Ancient DNA from lentils (Lens culinaris) illuminates human - plant - culture interactions in the Canary Islands

Svante Pääbo: pushing ancient DNA to the limit

Ancient DNA (aDNA) analysis offers valuable insights into the domestication and spread of foxtail millet (Setaria italica) across northern China and the Tibetan Plateau. This study leverages advanced genomic techniques to reconstruct the evolutionary history and adaptation of this crucial crop.To overcome the limitations of ancient environmental DNA (aeDNA) in paleoecology and evolutionary studies, we developed eProbe, a flexible toolkit for designing, assessing, and validating hybridization capture probes. Benchmarking a foxtail millet probe set generated by eProbe demonstrated a 455-fold increase in target DNA recovery and high genome coverage, enabling detailed population and evolutionary genetic analyses.Using these custom-designed probes, we enriched foxtail millet aDNA from archaeological and lake sediment samples across the Tibetan Plateau and northern China. This approach provides unprecedented insights into the spread and adaptation of foxtail millet as it ascended the plateau and underwent domestication. Combined with data from ancient seed enrichment, this dual analysis offers a comprehensive understanding of foxtail millet's evolutionary history and its role in high-altitude agricultural adaptation.By integrating data from both ancient seed enrichment and environmental samples, this study offers critical insights into the complex processes of foxtail millet domestication and its impact on ancient agricultural systems in East Asia. Furthermore, these findings provide valuable context for understanding how ancient trade networks, such as the Silk Road, may have facilitated the exchange and adaptation of staple crops, influencing agricultural development and cultural interactions across Eurasia.

Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds

Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities

The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people. The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity. 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort. This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism.

Genetic and toxinological characterization of North Atlantic strains of the dinoflagellate Ostreopsis and allelopathic interactions with toxic and non-toxic species from the genera Prorocentrum, Coolia and Gambierdiscus

This chapter explores the origin and dispersal of the Tai-Kadai language family from the perspectives of linguistics, archaeology, and genetics. From a linguistic standpoint, this section primarily focuses on linguistic features, internal classification, external relationships with other language families, and Tai-Kadai language prehistory. In terms of archaeology, the investigation delves into the cultural interactions and population migrations in southern Asia and Southeast Asia since the Mesolithic Age, combining ancient DNA (aDNA) studies to detect the relationship between ancient populations in Eastern Eurasia and the present-day Tai-Kadai-speaking people. This process can be viewed as a bidirectional assimilation, with northern migrants undergoing a process known as ‘Yueization (百越化)’ while the indigenous Bai-Yue (百越) populations experienced ‘Sinicization (汉化)’. Taking a genetic perspective into account, studies on Y-chromosome and mitochondrial DNA (mtDNA) suggest that the ancestral roots of Tai-Kadai people can be traced back to the Yangtze River Delta and the South China Coast. Furthermore, ancient DNA research indicates strong connections between the Tai-Kadai, Austronesian populations, and the South China ancients, implying a common origin for the Tai-Kadai and Austronesian language groups.

The Canary Islands were settled ca. 1,800 years ago by Amazigh/Berber farming populations originating in North Africa. This historical event represents the last and westernmost expansion of the Mediterranean farming package in Antiquity, and investigating it yields information about crop dispersal along the periphery of the Mediterranean world around the turn of the first millennium ce. The current study focuses on archaeobotanical evidence recorded in a series of pre-Hispanic/Amazigh sites of the Canary Islands (ca. 2nd–15th centuries ce). It offers new, unpublished archaeobotanical findings and direct radiocarbon datings of plant remains from the different islands. The general goal is to gain a better grasp of how the first settlers of the Canary Islands adapted their farming activities to the different natural conditions of each island. The results suggest a shared crop ‘package’ throughout the islands since at least the 3rd–5th centuries ce. This set of plants was likely introduced from north-western Africa and consists of Hordeum vulgare (hulled barley), Triticum durum (durum wheat), Lens culinaris (lentil), Vicia faba (broad bean), Pisum sativum (pea), and Ficus carica (fig). The crop ‘package’ probably arrived in a single episode during the initial colonisation and was not followed by any other plants. Subsequent to the initial settling and until the arrival of the European seafarers, the islands remained isolated from each other and from the outside world, a condition that over time led to a decline in crop diversity in all of the islands except Gran Canaria.

Ancient mitochondrial DNA sequences (378 base pairs of cytochrome b and 368 of 12S rRNA) extracted from a mummified extinct giant lizard, Gallotia goliath, from eastern Tenerife, Canary Islands, were used to assess the species status and relationship of this form within the genus. G. goliath is clearly a member of the G. simonyi group of the western Canary islands (Tenerife, La Gomera, El Hierro and La Palma) and is not closely related to the giant G. stehlini of Gran Canaria. Contrary to recent opinion, it is phylogenetically distinct, within the G. simonyi group, from the extant G. simonyi of El Hierro and also from the recently discovered live G. gomerana on La Gomera and from G. intermedia in north-western Tenerife. It may be the sister taxon of either all the other members of the G. simonyi group or of G. intermedia. The phylogenetic distinctness of G. goliath makes Tenerife unique among oceanic islands in having had one giant and two medium-sized lizard species that were probably substantially herbivorous, the others being G. intermedia and G. galloti. Gallotia shows great community differences on other islands in the Canaries, two having a single small species, one a single giant, and three a giant and a medium-sized form.

In 1998 the author published ‘Genetics, linguistics and prehistory: thinking big and thinking straight’, a critique of late twentieth-century attempts to synthesize the disciplines of genetics, linguistics and archaeology. This paper assesses subsequent progress, using examples from various parts of the world, including Britain, Denmark, Finland, France, Frisia, Germany, Hungary, Ireland, Italy, Micronesia, Portugal, Spain and the Canary Islands. The growing importance of mitochondrial DNA and the Y chromosome, rather than classical population genetics, is emphasized. The author argues that ancient DNA and early linguistic data should be used more. Languages mentioned include Aquitanian, Basque, Celtiberian, Etruscan, Finnish, Hungarian, Iberian, Lepontic, Lusitanian, Pictish, Raetic, ‘Tartessian’, Thracian and the Ladin dialect of the Italian Alps. Aspects of the ancient linguistic geography of Scotland and the Iberian peninsula are discussed, as is the difficulty of deciding the direction of spread of Indo-European and non-Indo-European languages. The potential of ancient place and personal names is illustrated from Celtic.

BackgroundAncient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems’ threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory’s shearwater (Calonectris borealis).FindingsWe analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia.ConclusionsOur findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

The archaeological signature for the first arrival of modern humans in Europe has been a focus of intensive research and for certain regions is now relatively well understood. The archaeological signature for modern human arrival in Arabia, India and much of Asia, on the other hand, is much debated despite the fact that genetic research provides a temporal window for colonisation of 60–75 thousand years ago (kya) (Oppenheimer 2009, 2012b, this volume; Sun et al. 2006; Rasmussen et al. 2011). Indeed, the issue of modern human colonisation east of Africa is emerging as one of the most important and hotly debated topics in Palaeolithic studies (Appenzeller 2012; Balter 2010). Unresolved questions include the exit route from Africa (e.g., Nile corridor or Horn of Africa), the date at which modern humans arrived in each region, the speed at which they dispersed, the alterations to subsistence and technology required at each step of the journey and the extent of cultural and biological interaction between hominin species encountered en route (Beyin 2006; Field & Lahr 2005; Foley & Lahr 1997; Petraglia et al. 2010; Peer 1998; Vermeersch 2001). Such questions are unanswered, and vast lacunae exist in the archaeological records of regions such as Arabia, India and Southeast Asia. The story of modern human spread and cultural change east of Africa therefore remains poorly sketched, and major challenges lie ahead in l eshing out this crucial period in human evolution. Recent analyses of modern and ancient human DNA have made important inroads into solving this puzzle, documenting relationships between populations, approximate ages for branching events, likely dispersa l pathways, and inter-species admixture and even identifying hitherto unknown species (e.g., Green et al. 2010; Liu et al. 2006; Oppenheimer 2009, 2012b; Rasmussen et al. 2011; Reich et al. 2011). Unfortunately, genetics research cannot yet provide precise dates for branching events or locate the geographic nodes at which such events took place.

Classic mitochondrial DNA phylogenetic and phylogeographic studies on the aboriginal, historical, and extant human populations of the Canary Islands have contributed to reconstructing the origin and settlement on the islands of the pre-European colonizers. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples has greatly improved these molecular results, but it has also revealed significant contamination in the islands' previous aboriginal genetic pool. Following a thorough review of these cases, new phylogeographic analysis revealed the existence of a heterogeneous aboriginal population, asymmetrically distributed across the various islands, and most likely descended from a unique main settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple on the Canary Islands.

Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans