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Post by Admin on Feb 27, 2017 20:19:14 GMT
Figure 4. Genome-wide population structure. A) Principal component analysis of ∼44,000 SNPs showing the top two components. B) Maximum likelihood tree showing populations relationships. We constructed trees that infer population relationships using TreeMix [62]. This method estimates both population splits and the possibility of population mixture. First, we build a maximum-likelihood tree setting the position of the root at the Yoruba (Figure 4B). South Moroccans and Saharawi appear close to Yoruba while Egyptians are on a branch leading to Middle Easterners and Basque. Next, we set TreeMix to allow migration edges (m) and test by increasing m sequentially up to m = 20. The initial tree structure remains mostly unchanged when migration edges are added. All North Africans except Tunisians appear admixed from an ancestral population to Yoruba. For figure clarity, we show plot m = 6 and the migration edges weights (Figure S4A). When m>6 the tree shows admixture among North Africans as well admixture with Middle Easterners/Europeans. To visually identify aspects of ancestry not captured by the tree at m = 6, we plot the residuals of the model's fit (Figure S4B). Positive residuals indicate populations where the fit might be improved by adding additional edges. TreeMix results show that relatedness of the tested populations cannot be explained by a simple tree; therefore we apply a 3-population test to all populations to measure treeness in the previous results. A negative value from ƒ3(A;B,C) implies that population A derives from at least two different groups that are related to B and C. Table S6 shows the two lowest values for each North African population. All North Africans except Tunisians appear to be a mixture of populations related to Yoruba and Eurasians (Basque and Lebanese Christians). Tunisians, Yoruba, Basque, and Lebanese Christians appear to be related to other groups by a simple tree implying a history of divergence without subsequent mixture. Our results from the maternally inherited mtDNA genome [45] and the paternally inherited Y-chromosome show that both males and females in North Africa underwent a similar admixture history and both are today a mixture of African and Eurasian lineages with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We should note here that although the pattern of admixture with the surrounding regions is similar in males and females, the demographic processes or historical events driving these admixtures could have been different. Also, differential sexual gene flow might have resulted in differences in the proportions of admixture components resulting in source lineage frequency differences [45]. Nevertheless, we show that a generally similar admixture history in male and female phylogenies consequently reflected on the entire genome diversity, resulting in genome-wide SNPs showing comparable patterns to uniparental markers, placing North Africans close to Eurasians. Furthermore, admixture tests using genome-wide SNPs also show that most North Africans are a mixture of populations related to current Africans and Eurasians. Although recent cultural expansions from the Middle East, like the Islamic expansion, could have introduced new lineages to North Africa and facilitated admixture between populations from both regions, our results show that the North African component mostly formed much earlier. This is shown in the admixture tests where Basque and Lebanese Christians but not Lebanese Muslims formed potential source populations to North Africans. In particular, Lebanese Christians were shown to have been isolated for at least the last 2,000 years and were proposed to be genetically close to the ancestral population of the Levant region from which current Europeans diverged ∼15,900–9,100 ya between the last glacial warming and the start of the Neolithic [26]. Our coalescence time estimate for the paternal lineages in North Africa is ∼15,000 ya for most populations. These dates coincide with major environmental changes in North Africa following the full glacial hyperarid conditions during the Last Glacial Maxima. Humid conditions started in North Africa ∼14,500 ya transforming the area into a verdant landscape vegetated with annual grasses and shrubs which attracted hunter-gatherers who spread into the region [64]–[66]. This period was accompanied by cultural connection between the Middle East and North Africa as suggested by the lithic similarity between the regions [65]. Median joining (MJ) networks. Plotted are MJ networks of Y-STR haplotypes within haplogroups A) E-M78, B) E-M81, C) J-M172, and D) J-M267. The circle sizes are proportional to the haplotype frequencies. The smallest area is equivalent to one individual. Branch lengths are proportional to the number of mutational steps separating two haplotypes. Although most North Africans appear as an admixture of populations from the surrounding regions, the Tunisian Berbers show long periods of genetic isolation, allowing a distinctive genetic component to evolve. Unlike other North Africans, our admixture tests propose that Berbers diverged from surrounding populations without subsequent mixture. We show that coalescence time estimate from paternal lineages are pushed back ∼15,000 years when Tunisians (Berbers and general population) are included in the analyses suggesting an early upper Paleolithic ancestral population with most North Africans (∼30,000–44,000 ya). There has been recent interest in North Africa as a source for modern human migrations after most early research studying the origins of Homo sapiens focused on the fossils of East Africa. Recent studies of hominin fossils from northwestern Africa present strong evidence of resemblances and possible evolutionary connections with fossils representing migrations out of Africa between 130,000 and 40,000 ya [67]. Our analysis of modern North Africans shows that most populations emerged recently from admixture of Africans and Eurasians and therefore are ineffective in resolving questions about ancient human expansions. Genetic isolates, like the Tunisian Berbers analyzed here, could provide some insights on early human movements in North Africa. However, information from today's populations is limited by factors such as migration, admixture, drift, and selection pressure. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum with no traces of genetic continuity with the first human settlers in the region. Therefore, reconstruction of modern humans' history would probably require analysis of indigenous ancient DNA from human fossils. Fadhlaoui-Zid K, Haber M, Martínez-Cruz B, Zalloua P, Benammar Elgaaied A, Comas D (2013) Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa. PLoS ONE 8(11): e80293.
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Post by Admin on Sept 6, 2017 19:09:21 GMT
The first humans arrived in Indonesia thousands of years before previously thought—which could mean they were present for an eruption at the Lake Toba supervolcano just over 71,000 years ago. Newly analyzed fossil evidence also places these early humans in rainforest environments, causing a major rethink of how these people migrated across the land after leaving Africa about 30,000 years earlier. Researchers have long theorized that early humans likely moved along the coast because it was safer and had better resources than the jungle terrain. How and when humans dispersed across the globe are ongoing questions that grow more difficult to answer as new fossil evidence is unearthed. For example, the earliest Homo sapiens fossils ever found were recently discovered in Morocco—far away from the parts of south and east Africa we tend to think of as the “cradle of humanity.”
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Post by Admin on Sept 7, 2017 19:14:28 GMT
In a study published in the journal Nature, scientists have now accurately dated two human teeth first discovered on the island of Sumatra in the late 19th century, showing our ancestors were living there between 73,000 and 63,000 years ago. Genetic studies have placed humans in Southeast Asia by 60,000 years ago, but the previous oldest fossil evidence dated to just 45,000 years. This new evidence pushes the timeline back thousands of years farther. Figure 2: Lida Ajer breccia; structure and stratigraphic relationships The teeth were found in the Lida Ajer cave in the Padang Highlands of Sumatra. They are the first evidence of humans in Indonesia and the first evidence of humans occupying a rainforest environment. The finding has surprised archaeologists. Until now, Kira Westaway, an environmental scientist at Macquarie University in Australia, tells Newsweek, “The earliest evidence for modern humans using rainforests environments [was from] around 45,000 years ago in Niah Cave, Borneo.” These regions seem an unlikely place for early humans to live. “Rainforests are difficult environments to live in,” says Westaway. “They require technological innovations and sophisticated hunting techniques for survival.” This research reveals that people inhabited the rainforest far earlier than previously suspected. “Finding an early modern human presence in a rainforest location is remarkable as it suggests that these skills were in place by this time,” says Westaway. The team also highlights the potential link with the supervolcano eruption at Lake Toba during this period. Had these early humans arrived at the upper limit of the new timeline—73,000 years ago—they would have been there for the event. Westaway explains that a recent recalibration indicates the Toba eruption occurred 71,600 years ago. “This means that there is a slim chance that the modern humans arrived in the region just before the event—in which case they would have been affected by the extensive volcanic ash cloud and the devastating effects on the environment,” However, Westaway acknowledges, “it’s more probable they arrived after the event.” Figure 3: A summary of the results from the Lida Ajer cave analysis. Genetic evidence for anatomically modern humans (AMH) out of Africa before 75 thousand years ago (ka)1 and in island southeast Asia (ISEA) before 60 ka (93–61 ka)2 predates accepted archaeological records of occupation in the region3. Claims that AMH arrived in ISEA before 60 ka (ref. 4) have been supported only by equivocal5 or non-skeletal evidence6. AMH evidence from this period is rare and lacks robust chronologies owing to a lack of direct dating applications7, poor preservation and/or excavation strategies8 and questionable taxonomic identifications9. Lida Ajer is a Sumatran Pleistocene cave with a rich rainforest fauna associated with fossil human teeth7, 10. The importance of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertainties regarding the age of the deposit, therefore it is rarely considered in models of human dispersal. Here we reinvestigate Lida Ajer to identify the teeth confidently and establish a robust chronology using an integrated dating approach. Using enamel–dentine junction morphology, enamel thickness and comparative morphology, we show that the teeth are unequivocally AMH. Luminescence and uranium-series techniques applied to bone-bearing sediments and speleothems, and coupled uranium-series and electron spin resonance dating of mammalian teeth, place modern humans in Sumatra between 73 and 63 ka. This age is consistent with biostratigraphic estimations7, palaeoclimate and sea-level reconstructions, and genetic evidence for a pre-60 ka arrival of AMH into ISEA2. Lida Ajer represents, to our knowledge, the earliest evidence of rainforest occupation by AMH, and underscores the importance of reassessing the timing and environmental context of the dispersal of modern humans out of Africa. Nature (2017) doi:10.1038/nature23452
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Post by Admin on Oct 3, 2017 19:32:35 GMT
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. Fig 1. Overview of populations investigated in this study. Following quality filtering (~3.9 million SNPs remained, see SI), we merged the Sudan and South Sudan genotype dataset to relevant published genotype datasets from neighboring and other relevant populations [19–24] (Fig 1A, S1 Table) in order to bring the genetic variation into a regional and global context (SI, Method Section). This dataset is likely the most comprehensive dataset assembled to date of northeast African populations. Northeast African individuals and groups displayed marked levels of population structure and differentiation (Figs 1B and 2, S1–S6 Figs), and some groups showed strong affinities to groups from other areas, including Europe, Middle East and western Africa (Fig 2, S1–S6 Figs). Focusing on population structure in Sudan and South Sudan, we found that genetic variation was correlated with geography (r = 0.39, p<0.01, Mantel test), to a greater extent than to linguistic classification (r = 0.28, p<0.01), indicating that geography drives population structure in the area. Several populations, in particular from the North and East of Sudan displayed genetic affinities to non-Africans, which is consistent with recent admixture into these groups (Fig 2, S1–S6 Figs). This admixture unifies the Nubian, Arabic and Beja populations from the north, and it is almost completely absent in the western Sudanese and South Sudanese populations.
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Post by Admin on Oct 4, 2017 18:58:31 GMT
Fig 2. Inferred admixture fractions [51] for difference choices of number of clusters. 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. Fig 3. Maps showing the amount of Nilotic and Eurasian admixture and admixture dates in investigated populations. 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. Little admixture in northeast Africa with Bantu-speaking groups 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 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.
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