Tweet
Eurasian Back-Migration Into Northeast Africa Was A Complex And Multifaceted Process November 2023
It is clear that back migrations into Northeast Africa have had a major impact on the genetic ancestries of the peoples in the region today [4–6]. Ethiopian populations, for instance, harbor a large proportion of “non-African” ancestry, as high as, ∼ 40% in some groups—see for instance the Amhara in Fig 1c in [7]. What is clear is that some current-day Northeast Africans can trace much of their ancestry from other sources than the original hunter-gatherers in the region, such as the Mota individual, an Ethiopian male who lived around 4500 years ago [8, 9]. It is also clear that these back migrations into Africa have been ongoing for a long time period. For North Africa, seven individuals from Morocco that had a high affinity to Middle Eastern populations, dated to 15 000 years ago, suggesting the possibility that similar deep-in-time admixtures might have occurred in other parts of Africa [10].
[...] They proposed a four-stage model where initially Sudanese Nilotic speakers admixed with groups with Eurasian ancestry (either from Northern Africa or the Levant) within Northeast Africa. In step two, the descendants of these groups migrated to East Africa reaching Lake Turkana by around 5 000—4 000 BP and central Tanzania by around 3000 BP and mixed with local hunter-gatherer groups throughout this process [5]. The first signs of pastoralism in East Africa coincide with these events. Thirdly the second wave of Sudanese-related groups migrated into the area and contributed to the pastoral Iron Age populations. Lastly, West African ancestry (genetically similar to Bantu speakers) appeared alongside the advent of crop farming in the region.
[...]
By leveraging one of the largest datasets of Northeast African populations to date, we aim to add resolution to Eurasian admixture in Northeast African populations. Specifically, we aim to improve the estimation of the best proxies for the origin of Eurasian admixture in modern-day Northeast African populations by using more Northeast African and Middle Eastern, and Eurasian reference populations. In this study, we follow the approach of [4, 6, 16] in that we employ local ancestry methods to identify the Eurasian fragments of East African genomes and extract those segments from the surrounding genomes, a process referred to here as ancestry-deconvolution. We then identify the current-day populations that best match those segments. We also date the events to get a better understanding of historic and prehistoric movements in the region. Using the information of possible sources for admixture and dating of these, we construct a model representative of the population history in the region. Overall we find a complex history of Eurasian admixture in Northeastern Africa, related to the spread of languages, the Muslim conquest, and trade routes along the Red Sea.
[...]
The first division in the data is between Africans and non-Africans, and it is clear that North- and East- Africans have a much larger proportion of shared ancestry with Eurasian groups than other African groups (K = 3 in S2 Fig). East African groups break away from other African groups at K = 5 via a component (black) maximized in the Nuba at 80.1%. Of particular interest for the present investigation is also the component that emerges is K = 8 (light orange) maximized in the Ari, Sabue and Gumuz populations. The Sabue is one of the few remaining hunter-gatherer groups in East Africa today and they share genetic continuity with earlier hunter-gatherer ancestry from the region [38] represented by the Mota individual [8]. The Ari, Gumuz and Sabue have been suggested to retain a high degree of ancient East African hunter-gatherer ancestry, [4, 26, 38] and our demographic analyses indicate a high degree of similarity between these populations. This component is shared with many other East African groups, displaying fractions of ancestry that show deep continuity in the region.
At K = 11 another East African component appears, maximized in the Somali populations and might represent Cushitic-related ancestry. Levantine populations separate from the Arabic populations at K = 14 and we visualized these two components using a Kriging interpolation across the study area, Fig 1. These two ancestries were the component maximized in the Lebanese Druze (dark blue) and the component highest in the Yemeni (blush pink).
To investigate the differences in affinities of our target populations to either Levantine and Yemenite ancestry we performed a f4 test. The test took the following form Yemen_YEMEN |Lebanese_Christian|Target S22 Fig. It showed significant association with Levantine for the populations north of the Sudanese BeniAmer as well as for the Oromo and Tygray from Ethiopia, the Kenyan Luhya and the Maasai from Kenya. No populations had a significantly higher association to Yemenite ancestry when compared to Levantine ancestry in this more stringent test. The test however highlight the importance of Levantine admixture for more northern populations in particular.
In our Principal Component (PC) analyses, the first PC differentiates between African and non-African groups S5 Fig. Several African populations fall on the cline between African and non-African variation, in particular North Africans, such as the Egyptians and populations from Sudan who are known to have Eurasian admixture [15]. We also observe a grouping according to linguistics where Omotic, Afro-Asiatic, and Nilo-Saharan speakers separate from each other. East African groups are positioned on the diagonal between PC 1 and PC 3, with the Ari, Sandawe, and Sabue populations forming their own cluster in the direction of the southern African Khoe-San, indicating shared ancestries between these hunter-gatherer groups S5 Fig. This cline is similar to what was found in studies using aDNA [5, 11] and is a reflection of the cline between southern and East African hunter-gather ancestry.
UMAP was also performed in the genotype information in our dataset, see S20 Fig. This analysis produces two larger clusters of populations, one consisting of West African groups, Eastern Bantu speakers, the Saharan speakers, the Nuer, Dinka, and Shiluk from Sudan. The other cluster contains mainly Middle Eastern populations and Ethiopians, as well as the remaining Sudanese populations.
[...]
As has been shown in previous studies, and indicated by our demographic inference Fig 1 and S6 Fig, there are generally four main components of modern-day East African genetic ancestry [5, 12]. Namely, basal East African hunter-gatherer ancestry, Sudanese/Nilotic ancestry, Eurasian ancestry, and West African ancestry associated with Bantu speakers. Since the aim of this study is to identify the best proxy for the source of the Eurasian ancestry of the Northeast African populations, we constructed a scenario where we could use these four ancestral sources to paint the haplotypes of our chosen target populations using MOSAIC [34]. We set up an initial scenario to try and identify the best Eurasian source to use for further analyses. In this scenario we used the following populations: To represent the basal East African hunter-gatherer ancestry we chose the Sabue [26, 38]. The Sabue has been referred to by many different names in the literature, for instance, Shabo and Chabu, here we use the name used in the original publication of the data [26]. The CEU (Utah residents with Northern and Western European ancestry) population from the 1000 genomes consortium was chosen as a proxy for general Eurasian ancestry. The Sudanese Dinka was chosen to represent Sudanese ancestry (the group that defines the black component in the ADMIXTURE analysis associated with Sudanese ancestry). The YRI (Yoruba in Ibadan, Nigeria) was used as a proxy for West African Niger-Congo and Bantu-speaker-associated ancestry.
[...]
Population structure inferences illustrate the complex genetic history of Northeast African populations. Larger patterns of genetic associations between many of the world’s distinct human lineages are reflected in Northeast African genomes. The hunter-gatherer’s ancestry highlights the deep history of the region and its people and that this ancestry remains within the East African populations. The southern part of the region has a closer genetic affinity to West African groups, a result of the Bantu expansion and several of these populations also speak Bantu languages today. That the Bantu expansion did not continue further into the region could be a result of geographical barriers such as the Ethiopian Highlands and the dry regions of the Horn of Africa, indicated by our FEEMS analysis in Fig 1D or as suggested by [15] that the Northeast African Nilotic speaking herders (such as the Dinka and Nuer), who have remained relatively isolated from other groups, could have formed a buffer against the Bantu expansion continuing further into Northeast Africa.
Eurasian admixture has had a large influence on the genomes of Northeast African groups. The Egyptian and Sudanese Copt populations for instance are genetically very similar to Middle Eastern groups rather than to other African populations. The pattern is true also for the rest of North Africa and present as early as at least 15 000 years ago [10] though not investigated here. The Copts look genetically similar to the Egyptians from Cairo, see Fig 1A and 1C, this is not unsurprising given that the Copts arrived in Sudan around 200 years ago from Egypt and seem to have lived relatively isolated since then [15]. Our admixture date for the Copts (with Eurasians) was inferred to be 27.5 for the f3 analysis and 25.7 for the R2 and around 22 generations for the Egyptians. Thus this admixture took place around the 14th century.
Further south in the region, we continue to see the impact of past Eurasian admixture. Northeast African populations from Sudan and Ethiopia positions’ in the PCA plots are being drawn towards Eurasian populations, S6 Fig. ADMIXTURE analyses recapitulate this pattern where Northeast African groups share the component maximized in Middle Eastern groups (pink component at K = 6, Fig S2 Fig). The Sudanese data in our study is mainly from [15] who also investigated the time and sources of admixture in Sudanese populations. [15] investigated a simpler admixture scenario with only two putative sources, namely the Sudanese Nuer and the TSI (Tuscan) to represent the admixture of a Sudanese basal population with a Eurasian source. This is most similar to our R2 approach in which we picked the scenario with the best genomic fit (R2) and for two Eurasian sources in each run and then picked the two Eurasian sources that produced the best genomic fit (R2 value). Our findings are generally in agreement, particularly for the Eurasian admixture dates that is the primary focus of our study.
In the area of current-day Sudan and South Sudan, there is a clear divide between the Eastern Sudanic- and Semitic-speaking groups from Sudan, and the South Sudanese groups, as well as the Saharan-speaking Sudanese groups. This divide can be seen both with regards to global ancestry as well as their inferred admixture dates for their Eurasian ancestries. Dongola had been the capital of the Nubian Kingdom and the fall of Dongola in 1317 to Mameluke forces meant the start of Arab and Islamic dominance south of the borders of Egypt. Many of the Semitic speakers in our dataset have their Eurasian admixture dated to this time—around 20 generations ago. The exception is mainly the Southern Semitic speakers such as the Beni-Amer and Tygray whose dates are slightly older at around 30 generations ago. Around 30 generations ago is also the inferred date for the Ethiopian Cuschitic-speaking Afar and Oromo (though Oromo had a generation time of 21 for the best by f3). South Sudanese groups however stayed largely isolated, this pattern is evident in the ADMIXTURE analysis, as the populations around South Sudan are represented by a specific component (the black component at K = 5 and onward) with very little of the non-African (pink) component that we find in most other North-East African groups, indicating their isolation and genetic homogeneity compared to other populations.
[...]
Along the Red Sea coast of Eritrea and Sudan, we find a region of high gene flow extending into northern Ethiopia and into the Great Rift Valley, Fig 1D. This region corresponds well to the pink component in Fig 1A and 1B which seems to represent Yemeni ancestry. f3 visualizations also indicates higher geneflow from Arabian groups in this area relative to more northern and southern latitudes, Fig 2. It is also a region in which we infer some of the oldest inferred admixture dates. These observations, as well as the shared linguistics of South Semitic (as South Semitic languages that are found in Yemen, Oman, Eritrea, and Ethiopia [44]), indicate a close connection between Eritrea, and Ethiopia to the south of the Arabian peninsula and present-day Yemen. The Kingdom of Aksum (or the Aksumite Empire) encompassing Eastern Sudan, Northern Ethiopia, Eritrea, Djibouti and across the Red Sea into Yemen, thrived between the 1:th and 7:th century AD, as trade along the Red Sea increased and the trade along the Nile decreased. Both Rome and Byzantium traded with the Indian Subcontinent and artifacts from these Kingdoms can be found at Aksumite sites, [45, 46]. The Semitic-speaking Ethiopian populations also group together with the Middle Eastern populations in the UMAP analysis, S20 Fig. These admixture events could come as the result of the Red Sea trade. Aksum collapsed in the 8th century as Islam started to expand and control over the Red Sea trade shifted to the Near East [47].
Previous ancestry deconvolution studies pointed at Levantine sources for the Eurasian admixture in Northeast Africans rather than Arabic groups [4, 6]. We find that the pattern is more complex with different source populations in different regions, see Fig 1B and 1C as well as Fig 2. Levantine contributions are seen more towards the north and contributions from Arabian peninsula groups are seen more at lower latitudes, Figs 1B, 1C and 2.
[...]
The major linguistic family was the only factor that was significant (and only for the best by f3) in our ANOVA test of the available categories, S4 Table. The linear regression analysis of distance from the Levant, S21A and S21B Fig, also produced a significant fit with a negative coefficient indicating more recent admixture dates further from the Levant—this is likely driven by the younger dates for the populations in and around South Sudan. The same pattern was observed when comparing the distance to Sanaa, albeit with a smaller slope of the line and larger p-values (S21C and S21D Fig).
One possible explanation for this phenomenon could be that populations with little or no previous Eurasian admixture would have their inferred admixture date affected more by recent Eurasian admixture than populations that experienced larger admixture in the past. In other words, most, if not all, of the populations in this study have or have had admixture with populations from the Middle East during the Arab expansion, and this newer admixture is obscuring older admixture patterns. The groups with younger inferred dates in our analysis thus likely have less older admixture contributions.
Our study thus points to that the distribution of Eurasian-like ancestry in Eastern and North-Eastern African populations is mostly an effect of more recent migrations (many of them recorded in historical texts) rather than ancient events related to the advent of pastoralism in the region at large, as indicated by ancient DNA studies [5]). Identifying the impact of ancient events on populations was not feasible when the original pattern has been distorted or masked by subsequent admixture events. To fully explore the question of Eurasian admixture into Africa over larger timescales likely requires population-level aDNA, especially of the early East African hunter-gatherers such as Mota, and the various in-moving groups, including those containing Eurasian admixture.
North-Eastern Africa is a vast region with complex histories of migrations and admixture. It was not possible to identify one source or origin of Eurasian admixture in the region, rather different populations have experienced admixture at different times, at varying degrees, and from different external sources. Although slight trends were observed linked to language grouping and geography, the overall pattern proved to be complex and specific to certain population groups. Previous studies have highlighted these events in distinct regions or countries in Northern and Eastern Africa, whilst we in this study have tried to combine them with a specific emphasis on the Eurasian admixture in modern-day populations.
https://journals.plos.org/plosone/ar...l.pone.0290423
It is clear that back migrations into Northeast Africa have had a major impact on the genetic ancestries of the peoples in the region today [4–6]. Ethiopian populations, for instance, harbor a large proportion of “non-African” ancestry, as high as, ∼ 40% in some groups—see for instance the Amhara in Fig 1c in [7]. What is clear is that some current-day Northeast Africans can trace much of their ancestry from other sources than the original hunter-gatherers in the region, such as the Mota individual, an Ethiopian male who lived around 4500 years ago [8, 9]. It is also clear that these back migrations into Africa have been ongoing for a long time period. For North Africa, seven individuals from Morocco that had a high affinity to Middle Eastern populations, dated to 15 000 years ago, suggesting the possibility that similar deep-in-time admixtures might have occurred in other parts of Africa [10].
[...] They proposed a four-stage model where initially Sudanese Nilotic speakers admixed with groups with Eurasian ancestry (either from Northern Africa or the Levant) within Northeast Africa. In step two, the descendants of these groups migrated to East Africa reaching Lake Turkana by around 5 000—4 000 BP and central Tanzania by around 3000 BP and mixed with local hunter-gatherer groups throughout this process [5]. The first signs of pastoralism in East Africa coincide with these events. Thirdly the second wave of Sudanese-related groups migrated into the area and contributed to the pastoral Iron Age populations. Lastly, West African ancestry (genetically similar to Bantu speakers) appeared alongside the advent of crop farming in the region.
[...]
By leveraging one of the largest datasets of Northeast African populations to date, we aim to add resolution to Eurasian admixture in Northeast African populations. Specifically, we aim to improve the estimation of the best proxies for the origin of Eurasian admixture in modern-day Northeast African populations by using more Northeast African and Middle Eastern, and Eurasian reference populations. In this study, we follow the approach of [4, 6, 16] in that we employ local ancestry methods to identify the Eurasian fragments of East African genomes and extract those segments from the surrounding genomes, a process referred to here as ancestry-deconvolution. We then identify the current-day populations that best match those segments. We also date the events to get a better understanding of historic and prehistoric movements in the region. Using the information of possible sources for admixture and dating of these, we construct a model representative of the population history in the region. Overall we find a complex history of Eurasian admixture in Northeastern Africa, related to the spread of languages, the Muslim conquest, and trade routes along the Red Sea.
[...]
The first division in the data is between Africans and non-Africans, and it is clear that North- and East- Africans have a much larger proportion of shared ancestry with Eurasian groups than other African groups (K = 3 in S2 Fig). East African groups break away from other African groups at K = 5 via a component (black) maximized in the Nuba at 80.1%. Of particular interest for the present investigation is also the component that emerges is K = 8 (light orange) maximized in the Ari, Sabue and Gumuz populations. The Sabue is one of the few remaining hunter-gatherer groups in East Africa today and they share genetic continuity with earlier hunter-gatherer ancestry from the region [38] represented by the Mota individual [8]. The Ari, Gumuz and Sabue have been suggested to retain a high degree of ancient East African hunter-gatherer ancestry, [4, 26, 38] and our demographic analyses indicate a high degree of similarity between these populations. This component is shared with many other East African groups, displaying fractions of ancestry that show deep continuity in the region.
At K = 11 another East African component appears, maximized in the Somali populations and might represent Cushitic-related ancestry. Levantine populations separate from the Arabic populations at K = 14 and we visualized these two components using a Kriging interpolation across the study area, Fig 1. These two ancestries were the component maximized in the Lebanese Druze (dark blue) and the component highest in the Yemeni (blush pink).
To investigate the differences in affinities of our target populations to either Levantine and Yemenite ancestry we performed a f4 test. The test took the following form Yemen_YEMEN |Lebanese_Christian|Target S22 Fig. It showed significant association with Levantine for the populations north of the Sudanese BeniAmer as well as for the Oromo and Tygray from Ethiopia, the Kenyan Luhya and the Maasai from Kenya. No populations had a significantly higher association to Yemenite ancestry when compared to Levantine ancestry in this more stringent test. The test however highlight the importance of Levantine admixture for more northern populations in particular.
In our Principal Component (PC) analyses, the first PC differentiates between African and non-African groups S5 Fig. Several African populations fall on the cline between African and non-African variation, in particular North Africans, such as the Egyptians and populations from Sudan who are known to have Eurasian admixture [15]. We also observe a grouping according to linguistics where Omotic, Afro-Asiatic, and Nilo-Saharan speakers separate from each other. East African groups are positioned on the diagonal between PC 1 and PC 3, with the Ari, Sandawe, and Sabue populations forming their own cluster in the direction of the southern African Khoe-San, indicating shared ancestries between these hunter-gatherer groups S5 Fig. This cline is similar to what was found in studies using aDNA [5, 11] and is a reflection of the cline between southern and East African hunter-gather ancestry.
UMAP was also performed in the genotype information in our dataset, see S20 Fig. This analysis produces two larger clusters of populations, one consisting of West African groups, Eastern Bantu speakers, the Saharan speakers, the Nuer, Dinka, and Shiluk from Sudan. The other cluster contains mainly Middle Eastern populations and Ethiopians, as well as the remaining Sudanese populations.
[...]
As has been shown in previous studies, and indicated by our demographic inference Fig 1 and S6 Fig, there are generally four main components of modern-day East African genetic ancestry [5, 12]. Namely, basal East African hunter-gatherer ancestry, Sudanese/Nilotic ancestry, Eurasian ancestry, and West African ancestry associated with Bantu speakers. Since the aim of this study is to identify the best proxy for the source of the Eurasian ancestry of the Northeast African populations, we constructed a scenario where we could use these four ancestral sources to paint the haplotypes of our chosen target populations using MOSAIC [34]. We set up an initial scenario to try and identify the best Eurasian source to use for further analyses. In this scenario we used the following populations: To represent the basal East African hunter-gatherer ancestry we chose the Sabue [26, 38]. The Sabue has been referred to by many different names in the literature, for instance, Shabo and Chabu, here we use the name used in the original publication of the data [26]. The CEU (Utah residents with Northern and Western European ancestry) population from the 1000 genomes consortium was chosen as a proxy for general Eurasian ancestry. The Sudanese Dinka was chosen to represent Sudanese ancestry (the group that defines the black component in the ADMIXTURE analysis associated with Sudanese ancestry). The YRI (Yoruba in Ibadan, Nigeria) was used as a proxy for West African Niger-Congo and Bantu-speaker-associated ancestry.
[...]
Population structure inferences illustrate the complex genetic history of Northeast African populations. Larger patterns of genetic associations between many of the world’s distinct human lineages are reflected in Northeast African genomes. The hunter-gatherer’s ancestry highlights the deep history of the region and its people and that this ancestry remains within the East African populations. The southern part of the region has a closer genetic affinity to West African groups, a result of the Bantu expansion and several of these populations also speak Bantu languages today. That the Bantu expansion did not continue further into the region could be a result of geographical barriers such as the Ethiopian Highlands and the dry regions of the Horn of Africa, indicated by our FEEMS analysis in Fig 1D or as suggested by [15] that the Northeast African Nilotic speaking herders (such as the Dinka and Nuer), who have remained relatively isolated from other groups, could have formed a buffer against the Bantu expansion continuing further into Northeast Africa.
Eurasian admixture has had a large influence on the genomes of Northeast African groups. The Egyptian and Sudanese Copt populations for instance are genetically very similar to Middle Eastern groups rather than to other African populations. The pattern is true also for the rest of North Africa and present as early as at least 15 000 years ago [10] though not investigated here. The Copts look genetically similar to the Egyptians from Cairo, see Fig 1A and 1C, this is not unsurprising given that the Copts arrived in Sudan around 200 years ago from Egypt and seem to have lived relatively isolated since then [15]. Our admixture date for the Copts (with Eurasians) was inferred to be 27.5 for the f3 analysis and 25.7 for the R2 and around 22 generations for the Egyptians. Thus this admixture took place around the 14th century.
Further south in the region, we continue to see the impact of past Eurasian admixture. Northeast African populations from Sudan and Ethiopia positions’ in the PCA plots are being drawn towards Eurasian populations, S6 Fig. ADMIXTURE analyses recapitulate this pattern where Northeast African groups share the component maximized in Middle Eastern groups (pink component at K = 6, Fig S2 Fig). The Sudanese data in our study is mainly from [15] who also investigated the time and sources of admixture in Sudanese populations. [15] investigated a simpler admixture scenario with only two putative sources, namely the Sudanese Nuer and the TSI (Tuscan) to represent the admixture of a Sudanese basal population with a Eurasian source. This is most similar to our R2 approach in which we picked the scenario with the best genomic fit (R2) and for two Eurasian sources in each run and then picked the two Eurasian sources that produced the best genomic fit (R2 value). Our findings are generally in agreement, particularly for the Eurasian admixture dates that is the primary focus of our study.
In the area of current-day Sudan and South Sudan, there is a clear divide between the Eastern Sudanic- and Semitic-speaking groups from Sudan, and the South Sudanese groups, as well as the Saharan-speaking Sudanese groups. This divide can be seen both with regards to global ancestry as well as their inferred admixture dates for their Eurasian ancestries. Dongola had been the capital of the Nubian Kingdom and the fall of Dongola in 1317 to Mameluke forces meant the start of Arab and Islamic dominance south of the borders of Egypt. Many of the Semitic speakers in our dataset have their Eurasian admixture dated to this time—around 20 generations ago. The exception is mainly the Southern Semitic speakers such as the Beni-Amer and Tygray whose dates are slightly older at around 30 generations ago. Around 30 generations ago is also the inferred date for the Ethiopian Cuschitic-speaking Afar and Oromo (though Oromo had a generation time of 21 for the best by f3). South Sudanese groups however stayed largely isolated, this pattern is evident in the ADMIXTURE analysis, as the populations around South Sudan are represented by a specific component (the black component at K = 5 and onward) with very little of the non-African (pink) component that we find in most other North-East African groups, indicating their isolation and genetic homogeneity compared to other populations.
[...]
Along the Red Sea coast of Eritrea and Sudan, we find a region of high gene flow extending into northern Ethiopia and into the Great Rift Valley, Fig 1D. This region corresponds well to the pink component in Fig 1A and 1B which seems to represent Yemeni ancestry. f3 visualizations also indicates higher geneflow from Arabian groups in this area relative to more northern and southern latitudes, Fig 2. It is also a region in which we infer some of the oldest inferred admixture dates. These observations, as well as the shared linguistics of South Semitic (as South Semitic languages that are found in Yemen, Oman, Eritrea, and Ethiopia [44]), indicate a close connection between Eritrea, and Ethiopia to the south of the Arabian peninsula and present-day Yemen. The Kingdom of Aksum (or the Aksumite Empire) encompassing Eastern Sudan, Northern Ethiopia, Eritrea, Djibouti and across the Red Sea into Yemen, thrived between the 1:th and 7:th century AD, as trade along the Red Sea increased and the trade along the Nile decreased. Both Rome and Byzantium traded with the Indian Subcontinent and artifacts from these Kingdoms can be found at Aksumite sites, [45, 46]. The Semitic-speaking Ethiopian populations also group together with the Middle Eastern populations in the UMAP analysis, S20 Fig. These admixture events could come as the result of the Red Sea trade. Aksum collapsed in the 8th century as Islam started to expand and control over the Red Sea trade shifted to the Near East [47].
Previous ancestry deconvolution studies pointed at Levantine sources for the Eurasian admixture in Northeast Africans rather than Arabic groups [4, 6]. We find that the pattern is more complex with different source populations in different regions, see Fig 1B and 1C as well as Fig 2. Levantine contributions are seen more towards the north and contributions from Arabian peninsula groups are seen more at lower latitudes, Figs 1B, 1C and 2.
[...]
The major linguistic family was the only factor that was significant (and only for the best by f3) in our ANOVA test of the available categories, S4 Table. The linear regression analysis of distance from the Levant, S21A and S21B Fig, also produced a significant fit with a negative coefficient indicating more recent admixture dates further from the Levant—this is likely driven by the younger dates for the populations in and around South Sudan. The same pattern was observed when comparing the distance to Sanaa, albeit with a smaller slope of the line and larger p-values (S21C and S21D Fig).
One possible explanation for this phenomenon could be that populations with little or no previous Eurasian admixture would have their inferred admixture date affected more by recent Eurasian admixture than populations that experienced larger admixture in the past. In other words, most, if not all, of the populations in this study have or have had admixture with populations from the Middle East during the Arab expansion, and this newer admixture is obscuring older admixture patterns. The groups with younger inferred dates in our analysis thus likely have less older admixture contributions.
Our study thus points to that the distribution of Eurasian-like ancestry in Eastern and North-Eastern African populations is mostly an effect of more recent migrations (many of them recorded in historical texts) rather than ancient events related to the advent of pastoralism in the region at large, as indicated by ancient DNA studies [5]). Identifying the impact of ancient events on populations was not feasible when the original pattern has been distorted or masked by subsequent admixture events. To fully explore the question of Eurasian admixture into Africa over larger timescales likely requires population-level aDNA, especially of the early East African hunter-gatherers such as Mota, and the various in-moving groups, including those containing Eurasian admixture.
North-Eastern Africa is a vast region with complex histories of migrations and admixture. It was not possible to identify one source or origin of Eurasian admixture in the region, rather different populations have experienced admixture at different times, at varying degrees, and from different external sources. Although slight trends were observed linked to language grouping and geography, the overall pattern proved to be complex and specific to certain population groups. Previous studies have highlighted these events in distinct regions or countries in Northern and Eastern Africa, whilst we in this study have tried to combine them with a specific emphasis on the Eurasian admixture in modern-day populations.
https://journals.plos.org/plosone/ar...l.pone.0290423