Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.

The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people1,2. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast3. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia4. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

Ancient DNA and deep population structure in sub-Saharan African foragers.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

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.

Earliest known human burial in Africa.

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.

The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.

Total daily energy expenditure and elevated water turnover in a small-scale semi-nomadic pastoralist society from Northern Kenya.

BACKGROUND: Pastoralists live in challenging environments, which may be accompanied by unique activity, energy, and water requirements. AIM: Few studies have examined whether the demands of pastoralism contribute to differences in total energy expenditure (TEE) and water turnover (WT) compared to other lifestyles. SUBJECTS AND METHODS: Accelerometer-derived physical activity, doubly labelled water-derived TEE and WT, and anthropometric data were collected for 34 semi-nomadic Daasanach adults from three northern Kenyan communities with different levels of pastoralist activity. Daasanach TEEs and WTs were compared to those of other small-scale and industrialised populations. RESULTS: When modelled as a function of fat-free-mass, fat-mass, age, and sex, TEE did not differ between Daasanach communities. Daasanach TEE (1564-4172 kcal/day) was not significantly correlated with activity and 91% of TEEs were within the range expected for individuals from comparison populations. Mean WT did not differ between Daasanach communities; Daasanach absolute (7.54 litres/day men; 7.46 litres/day women), mass-adjusted, and TEE-adjusted WT was higher than most populations worldwide. CONCLUSIONS: The similar mass-adjusted TEE of Daasanach and industrialised populations supports the hypothesis that habitual TEE is constrained, with physically demanding lifestyles necessitating trade-offs in energy allocation. Elevated WT in the absence of elevated TEE likely reflects a demanding active lifestyle in a hot, arid climate.

Early childhood growth in Daasanach pastoralists of Northern Kenya: Distinct patterns of faltering in linear growth and weight gain.

OBJECTIVES: Investigations of early childhood growth among small-scale populations are essential for understanding human life history variation and enhancing the ability to serve such communities through global public health initiatives. This study characterizes early childhood growth trajectories and identifies differences in growth patterns relative to international references among Daasanach semi-nomadic pastoralist children living in a hot, arid region of northern Kenya. METHODS: A large sample of height and weight measures were collected from children (N = 1756; total observations = 4508; age = 0-5 years) between 2018 and 2020. Daasanach growth was compared to international reference standards and Daasanach-specific centile growth curves and pseudo-velocity models were generated using generalized additive models for location scale and size. RESULTS: Compared to World Health Organization (WHO) reference, relatively few Daasanach children were stunted (14.3%), while a large proportion were underweight (38.5%) and wasted (53.6%). Additionally, Daasanach children had a distinctive pattern of growth, marked by an increase in linear growth velocity after 24 months of age and relatively high linear growth velocity throughout the rest of early childhood. CONCLUSIONS: These results identify a unique pattern of early childhood growth faltering among children in a small-scale population and may reflect a thermoregulatory adaptation to their hot, arid environment. As linear growth and weight gain remain important indicators of health, the results of this study provide insight into growth velocity variations. This study has important implications for global public health efforts to identify and address sources of early growth faltering and undernutrition in small-scale populations.

Water Insecurity, Water Borrowing, and Psychosocial Stress Among Daasanach Pastoralists in Northern Kenya.

This article quantifies Daasanach water insecurity experiences in Northern Kenya, examines how water insecurity is associated with water borrowing and psychosocial stress, and evaluates if water borrowing mitigates the stress from water insecurity. Of 133 households interviewed in 7 communities, 94% were water insecure and 74.4% borrowed water three or more times in the prior month. Regression analyses demonstrate water borrowing frequency moderates the relationship between water insecurity and psychosocial stress. Only those who rarely or never borrowed water reported greater stress with higher water insecurity. The coping mechanism of water borrowing may help blunt water insecurity-related stress.

Cross-cultural variation in thirst perception in hot-humid and hot-arid environments: Evidence from two small-scale populations.

OBJECTIVES: Thirst is an evolved central homeostatic feedback system that helps regulate body water for survival. Little research has examined how early development and exposure to extreme environments and water availability affect thirst perception, particularly outside Western settings. Therefore, we compared two indicators of perceived thirst (current thirst and pleasantness of drinking water) using visual scales among Tsimane' forager-horticulturalists in the hot-humid Bolivian Amazon and Daasanach agro-pastoralists in hot-arid Northern Kenya. METHODS: We examined how these measures of perceived thirst were associated with hydration status (urine specific gravity), ambient temperatures, birth season, age, and population-specific characteristics for 607 adults (n = 378 Tsimane', n = 229 Daasanach) aged 18+ using multi-level mixed-effect regressions. RESULTS: Tsimane' had higher perceived thirst than Daasanach. Across populations, hydration status was unrelated to both measures of thirst. There was a significant interaction between birth season and temperature on pleasantness of drinking water, driven by Kenya data. Daasanach born in the wet season (in utero during less water availability) had blunted pleasantness of drinking water at higher temperatures compared to those born in the dry season (in utero during greater water availability). CONCLUSIONS: Our findings suggest hydration status is not a reliable predictor of thirst perceptions in extreme-hot environments with ad libitum drinking. Rather, our findings, which require additional confirmation, point to the importance of water availability during gestation in affecting thirst sensitivity to heat and water feedback mechanisms, particularly in arid environments. Thirst regulation will be increasingly important to understand given climate change driven exposures to extreme heat and water insecurity.

The co-occurrence of water insecurity and food insecurity among Daasanach pastoralists in northern Kenya.

OBJECTIVE: Water plays a critical role in the production of food and preparation of nutritious meals, yet few studies have examined the relationship between water and food insecurity. The primary objective of this study, therefore, was to examine how experiences of household water insecurity (HWI) relate to experiences of household food insecurity (HFI) among a pastoralist population living in an arid, water-stressed region of northern Kenya. DESIGN: We implemented the twelve-item Household Water Insecurity Experiences (HWISE, range 0-36) Scale and the nine-item Household Food Insecurity Access Scale (HFIAS, range 0-27) in a cross-sectional survey to measure HWI and HFI, respectively. Data on socio-demographic characteristics and intake of meat and dairy in the prior week were collected as covariates of interest. SETTING: Northern Kenya, June-July 2019. PARTICIPANTS: Daasanach pastoralist households (n 136) from seven communities. RESULTS: In the prior 4 weeks, 93·4 % and 98·5 % of households had experienced moderate-to-severe HWI and HFI, respectively. Multiple linear regression analyses indicated a strong association between HWI and HFI. Each point higher HWISE score was associated with a 0·44-point (95 % CI: 0·22, 0·66, P = 0·003) higher HFIAS score adjusting for socio-economic status and other covariates. CONCLUSIONS: These findings demonstrate high prevalence and co-occurrence of HWI and HFI among Daasanach pastoralists in northern Kenya. This study highlights the need to address HWI and HFI simultaneously when developing policies and interventions to improve the nutritional well-being of populations whose subsistence is closely tied to water availability and access.