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Angela
01-03-18, 20:14
Another one from the Reich group. The technology is getting better and better, which is great news. Some interesting info from a pop gen perspective as well.

See: Odile Loreille et al
"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"


http://www.mdpi.com/2073-4425/9/3/135/htm

"Abstract: 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."

Angela
01-03-18, 20:29
This is Middle Kingdom, so it's big.

"A mummified head, which could neither be attributed to the governor nor to his wife, was found atop the governor’s coffin (Figure 1 (http://www.mdpi.com/2073-4425/9/3/135/htm#fig_body_display_genes-09-00135-f001)).http://www.mdpi.com/genes/genes-09-00135/article_deploy/html/images/genes-09-00135-g001-550.jpg

Figure 1. Head of the Djehutynakht mummy (2010–1961 BC). Photograph © 2018 Museum of Fine Arts, Boston, USA.

"In order to unequivocally determine the biological sex of the individual, the MFA contacted the Federal Bureau of Investigation (FBI) Laboratory to perform DNA analysis.At the time the FBI was contacted, the ancient DNA community had largely given up on the testing of ancient Egyptian human remains. Though DNA extraction and amplification from ancient Egyptian samples had been attempted in the early days of paleogenetics, these initial attempts either resulted in failure (4500-year-old human femurs [9 (http://www.mdpi.com/2073-4425/9/3/135/htm#B9-genes-09-00135)]) or yielded data that turned out to be the product of modern DNA contamination (2400-year-old mummy [10 (http://www.mdpi.com/2073-4425/9/3/135/htm#B10-genes-09-00135)] and 1600-year-old sacred monkey bones from the Saqqara Baboon Galleries [11 (http://www.mdpi.com/2073-4425/9/3/135/htm#B11-genes-09-00135)]), both contaminated with modern human DNA)."

"Recently, a number of commercial high throughput sequencing (HTS) assays, designed specifically for forensic applications, have become available [16 (http://www.mdpi.com/2073-4425/9/3/135/htm#B16-genes-09-00135),17 (http://www.mdpi.com/2073-4425/9/3/135/htm#B17-genes-09-00135)]. While these assays overcome many of the limitations of traditional capillary electrophoresis-based forensic DNA analyses, they are still based on targeted amplification of defined genomic regions. As a result, their utility is limited to samples harboring DNA fragments large enough for PCR amplification.
One of the primary advantages of HTS is that DNA fragments of very short size can be recovered and sequenced, thus obviating the need for targeted PCR. Here, we exploit this feature and describe the use of shotgun sequencing to determine the biological sex of a 4000-year-old Egyptian mummy."

The mummy belonged to a man. They also got his mtDna.

"The mtGenome profile independently obtained from the tooth by the FBI and HMS laboratories were identical and can be found in Table S2 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]); 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B68-genes-09-00135),69 (http://www.mdpi.com/2073-4425/9/3/135/htm#B69-genes-09-00135),70 (http://www.mdpi.com/2073-4425/9/3/135/htm#B70-genes-09-00135),71 (http://www.mdpi.com/2073-4425/9/3/135/htm#B71-genes-09-00135),72 (http://www.mdpi.com/2073-4425/9/3/135/htm#B72-genes-09-00135),73 (http://www.mdpi.com/2073-4425/9/3/135/htm#B73-genes-09-00135)]. The dominant haplogroups among this dataset were haplogroup T (11.98%) and L3 (11.23%; Table S3 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]. 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]."

"Given limited available data and the fact that U5 is the dominant mitochondrial haplogroup found among hunter-gatherers in Europe [83 (http://www.mdpi.com/2073-4425/9/3/135/htm#B83-genes-09-00135),84 (http://www.mdpi.com/2073-4425/9/3/135/htm#B84-genes-09-00135)], the recovery of a haplogroup U5b2b5 sequence from the mummy of Djehutynakht raises the question of data authenticity, despite the molecular metrics suggesting otherwise. When the mummy’s mtDNA sequence is viewed in the context of modern mtDNA diversity, however, the observed U5 lineage could potentially reflect interactions between Egypt and the Near East that date as far back as the Predynastic and Early Dynastic periods [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135)]. Trade between Egypt and the Near East is evidenced by, among other things, ceramic imports to Egypt [86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. In addition, dwellings similar to those found in Palestine suggest some immigration to Egypt from more arid Near Eastern areas from the late Predynastic to the Old Kingdom [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),87 (http://www.mdpi.com/2073-4425/9/3/135/htm#B87-genes-09-00135)]. Both trade and immigration between Egypt and the Near East continued to increase over time. Demand in Egypt for cedar of Lebanon wood (a wood available and harvested in Lebanon and Syria during the MK) led to the further establishment of trade routes between Egypt and the Levant [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. It is interesting, and perhaps not coincidental, that the individual with the mtDNA sequence most similar to Djehutynakht comes from a Lebanese individual."

"On top of this historical information offering an explanation for the observed mtDNA data are now additional, recently published, mtGenomes from Africa, and Egypt in particular. MtDNA haplotypes recently obtained from ancient human remains from sub-Saharan Africa belong only to haplogroup L subgroups [65 (http://www.mdpi.com/2073-4425/9/3/135/htm#B65-genes-09-00135),88 (http://www.mdpi.com/2073-4425/9/3/135/htm#B88-genes-09-00135)]. However, nearly all of the remains excavated in the Northern part of the continent belong to Eurasian mtDNA lineages [63 (http://www.mdpi.com/2073-4425/9/3/135/htm#B63-genes-09-00135),67 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135),74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135),89 (http://www.mdpi.com/2073-4425/9/3/135/htm#B89-genes-09-00135),90 (http://www.mdpi.com/2073-4425/9/3/135/htm#B90-genes-09-00135)]. In fact, of the 114 mtDNA genomes now available from northern African ancient human remains, only one belongs to an African lineage (L3 observed in a skeleton from Abusir el-Meleq [74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]). The deep presence of Eurasian mtDNA lineages in Northern Africa has, therefore, been clearly established with these recent reports and offers further support for the authenticity of the Eurasian mtDNA sequence observed in the Djehutynakht mummy. In the present study, Near Eastern influence has been found in an individual of high social status who lived in Upper Egypt during the Middle Kingdom."

Good stuff in lots of ways. It's a good reminder also that some conclusions drawn from uniparental markers are rather naeve. It would be incorrect, in this case, to attribute "northern" or "European" ethnicity to this individual on the basis of a "European mtdna". One has to interpret uniparental markers not only in the context of where most of marker X exists today, but what ancient samples have been found, and what archaeology tells us of interactions between ancient peoples.

Angela
01-03-18, 21:32
This is Middle Kingdom, so it's big.

"A mummified head, which could neither be attributed to the governor nor to his wife, was found atop the governor’s coffin (Figure 1 (http://www.mdpi.com/2073-4425/9/3/135/htm#fig_body_display_genes-09-00135-f001)).http://www.mdpi.com/genes/genes-09-00135/article_deploy/html/images/genes-09-00135-g001-550.jpg

Figure 1. Head of the Djehutynakht mummy (2010–1961 BC). Photograph © 2018 Museum of Fine Arts, Boston, USA.

"In order to unequivocally determine the biological sex of the individual, the MFA contacted the Federal Bureau of Investigation (FBI) Laboratory to perform DNA analysis.At the time the FBI was contacted, the ancient DNA community had largely given up on the testing of ancient Egyptian human remains. Though DNA extraction and amplification from ancient Egyptian samples had been attempted in the early days of paleogenetics, these initial attempts either resulted in failure (4500-year-old human femurs [9 (http://www.mdpi.com/2073-4425/9/3/135/htm#B9-genes-09-00135)]) or yielded data that turned out to be the product of modern DNA contamination (2400-year-old mummy [10 (http://www.mdpi.com/2073-4425/9/3/135/htm#B10-genes-09-00135)] and 1600-year-old sacred monkey bones from the Saqqara Baboon Galleries [11 (http://www.mdpi.com/2073-4425/9/3/135/htm#B11-genes-09-00135)]), both contaminated with modern human DNA)."

"Recently, a number of commercial high throughput sequencing (HTS) assays, designed specifically for forensic applications, have become available [16 (http://www.mdpi.com/2073-4425/9/3/135/htm#B16-genes-09-00135),17 (http://www.mdpi.com/2073-4425/9/3/135/htm#B17-genes-09-00135)]. While these assays overcome many of the limitations of traditional capillary electrophoresis-based forensic DNA analyses, they are still based on targeted amplification of defined genomic regions. As a result, their utility is limited to samples harboring DNA fragments large enough for PCR amplification.
One of the primary advantages of HTS is that DNA fragments of very short size can be recovered and sequenced, thus obviating the need for targeted PCR. Here, we exploit this feature and describe the use of shotgun sequencing to determine the biological sex of a 4000-year-old Egyptian mummy."

The mummy belonged to a man. They also got his mtDna.

"The mtGenome profile independently obtained from the tooth by the FBI and HMS laboratories were identical and can be found in Table S2 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]); 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B68-genes-09-00135),69 (http://www.mdpi.com/2073-4425/9/3/135/htm#B69-genes-09-00135),70 (http://www.mdpi.com/2073-4425/9/3/135/htm#B70-genes-09-00135),71 (http://www.mdpi.com/2073-4425/9/3/135/htm#B71-genes-09-00135),72 (http://www.mdpi.com/2073-4425/9/3/135/htm#B72-genes-09-00135),73 (http://www.mdpi.com/2073-4425/9/3/135/htm#B73-genes-09-00135)]. The dominant haplogroups among this dataset were haplogroup T (11.98%) and L3 (11.23%; Table S3 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]. 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]."

"Given limited available data and the fact that U5 is the dominant mitochondrial haplogroup found among hunter-gatherers in Europe [83 (http://www.mdpi.com/2073-4425/9/3/135/htm#B83-genes-09-00135),84 (http://www.mdpi.com/2073-4425/9/3/135/htm#B84-genes-09-00135)], the recovery of a haplogroup U5b2b5 sequence from the mummy of Djehutynakht raises the question of data authenticity, despite the molecular metrics suggesting otherwise. When the mummy’s mtDNA sequence is viewed in the context of modern mtDNA diversity, however, the observed U5 lineage could potentially reflect interactions between Egypt and the Near East that date as far back as the Predynastic and Early Dynastic periods [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135)]. Trade between Egypt and the Near East is evidenced by, among other things, ceramic imports to Egypt [86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. In addition, dwellings similar to those found in Palestine suggest some immigration to Egypt from more arid Near Eastern areas from the late Predynastic to the Old Kingdom [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),87 (http://www.mdpi.com/2073-4425/9/3/135/htm#B87-genes-09-00135)]. Both trade and immigration between Egypt and the Near East continued to increase over time. Demand in Egypt for cedar of Lebanon wood (a wood available and harvested in Lebanon and Syria during the MK) led to the further establishment of trade routes between Egypt and the Levant [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. It is interesting, and perhaps not coincidental, that the individual with the mtDNA sequence most similar to Djehutynakht comes from a Lebanese individual."

"On top of this historical information offering an explanation for the observed mtDNA data are now additional, recently published, mtGenomes from Africa, and Egypt in particular. MtDNA haplotypes recently obtained from ancient human remains from sub-Saharan Africa belong only to haplogroup L subgroups [65 (http://www.mdpi.com/2073-4425/9/3/135/htm#B65-genes-09-00135),88 (http://www.mdpi.com/2073-4425/9/3/135/htm#B88-genes-09-00135)]. However, nearly all of the remains excavated in the Northern part of the continent belong to Eurasian mtDNA lineages [63 (http://www.mdpi.com/2073-4425/9/3/135/htm#B63-genes-09-00135),67 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135),74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135),89 (http://www.mdpi.com/2073-4425/9/3/135/htm#B89-genes-09-00135),90 (http://www.mdpi.com/2073-4425/9/3/135/htm#B90-genes-09-00135)]. In fact, of the 114 mtDNA genomes now available from northern African ancient human remains, only one belongs to an African lineage (L3 observed in a skeleton from Abusir el-Meleq [74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]). The deep presence of Eurasian mtDNA lineages in Northern Africa has, therefore, been clearly established with these recent reports and offers further support for the authenticity of the Eurasian mtDNA sequence observed in the Djehutynakht mummy. In the present study, Near Eastern influence has been found in an individual of high social status who lived in Upper Egypt during the Middle Kingdom."

Good stuff in lots of ways. It's a good reminder also that some conclusions drawn from uniparental markers are rather naeve. It would be incorrect, in this case, to attribute "northern" or "European" ethnicity to this individual on the basis of a "European mtdna". One has to interpret uniparental markers not only in the context of where most of marker X exists today, but what ancient samples have been found, and what archaeology tells us of interactions between ancient peoples.




Fwiw I think he has a "Middle Eastern" look as well.

IronSide
01-03-18, 21:38
Fwiw I think he has a "Middle Eastern" look as well.

Well if it wasn't Egyptian I would at least say "Caucasoid", but I wouldn't be able to pinpoint exactly where it's from.

Angela
01-03-18, 21:48
Well if it wasn't Egyptian I would at least say "Caucasoid", but I wouldn't be able to pinpoint exactly where it's from.

Generally speaking, although it might not apply in certain specific instances, North Africans are "Caucasoid", and so are a lot of Indians, yes?

Last time I checked, that is. :)

Jovialis
01-03-18, 21:55
This is Middle Kingdom, so it's big.

"A mummified head, which could neither be attributed to the governor nor to his wife, was found atop the governor’s coffin (Figure 1 (http://www.mdpi.com/2073-4425/9/3/135/htm#fig_body_display_genes-09-00135-f001)).http://www.mdpi.com/genes/genes-09-00135/article_deploy/html/images/genes-09-00135-g001-550.jpg

Figure 1. Head of the Djehutynakht mummy (2010–1961 BC). Photograph © 2018 Museum of Fine Arts, Boston, USA.

"In order to unequivocally determine the biological sex of the individual, the MFA contacted the Federal Bureau of Investigation (FBI) Laboratory to perform DNA analysis.At the time the FBI was contacted, the ancient DNA community had largely given up on the testing of ancient Egyptian human remains. Though DNA extraction and amplification from ancient Egyptian samples had been attempted in the early days of paleogenetics, these initial attempts either resulted in failure (4500-year-old human femurs [9 (http://www.mdpi.com/2073-4425/9/3/135/htm#B9-genes-09-00135)]) or yielded data that turned out to be the product of modern DNA contamination (2400-year-old mummy [10 (http://www.mdpi.com/2073-4425/9/3/135/htm#B10-genes-09-00135)] and 1600-year-old sacred monkey bones from the Saqqara Baboon Galleries [11 (http://www.mdpi.com/2073-4425/9/3/135/htm#B11-genes-09-00135)]), both contaminated with modern human DNA)."

"Recently, a number of commercial high throughput sequencing (HTS) assays, designed specifically for forensic applications, have become available [16 (http://www.mdpi.com/2073-4425/9/3/135/htm#B16-genes-09-00135),17 (http://www.mdpi.com/2073-4425/9/3/135/htm#B17-genes-09-00135)]. While these assays overcome many of the limitations of traditional capillary electrophoresis-based forensic DNA analyses, they are still based on targeted amplification of defined genomic regions. As a result, their utility is limited to samples harboring DNA fragments large enough for PCR amplification.
One of the primary advantages of HTS is that DNA fragments of very short size can be recovered and sequenced, thus obviating the need for targeted PCR. Here, we exploit this feature and describe the use of shotgun sequencing to determine the biological sex of a 4000-year-old Egyptian mummy."

The mummy belonged to a man. They also got his mtDna.

"The mtGenome profile independently obtained from the tooth by the FBI and HMS laboratories were identical and can be found in Table S2 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]); 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B68-genes-09-00135),69 (http://www.mdpi.com/2073-4425/9/3/135/htm#B69-genes-09-00135),70 (http://www.mdpi.com/2073-4425/9/3/135/htm#B70-genes-09-00135),71 (http://www.mdpi.com/2073-4425/9/3/135/htm#B71-genes-09-00135),72 (http://www.mdpi.com/2073-4425/9/3/135/htm#B72-genes-09-00135),73 (http://www.mdpi.com/2073-4425/9/3/135/htm#B73-genes-09-00135)]. The dominant haplogroups among this dataset were haplogroup T (11.98%) and L3 (11.23%; Table S3 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]. 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]."

"Given limited available data and the fact that U5 is the dominant mitochondrial haplogroup found among hunter-gatherers in Europe [83 (http://www.mdpi.com/2073-4425/9/3/135/htm#B83-genes-09-00135),84 (http://www.mdpi.com/2073-4425/9/3/135/htm#B84-genes-09-00135)], the recovery of a haplogroup U5b2b5 sequence from the mummy of Djehutynakht raises the question of data authenticity, despite the molecular metrics suggesting otherwise. When the mummy’s mtDNA sequence is viewed in the context of modern mtDNA diversity, however, the observed U5 lineage could potentially reflect interactions between Egypt and the Near East that date as far back as the Predynastic and Early Dynastic periods [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135)]. Trade between Egypt and the Near East is evidenced by, among other things, ceramic imports to Egypt [86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. In addition, dwellings similar to those found in Palestine suggest some immigration to Egypt from more arid Near Eastern areas from the late Predynastic to the Old Kingdom [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),87 (http://www.mdpi.com/2073-4425/9/3/135/htm#B87-genes-09-00135)]. Both trade and immigration between Egypt and the Near East continued to increase over time. Demand in Egypt for cedar of Lebanon wood (a wood available and harvested in Lebanon and Syria during the MK) led to the further establishment of trade routes between Egypt and the Levant [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. It is interesting, and perhaps not coincidental, that the individual with the mtDNA sequence most similar to Djehutynakht comes from a Lebanese individual."

"On top of this historical information offering an explanation for the observed mtDNA data are now additional, recently published, mtGenomes from Africa, and Egypt in particular. MtDNA haplotypes recently obtained from ancient human remains from sub-Saharan Africa belong only to haplogroup L subgroups [65 (http://www.mdpi.com/2073-4425/9/3/135/htm#B65-genes-09-00135),88 (http://www.mdpi.com/2073-4425/9/3/135/htm#B88-genes-09-00135)]. However, nearly all of the remains excavated in the Northern part of the continent belong to Eurasian mtDNA lineages [63 (http://www.mdpi.com/2073-4425/9/3/135/htm#B63-genes-09-00135),67 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135),74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135),89 (http://www.mdpi.com/2073-4425/9/3/135/htm#B89-genes-09-00135),90 (http://www.mdpi.com/2073-4425/9/3/135/htm#B90-genes-09-00135)]. In fact, of the 114 mtDNA genomes now available from northern African ancient human remains, only one belongs to an African lineage (L3 observed in a skeleton from Abusir el-Meleq [74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]). The deep presence of Eurasian mtDNA lineages in Northern Africa has, therefore, been clearly established with these recent reports and offers further support for the authenticity of the Eurasian mtDNA sequence observed in the Djehutynakht mummy. In the present study, Near Eastern influence has been found in an individual of high social status who lived in Upper Egypt during the Middle Kingdom."

Good stuff in lots of ways. It's a good reminder also that some conclusions drawn from uniparental markers are rather naeve. It would be incorrect, in this case, to attribute "northern" or "European" ethnicity to this individual on the basis of a "European mtdna". One has to interpret uniparental markers not only in the context of where most of marker X exists today, but what ancient samples have been found, and what archaeology tells us of interactions between ancient peoples.




Really fascinating, Egypt has such a rich archaeological history. Thankfully they had the cultural practices they did. Because we are able to learn so much from it today.

Jovialis
01-03-18, 22:24
This is Middle Kingdom, so it's big.

"A mummified head, which could neither be attributed to the governor nor to his wife, was found atop the governor’s coffin (Figure 1 (http://www.mdpi.com/2073-4425/9/3/135/htm#fig_body_display_genes-09-00135-f001)).http://www.mdpi.com/genes/genes-09-00135/article_deploy/html/images/genes-09-00135-g001-550.jpg

Figure 1. Head of the Djehutynakht mummy (2010–1961 BC). Photograph © 2018 Museum of Fine Arts, Boston, USA.

"In order to unequivocally determine the biological sex of the individual, the MFA contacted the Federal Bureau of Investigation (FBI) Laboratory to perform DNA analysis.At the time the FBI was contacted, the ancient DNA community had largely given up on the testing of ancient Egyptian human remains. Though DNA extraction and amplification from ancient Egyptian samples had been attempted in the early days of paleogenetics, these initial attempts either resulted in failure (4500-year-old human femurs [9 (http://www.mdpi.com/2073-4425/9/3/135/htm#B9-genes-09-00135)]) or yielded data that turned out to be the product of modern DNA contamination (2400-year-old mummy [10 (http://www.mdpi.com/2073-4425/9/3/135/htm#B10-genes-09-00135)] and 1600-year-old sacred monkey bones from the Saqqara Baboon Galleries [11 (http://www.mdpi.com/2073-4425/9/3/135/htm#B11-genes-09-00135)]), both contaminated with modern human DNA)."

"Recently, a number of commercial high throughput sequencing (HTS) assays, designed specifically for forensic applications, have become available [16 (http://www.mdpi.com/2073-4425/9/3/135/htm#B16-genes-09-00135),17 (http://www.mdpi.com/2073-4425/9/3/135/htm#B17-genes-09-00135)]. While these assays overcome many of the limitations of traditional capillary electrophoresis-based forensic DNA analyses, they are still based on targeted amplification of defined genomic regions. As a result, their utility is limited to samples harboring DNA fragments large enough for PCR amplification.
One of the primary advantages of HTS is that DNA fragments of very short size can be recovered and sequenced, thus obviating the need for targeted PCR. Here, we exploit this feature and describe the use of shotgun sequencing to determine the biological sex of a 4000-year-old Egyptian mummy."

The mummy belonged to a man. They also got his mtDna.

"The mtGenome profile independently obtained from the tooth by the FBI and HMS laboratories were identical and can be found in Table S2 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]); 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B68-genes-09-00135),69 (http://www.mdpi.com/2073-4425/9/3/135/htm#B69-genes-09-00135),70 (http://www.mdpi.com/2073-4425/9/3/135/htm#B70-genes-09-00135),71 (http://www.mdpi.com/2073-4425/9/3/135/htm#B71-genes-09-00135),72 (http://www.mdpi.com/2073-4425/9/3/135/htm#B72-genes-09-00135),73 (http://www.mdpi.com/2073-4425/9/3/135/htm#B73-genes-09-00135)]. The dominant haplogroups among this dataset were haplogroup T (11.98%) and L3 (11.23%; Table S3 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#app1-genes-09-00135)). 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135)]. 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 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]."

"Given limited available data and the fact that U5 is the dominant mitochondrial haplogroup found among hunter-gatherers in Europe [83 (http://www.mdpi.com/2073-4425/9/3/135/htm#B83-genes-09-00135),84 (http://www.mdpi.com/2073-4425/9/3/135/htm#B84-genes-09-00135)], the recovery of a haplogroup U5b2b5 sequence from the mummy of Djehutynakht raises the question of data authenticity, despite the molecular metrics suggesting otherwise. When the mummy’s mtDNA sequence is viewed in the context of modern mtDNA diversity, however, the observed U5 lineage could potentially reflect interactions between Egypt and the Near East that date as far back as the Predynastic and Early Dynastic periods [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135)]. Trade between Egypt and the Near East is evidenced by, among other things, ceramic imports to Egypt [86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. In addition, dwellings similar to those found in Palestine suggest some immigration to Egypt from more arid Near Eastern areas from the late Predynastic to the Old Kingdom [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),87 (http://www.mdpi.com/2073-4425/9/3/135/htm#B87-genes-09-00135)]. Both trade and immigration between Egypt and the Near East continued to increase over time. Demand in Egypt for cedar of Lebanon wood (a wood available and harvested in Lebanon and Syria during the MK) led to the further establishment of trade routes between Egypt and the Levant [85 (http://www.mdpi.com/2073-4425/9/3/135/htm#B85-genes-09-00135),86 (http://www.mdpi.com/2073-4425/9/3/135/htm#B86-genes-09-00135)]. It is interesting, and perhaps not coincidental, that the individual with the mtDNA sequence most similar to Djehutynakht comes from a Lebanese individual."

"On top of this historical information offering an explanation for the observed mtDNA data are now additional, recently published, mtGenomes from Africa, and Egypt in particular. MtDNA haplotypes recently obtained from ancient human remains from sub-Saharan Africa belong only to haplogroup L subgroups [65 (http://www.mdpi.com/2073-4425/9/3/135/htm#B65-genes-09-00135),88 (http://www.mdpi.com/2073-4425/9/3/135/htm#B88-genes-09-00135)]. However, nearly all of the remains excavated in the Northern part of the continent belong to Eurasian mtDNA lineages [63 (http://www.mdpi.com/2073-4425/9/3/135/htm#B63-genes-09-00135),67 (http://www.mdpi.com/2073-4425/9/3/135/htm#B67-genes-09-00135),74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135),89 (http://www.mdpi.com/2073-4425/9/3/135/htm#B89-genes-09-00135),90 (http://www.mdpi.com/2073-4425/9/3/135/htm#B90-genes-09-00135)]. In fact, of the 114 mtDNA genomes now available from northern African ancient human remains, only one belongs to an African lineage (L3 observed in a skeleton from Abusir el-Meleq [74 (http://www.mdpi.com/2073-4425/9/3/135/htm#B74-genes-09-00135)]). The deep presence of Eurasian mtDNA lineages in Northern Africa has, therefore, been clearly established with these recent reports and offers further support for the authenticity of the Eurasian mtDNA sequence observed in the Djehutynakht mummy. In the present study, Near Eastern influence has been found in an individual of high social status who lived in Upper Egypt during the Middle Kingdom."

Good stuff in lots of ways. It's a good reminder also that some conclusions drawn from uniparental markers are rather naeve. It would be incorrect, in this case, to attribute "northern" or "European" ethnicity to this individual on the basis of a "European mtdna". One has to interpret uniparental markers not only in the context of where most of marker X exists today, but what ancient samples have been found, and what archaeology tells us of interactions between ancient peoples.




https://i.imgur.com/ZghtaMA.jpg

The coffin was renowned as one of the finest painted in Egypt.

https://en.wikipedia.org/wiki/Djehutynakht_(10A)

Jovialis
02-03-18, 01:29
This link has some really great pictures of the coffin.

http://www.mfa.org/collections/object/front-side-panel-of-outer-coffin-of-djehutynakht-142815

FIREYWOTAN
02-03-18, 21:45
Thank you for sharing the findings and opening the doors to a number of interesting articles. The challenge at times is which way to look even before the words can be digested.
Wow they sure do capture the scenes that tell the story. The process is infectious the more time I spend the more passion I find in the search.:thinking::thinking:
Table S3: Haplogroup distribution among 668 modern Egyptians
mtDNA haplogroup
T
L3
R0
U
H
M
J
HV
L2
N
K
I
L1
X
R
L0
W
L4&5
B
Table S2a: Haplogroup U distribution among 64 modern Egyptians
mtDNA haplogroup
U3
U6
U7
U5
U4
U1
U2
U9
U8

Alyan
02-02-19, 02:06
We need more research on this mummy. Surely we can get more thorough DNA?

Alyan
05-02-19, 01:16
10686
This is a double post but a relevant one. I have confirmation that the researchers did get at least Y-DNA from the mummy with the info apparently ready to be put in another paper.

Combining the mummy's age, location, and position in Egyptian society we just might know what the founders of Egypt were like genetically.

ToBeOrNotToBe
05-02-19, 01:49
10685
This is a double post but a relevant one. I have confirmation that the researchers did get at least Y-DNA from the mummy with the info apparently ready to be put in another paper.

Combining the mummy's age, location, and position in Egyptian society we just might know what the founders of Egypt were like genetically.

If Middle Kingdom and elite, then presumably E1b1b. For New Kingdom elite, I'd guess J and R1b play a big role (from the Hyksos).

Alyan
05-02-19, 01:55
The mummy is really early in the Middle Kingdom. The paper even notes it had continuity with Old Kingdom Egypt.

ToBeOrNotToBe
05-02-19, 02:00
The mummy is really early in the Middle Kingdom. The paper even notes it had continuity with Old Kingdom Egypt.

Then E1b1b, unless there's some surprises (perhaps it could be Y DNA T, like those from Chalcolithic Israel). Main Egyptian population throughout will be E1b1b for sure though, I don't think anything is likely to go against that. I'm very confident in a shift in elite Y DNA dating to the Hyksos though, and also very confident it would be to Y DNA J and R1b (New Kingdom is where you see a lot of elite Egyptians with light hair; also some of the elite (e.g. Seti I and his son, Ramses II) were linked to the usurper god of foreigners and violence, Seth (https://en.wikipedia.org/wiki/Set_(deity)#Set_in_the_Second_Intermediate_and_Ram esside_Periods)).

From Wikipedia:

The Hyksos practised horse burials (https://en.wikipedia.org/wiki/Horse_burial), and their chief deity, their native storm god (https://en.wikipedia.org/wiki/Weather_god), Hadad (https://en.wikipedia.org/wiki/Hadad), they associated with the Egyptian storm and desert god, Set (https://en.wikipedia.org/wiki/Set_(deity)).[3] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Hyksos-3)[7] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Morenz2013-7) The Hyksos were a mixed people of mainly Semitic-speaking (https://en.wikipedia.org/wiki/Ancient_Semitic-speaking_peoples) origin.[3] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Hyksos-3)[8] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Starr1991-8) The Hyksos are generally held to have contained Hurrian (https://en.wikipedia.org/wiki/Hurrians) and Indo-European (https://en.wikipedia.org/wiki/Proto-Indo-Europeans) elements, particularly among the leadership,[9] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Stiebing-9)[10] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Syria-10) but this has been vigorously opposed in some quarters, often for political reasons.[11] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Bernal39-11)
The Hyksos brought several technical innovations to Egypt, as well as cultural imports such as new musical instruments and foreign loanwords.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12)The changes introduced include new techniques of bronze-working and pottery, new breeds of animals, and new crops.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12) In warfare, they introduced the horse (https://en.wikipedia.org/wiki/Horse) and chariot (https://en.wikipedia.org/wiki/Chariot),[13] (https://en.wikipedia.org/wiki/Hyksos#cite_note-13) the composite bow (https://en.wikipedia.org/wiki/Composite_bow), improved battle axes (https://en.wikipedia.org/wiki/Battle_axe), and advanced fortification techniques.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12) Because of these cultural advances, Hyksos' rule became decisive for Egypt's later empire in the Middle East during the New Kingdom (https://en.wikipedia.org/wiki/New_Kingdom_of_Egypt).[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12)

There's even the possibility of R1a of all things in the New Kingdom, given the Hyksos' Indo-European elite has been linked to the Iranian branch (with the spread of chariots).

Alyan
06-02-19, 12:37
The best part will be hearing the usual suspects (Nordicists, Afrocentrists) try to be spin the findings once the mummy is found to have no ties to Europe or Africa below the Sahara paternally.

ToBeOrNotToBe
06-02-19, 12:40
The best part will be hearing the usual suspects (Nordicists, Afrocentrists) try to be spin the findings once the mummy is found to have no ties to Europe or Africa below the Sahara paternally.

Yeah, I'd bet money it's going to be E1b1b, G or T

matty74
06-02-19, 14:47
Why would a 4000 year old Egyptian mummy be European?

Alyan
06-02-19, 17:16
Tell that to Nordicists.

Sile
06-02-19, 18:28
Then E1b1b, unless there's some surprises (perhaps it could be Y DNA T, like those from Chalcolithic Israel). Main Egyptian population throughout will be E1b1b for sure though, I don't think anything is likely to go against that. I'm very confident in a shift in elite Y DNA dating to the Hyksos though, and also very confident it would be to Y DNA J and R1b (New Kingdom is where you see a lot of elite Egyptians with light hair; also some of the elite (e.g. Seti I and his son, Ramses II) were linked to the usurper god of foreigners and violence, Seth (https://en.wikipedia.org/wiki/Set_(deity)#Set_in_the_Second_Intermediate_and_Ram esside_Periods)).

From Wikipedia:

The Hyksos practised horse burials (https://en.wikipedia.org/wiki/Horse_burial), and their chief deity, their native storm god (https://en.wikipedia.org/wiki/Weather_god), Hadad (https://en.wikipedia.org/wiki/Hadad), they associated with the Egyptian storm and desert god, Set (https://en.wikipedia.org/wiki/Set_(deity)).[3] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Hyksos-3)[7] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Morenz2013-7) The Hyksos were a mixed people of mainly Semitic-speaking (https://en.wikipedia.org/wiki/Ancient_Semitic-speaking_peoples) origin.[3] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Hyksos-3)[8] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Starr1991-8) The Hyksos are generally held to have contained Hurrian (https://en.wikipedia.org/wiki/Hurrians) and Indo-European (https://en.wikipedia.org/wiki/Proto-Indo-Europeans) elements, particularly among the leadership,[9] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Stiebing-9)[10] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Syria-10) but this has been vigorously opposed in some quarters, often for political reasons.[11] (https://en.wikipedia.org/wiki/Hyksos#cite_note-Bernal39-11)
The Hyksos brought several technical innovations to Egypt, as well as cultural imports such as new musical instruments and foreign loanwords.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12)The changes introduced include new techniques of bronze-working and pottery, new breeds of animals, and new crops.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12) In warfare, they introduced the horse (https://en.wikipedia.org/wiki/Horse) and chariot (https://en.wikipedia.org/wiki/Chariot),[13] (https://en.wikipedia.org/wiki/Hyksos#cite_note-13) the composite bow (https://en.wikipedia.org/wiki/Composite_bow), improved battle axes (https://en.wikipedia.org/wiki/Battle_axe), and advanced fortification techniques.[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12) Because of these cultural advances, Hyksos' rule became decisive for Egypt's later empire in the Middle East during the New Kingdom (https://en.wikipedia.org/wiki/New_Kingdom_of_Egypt).[12] (https://en.wikipedia.org/wiki/Hyksos#cite_note-EB_Ancient_Egypt-12)

There's even the possibility of R1a of all things in the New Kingdom, given the Hyksos' Indo-European elite has been linked to the Iranian branch (with the spread of chariots).

Hurrians from south-caucasus, most likely part of kura-Araxes culture have never been semetic unless you are talking only in the last 1500 years.............you can add all ancient anatolian languages as non-semetic as well

Corrado
06-02-19, 18:37
Can someone post the mtdna Table S3 from the supplements? For some reason I'm having trouble opening it.

Megalophias
06-02-19, 18:54
Can someone post the mtdna Table S3 from the supplements? For some reason I'm having trouble opening it.



Table S3: Haplogroup distribution among 668 modern Egyptians






mtDNA haplogroup
Number of individuals


T
80


L3
75


R0
64


U
64


H
59


M
53


J
49


HV
37


L2
31


N
31


K
21


I
20


L1
19


X
19


R
17


L0
15


W
8


L4&5
5


B
1

Corrado
06-02-19, 19:21
No further subclade resolution? Disappointing. I'm a bit surprised L3 is the second most common though.

Alyan
07-02-19, 08:19
Wait for the final paper with the mummy's nuclear data.

FIREYWOTAN
07-02-19, 21:43
Thank you for sharing the latest news it demonstrates just how much continues to change. The toolkits are so much more aggressive and the focus makes each discovery a unique experience. The stories that we can tell and the opportunity to learn a little more each day. The direction of each line challenges another reason to keep reading. What's next and there's always something more to explore. It's been close to a year now and I'm thrilled everyday to have so much to chew on.
Thanks again for making me feel so welcome.

Alyan
08-02-19, 16:12
1. Neolithic Morocco.

2. Neolithic Tunisia.

3. Neolithic Levant.

4. Nuclear DNAfrom Djehutynakht's mummy combined with past DNA peer reviewed studies in the proper channels for Egypt.

That should do for figuring out Ancient Egyptian DNA, at least if we can't get more sources of DNA.