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Individual ancestry proportions a, Inferences from qpAdm (see Extended Data Table 2 and Supplementary Information for model details and statistical fit). Blue represents African ancestry: the most common are Bantu-associated (common at southern sites) and Makwasinyi associated (northern sites), which itself is approximately 80% Bantu-related and 20% pastoralist-related. Yellow represents Southwest Asian ancestry: Persian or Arabian. Grey represents Indian ancestry. Bars represent s.e.m., computed using a block jackknife across all 5-centimorgan (cM) segments of the autosomes, and are meaningful even for single individuals as the genome contains information from a large sample size of ancestors. b, Ternary plot of Makwasinyi, Persian and Indian ancestry components in Mtwapa and Faza (red (high coverage) and yellow (low coverage)) and Manda (blue (high coverage) and green (low coverage)). Individuals with higher coverage (>100,000 SNPs overlapping positions on the Human Origins SNP array) are used to fit a linear regression (dashed line), which intersects at nearly 100% Makwasinyi and 0% Persian and Indian, consistent with a Makwasinyi-related population with little or no recent Asian ancestry mixing with an already-mixed Persian–Indian population. c, Bar graph showing P values from Hotelling T-squared tests for a qpAdm model with a mixed Persian–Indian source. The x-axis specifies the proportion of Persian ancestry in the source.
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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...
Citations
... Involving Indigenous knowledge and meaningfully collaborating with Indigenous peoples in knowledge building are also key to this goal. A recent genetic study of Holocene Swahili skeletons that included a diversity of global South authors demonstrated how a centuries-old local oral tradition for Swahili origins was correct and overturned other scientific explanations (Brielle et al. 2023), providing an important example of how Western scientists often dismiss other kinds of knowledge (e.g., oral histories) as nonscientific. Similar recent research designs include studies of both oral and genetic histories of southwest Indian Adivasis (Biddanda et al. 2022) and the incorporation of cultural narratives of coastal Australian populations in studies of post-Pleistocene sea-level rise (Nunn and Cook 2022). ...
The study of human evolution, also known as palaeoanthropology, focuses on our distant and more recent human past; what shaped us as a lineage, genus, and species; and how we came to be the diverse single species we are today. However, the bulk of this research, knowledge production, and understanding has been driven by the global North to the exclusion of non‐Western scientists, despite the deep and rich fossil record of formerly colonized regions (Africa, Australia, South and Southeast Asia, North/South America), maintaining a neocolonial dynamic to this day. Coloniality manifests itself in paleoanthropology in multiple ways: who conducts research, who gets recognition and reward, whose voices and worldviews get centered in paleoanthropological models, what is considered to constitute scientific knowledge, where fossil/archaeological material is housed and curated, and who controls access to these collections. This entry explores these manifestations of coloniality, offering corrective practices.
... Arabic, and the Omani variety in particular, has by far been the most influential language (see, inter alia, Krumm 1932Krumm , 1940Zawawi 1979;Nurse & Hinnebusch 1993: 321), with a strong influence on Swahili in political, religious, educational, and other cultural terms (see, inter alia, Nurse & Hinnebusch 1993: 321;Lodhi 2000: 91-97;Mazrui 2022). Arabic influences on Swahili have probably existed since the language first emerged, through trade and the early adoption of Islam by its speakers (Lodhi 2000: 53-57;Mazrui 2022;Brielle & al. 2023), but most Arabic loanwords were introduced into Swahili during the Omani suzerainty over Zanzibar and other parts of the East African coast (see Schadeberg 2009;Nurse & Hinnebusch 1993: 286, 321;Hinnebusch 1996). ...
In this study I explore the transfer and further adaptation of Arabic lazima, first into Swahili and its many varieties and then from Swahili into several local language varieties spoken in East Africa. Establishing the function of lazima as a modal marker, used for conveying strong necessity, I examine the various structural and semantic types of integration that lazima has been exposed to. In this pursuit, the investigation contributes both to the growing interest in studies on modality and the influence of Swahili in this area. Drawing on a wide range of Swahili varieties and Swahilized varieties, the analysis challenges the traditional understanding of lazima as a nominal form confined to a superordinate copula clause and as only operating on predicate verbs inflected in dependent and/or non-indicative forms. I argue that there are structural, interactional and ultimately socio-cognitive and socio-historical reasons behind the introduction of this linguistic element in the East African region, where lazima in some local languages even seems to serve as the sole marker of strong necessity, or even of necessity more generally, in a particular semantic domain.
... These factors should be carefully taken into account when interpreting results for sex-biased admixture, as they directly impact a number of analysable SNPs on the X chromosome and can pose challenges in observing statistical significance. Nevertheless, the growing number of higher-resolution ancient genomes holds promise for unravelling the diverse processes of sex-biased demography, which may mirror sex differences in cultural practices and social structures (Brielle et al., 2023;Gnecchi-Ruscone et al., 2024). ...
Agriculture was arguably the most profound innovation in human history, and while it eventually spread throughout the planet its specific origins and dispersals are unique across different regions. It is therefore important to take into account diverse geographic and cultural contexts when trying to understand independent transitions to farming in different regions. In recent years, there has been a significant increase in sequencing ancient human genomes, enabling more regionally specific questions to be asked regarding the genetic impact of the local adoption of agriculture. One particularly informative approach is to explore the imbalance of genetic admixture from male versus female sources, which offers valuable insights into the social structures and cultural interactions of prehistoric populations. Here, we utilize publicly available data of ancient genomes from northern China, an area that is well known for one of the earliest centres for agricultural revolution, to look at potential sex biases in genetic admixture from different time periods based on autosomal and sex-specifically inherited X chromosomal variation. Our analysis identifies a higher influx of males from the Yellow River basin to the West Liao River basin during the Late Neolithic period associated with an increase in the reliance on millet farming in this region. This result underscores a distinction in farming transitions in northern China, particularly when compared to agricultural transitions in Europe, where there is no evidence of sex-biased admixture.
... Historical linguistics and archaeology attest that a sphere of cultural interaction formed around the 7th century CE, when agro-pastoral, iron-working communities across nearly 3000 km of coast began speaking similar languages (Nurse and Spear 1985;Walsh 2018), making pots in similar ways (Fleisher and Wynne-Jones 2011), and engaging in similar marine subsistence foodways as they founded village communities on the direct East African littoral and on off-shore islands, like Unguja, Pemba, and Mafia . Around 1000 CE there was a significant shift in Swahili societies, as the broad regional similarities between the East African coast and hinterland of the late first millennium transformed into regionally specific zones with unique trajectories of social development (Brielle et al. 2023;Fleisher et al. 2015;Quintana Morales et al. 2022;Wynne-Jones 2016). This was the result of multiple entangled factors like the arrival and spread of Islam, the initiation of social stratification, urbanism, the intensification of western Indian Ocean trade networks, and the spread and diversification of new subsistence strategies related to rice cultivation and deep-water fishing. ...
Ceramic trends on Unguja Island in Zanzibar, Tanzania provide insights into non-elite political strategies on the East African Swahili Coast. Synthesizing imported ceramic data from two seasons of systematic field survey across rural Unguja with historical, ethnographic, and archaeological evidence from coastal East Africa, this paper argues that an integrative orientation toward power characterized bottom-up action on the Swahili Coast over the second millennium CE. While theories of bottom-up action have emphasized commoner autonomy and resistance to clientage, debt, and social inequality, evidence from the Swahili Coast attests to efforts by non-elites to seek entrance into cycles of reciprocal obligation as a means for recognition and social mobility-a specifically non-egalitarian orientation toward power. In response, elites competed with one another to accumulate wealth-in-people, resulting in a competitive patron-client system that prevented political consolidation. Elucidating these dynamics contributes to an understanding of how non-elite political strategies have shaped sociopolitical systems globally.
... We merged the newly published ancient DNA data with previously published data from ancient Africans and Eurasians and present-day people from around the world whose genomes had been shotgun sequenced or enriched for sequences covering a canonical set of ~1,233,013 million SNPs (1240k data) [60][61][62][63] , as well as whole-genome sequence data from ancient and present-day African and Near Eastern groups 16,[23][24][25][27][28][29][30]33,[75][76][77][78][79][80][81][82][83][84][85][86][87][88][89][90][91][92] . We also merged the new data with Affymetrix HO SNP genotyping data (597,573 SNPs), which allows us to leverage data from a more diverse range of present-day populations from Eurasia and Africa 15,17,25,75,82,[92][93][94][95][96][97][98][99][100][101][102][103][104][105][106] . ...
... We merged the newly published ancient DNA data with previously published data from ancient Africans and Eurasians and present-day people from around the world whose genomes had been shotgun sequenced or enriched for sequences covering a canonical set of ~1,233,013 million SNPs (1240k data) [60][61][62][63] , as well as whole-genome sequence data from ancient and present-day African and Near Eastern groups 16,[23][24][25][27][28][29][30]33,[75][76][77][78][79][80][81][82][83][84][85][86][87][88][89][90][91][92] . We also merged the new data with Affymetrix HO SNP genotyping data (597,573 SNPs), which allows us to leverage data from a more diverse range of present-day populations from Eurasia and Africa 15,17,25,75,82,[92][93][94][95][96][97][98][99][100][101][102][103][104][105][106] . Whenever we needed to co-analyse 1240k data and HO array data, we restricted to SNPs also covered on the HO SNP array. ...
Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 ce at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter–gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.
... We are now witnessing a proliferation of scientific studies pertaining to the African past, many of which disclose important new knowledge about how African peoples conducted their lives. One recent aDNA study, for example, tells us how Persian traders developed relationships along the Swahili coast from 1000 to 1500 CE with powerful women who headed matrilineal clans (Brielle et al., 2023). What makes this study significant is a powerful social narrative that overcomes the technical DNA statistics that are incomprehensible to most archaeologists, let alone lay people. ...
... Bringing evidence of environmental and climatic changes into discourse for understanding human history and behavior is not new (1). However, recent years have seen more concerted efforts to promote consilience through dialogue between the sciences and humanities (2,3), as well as the application of genetics to questions of past human geography and demography (4,5). Such studies are generally published in scientific journals (6)(7)(8)(9), arguably limiting their influence on historians for whom monographs and a small number of history journals remain vital academic currency (10)(11)(12)(13). ...
Investigation into the nexus of human-environmental behavior has seen increasing collaboration of archaeologists, historians, and paleo-scientists. However, many studies still lack interdisciplinarity and overlook incompatibilities in spatiotemporal scaling of environmental and societal data and their uncertainties. Here, we argue for a strengthened commitment to collaborative work and introduce the “dahliagram” as a tool to analyze and visualize quantitative and qualitative knowledge from diverse disciplinary sources and epistemological backgrounds. On the basis of regional cases of past human mobility in eastern Africa, Inner Eurasia, and the North Atlantic, we develop three dahliagrams that illustrate pull and push factors underlying key phases of population movement across different geographical scales and over contrasting periods of time since the end of the last Ice Age. Agnostic to analytical units, dahliagrams offer an effective tool for interdisciplinary investigation, visualization, and communication of complex human-environmental interactions at a diversity of spatiotemporal scales.
... In Africa, a recent study of the Swahili coast indicated asymmetric social interactions and sex-biased admixture between groups during back-to-Africa gene flow from various traders introducing different Eurasian components at different time periods (23). The study showed substantial genetic mixing between African and Asian populations, particularly those from Persia and India, between 1250 and 1800 CE, coinciding with the spread of Islam in the region. ...
... Feedback to communities varies depending on previous engagement between them and collaborating institutions, with different teams adopting different approaches. Many aDNA projects in Africa were initiated through longstanding community-based archaeology projects spanning several decades [e.g., (23)] or established collaborations initially focused on modernday population genetics research (48). Ethical concerns particularly relating to African aDNA research, the dignified treatment of human remains, and the protection of cultural heritage are important discussion topics and have been addressed in specific publications (49). ...
Ancient DNA (aDNA) has added a wealth of information about our species’ history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
... For generating usable archaeogenetic data from Africa, targeted enrichment of human DNA on dedicated single nucleotide polymorphism (SNP) capture panels is almost always necessary. A majority of ancient DNA studies on African populations [6][7][8][9][10][11][12][13] relied on a SNP capture panel usually termed "1240K" [14,15], and some studies on Upper Paleolithic humans relied on a supplementary panel ("1000K", comprising transversion polymorphisms found in two Yoruba individuals and transversion polymorphisms in the Altai Neanderthal genome) or on its union with 1240K [4,14], or on standalone 1240K [5]. The 1240K panel was constructed of the following elements: all SNPs on the Human Origins array (itself composed of 13 sub-panels, each ascertained as heterozygous in a single high-coverage human genome [16]), all SNPs on the Illumina 650Y array, all SNPs on the Affymetrix 50k XBA array, and smaller numbers of SNPs chosen for other purposes [14]. ...
... Results for ascertainment on variants common in Africans (either those having no detectable West Eurasian ancestry or all Africans in the SGDP dataset) are circled in red. Thirty eight site subsampling schemes were analyzed (see panel a): 1) AT/GC; 2) random thinning of the AT/GC dataset to the 1240K SNP count for a given combination of groups (no missing data allowed at the group level), results for 100 thinned replicates are shown; 3) random thinning of all sites to the 1240K SNP count, results for 100 thinned replicates are shown; 4) the 1240K enrichment panel; 5) major components of the 1240K panel: sites included in the Illumina 650Y and/or Human Origins (HO) SNP arrays, sites included exclusively in one of them, and remaining sites; 6) the 1000K and 2200K SNP panels; 7) archaic ascertainment (either all such sites or transversions only); 8) the largest HO panels (4,5,13) or their union (4+5); 9) MAF ascertainment in one of nine continental-scale groups; 10) the same procedure repeated on AT/GC sites. The size of the resulting SNP panels is coded by point size, and the ten broad ascertainment types are coded by color according to the legend. ...
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data—that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed—but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True “outgroup ascertainment” is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the “Affymetrix Human Origins array” which has been genotyped on thousands of modern individuals from hundreds of populations, or the “1240k” in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
... Critical sources of information that need to be elevated are the perspectives and knowledge of indigenous voices that have long term observational records and environmental stewardship. Examples include the recent report that oral traditions of the people from the Swahili coast resolved long-standing questions about the origins of its people (Brielle et al. 2023); and key insights into aquatic systems obtained from m atauranga M aori (encompassing not only M aori knowledge, but also M aori culture, values and worldview; Hikuroa 2017), which have led to sustainable management practices across both freshwater (Kusabs and Quinn 2009) and marine environments (Paul-Burke et al. 2018). ...
Climate‐change is rapidly and intensively altering aquatic communities and habitats. While previous work has focused on direct effects of potential drivers, indirect and interactive effects on organisms and ecosystems have received less attention. Here, we give an overview of contributions to a special issue in Limnology and Oceanography that addresses this knowledge gap. Contributions covered diverse habitats, from polar to tropical regions, alpine streams to coral reefs. Several studies relied on time‐series to identify indirect effects, thus emphasizing our need to maintain high‐quality time‐series data. Time‐series are particularly crucial now that the pace of climate‐change on aquatic‐ecosystems is accelerating. Another common theme is the role of species‐specific characteristics in physiology, behavior or genetics in aquatic ecosystem function. The addition of inter‐ and intra‐specific variability to investigations of climate‐change may be challenging particularly since ecosystem studies typically involve a large parameter space of environmental and biological variables across spatial and temporal scales. However, the results demonstrate that inclusion of species‐specific dynamics, although challenging, can deliver mechanistic insights into aquatic ecosystem patterns and processes. Some contributions leverage habitat changes from disturbances or climate shifts to document capacity for resilience or recovery of pelagic and benthic communities. Jointly, the results in this special issue document fruitful approaches and provide urgent information needed for deciphering aquatic ecosystem responses to climate forcings. This information is foundational if we wish to tackle the combined effects of climate change and other human impacts with maximum efficacy and minimize unintended consequences for biodiversity and ecosystem functioning.
