quote:Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the site of Kadruka. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kilometres away. Our findings support established models for the southwards dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide the first direct evidence for a genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
posted
Good. Now we need a mature and professional aDNA study that will compare available aDNA from Ancient Egypt and the Levant of similar age, and this genome and PN genomes from Tanzania and Kenya to see which ancient populations were closest to Ancient Egypt.
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quote:Originally posted by Mansamusa: Good.Now we need a mature and professional aDNA study that will compare available aDNA from Ancient Egypt and the Levant of similar age, and the PN genomes from Tanzania and Kenya to see which ancient populations were closest to Ancient Egypt.
there is one 4K mummy head tested, a male Djehutynakht. "Overlord of the Hare nome" (the 15th nome of Upper Egypt) during the very end of the 11th Dynasty or the early 12th Dynast They were only able to determine mtDNA U5, but not paternal
"This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens."
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quote:Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the site of Kadruka. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kilometres away. Our findings support established models for the southwards dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide the first direct evidence for a genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
So are they implying this that this population is the source of the Savanna Pastoral Neolithic (which was discussed here and here)??
-------------------- Mahirap gisingin ang nagtutulog-tulugan. Posts: 26238 | From: Atlanta, Georgia, USA | Registered: Feb 2005
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quote:Originally posted by Mansamusa: Good.Now we need a mature and professional aDNA study that will compare available aDNA from Ancient Egypt and the Levant of similar age, and the PN genomes from Tanzania and Kenya to see which ancient populations were closest to Ancient Egypt.
there is one 4K mummy head tested, a male Djehutynakht. "Overlord of the Hare nome" (the 15th nome of Upper Egypt) during the very end of the 11th Dynasty or the early 12th Dynast They were only able to determine mtDNA U5, but not paternal
"This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens."
Bro, that's not even a whole-genome sample and has no relevance to the point being made. Correct me if I am wrong.
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Djehutynakht is a 4,000 year old mummy. The mummy has well preserved hair which could be analyzed by this new method. That could be compared to the 4000-year-old individual from Sudan. One study on the Siwa indicated 18% haplogroup U5 whilst U6 zero U4 was reported by Kefi at Taforalt Maybe Y DNA results could be extracted from this mummy's hair
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posted
I wonder what they mean by indistinguishable, they couldn't have possibly had that much Mota-like ancestry, so it either means indistinguishable in terms of Natufian + Neolithic Farmer-like to total SSA proportions or they mean indistinguishable from the perspective of being a source, so once the Mota is accounted for its identical.
In the former scenario, it will be 50-55% Natufian/Taf like + Levantine Farmer and the rest Dinka-like. In the latter, it'd be 70-75% Natufian/Taf + Levantine Farmer, so 25-30% Dinka.
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quote:Originally posted by SlimJim: I wonder what they mean by indistinguishable, they couldn't have possibly had that much Mota-like ancestry, so it either means indistinguishable in terms of Natufian + Neolithic Farmer-like to total SSA proportions or they mean indistinguishable from the perspective of being a source, so once the Mota is accounted for its identical.
In the former scenario, it will be 50-55% Natufian/Taf like + Levantine Farmer and the rest Dinka-like. In the latter, it'd be 70-75% Natufian/Taf + Levantine Farmer, so 25-30% Dinka.
Just guessing, but they likely used recent "ancient" DNA from Kenya:
quote: In our new research, our team sequenced the genomes of 41 people buried at archaeological sites in Kenya and Tanzania, more than doubling the number of ancient individuals with genome-wide data from sub-Saharan Africa. We obtained radiocarbon dates from the bones of 35 of these people—important because direct dates on human remains are virtually nonexistent in East Africa. Working as a team meant forging partnerships among curators, archaeologists, and geneticists, despite our different work cultures and specialized vocabularies.
The people we studied were buried with a wide variety of archaeological evidence linking them to foraging, pastoralism, and, in one case, farming. These associations are not airtight—people may have shifted between foraging and herding—but we rely on cultural traditions, artifact types, and food remains to try to understand how people were getting their meals.
After we grouped individuals based on the lifestyles we inferred from associated archaeological evidence, we compared their ancient genomes to those of hundreds of living people and a few dozen ancient people from across Africa and the adjacent Middle East. We were looking for patterns of genetic relatedness.
Some of our ancient samples did not resemble other known groups. Despite major efforts to document the vast genetic variation in Africa, there’s a long way to go. There are still gaps in modern data and no ancient data at all for much of the continent. Although we can identify groups that share genetic similarities with the ancient herders, this picture no doubt will become clearer as more data become available.
Published: 03 December 2022 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists
Ke Wang, Madeleine Bleasdale, Charles Le Moyne, Cacilia Freund, Johannes Krause, Nicole Boivin & Stephan Schiffels Scientific Reports volume 12, Article number: 20939 (2022)
Abstract Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.
Here, we extract DNA from five specimens (including petrous, teeth and hair) deriving from four individuals from middle Holocene cemeteries in the Dongola Reach of Upper Nubia, northern Sudan. Selected samples for this study represent three individuals from the early 7th millennium BP Neolithic site of Kadruka 21, and one Kerma period individual, directly dated to 4033 cal. BP, from Kadruka 1. Of all the tissues and samples tested, only one sample of preserved hair, from the Kerma period individual, yielded a sufficient amount of authentic ancient human DNA to study.
The very low coverage data resulting from this unique sample posed a challenge for downstream population genetic analyses. Nevertheless, we see from f3-statistics that this individual, from a rural agro-pastoral population linked with the Kerma culture of Upper Nubia16, shares close genetic affinity with Levantine groups. Moreover, we could show that this individual is genetically indistinguishable from early Pastoral Neolithic individuals dated to 4000BP living over 2500 km away in Kenya and Tanzania, even when correcting for relatively large standard errors in population genetic estimates due to the low coverage.
The PCA shows Sudan_Kadruka1_4000BP located close to previously published early pastoralists in eastern Africa4,5, such as Kenya_EarlyPastoral_N (3800–4000 calBP) and Kenya_Pastoral_Neolithic (1500–3000 calBP). Kenya_EarlyPastoral_N is a group of two pastoralist individuals dated to the early stage of the eastern African Pastoral Neolithic, both of whom are genetically derived from admixture between two early northeastern African-related ancestries from Sudan and Northern Africa/Levant
This close relatedness to early pastoral populations in eastern Africa is consistent with archaeological evidence for the dispersal of herding populations southwards along the Nile River Valley following their establishment in the Kadruka region from the early 7th millennium BP29,30, although we caution that inference from a single sample can at best be tentative.
The high affinity of the Kerma period individual from Kadruka 1 with Neolithic pastoral groups far to the south, and genetic indistinguishability of their sequenced DNA, would be consistent with this sample representing a possible genetic source population for the earliest eastern African pastoralists who settled in the Rift Valley. This in turn would point to a high degree of mobility of pastoralists between the Middle Nile Valley and present-day Kenya, potentially before or around the Pastoral Neolithic. It would imply that the southward dispersal of pastoralists from the Middle Nile Valley did not involve genetic exchange with pre-existing human groups along the migration route, particularly local foragers, and may therefore have been relatively rapid. Indeed, archaeological research suggests that dispersals were likely driven in part by increasing population pressure and regional aridification, with a marked period of aridity in Upper Nubia preceding the first appearance of pastoral groups in the Turkana Basin of eastern Africa at 5000 BP29,30,31. These early eastern African pastoralists at sites like Lothagam in the Turkana Basin29,32, while featuring regional forms of cultural expression, also broadly maintained traditions of monumental mortuary expression, as well as traditions of burial with elaborate grave goods for which the Neolithic and Kerma period cemeteries of the Middle Nile Valley, including Kadruka 1, are recognised9.
While much archaeogenetic research in Africa has focused on the Neolithic populations of eastern Africa, their source populations have, from a genetic standpoint, remained elusive. Highlighting the need for additional aDNA from ancient northeastern African populations, the aDNA recovered from ancient human hair in this study provides important new genetic data relevant to the detailed reconstruction of early pastoral dispersals from northeastern to eastern Africa. Our findings also point to the value of preserved ancient hair as a source of aDNA, particularly in regions where more typical aDNA archives are unavailable or poorly preserved, with exciting implications for future aDNA research.
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Ecological flexibility and adaptation to past climate change in the Middle Nile Valley: A multiproxy investigation of dietary shifts between the Neolithic and Kerma periods at Kadruka 1 and Kadruka 21 Charles Le Moyne ,Patrick Roberts,Quan Hua,Madeleine Bleasdale,Jocelyne Desideri,Nicole Boivin,Alison Crowther Published: February 2, 2023 https://doi.org/10.1371/journal.pone.0280347
Abstract Human responses to climate change have long been at the heart of discussions of past economic, social, and political change in the Nile Valley of northeastern Africa. Following the arrival of Neolithic groups in the 6th millennium BCE, the Northern Dongola Reach of Upper Nubia witnessed a cultural florescence manifested through elaborate funerary traditions. However, despite the wealth of archaeological data available from funerary contexts, including evidence for domesticated animals and plants as grave goods, the paucity of stratified habitation contexts hinders interpretation of local subsistence trajectories. While it is recognised archaeologically that, against the backdrop of increasing environmental deterioration, the importance of agriculture based on Southwest Asian winter cereals increased throughout the Kerma period (2500–1450 BCE), the contribution of domesticated cereals to earlier Neolithic herding economies remains unclear. This paper presents direct dietary data from a total of 55 Middle Neolithic and Kerma period individuals from Kadruka 21 and Kadruka 1. Microbotanical data obtained from human dental calculus and grave sediments are integrated with human and faunal stable isotopes to explore changes in dietary breadth over time. The combined results demonstrate the consumption of wild plant species, including C4 wetland adapted grasses, by Middle Neolithic individuals at Kadruka 1. Despite existing evidence for domesticated barley in associated graves, the results obtained in this study provide no clear evidence for the routine consumption of domesticated cereals by Middle Neolithic individuals. Rather, direct microparticle evidence for the consumption of Triticeae cereals is only associated with a single Kerma period individual and corresponds with an isotopic shift indicating a greater contribution of C3-derived resources to diet. These results provide evidence for Neolithic dietary flexibility in Upper Nubia through the persistence of foraging activities and support existing evidence linking increased agricultural reliance to the development of the Kerma culture.
Evidence for the arrival of Neolithic food producing groups in the Northern Dongola Reach of Upper Nubia, situated in the Middle Nile Valley (Fig 1), dates to the 6th millennium BCE and coincides with Nile channel and floodplain contraction between 6250 and 5750 BCE [26–29]. At the sites of El-Barga and Wadi El-Arab on the desert plateau, human remains with more gracile skeletal morphology appear alongside new classes of grave goods, new building techniques and some limited evidence for food production in the form of a single cattle bucranium at El-Barga [28, 30]. With increasing aridity and further contraction of floodplains in the late 6th millennium BCE, Neolithic populations shifted from the desert plateau to occupy the alluvial plain [27, 29]. Extensive surface scatters indicate widespread occupation along palaeochannel margins, while numerous cemeteries, as observed throughout the wider Nile Valley, attest to the elaboration of funerary traditions over the course of the 5th millennium BCE
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Although previous studies have suggested that the Neolithic evidence for domesticated cereals supports an early agricultural transition as part of a Neolithic ‘package’, presence within funerary contexts and absence within corresponding dietary signatures is more reflective of high value associations of trade items [4, 234, 235]. The results of this study correlate with existing studies of early low-level food production systems [261–263], demonstrating that Middle Neolithic populations on the alluvial plain maintained dietary flexibility through the use of domesticated animal products and readily available wild resources. While Neolithic populations in Upper Nubia had access to domesticated cereals and small-scale cultivation may have formed a limited contribution to local diets, current evidence suggests a later economic transition linked to broader socio-cultural changes occurring amidst increasingly arid environmental conditions.
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quote:Of all the tissues and samples tested, only one sample of preserved hair, from the Kerma period individual (Kadruka), yielded a sufficient amount of authentic ancient human DNA to study...
We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses
~ 4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists December 2022
quote:Originally posted by Djehuti: ^ Yet we have Hassan's thesis from 2009
Yes we have that thesis and after many posts you have not been able to quote anything in that thesis or any article by Hassan that even mentions Kadruka
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Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan
Hisham Yousif Hassan Mohamed B.sc. (Honors) of Zoology, University of Khartoum, 1999 Upgrading to PhD. Institute of Endemic Diseases, 2004 Thesis Submitted for the Fulfillment of Requirements for Philosophy Degree of Science in Molecular Biology Supervisor: Prof. Muntaser Eltayeb Ibrahim Department of Molecular Biology Institute of Endemic Diseases University of Khartoum July 2009 231 pages The area known today as Sudan may have been the scene of pivotal human evolutionary events, both as a corridor for ancient and modern migrations, as well as the venue of crucial past cultural evolution. Several questions pertaining to the pattern of succession of the different groups in early Sudan have been raised. To shed light on these aspects, ancient DNA (aDNA) and present DNA collection were made and studied using Y-chromosome markers for aDNA, and Y-chromosome and mtDNA markers for present DNA. Bone samples from different skeletal elements of burial sites from Neolithic, Meroitic, Post-Meroitic and Christian periods in Sudan were collected from Sudan National Museum. aDNA extraction was successful in 35 out of 76 samples, PCR was performed for sex determination using Amelogenin marker. Fourteen samples were females and 19 were males. To generate Y-chromosome specific haplogroups A-M13, B-M60, F-M89 and Y Alu Polymorphism (YAP) markers, which define the deep ancestral haplotypes in the phylogenetic tree of Y-chromosome were used. Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post Meroitic and Christian periods. Haplogroup B-M60 was not observed in the sample analyzed. For extant DNA, Y-chromosome and mtDNA haplogroup variations were studied in 15 Sudanese populations representing the three linguistic families in Sudan by typing the major Y haplogroups in 445 unrelated males, and 404 unrelated individuals were sequenced for the mitochondrial hypervariable region. Y-chromosome analysis shows Sudanese populations falling into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 8.1, 34.2, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel test reveal a strong correlation between genetic and linguistic structures (r= 0.30, p= 0.007), and a similar correlation between genetic and geographic distances (r= 0.29, p= 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. For mtDNA analysis, a total of 56 haplotypes were observed, all belonging to the major sub-Saharan African and Eurasian mitochondrial macrohapolgroups L0, L1, L2, L4, L5, L3A, M and N in frequencies of 12.1, 11.9, 22, 4.2, 6.2, 29.5, 2, and 12.2% respectively. Haplogroups L6 was not observed in the sample analyzed. The considerable frequencies of macrohaplogroup L0 in Sudan is interesting given the fact that this macrohaplogroup occurs near the root of the mitochondrial DNA tree. Afro-Asiatic speaking groups appear to have sustained high gene flow form Nilo-Saharan speaking groups. Mantel test reveal no correlations between genetic, linguistic (r = 0.12, p = 0.14), and geographic distances (r = -0.07, p = 0.67). Accordingly, though limited on number of aDNA samples, there is enough data to suggest and to tally with the historical evidence of the dominance by Nilotic elements during the early state formation in the Nile Valley, and as the states thrived there was a dominance by other elements particularly Nuba/Nubians. In Y-chromosome terms this mean in simplest terms introgression of the YAP insertion (haplogroups E and D), and Eurasian Haplogroups which are defined by F-M89 against a background of haplogroup A-M13. The data analysis of the extant Y-chromosomes suggests that the bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared to the Nilo-Saharan family of languages, and a generally higher effective population size for the former. While the mtDNA data suggests that regional variation and diversity in mtDNA sequences in Sudan is likely to have been shaped by a longer history of in-situ evolution and then by human migrations form East, west-central and North Africa and to a lesser extent from Eurasia to the Nile Valley.
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