors in Europe, left their homelands in the Balkans (where most of their own ancestors had arrived earlier from Anatolia), and settled new areas to the northwest. Contacts with local Mesolithic groups and exchange of products would have resulted in the co-optation of hunter-gatherers into farming communities, where they

The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1–3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the 10th millennium and early 9th millennium cal BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early 7th millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later-coming Anatolian farmers and 3rd-4th millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread, but before the Yamnaya migrations. We propose that the earliest farming societies demographically resembled foragers and only after regional gene flow and rising heterogeneity, did the farming population expansions into Europe occur.

• Newly generated pre-Neolithic European mtDNA genomes triple the number available
• Clade M found for the first time in Europe, prior to the Last Glacial Maximum bottleneck
• Rapid single dispersal of all non-Africans less than 55,000 years ago
• Previously unknown major population shift in Europe at the end of the Pleistocene

Farming was first introduced to Europe in the mid-seventh millennium BC, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 BC. 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.

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The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops’ progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wild Cucurbita, whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. First, we used high-throughput sequencing to analyze complete plastid genomes of 91 total Cucurbita samples, comprising ancient (n = 19), modern wild (n = 30), and modern domestic (n = 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wild Cucurbita, and we take initial steps to consider this hypothesis through cross-mammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumed Cucurbita fruits and dispersed their seeds; wild Cucurbita were likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal for Cucurbita, and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome’s population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.