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Post by Admin on Apr 11, 2023 18:25:45 GMT
A new analysis of medieval DNA has revealed that around the turn of the first millennium, Swahili ancestors from Africa and Asia began intermingling and having children, giving rise to a Swahili civilization with a multiracial identity, at least among its elites. The discovery matches local stories passed down through generations that were previously dismissed as myth by outside researchers. “This oral tradition was always maligned,” George Abungu, an archaeologist and former director-general of the National Museums of Kenya who was not involved in the genetic analysis, tells the New York Times’ Elie Dolgin. “Now, with this DNA study, we see there was some truth to it.” Members of the medieval and early modern Swahili culture lived in towns and villages along the coast of East Africa, shared the Kiswahili language, and largely practiced a common religion of Islam. The new research, published Wednesday in the journal Nature, sheds some light on how this culture formed. To start, the research team—made up of 44 scientists, including 17 African scholars—worked with locals to excavate cemeteries along the Swahili coast. They gathered DNA samples from 80 people who lived between 1250 to 1800 C.E. and compared that data with saliva samples from modern-day coastal Swahili-speaking people, as well as individuals living in the Middle East, Africa and other areas of the world. Afterward, the team ensured the exhumed bodies were replaced in their cemetery plots. They found that about half of the DNA from the medieval individuals came from African women, while the other half primarily came from Asian men. Of the Asian DNA, about 80 to 90 percent revealed Persian ancestry, while approximately 10 percent was linked to India. The genetic material from modern-day individuals supported this mixed ancestry, though people who identify as Swahili today have inherited varying amounts of DNA from medieval peoples. The traditional Swahili society is strongly matriarchal. Because mothers were largely African, medieval children retained their language and culture, while certain outside influences like architecture, fashion and art were absorbed into their predominantly African traditions, per the Times. Essentially, the paper reveals a timeline of intermarriage that matches a narrative told by the Swahili people called the Kilwa Chronicle. Early scholars had dismissed this oral history as “a kind of fairy tale,” write co-authors Chapurukha Kusimba, an anthropologist at the University of South Florida, and David Reich, a human evolutionary biologist at Harvard University, in the Conversation. “Ironically, the story of Swahili origins has been molded almost entirely by non-Swahili people, a challenge shared with many other marginalized and colonized peoples who are the modern descendants of cultures of the past with extraordinary achievements.” The Kilwa Chronicle tells a story of mixed Asian and African ancestry, suggesting that an influx of Persian sultans helped give rise to the Swahili culture. But prejudiced researchers have cast doubt on the story, assuming that the thriving East African port cities were built by Europeans, writes Popular Science’s Jocelyn Solis-Moreira. It has also been questioned by some African natives, who accused the elites of exaggerating their Asian connection to raise their social status, per the publication. In addition to the DNA analyses, the team consulted oral traditions, used systematic surveys and excavated material such as pottery, beads, house remains and imported objects. “Together they revealed the complexity of Swahili everyday life and the peoples’ cosmopolitan Indian Ocean heritage,” write the authors in the Conversation. Still, this research has a notable caveat: The team only took samples from people buried in elite Muslim cemeteries, which may not be representative of everyday citizens in the Swahili civilization. The researchers intend to gather more samples to continue to fill in the missing pieces of Swahili ancestry. “This research has been my life’s work—this journey to recover the past of the Swahili and restore them to rightful citizenship,” Kusimba says in a statement. “These findings bring out the African contributions, and indeed, the Africanness of the Swahili, without marginalizing the Persian and Indian connection.” www.nature.com/articles/s41586-023-05754-w
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Post by Admin on Apr 12, 2023 20:59:35 GMT
Entwined African and Asian genetic roots of medieval peoples of the Swahili coast Abstract 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. Main The medieval and early modern Swahili culture of eastern Africa from the seventh century AD was defined by a set of shared features: a common language of African origin (Kiswahili), a shared predominant religion (Islam) and a geographic distribution in coastal towns and villages. People of the Swahili culture lived across a vast coastal region that included northern Mozambique, southern Somalia, Madagascar and the archipelagos of Comoros, Kilwa, Mafia, Zanzibar and Lamu1 (yellow outlines in Fig. 1a). Millions of present-day coastal people identify as Swahili, although for many this is a secondary identity, with primary identities often being more based on town of origin, family history or traditional social status5. How people who identify as Swahili in the present day relate to people of the medieval and early modern Swahili culture has been difficult to elucidate in the absence of ancient DNA. Fig. 1: Dataset overview. a, Coastal areas associated with the medieval Swahili culture are shown in yellow. Sites represented in the ancient DNA samples are marked with black shapes. Numbers in parentheses are formatted X|Y, where X is the number of individuals for whom there are data, and Y is the number of individuals for whom we report high-resolution analyses. The chronology is given as the union of 95% confidence intervals for direct radiocarbon dates on the skeletons rounding to the nearest 50 years and is shown as calibrated (cal.) yr AD, or as AD for sites with only archaeological context (Supplementary Information; Extended Data Table 1). The base map was made with the Natural Earth R package using a CC BY license. Bodies of water were added from the RCMRD Geoportal with a CC BY license in R. All points were added and modifications were performed in R and Adobe Illustrator. The map is published for the first time in this Article. b, In a principal component analysis, eigenvector 1 correlates to variation maximized in sub-Saharan Africa, and eigenvector 2 correlates to Eurasian variation. c, Ancestry component assignment using ADMIXTURE with K = 9 clusters (selected on the basis of low cross-validation errors, high log-likelihood scores, and a low number of reference populations to not overfit; groups that maximize each components are shown on the right). Individuals with sufficient data for high-resolution analysis are plotted in approximate chronological order from left to right. Ancient individuals are labelled and plotted at four times the width of present-day individuals.
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Post by Admin on Apr 14, 2023 4:06:54 GMT
The medieval largely autonomous towns and polities known as the Swahili states arose out of fishing and agropastoral settlements on the eastern African coast during the late first millennium AD6. First millennium AD sites on the littoral, beginning in the seventh century, were part of a shared material culture and practice network across the eastern African region7. These sites were engaged in the Indian Ocean trading system, facilitated by southwest monsoons from May to October that enabled merchant vessels to travel from India or the Arabian Peninsula to the eastern African coast, and northeast monsoons from November to March enabling their return in the same year8.
Muslims were present from the eighth century AD, probably as a minority9. A major archaeological transition is evident during the eleventh century, with the establishment of new settlements and the elaboration of older ones with coral-built mosques and tombs, a set of changes generally understood as coinciding with the widespread adoption of Islam10. At this time, clearer distinctions also emerged between coastal ceramics and material traditions and those of inland assemblages2,11, even as many aspects of material culture remained deeply linked with inland African groups.
The political and administrative independence of Swahili towns diminished in the sixteenth century as the Portuguese naval and economic dominance in the Indian Ocean spread12. In the early eighteenth century, the Portuguese influence waned and the Sultanates of Oman and later Zanzibar became dominant4. In the nineteenth century, the growth of overseas trade, including in enslaved people, led to large-scale population movements from central regions of Africa and settlers from the Yemeni region of Hadramawt4,13. In the mid-nineteenth century, Britain and other European powers became dominant, leading to the settlement of Europeans, the arrival of labourers from South Asia, and further interactions with non-coastal eastern Africans.
In light of this multi-layered history, the extent to which people who identify as Swahili in the present day are genetically linked with people who built the medieval trading towns is unclear, as is the relationship of the medieval groups to earlier groups. Although the intercontinental connections maintained as part of the Indian Ocean trading network meant that foreigners were consistently present along the coast, the extent to which they had families with African residents has long been debated14.
Swahili traditions suggest that foreigners had an important impact; a set of common oral histories relates the founding of coastal towns to the arrival of a group known as the Shirazi, referring to a region in Persia3. This Shirazi tradition was put into writing in the Kilwa Chronicle in the sixteenth century15. These accounts of Shirazi roots were central to the narrative constructed by mid-twentieth century colonialist archaeologists, who interpreted second millennium coastal eastern African sites as having been built by Persian and Arab settlers, and focused on connections with the broader Indian Ocean world16.
However, narratives of foreign origin have the potential to be misleading, as Swahili social ‘elites’ used claims of foreign origin and rejection of cultural connections within Africa to establish their social status and to signal their religious and cultural affinities17,18.
Recent research has shown that archaeology during colonial times tended to ignore the evidence of deep African roots, emphasizing foreign objects at medieval Swahili sites rather than providing a balanced picture of the archaeological record2. Imports at most coastal sites typically comprise less than 5% of total assemblages2,9. Other aspects of the material culture also show continuity with earlier settlements, including the persistence of crops, domesticated animals, craft styles and ceramics9,19. Linguistic evidence provides additional evidence of African roots: Kiswahili is an African Bantu language with Asian loanwords20. However, without ancient DNA evidence, it is not possible to directly address questions of how genetic ancestry changed over time.
We generated ancient DNA data from the skeletal remains of individuals found at six coastal or island towns: Mtwapa, Manda, Faza, Kilwa, Songo Mnara and Lindi. These individuals date to AD 1250–1800 but provide insight into genetic events from the tenth century AD onwards. We also generated ancient DNA from the remains of individuals found at the site of Makwasinyi (postdating around AD 1650), about 100 km inland from the southern Kenyan coast, which was inhabited by people who were in cultural contact with coastal groups. We compare the newly reported data from the ancient individuals with that of present-day coastal Swahili speakers and with previously published data from diverse ancient and present-day eastern African and Eurasian groups.
Dataset overview We generated 179 ancient DNA libraries from 156 distinct skeletal samples (Supplementary Data File 1 and Methods). We applied in-solution enrichment for a targeted set of about 1.2 million single nucleotide polymorphisms (SNPs) to obtain genome-wide data passing standard measures of ancient DNA authenticity from 80 distinct individuals. The individuals were buried at seven second millennium AD sites in eastern Africa (black shapes in Fig. 1a; individuals are listed in Extended Data Table 1 and Supplementary Data File 2; see Methods, ‘Inclusion and ethics’ and Supplementary Information for details of archaeological and genetic permissions and sampling). We obtained direct radiocarbon dates (Supplementary Data File 3) for 33 of the skeletons, and estimated date ranges for the other individuals on the basis of archaeological context or genetic evidence of relatedness to individuals for whom we had direct dates (Extended Data Table 1 and Supplementary Data File 2). Because of the reliance on seafood, old carbon entering the food chain (marine reservoir effects) could mean that the radiocarbon dates of some individuals are older than their true dates. Moreover, differences in the dependence on marine food across the archaeological sites could mean that the relative chronology of the coastal individuals and sites may not be possible to determine with full confidence. We also generated new genome-wide data on the Affymetrix Human Origins SNP array from 93 present-day individuals who identified as Swahili and indicated that their ancestors lived for many generations in coastal towns21 (Supplementary Data File 4). Finally, we generated new genome-wide data from 19 individuals from Madagascar, and 10 from the United Arab Emirates.
Three sites were northern coastal towns: Mtwapa (Supplementary Fig. 1, 48 individuals spanning AD 1250 to AD 1650), Faza on Pate Island (1 individual), and Manda Island (Supplementary Fig. 2, 8 individuals spanning AD 1450 to AD 1650). Three additional sites were southern coastal towns: Songo Mnara (Supplementary Fig. 3 and Supplementary Table 1, 7 individuals spanning AD 1300 to AD 1800), Lindi (1 individual at AD 1500 to AD 1650), and Kilwa Kisiwani (2 individuals spanning AD 1300 to AD 1600). The remains at Mtwapa, Manda and Songo Mnara were mainly from Muslim burials of elites, often located near mosques. We do not have enough context for the Faza, Kilwa and Lindi burials to know if they followed the same pattern. We also analysed 13 individuals from Makwasinyi (AD 1650–1950), approximately 100 km inland from the coast of present-day Kenya. Although these burials post-date the coastal sites, the Makwasinyi community traded with coastal peoples while remaining isolated in most respects. We hypothesized that the ancestry of Makwasinyi people might be a good proxy to represent inland African groups that may have been in contact with people from medieval towns on the northern Swahili coast in previous centuries22.
Of the 80 individuals for whom we report data, we exclude 26 in genome-wide analyses, although their data remain valuable. Of these, 18 had too few SNPs for high-resolution whole-genome analyses although they yielded useful data such as reliably determined mitochondrial sequences; 5 were first- or possibly second-degree relatives of other individuals in the dataset with higher-quality data; 2 showed evidence of contamination; and 1 was a population genetic outlier with limited data, raising the possibility of contamination (Supplementary Data File 2).
Ancient DNA data from four individuals from the eastern African coast have previously been published (Supplementary Data File 5), but none have been published from a Swahili town23. An individual from around AD 1400 whose remains were recovered from Makangale Cave on Pemba Island had ancestry predominantly related to western African groups23 (an ancestry common today in speakers of Bantu languages and prevalent in eastern Africa—hereafter referred to as ‘Bantu-associated’). Another individual from Makangale Cave on Pemba Island dated to around AD 600, an individual from around AD 600 from Kuumbi Cave on Zanzibar Island, and an individual from around AD 1500 from Panga ya Saidi in Kenya all had predominantly sub-Saharan African forager-associated ancestry23. There is no indication of Eurasian ancestry deriving from migrations in the last 2,000 years in any of these individuals, which differs from nearly all of the individuals from medieval coastal towns newly reported here.
In this Article, we use ‘African ancestry’ to refer to DNA deriving from people who can be genetically well-proxied by sub-Saharan Africans for whom there is published ancient DNA data dating to between 2000 BC and AD 1000. We use the terms ‘Eurasian’, ‘Persian’, ‘Arabian’ and ‘Indian’ to refer to ancestry that can be proxied by modern populations from these regions and that are not known to be similar to ancestry in sub-Saharan Africans between 2000 BC and AD 1000. The evidence that a proportion of the ancestors of Africans from between 2000 BC and AD 1000 may have come from Eurasia—for example, approximately 40% of the ancestry of people of the eastern African Pastoral Neolithic culture24—does not contradict these definitions, as all humans are mixed at multiple time depths of history. As long as we specify both the time and the geography for the source populations, we can be precise in the use of the term ‘African ancestry’25.
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Post by Admin on Apr 22, 2023 17:59:26 GMT
Genetic affinities To obtain a qualitative picture of the sources of the ancestry in the ancient individuals, we performed principal component analysis (PCA) (Fig. 1b). We used 1,286 present-day Eurasian and African individuals to compute the axes (Supplementary Data File 6). We projected the newly reported ancient individuals onto this PCA and found that they form a cline, with one end overlapping with ancient and present-day African groups and the other falling between present-day Persians and Indians. This suggests mixtures of different proportions of source populations at either end of the cline, with these sources potentially having multiple deeper ancestry components. Some coastal individuals—particularly from Songo Mnara and Lindi, do not fall on this cline—suggesting additional complexity, although our power to understand this variability is limited by the small sample sizes. Similar patterns are evident with unsupervised clustering using ADMIXTURE, which further suggests sub-Saharan African-associated components, southwest Asian-associated components, and East Asian or Indian-associated components (Fig. 1c and Extended Data Fig. 1). Proportions of African, Persian and Indian DNA Using qpAdm26, we find that most medieval and early modern individuals can only be fit by a model with at least three ancestry components that can be proxied with ancient African, present-day Iranian and present-day Indian populations (Fig. 2a, Extended Data Table 2, Supplementary Tables 2–10 and Supplementary Information). Such a three-source model fits the pool of 48 Mtwapa individuals and the Faza individual (P value for fit = 0.23); the pool of Manda (P = 0.28) individuals, and at least one Songo Mnara individual (I19550) (P = 0.38). One Kilwa individual (I8816) had a relatively high proportion of ancestry related to inland sub-Saharan Africans, and so the Indian proportion, which is the smallest contributor, falls below threshold of definitive detection (a two-source model fits; P = 0.27). Fig. 2: 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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Post by Admin on Apr 23, 2023 17:27:11 GMT
The type of African ancestry needed to make the models fit differed between individuals from the north (Mtwapa, Faza and Manda) and south (Kilwa and Songo Mnara) of the studied region. In Kenya, the best-fitting proxy African source is the inland Makwasinyi individuals (Extended Data Table 2), who are themselves well-modelled as mixtures of about 80% Bantu-associated and 20% ancient eastern African Pastoral Neolithic ancestry24 (Fig. 3a, Extended Data Table 3, Supplementary Tables 2 and 3 and Supplementary Information). In Tanzania, the best-fitting African proxy source is Bantu-associated without evidence of a Pastoral Neolithic contribution. We use the individual buried at around AD 1600 in Lindi as a proxy Bantu-associated source for the Kilwa individual and individual I19550 from Songo Mnara (Extended Data Table 2). Fig. 3: Inferred admixture events along the eastern African coast. Although three continental sources are required to fit the data, the individuals from Manda, Faza and Mtwapa form a cline in PCA, suggesting two proximal source populations (Fig. 2b). Using linear regression, we extrapolate the ancestry of these two sources and infer that one was consistent with a 100% African origin (Supplementary Fig. 5 and Supplementary Information). The same analysis concludes that the other source had both Persian and Indian ancestry. This is consistent with sub-Saharan Africans mixing with a group that already had a mixture of Persian and Indian ancestry components. Given the two different African sources for the northern and southern individuals, there must have been at least two, but possibly more, admixture events. This would be expected if people of mixed Persian and Indian ancestry had children with people from different local African populations at different locations along the coast. When we analyse the Mtwapa and Faza, Manda, Kilwa and Songo Mnara individuals separately, the estimated proportions of Eurasian ancestry from India overlap, which could be consistent with a homogeneous source population of mixed Indian–Persian ancestry for all sites (Fig. 2c). However, a variable proportion among the early immigrants cannot be ruled out, and thus we cannot distinguish between scenarios of two or more streams of Persian–Indian migrants. Our statistical power to detect Indian ancestry relies on pooling of data from multiple individuals. There are a number of individuals with limited data or low Eurasian ancestry, for example individual I8816 from Kilwa, for which we have little power to detect Indian ancestry and cannot definitely document it (Supplementary Information).
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