...
Post A Reply
my profile
|
directory
login
|
register
|
search
|
faq
|
forum home
»
EgyptSearch Forums
»
Deshret
»
2017 article claims: Nubians an admixed group with gene-flow from outside of Africa
» Post A Reply
Post A Reply
Login Name:
Password:
Message Icon:
Message:
HTML is not enabled.
UBB Code™ is enabled.
[QUOTE]Originally posted by the lioness,: [QB] http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006976&rev=2 [b]Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations[/b] Nina Hollfelder, Carina M. Schlebusch, Torsten Günther, Hiba Babiker, Hisham Y. Hassan, Mattias Jakobsson Published: August 24, 2017https://doi.org/10.1371/journal.pgen.1006976 (excerpt) Abstract Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa. Author summary Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa. [IMG]https://images2.imgbox.com/8e/d5/neEdRCHV_o.jpg[/IMG] [IMG]https://images2.imgbox.com/a1/68/mdf37ckN_o.jpg[/IMG] Introduction The Nile River Valley and northeast Africa have experienced a long history of human habitation. The region harbored some of the most ancient civilizations in the world and contains fossil finds of the earliest anatomically modern humans [1–3]. Agriculture has a long history in the Nile River valley, and crops of potential Near Eastern origin as well as sorghum found in Sudan have been dated to 3000BC [4]. Livestock was introduced into northeast African and Sudan in the 5th millennium BC (likely from the North) and pastoralism spread rapidly across sedentary agriculturalists who lived along the Nile as well as to the nomadic populations inhabiting the drier surrounding regions [4]. Following the introduction of agriculture and pastoralism, settlements started growing, which led to the forming of political units. In Nubia (roughly the northern parts of current-day Sudan), the Kingdom of Kerma emerged around 3000 BC. Nubia has successively been at the center of several ensuing states, and the historical records show interactions with neighboring states through trade and confrontation, possibly reaching back to predynastic times [4–6]. Modern-day Sudan and South Sudan cover parts of the Nile River and the joining of the Blue and the White Nile, areas that link the northern part of the Nile Valley and North Africa with East Africa. Today, these areas display great linguistic diversity, with Sudan and South Sudan housing 137 living languages [7], which belong to three of the four linguistic macro-families found on the African continent: Afro-Asiatic, Nilo-Saharan, and Niger-Congo. Previous genetic studies focusing on human history in Sudan and South Sudan have used uniparentally inherited markers [8–10], low density polymorphic autosomal markers [11–17], or were only covering a limited number of populations [18]. These studies have found substantial genetic differentiation in northeast Africa and indications of migration and admixture. For instance, Tishkoff, Reed [18] investigated more than one hundred African populations using some 800 microsatellites, including six populations from Sudan and South Sudan and showed that eastern Africa harbors substantial amounts of genetic diversity. However, wide ranges of populations, representative of all the main linguistic groupings, in and around Sudan and South Sudan have not been studied in order to decipher population history using high-resolution genome-wide data. In this study we genotyped some 3.9 million SNPs in 221 individuals from a total of 18 populations from South Sudan and Sudan to investigate population structure and admixture patterns, which we use to reconstruct the genetic history of this region of northeast Africa. We find a genetic differentiation within the Sudanese and South Sudanese groups that is driven by Eurasian admixture, which may have followed the Nile southward and coincides with the time of the Arab conquest. [b] Nilotic groups emerged from an ancestral group of East Africa[/b] Among the populations from Sudan and South Sudan, the four Nilotic populations formed a notable population cluster based on the genome-wide data. They were genetically uniform with little genetic differentiation among themselves (pairwise FST values ≤ 0.0028, Fig 1B, S7A Fig). In the ADMIXTURE analyses, the Nilotic populations retained a specific ancestry component (blue), which is shared with other northeast African groups at low values of K, where most of the Sudanese populations have a substantial fraction of this ancestry (Figs 2 and S1–S6). Even at higher values of K, the Nilotes formed their own ancestry component, a component found in modest proportions in populations from Sudan and South Sudan. The Nilotes also appeared as one of the most common source populations for other Sudanese and South Sudanese populations (Figs 2 and 3A). We furthermore compare the affinity between the Nilotes and Neolithic European farmers (represented by an individual from the Linearbandkeramik (LBK)), using the 4,500 year old Mota individual from Ethiopia to represent an East African group that has not been affected by Eurasian admixture in the last 4,500 years [25]. Testing the population tree D(Ju|’hoansi,LBK;Mota,Nilote) shows no support for an affinity between Neolithic European farmers and Nilotes (S8A Fig), as can also be seen from the f4-ratio estimates of Eurasian ancestry in Nilotes (Fig 3B, S9A Fig). Previous studies of uniparental or few markers also found little support for incoming gene-flow to the Nilotic populations [9, 11, 15, 25], and, taken together with our results, Nilotic populations appear to have remained relatively isolated over time. The Nilotes are predominantly pastoralist populations, they live in Uganda, Ethiopia, Kenya, Tanzania, and are the most prominent ethnicity in South Sudan. They are traditionally strongly endogamic which could account for low levels of admixture. In terms of specific Nilotic populations, the f3 test showed no significant signal of gene flow with external populations for the Nuer and Baria (Fig 3A), however, we detected indications of external gene flow from West Africa (YRI) into Dinka (f3 = -0.001038, Z = -5.283) and TSI to Shilluk (f3 = -0.002565, Z = -7.951, S2 Table). These observations taken together, suggest long term isolation and continuity between the current-day Nilotic populations and the ancestral populations of northeast Africa. [b]Little admixture in northeast Africa with Bantu-speaking groups[/b] All the investigated Sudanese and South Sudanese populations, except the Hausa, showed almost no West African (orange in Fig 2) component or, at a higher K, Bantu component (Fig 2, yellow in S3 Fig) in the ADMIXTURE analysis. The Bantu migration that swept over most of sub-Saharan Africa 3–4 thousand years ago (kya) [26] did not cause massive admixture in northeast Africa, contrary to what has been found in many other sub-Saharan African regions, e.g. East Africa and southern Africa [18, 27, 28]. This expansion seems to have passed south of the Sudanese Nilotic populations in an eastward direction from West-Africa. The strongly endogamic Nilotic populations could have acted as a migration barrier for northeast Africa preventing admixture with Bantu-speaking groups of West African origin during the migrations of the Bantu expansion, potentially in addition to climatic barriers connected to the agriculture of the Bantu-speakers. Although there are a few Bantu speaking populations in South Sudan [29] that likely migrated during the Bantu expansion, they do not appear to have mixed much with local Nilotic groups. The Afro-Asiatic speaking Hausa population from northeastern Sudan was the exception to the observation of little West African affinity in Sudan and South Sudan (Fig 1). The Hausa, originally of western Africa, comprises the largest West African population that have migrated to Sudan during the past 300 years, traditionally employed mainly in agricultural activities [30, 31]. In S11 Fig they cluster in between the West African Yoruba and Nzime, and the Darfurian/Kordofanian and Nilotic populations. This finding is consistent with previous analyses [18, 30, 32, 33]. Even though the ADMIXTURE analysis showed some level of local Nilotic genetic material (~30% at K11 and higher, Fig 2, S3 Fig), the f3 statistics did not provide significant evidence for admixture with Darfurian/Kordofanian and Nilotic populations. Using LD decay patterns [34], we estimate an admixture event in the Hausa to 31.2 ± 9.3 generations ago (Z = 3.34683) from a Eurasian source. This is before the historically documented settlement of the Hausa in the Sudan and it is still unknown if the Hausa populations of West Africa also show this admixture signal. These observations point to that the Hausa originated in West Africa and migrated recently to Sudan, where they have stayed relatively isolated from neighboring populations. [b]Nubians are an admixed group with gene-flow from outside of Africa[/b] The Nubians inhabit the Nile valley in the arid desert of northern Sudan and speak Eastern Sudanic languages of the Nilo-Saharan linguistic family that are close to the languages spoken by Nilotic populations (Table 1, Fig 1A). The Nubian populations have a long history in the region, dating back to dynastic Egypt [5]. They showed little genetic differentiation among individuals and groups, with a maximum (across all pairwise comparisons) pairwise FST (Weir and Cockerham’s estimator) of 0.004513 between the Mahas and the Halfawieen (Fig 1B, S7A Fig). The FST values to the surrounding Arabic and Beja populations were also low, which hints at gene-flow or shared ancestry with the neighboring populations. Even though the Nubians and the Nilotes are linguistically closer to each other than to the Afro-Asiatic groups, the Nubians showed the greatest genetic differentiation (FST between 0.02 and 0.04) to the Nilotes (Fig 1, S7A Fig). To investigate whether this signal of genetic differentiation is driven by the Eurasian admixture into the Nubians (as seen in Fig 2), we created pseudo-‘unadmixed’ (in terms of not having Eurasian admixture) allele frequencies (see SI) and calculated Wright’s FST, which showed that an ‘unadmixed’ Nubian gene-pool is genetically similar to Nilotes (S7B Fig). The strongest signal of admixture into Nubian populations came from Eurasian populations (S10 Fig, S2 Table) and was likely quite extensive: 39.41%-47.73% (f4-ratio, Z-scores between 22.8 and 26.7 Fig 3B, S9 Fig). Interestingly, the Nubians showed the highest level of allelic richness, number of private alleles and shared private alleles (ADZE, between Danagla and Halfawieen, S12 Fig) among all Sudanese and South Sudanese groups. This observation together with a smaller total length of runs of homozygosity, between lengths of 0.5–1 kilobases, points to substantial admixture in Nubians (Fig 4). Hence, the Nubians can be seen as a group with substantial genetic material relating to Nilotes that later have received much gene-flow from Eurasians (likely Middle Eastern) and from East Africans [b] West-Eurasian migration from the north[/b] All the populations that inhabit the Northeast of Sudan today, including the Nubian, Arab, and Beja groups showed admixture with Eurasian sources and the admixture fractions were very similar. The admixture component in the northeastern groups cluster with the greater European and Middle Eastern group assuming few clusters, and for greater number of assumed clusters, when a predominantly Middle Eastern cluster emerged, the admixture in northeastern Sudan connected to the Middle East (ADMIXTURE, Fig 2, f3, S10 Fig). According to historical and linguistic studies, and recent Y-chromosome data it has been suggested that the northeastern Sudanese populations especially Nubians and Beja were strongly affected by Eurasian migrations since the introduction of Islam from the Arabian Peninsula through Egypt and the Red Sea starting around 651 A.D [9, 35]. Assuming that the Nubian population is a mixture of an incoming Eurasian (TSI is used as a proxy) group and a resident group that is genetically similar to the current day Nilotes (Nuer is used as a proxy), first contact is dated using patterns of LD-decay [34] to roughly 56 generations ago for the Danagla (54.45 ± 10.34, Z = 5.26437) and the Mahas (58.35 ± 12.2, Z = 4.78402); the Halfawieen have received Eurasian admixture later, around 19 generations ago (19.31 ± 3.81, Z = 5.05949, S7 Table, Fig 3C). Assuming a generation time of 30 years, the admixture dates for Danagla and Mahas predate the Arab expansion in the 7th century, and may suggest that the migrations and admixture predate Islamic conquest. However, the confidence intervals overlap with the 7th century, and these admixture estimates largely coincide with the Arab expansion into the northeast of Sudan. It is known from historic sources that Arabic groups encountered the Nubians first in the 7th century, and were held back from advancing further into the Sahel until the fall of Dongola in 1315/1316AD [36] and the collapse of the Kingdom of Makuria. This is consistent with the later date for the admixture into Halfawieen and the Arabic populations of Sudan. Previous studies [37, 38] have found a similar pattern for populations of Maghreb, where admixture times coincide with the time of the historically documented Arab conquest. The Eurasian migrations also appear to have expanded and migrated into northeast Africa where they admixed with local populations giving rise to Arabic-speaking groups (Shaigia, Gaalien and Bataheen) that today inhabit areas of central Sudan (Fig 2). We further tested the source of admixture into the central Sudan Semitic speaking Arab groups (Shaigia, Gaalien and Bataheen) using ancient samples from Europe (LBK) and East Africa (Mota) and the population history of D(Ju|’hoansi,LBK;Mota,X), (where the Ju|’hoansi is an outgroup Khoe-San population from Namibia), which suggested Eurasian admixture into central Sudan Arab groups (see SI, S8A Fig). This migration and admixture occurred later than the events that brought Eurasian gene-flow into the Nubians (S3 Table, Fig 3C). Interestingly, when we overlay the Eurasian genetic component onto a geographic map, it appears as if the expansion could have spread along the Blue Nile (Fig 3B and 3C), showing a gradient of higher to lower admixture proportion and older to younger admixture dates from northern Sudan to South Sudan. The Eurasian admixture proportion in the Arab populations is high, ranging between ~40%–48% (SI, Fig 3B and S9A Fig). The presence of a northeast African genetic signature similar to Nilotic populations and the recent admixture signal from Eurasia indicates that the populations in central Sudan that self-identify as Arab were originally a local northeast African population (similar to the Nubians and the Beja) that mixed with a Eurasian population during the Arab expansion, or possibly earlier. However, the mixed groups kept the language and culture of the incoming migrants. Beja groups, who generally reside in eastern areas of Sudan close to the sea, show high non-African admixture in all tests (Figs 2 and 3B, S1–S6 and S8–S10 Figs). The Beni Amer also showed a strong admixture signal with a Eurasian population as well as a shared ancestry component with the Somali population (pink component in Fig 2), which suggest admixture with the East African Cushitic-speaking populations, perhaps as a result of migration along the coast. We dated the admixture of the Beja populations with the Cushitic-speaking Somalian population [39], and the admixture dates go far back in time, about 59 generations ago for the Hadendowa and about 68–75 generations for the Beni Amer (S3 and S4 Tables). The large proportion of the East African (pink in Fig 2) component is therefore not a result of recent admixture of East Africans into the Beni Amer. Admixture of non-Africans into the Beni Amer was also dated to an early event about 107.7 ± 24.4 generations ago (Z = 4.41711) and a younger event, 34.2 generations ago (± 9.6, Z-score = 3.55532 Fig 3C, S7 Table) suggesting an early migration from Eurasian into these coastal African populations, possibly across the sea. However, these old admixture events into the Beni Amer could be driven by admixture from the Cushitic-speaking populations of the Horn of Africa, which themselves have received 30–50% non-African ancestry about 100 generations ago, or 3kya [22, 40]. [b]The population history of the Copts and their relation to Egyptians[/b] The Copts represent a well-known ethnic group, generally practicing Christianity, which migrated from Egypt to Sudan around 200 years ago, settling in a predominately Muslim region. The ADMIXTURE analyses and the PCA displayed the genetic affinity of the Copts to the Egyptian population (Fig 2, S1–S6, S11 and S13–S16 Figs). Assuming few clusters, the Copts appeared admixed between Near Eastern/European populations and northeastern Sudanese and look similar in their genetic profile to the Egyptians. Assuming greater number of clusters (K≥18), the Copts formed their own separate ancestry component that was shared with Egyptians but can also be found in Arab populations (Fig 2). This behavior in the admixture analyses is consistent with shared ancestry between Copts and Egyptians and/or additional genetic drift in the Copts [41, 42]. The Copts and the Egyptians have a historically documented shared history. We further investigate the relationships of the Copts and the Egyptians to other groups. All population histories tested in every possible combination of either Copts or Egyptians, and Bedouin and Nuer, with Ju|’hoansi as outgroup to the others were rejected (D-statistic, |Z|>5.5), which points to a non-tree-like history of the Copts and Egyptians. Our results instead indicate that they are an admixed population of at least one sub-Saharan population and one Eurasian population, but had subsequent admixture with additional groups. The population tree that has the most support finds the Nuer (Nilotic) as an outgroup to the Bedouin and Copts (D(Ju|’hoansi,Nuer;Bedouin,Copts) = 0.0103, Z = 5.550). The Copts were estimated to be of 69.54% ± 2.57 European ancestry and the Egyptians of 70.65% ± 2.47 European ancestry (f4-ratio, Fig 3B, S9A Fig). The Egyptians and Copts showed low levels of genetic differentiation (FST = 0.00236, Fig 1B), lower levels of genetic diversity (S17 Fig) and greater levels of RoH (Fig 4) compared to other northeast African groups, including Arab and Middle Eastern groups that share ancestry with the Copts and Egyptians (Fig 2) [41]. A formal test (D(Ju|’hoansi,X;Egypt,Copt)), did not find significant admixture into the Egyptians from other tested groups (X) as the explanation of the (admittedly low level of) differentiation between the two groups, and the Copts and Egyptians displayed similar levels of European or Middle Eastern ancestry (S8A and S8B Fig). Taken together, these results point to that the Copts and the Egyptians have a common history linked to smaller population sizes, and that the Copts have remained relatively isolated since the arrival to Sudan with only low levels of admixture with local northeastern Sudanese groups (S8B Fig). [b]Conclusion[/b] We have shown that there has been long-term migration into Sudan, moving in a southward direction possibly along the Nile and the Blue Nile. From historic documents, we know that the ancient Egyptians were in contact with the ancient Nubians that inhabited the Nile area in the north of modern-day Sudan. Our study suggests that the later migration followed along the Nile, likely being held up by the Nubians until the fall of the Kingdom of Makuria in the 14th Century [4]. Following that historic event, the Arab expansion spread further southward, which can be seen in a succession of admixture events that occur more recent in time as one travels south. Many populations in Sudan that self-identity as Arab, displayed a population history of local Sudanese populations that have admixed with incoming Eurasian populations, and adopted the language and culture of the incoming migrants. In fact most populations from northeast Sudan (Nubian, Arab and Beja groups) seem to be a mixture of Middle Eastern and local northeast African genetic components, although only the Arab groups shifted to the Semitic languages. Cultural and linguistic replacement following the Arab conquest has been described previously in populations of the Maghreb [37, 38, 43]. The Eurasian admixture had less impact on the populations of western Sudan and South Sudan. The Darfurian and Kordofanian populations showed overall less admixture from non-African groups than the northeastern populations (and the limited admixture that does exist is more recent in time). The Nilotic populations have stayed largely un-admixed, which appears to be the case in Ethiopia too, where a similar observation has been made for the Gumuz [23, 44], an Ethiopian Nilotic population that is genetically similar to South Sudan Nilotes. Northeast African Nilotes showed some distinction from an ancient Ethiopian individual (Mota, found in the Mota Cave in the southern Ethiopian highlands), which suggests population structure between northeast and eastern Africa already 4,500 years ago. The modern-day Nilotic groups are likely direct descendants of past populations living in northeast Africa many thousands of years ago. [/QB][/QUOTE]
Instant Graemlins
Instant UBB Code™
What is UBB Code™?
Options
Disable Graemlins in this post.
*** Click here to review this topic. ***
Contact Us
|
EgyptSearch!
(c) 2015 EgyptSearch.com
Powered by UBB.classic™ 6.7.3