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DNA Is The Key To Unlocking Our Ancient African Past - 2020
African aDNA studies are few to date, as early aDNA research focused on Europe, and early DNA sequencing technology was not yet developed enough to be able to handle samples from warm climates. However, in recent years molecular genetics methods and tools have continued to improve, so that not only have researchers had more success with remains preserved in poor conditions, but aDNA has been successfully extracted from far more ancient remains compared with even a decade ago. At the time of writing, eight studies in total have published ancient genomic DNA results from Africa, four studies with aDNA from North Africa and four studies with aDNA from sub-Saharan Africa. Human population history in North Africa has a unique standing in Africa. Modern-day groups are largely related to Eurasian and Middle Eastern populations with minimal levels of genetic contributions from sub-Saharan Africa (blue dots, Figure 3). is was suggested to be the result of back to Africa migrations during the Neolithic period, and migrations related to the introduction of farming practices to North Africa. aDNA studies of early Neolithic (~7000 before present [BP]) Moroccan remains (blue skulls, Figure 3) indeed found the individuals to be most genetically similar to Anatolian farmers and Natufians from the Middle East, suggesting a potential early westward migration of these groups. However, a more recent study on 15,000 BP remains from Morocco demonstrated that northern Africa received significant amounts of gene ow from Eurasia predating the start of the Holocene. Gene flow from the south, across the Sahara into North Africa, was limited, and seemed to have occurred only recently. This was apparent as low levels of genetic ancestry from sub-Saharan groups in ancient North African individuals dated to the Neolithic. Mummies from the easternmost part of North Africa also demonstrated that admixture between sub-Saharan Africans and northern Africans was recent, in that people from ancient Egypt (~3400BP) displayed less sub-Saharan admixture compared with present-day Egyptians.
Modern and aDNA studies on sub-Saharan Africa indicated that the history of this part of the continent may be divided into two very different phases. Before the invention and spread of farming practices in Africa, hunter-gatherer groups were related in an ‘isolation-by-distance’ fashion influenced by geography. This means that groups were most closely related to their neighbours, and less related to groups that were geographically further away. This stands in stark contrast to the large population movements that followed the invention of farming practices in Africa. As farming populations rapidly spread across the whole continent, their genetic signature ‘erased’ the ‘isolation-by-distance’ pattern observed in hunter-gatherer populations. Currently, it is believed that three regions in Africa developed agriculture independently of one another: the Sahara/Sahel (around 7000 BP), the Ethiopian highlands (~7000–4000 BP) and western Africa (~5000–3000 BP). The Nile River Valley is thought to have adopted agriculture (~7000–8000 BP) from the Neolithic transition in the Middle East (~10,000–11,000 BP). From these centres of origin, farming practices spread to the rest of Africa, with domesticated animals reaching the southern tip of Africa around 2000 BP and crop farming around 1800 BP.
The first ancient nuclear genome to be sequenced from sub-Saharan Africa was that of a 4500-year-old Ethiopian individual (named Mota, Figure 3). This genome revealed that East African populations younger than 4500 years (brown dots and brown skulls, Figure 3) were influenced by a single or multiple migrations from outside Africa back into the continent of populations who were genetically similar to early Neolithic farmers from western Eurasia. The PCA demonstrates this (Figure 3B), where current-day East African populations (brown dots) and ancient East African individuals from farming contexts (brown skulls) lie between the Mota individual (a representative non-admixed East African hunter-gatherer) and non-Africans (blue dots). This study clearly indicated migration from Eurasia back into East Africa after 4500 years ago, and showed that current-day East African groups’ ancestries link them to their East African ancestors as well as Eurasian groups that migrated back into Africa. This finding was was confirmed multiple times in subsequent aDNA studies that included ancient East African individuals. A study that sequenced 16 ancient Africans across East and southern Africa showed that ancient herders carrying this mixed East African-Eurasian ancestry migrated all the way down into southern Africa. These groups introduced herding practices to the south of the continent (brown skulls and dots in eastern and southern Africa, Figure 3A and B). The ancient genomes also revealed how hunter-gatherer genetic ancestry looked before the spread of farming through the continent. The ancestry of hunter-gatherer populations of East and southern Africa (yellow to red skull cline a gradation in biological features over geographic space, on PCA – Figure 3B) fit on a cline, where neighbouring groups were more related to one another than groups further away. Subsequent African demographic history was ever more complex, with repeated gene flow between different groups, and varying levels of population replacement by especially western African Bantu-speaking farmers. The Bantu expansion is one of the largest expansion events of farmers globally and began around ~5000–3000 BP in western Africa (in the region of current eastern Nigeria and western Cameroon). It is visible in the archaeological record via increased sedentism, the spread of agricultural practices and the use of iron. Today, the majority of sub-Saharan Africans speak one of ~500 closely related Bantu languages despite their distribution over an area of ~500,000 km2. Earlier genetic studies indicated that the current distribution of Bantu-speaking populations is largely a consequence of the movement of people (demic diffusion) rather than a diffusion of only language. is has been confirmed by aDNA studies; i.e., where ancient remains found in Iron Age archaeological contexts in East and southern Africa (grey skulls on Figure 3A) group genetically with current-day West African populations on the PCA (Figure 3B). The effects of the Bantu expansion may also be seen in aDNA studies on southern Africa. A study that sequenced the nuclear genomes of seven ancient southern African individuals, three dating to the Late Stone Age (2000 years old – red skulls in southern Africa – Figure 3A), and four dating to the Iron Age (300 to 400 years old – grey skulls in southern Africa – Figure 3A) found that the Later Stone Age individuals were related to current-day Khoe-San hunter-gatherer individuals (red dots) and the Iron Age individuals to current-day West Africans (grey dots). The study confirmed extensive population replacement in southern Africa, where Later Stone Age ancestors of the Khoe-San hunter-gatherers were replaced by incoming Bantu-speaking farmer groups with West African genetic ancestry. Interestingly, one of the 2000-year-old individuals related to Khoe-San groups yielded enough ancient DNA to reach 13× coverage, a very high yield with regards to aDNA. When using this high coverage ancient individual as a reference, it was revealed that all modern Khoe-San groups have 9–22% admixture from the admixed group of Eurasian-East African ancestry that introduced herding into southern Africa. This can be noted on the PCA (Figure 3B) as a shift in modern-day Khoe-San groups (red dots) towards the East African side of the PCA. The high coverage ancient individual was further compared with other Africans to re-estimate the time when the first modern human groups genetically diverged from one another. Whereas past research estimated a divergence time of 100,000 years, (200,000, using the updated human mutation rate) using the non-admixed Stone Age individual pushed back the divergence time to between 260,000–350,000 years, towards the genesis of the Middle Stone Age when humans became morphologically and behaviourally modern. African genomes and future aDNA studies in Africa will continue to clarify the picture of our deep genetic history and bring us closer to answering the questions of human origins in Africa. Concurrently, it will continue to clarify the large-scale but complex movements associated with the spread of farming practices in Africa.
https://watermark.silverchair.com/bi...O56wiiC4plZRPM
African aDNA studies are few to date, as early aDNA research focused on Europe, and early DNA sequencing technology was not yet developed enough to be able to handle samples from warm climates. However, in recent years molecular genetics methods and tools have continued to improve, so that not only have researchers had more success with remains preserved in poor conditions, but aDNA has been successfully extracted from far more ancient remains compared with even a decade ago. At the time of writing, eight studies in total have published ancient genomic DNA results from Africa, four studies with aDNA from North Africa and four studies with aDNA from sub-Saharan Africa. Human population history in North Africa has a unique standing in Africa. Modern-day groups are largely related to Eurasian and Middle Eastern populations with minimal levels of genetic contributions from sub-Saharan Africa (blue dots, Figure 3). is was suggested to be the result of back to Africa migrations during the Neolithic period, and migrations related to the introduction of farming practices to North Africa. aDNA studies of early Neolithic (~7000 before present [BP]) Moroccan remains (blue skulls, Figure 3) indeed found the individuals to be most genetically similar to Anatolian farmers and Natufians from the Middle East, suggesting a potential early westward migration of these groups. However, a more recent study on 15,000 BP remains from Morocco demonstrated that northern Africa received significant amounts of gene ow from Eurasia predating the start of the Holocene. Gene flow from the south, across the Sahara into North Africa, was limited, and seemed to have occurred only recently. This was apparent as low levels of genetic ancestry from sub-Saharan groups in ancient North African individuals dated to the Neolithic. Mummies from the easternmost part of North Africa also demonstrated that admixture between sub-Saharan Africans and northern Africans was recent, in that people from ancient Egypt (~3400BP) displayed less sub-Saharan admixture compared with present-day Egyptians.
Modern and aDNA studies on sub-Saharan Africa indicated that the history of this part of the continent may be divided into two very different phases. Before the invention and spread of farming practices in Africa, hunter-gatherer groups were related in an ‘isolation-by-distance’ fashion influenced by geography. This means that groups were most closely related to their neighbours, and less related to groups that were geographically further away. This stands in stark contrast to the large population movements that followed the invention of farming practices in Africa. As farming populations rapidly spread across the whole continent, their genetic signature ‘erased’ the ‘isolation-by-distance’ pattern observed in hunter-gatherer populations. Currently, it is believed that three regions in Africa developed agriculture independently of one another: the Sahara/Sahel (around 7000 BP), the Ethiopian highlands (~7000–4000 BP) and western Africa (~5000–3000 BP). The Nile River Valley is thought to have adopted agriculture (~7000–8000 BP) from the Neolithic transition in the Middle East (~10,000–11,000 BP). From these centres of origin, farming practices spread to the rest of Africa, with domesticated animals reaching the southern tip of Africa around 2000 BP and crop farming around 1800 BP.
The first ancient nuclear genome to be sequenced from sub-Saharan Africa was that of a 4500-year-old Ethiopian individual (named Mota, Figure 3). This genome revealed that East African populations younger than 4500 years (brown dots and brown skulls, Figure 3) were influenced by a single or multiple migrations from outside Africa back into the continent of populations who were genetically similar to early Neolithic farmers from western Eurasia. The PCA demonstrates this (Figure 3B), where current-day East African populations (brown dots) and ancient East African individuals from farming contexts (brown skulls) lie between the Mota individual (a representative non-admixed East African hunter-gatherer) and non-Africans (blue dots). This study clearly indicated migration from Eurasia back into East Africa after 4500 years ago, and showed that current-day East African groups’ ancestries link them to their East African ancestors as well as Eurasian groups that migrated back into Africa. This finding was was confirmed multiple times in subsequent aDNA studies that included ancient East African individuals. A study that sequenced 16 ancient Africans across East and southern Africa showed that ancient herders carrying this mixed East African-Eurasian ancestry migrated all the way down into southern Africa. These groups introduced herding practices to the south of the continent (brown skulls and dots in eastern and southern Africa, Figure 3A and B). The ancient genomes also revealed how hunter-gatherer genetic ancestry looked before the spread of farming through the continent. The ancestry of hunter-gatherer populations of East and southern Africa (yellow to red skull cline a gradation in biological features over geographic space, on PCA – Figure 3B) fit on a cline, where neighbouring groups were more related to one another than groups further away. Subsequent African demographic history was ever more complex, with repeated gene flow between different groups, and varying levels of population replacement by especially western African Bantu-speaking farmers. The Bantu expansion is one of the largest expansion events of farmers globally and began around ~5000–3000 BP in western Africa (in the region of current eastern Nigeria and western Cameroon). It is visible in the archaeological record via increased sedentism, the spread of agricultural practices and the use of iron. Today, the majority of sub-Saharan Africans speak one of ~500 closely related Bantu languages despite their distribution over an area of ~500,000 km2. Earlier genetic studies indicated that the current distribution of Bantu-speaking populations is largely a consequence of the movement of people (demic diffusion) rather than a diffusion of only language. is has been confirmed by aDNA studies; i.e., where ancient remains found in Iron Age archaeological contexts in East and southern Africa (grey skulls on Figure 3A) group genetically with current-day West African populations on the PCA (Figure 3B). The effects of the Bantu expansion may also be seen in aDNA studies on southern Africa. A study that sequenced the nuclear genomes of seven ancient southern African individuals, three dating to the Late Stone Age (2000 years old – red skulls in southern Africa – Figure 3A), and four dating to the Iron Age (300 to 400 years old – grey skulls in southern Africa – Figure 3A) found that the Later Stone Age individuals were related to current-day Khoe-San hunter-gatherer individuals (red dots) and the Iron Age individuals to current-day West Africans (grey dots). The study confirmed extensive population replacement in southern Africa, where Later Stone Age ancestors of the Khoe-San hunter-gatherers were replaced by incoming Bantu-speaking farmer groups with West African genetic ancestry. Interestingly, one of the 2000-year-old individuals related to Khoe-San groups yielded enough ancient DNA to reach 13× coverage, a very high yield with regards to aDNA. When using this high coverage ancient individual as a reference, it was revealed that all modern Khoe-San groups have 9–22% admixture from the admixed group of Eurasian-East African ancestry that introduced herding into southern Africa. This can be noted on the PCA (Figure 3B) as a shift in modern-day Khoe-San groups (red dots) towards the East African side of the PCA. The high coverage ancient individual was further compared with other Africans to re-estimate the time when the first modern human groups genetically diverged from one another. Whereas past research estimated a divergence time of 100,000 years, (200,000, using the updated human mutation rate) using the non-admixed Stone Age individual pushed back the divergence time to between 260,000–350,000 years, towards the genesis of the Middle Stone Age when humans became morphologically and behaviourally modern. African genomes and future aDNA studies in Africa will continue to clarify the picture of our deep genetic history and bring us closer to answering the questions of human origins in Africa. Concurrently, it will continue to clarify the large-scale but complex movements associated with the spread of farming practices in Africa.
https://watermark.silverchair.com/bi...O56wiiC4plZRPM