high-quality DNA obtained from bone samples of seven individuals from Taforalt in eastern Morocco dating from the Later Stone Age, about 15,000 years ago. The Taforalt individuals were found to be most closely related to populations from the Near East (Natufians), with a third of their ancestry from sub-Saharan Africa. No evidence was found for introgression with western Europeans, despite attribution to the Iberomaurusian culture.
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mtDNA analysis shows that the Taforalt individuals belonged to mtDNA haplogroups U6a and M1b. Y-DNA analysis shows that the Taforalt males all belonged to Y-DNA haplogroup E1b1b1a1 (M78), which is closely related to the E1b1b1b (M123) sub-haplogroup that has been observed in skeletal remains belonging to the Epipaleolithic Natufian and Pre-Pottery Neolithic cultures of the Levant
ref
Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations MARIEKE VAN DE LOOSDRECHT SCIENCE 4 May 2018
Malawi,Mount Hora (excerpt, oldest samples) 8100 BP
BT(xCT)
L0k2
f, L0a2 ..............
6100 BP
BT(xCT)
L0d1b2b L0d1c ________
2017-1748 BP
A1b1b2a
L0d1b2b1b
1282-1069 BP
L0d1a1a
Summary We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.
Reconstructing Prehistoric African Population Structure Pontus Skoglund, SCIENCE 4 May 2018 DOI: 10.1126/science.aar8380
The deposits at Shum Laka, a rock shelter located in the Grassfields region of western Cameroon, are among the most important archaeological sources for the study of Late Pleistocene and Holocene prehistory in western Central Africa1–4 . The oldest human-occupied layers at the site date to about 30,000 calendar years before present (bp; taken as ad 1950 in accordance with radiocarbon calibration convention), but of special interest are artefacts and skeletons dating to between the end of the Later Stone Age (about 8,000 bp) and the beginning of the Iron Age (about 2,500 bp)
All of the mtDNA and Y chromosome haplogroups we observe at Shum Laka are associated today with sub-Saharan Africans. The two earlier individuals carry mtDNA haplogroup L0a (specifically L0a2a1), which is widespread in Africa, and the two later individuals carry L1c (specifically L1c2a1b), which is found among both farmers and hunter-gatherers in Central and West Africa15,16. Individuals 2/SE I and 4/A have Y chromosomes from macrohaplogroup B (often found today in hunter-gatherers from Central Africa17), and 2/SE II has the rare Y chromosome haplogroup A00, which was discovered in 2013 and is present at appreciable frequencies only in Cameroon—in particular, among the Mbo and Bangwa in the western part of the country12,13. A00 is the oldest known branch of the modern human Y chromosome tree, with a split time of about 300,000–200,000 bp from all other known lineages12,18,19. At 1,666 positions (from whole-genome sequence data; Supplementary Table 4) that differ between present-day A0018 and all other Y chromosomes, the sequence of the Shum Laka individual carries the nonreference allele at a total of 1,521, translating to a within-A00 split at about 37,000–25,000 bp (95% confidence interval) (Fig. 1, Methods).
Nature. 2021 Aug 25. Published in final edited form as: Nature. 2020 Jan; 577(7792): 665–670. Published online 2020 Jan 22. doi: 10.1038/s41586-020-1929-1 PMCID: PMC8386425 NIHMSID: NIHMS1544948 PMID: 31969706
We used a maximum likelihood based approach to determine the Y chromosome haplogroup of Mota. We called genotypes along the Y chromosome with a minimum base threshold of 20 using GATK and employed YFitter (53) to predict the most likely haplogroup. Mota was assigned to haplogroup E1b1. We verified this haplogroup by looking for mutations in Mota that were described by the International Society of Genetic Genealogy (ISOGG) as defining the branches leading to haplogroup E1b1 (Table S4)
Mota was assigned to haplogroup L3x2a. Haplogroup L3 arose 60-70 kya (50) in Eastern Africa where the richest present-day haplogroup diversity is found (51). All mitochondrial haplogroups found outside Africa descend from the L3 lineage and hence this haplogroup is associated with the spread of Homo sapiens out of Africa to the rest of the world (52). The subhaplogroup L3x2 is restricted to the Horn of Africa and the Nile Valley in modern Ethiopian samples (12), suggesting a degree of maternal continuity in Ethiopia over the past 4,500 years.
Article Published: 22 January 2020 Ancient West African foragers in the context of African population history Mark Lipson, Isabelle Ribot, […]David Reich
Tracing the migrations of anatomically modern humans has been complicated by human movements both out of and into Africa, especially in relatively recent history. Gallego Llorente et al. sequenced an Ethiopian individual, “Mota,” who lived approximately 4500 years ago, predating one such wave of individuals into Africa from Eurasia. The genetic information from Mota suggests that present-day Sardinians were the likely source of the Eurasian backflow. Furthermore, 4 to 7% of most African genomes, including Yoruba and Mbuti Pygmies, originated from this Eurasian gene flow.__
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Djehutynakht, a governor in 11th or 12th Dynasty 4000 ya
U5b2b5 (maternal DNA only recovered)
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. 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
The mtGenome profile independently obtained from the tooth by the FBI and HMS laboratories were identical and can be found in Table S2. The haplotype (deposited in GenBank under accession number MG736653) belongs to mitochondrial DNA lineage U5b2b5, but the specific sequence has not been previously reported in the 35,942 mtGenomes stored in the NCBI GenBank database (as of October 2017). The sequence closest to the mummy’s belongs to a contemporary individual from Lebanon (KT779192 [67]); however, the two haplotypes still differ at five positions, three of them in the control region (CR). A comparison between the mummy CR and the 26,127 CR sequences from the EMPOP database produced no match.
To better understand the mtDNA lineage of the mummy in the context of known Egyptian mtDNA diversity, the mummy haplogroup was compared to the mtDNA haplogroup distribution of 668 Egyptians from various modern populations [68,69,70,71,72,73]. The dominant haplogroups among this dataset were haplogroup T (11.98%) and L3 (11.23%; Table S3). Out of the 64 individuals who belonged to haplogroup U, seven belonged to haplogroup U5 (1.05%), and three (0.5%) belonged to one of the U5b subgroups (U5b1c; U5b1d1a; U5b2a5).
The Djehutynakht sequence was also compared to available ancient human DNA sequences (Table S4). Not surprisingly, no direct matches to the Djehutynakht sequence have been reported. However, related U5b2b sequences have been observed in ancient human remains from Europe, and a haplogroup U5b2c1 haplotype was recently discovered in 2000-year-old remains from Phoenicia [67]. When only the mtDNA sequences recovered from ancient Egyptian human remains are considered, the Djehutynakht sequence most closely resembles a U5a lineage from sample JK2903, a 2000-year-old skeleton from Abusir el-Meleq [74].
Genes (Basel). 2018 Mar; 9(3): 135. Published online 2018 Mar 1. doi: 10.3390/genes9030135 PMCID: PMC5867856 PMID: 29494531 Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens _______
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quote:Originally posted by Doug M: T The second issue being that there is no ADNA from Africa over 8,000 years old, which means any DNA study in this region is always going to be skewed toward ADNA samples from Europe.
This is patently false. Hora (Malawi), Shum Laka (Cameroon) and Taforlat (Morocco) ancient genetic samples are all over 8000 years old.
quote:Originally posted by Elmaestro: This comes off as passive aggression. And it's incomplete.
I2966 of Hora, Malawi is 9,000 years old.
there was a 2020 Martiniano article referencing Skoglund where they apparently round off 8,100 to 9,000 (although I would have rounded to 8,000) but the primary article they reference below is more precise
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