Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.

Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.

The chronology of the human colonization of the Canary Islands.

The human colonization of the Canary Islands represents the sole known expansion of Berber communities into the Atlantic Ocean and is an example of marine dispersal carried out by an African population. While this island colonization shows similarities to the populating of other islands across the world, several questions still need to be answered before this case can be included in wider debates regarding patterns of initial colonization and human settlement, human-environment interactions, and the emergence of island identities. Specifically, the chronology of the first human settlement of the Canary Islands remains disputed due to differing estimates of the timing of its first colonization. This absence of a consensus has resulted in divergent hypotheses regarding the motivations that led early settlers to migrate to the islands, e.g., ecological or demographic. Distinct motivations would imply differences in the strategies and dynamics of colonization; thus, identifying them is crucial to understanding how these populations developed in such environments. In response, the current study assembles a comprehensive dataset of the most reliable radiocarbon dates, which were used for building Bayesian models of colonization. The findings suggest that i) the Romans most likely discovered the islands around the 1st century BCE; ii) Berber groups from western North Africa first set foot on one of the islands closest to the African mainland sometime between the 1st and 3rd centuries CE; iii) Roman and Berber societies did not live simultaneously in the Canary Islands; and iv) the Berber people rapidly spread throughout the archipelago.

The demography of the Canary Islands from a genetic perspective.

The establishment of European colonies across the world had important demographic consequences because it brought together diverse and distant civilizations for the first time. One clear example of this phenomenon is observed in the Canary Islands. The modern Canarian population is mainly the result of the admixture of natives of North African origin and European colonizers. However, additional migratory flows reached the islands due to the importation of enslaved Africans to cultivate sugarcane and the intense commercial contact with the American continent. In this review, we evaluate how the genetic analysis of indigenous, historical and current populations has provided a glimpse into the Canary Islands' complex genetic composition. We show that each island subpopulation's characterization is needed to fully disentangle the demographic history of the Canarian archipelago. Finally, we discuss what research avenues remain to be explored to improve our knowledge of the impact that the European colonization had on its native population.

Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain.

The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.

Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

Paleogenomics of the prehistory of Europe: human migrations, domestication and disease.

A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.

Aggressive or funerary cannibalism? Skull-cup and human bone manipulation in Cueva de El Toro (Early Neolithic, southern Iberia).

OBJECTIVE: We analyze the processing sequence involved in the manufacture of a skull-cup and the manipulation of human bones from the Early Neolithic of Cueva de El Toro (Málaga, Spain). MATERIALS AND METHODS: The Early Neolithic material studied includes human remains found in two separate assemblages. Assemblage A consists of one skull-cup, a non-manipulated adult human mandible, and four ceramic vessels. Assemblage B contains manipulated and non-manipulated human remains that appeared mingled with domestic waste. Using a taphonomic approach, we evaluate the skull-cup processing and the anthropogenic alteration of human bones. RESULTS: The skull-cup was processed by careful paring away of skin, fragmentation of the facial skeleton and base of the skull, and controlled percussion of the edges of the calotte to achieve a regular shape. It was later boiled for some time in a container that caused pot polish in a specific area. The other human bones appeared scattered throughout the living area, mixed with other remains of domestic activity. Some of these bones show cut marks, percussion damage for marrow extraction, and tooth/chewing marks. DISCUSSION: Evidence from Cueva de El Toro suggests that cannibalism was conducted in the domestic sphere, likely following ritualized practices where the skull-cup could have played a part. Interpretation of this evidence suggests two hypotheses: (a) aggressive cannibalism relates to extreme inter-group violence; and (b) funerary cannibalism is a facet of multi-stage burial practices. Similar evidence has been found in other Neolithic sites of this region and suggests that cannibalism and skull-cups were elements widespread in these communities. These practices may be linked to significant transformations associated with the end of the Early Neolithic in southern Iberia.

Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain.

Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe-where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.

The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain.

OBJECTIVES: 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. MATERIALS AND METHODS: 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. RESULTS: 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. DISCUSSION: 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.

The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents.

BACKGROUND: Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia. RESULTS: Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent. CONCLUSIONS: The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

Mitochondrial DNA and Y-chromosome structure at the Mediterranean and Atlantic façades of the Iberian Peninsula.

OBJECTIVES: The aim of this study is to analyze mitochondrial DNA and Y-chromosome lineages in a range of Atlantic and Mediterranean populations of the Iberian Peninsula in search of genetic differences between both façades and to uncover the most probable geographic origin and coalescence ages of lineages. METHODS: The control region of mitochondrial DNA and haplogroup diagnostic positions were analyzed in 575 subjects and Y-chromosome markers were typed in 260 unrelated males. Moreover, previously published data were compiled and used in the analyses. RESULTS: The level of genetic structure deduced from uniparental markers for the Iberian Peninsula was weak, with stronger Atlantic versus Mediterranean than North to South differentiation and larger diversities in the South. In general, mitochondrial DNA haplogroups had mainly Paleolithic and Mesolithic coalescences in Europe, although some of them, ruling out drift effects, seem to have younger implantation in Central Europe and the Atlantic areas than in the Mediterranean (I, J, J2a, T1, and W) while others as N1 and X could have reached the Iberian Peninsula at the Neolithic transition. On the other hand, younger coalescence ages are being proposed for the arriving or spread of the bulk of Y-chromosome lineages in Europe. CONCLUSIONS: The major haplotypic affinities found for all the Iberian Peninsula regions were always with North Africa and the Atlantic Islands. These results draw an Atlantic network that clearly resembles those of the Megalithic Copper and Bronze cultures at this part of Europe.

El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population.

El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.

The genomic history of the indigenous people of the Canary Islands.

The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.

Demographic history and genetic structure in pre-Hispanic Central Mexico.

Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled "ghost" populations.

The origin of the Carpathian Avar elites revealed.

In the sixth century, the Avar elites established themselves in the Carpathian Basin as evidenced today by the astounding archaeological sites with exquisite grave goods made of silver and gold. Recently reported in Cell, Gnecchi-Ruscone et al.1 obtained paleogenomic evidence from Avar sites in Hungary, placing the Avar elites' origin in Mongolia and confirming their own historical claims.

Mitochondrial DNA and Y-chromosome microstructure in Tunisia.

Mitochondrial DNA (mtDNA) and Y-chromosome variation has been studied in Bou Omrane and Bou Saâd, two Tunisian Berber populations. In spite of their close geographic proximity, genetic distances between them were high and significant with both uniparental markers. A global analysis, including all previously studied Tunisian samples, confirmed the existence of a high female and male population structure in this country. Analyses of molecular variance analysis evidenced that this differentiation was not attributable to ethnic differences. Mantel test showed that, in all cases, Y-chromosome haplotypic distances correlated poorly with geography, whereas after excluding the more isolated samples of Bou Omrane and Bou Saâd, the mtDNA pattern of variation is significantly correlated with geography. Congruently, the N(m) ratio of males versus females pointed to a significant excess of female migration rate across localities, which could be explained by patrilocality, a common marriage system in rural Tunisia. In addition, it has been observed that cultural isolation in rural communities promotes, by the effect of genetic drift, stronger loss of diversity and larger genetic differentiation levels than those observed in urban areas as deduced from comparisons of their respective mean genetic diversity and their respective mean genetic distances among populations. It is likely that the permanent exodus from rural to urban areas will have important repercussions in the future genetic structure of this country.

Improved ethanol precipitation of DNA.

In this Short Communication, a shorter version of the standard DNA ethanol precipitation and purification protocol is described. It uses a mixture of 70% ethanol, 75 mM ammonium acetate and different concentrations of different carriers to perform DNA precipitation and washing in only one step.

Mitochondrial DNA patterns in the Macaronesia islands: Variation within and among archipelagos.

Macaronesia covers four Atlantic archipelagos: the Azores, Madeira, the Canary Islands, and the Cape Verde islands. When discovered by Europeans in the 15th century, only the Canaries were inhabited. Historical reports highlight the impact of Iberians on settlement in Macaronesia. Although important differences in their settlement are documented, its influence on their genetic structures and relationships has yet to be ascertained. In this study, the hypervariable region I (HVRI) sequence and coding region polymorphisms of mitochondrial DNA (mtDNA) in 623 individuals from the Azores (120) and Canary Islands (503) were analyzed. Combined with published data, these give a total of 1,542 haplotypes from Macaronesia and 1,067 from the Iberian Peninsula. The results obtained indicate that Cape Verde is the most distinctive archipelago, with an mtDNA pool composed almost exclusively of African lineages. However, the other archipelagos present an mtDNA profile dominated by the presence of West-Eurasian mtDNA haplogroups with African lineages present in varying proportions. Moreover, no signs of integration of typical Canarian U6 lineages in the other archipelagos were detected. The four Macaronesia archipelagos currently have differentiated genetic profiles, and the Azores present the highest intra-archipelago differentiation and the lowest values of diversity. The analyses performed show that the present-day genetic profile of the Macaronesian archipelagos was mainly determined by the initial process of settlement and further microdifferentiation probably as a consequence of the small population size of some islands. Moreover, contacts between archipelagos seem to have had a low impact on the mtDNA genetic pool of each archipelago.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

BACKGROUND: The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times. RESULTS: Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today. CONCLUSION: The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.

Temporal evolution of the ABO allele frequencies in the Canary Islands: the impact of the European colonization.

The indigenous Canary Islands population suffered a strong cultural and genetic impact when they were colonized by Europeans in the fifteenth century. The molecular analysis of the ABO blood group gene on aboriginal and seventeenth to eighteenth century remains confirms the demographic history of the islands depicted by previous archaeological, anthropological, and genetic studies. ABO allele frequencies clearly related Canarian aborigines with North African Berber populations, its most probable source of origin, and is far related to Iberian and to the current population of the archipelago. The historical sample shows a congruent intermediate position testifying already a strong European influence that would go in augment since then to present times, affecting all the islands with the important exception of La Gomera.