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Howard23
04-04-2021, 02:09 AM
It is well known that mt-D1 is a typical matrilineal marker of Native Americans. However, mt-D1j was found in the slab grave of Mongolia about 2500 years ago, which is very unusual. Please confirm it for me.

ID:MIT001.A0101 M D1j Q1a1a1 (Q-M120) EIA

1. Jeong et al. 2020. A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe.
https://www.sciencedirect.com/science/article/pii/S0092867420313210

2. https://www.yfull.com/mtree/D1/

https://ars.els-cdn.com/content/image/1-s2.0-S0092867420313210-fx1.jpg

Shuzam87
04-04-2021, 12:14 PM
According to the supplmentart material of the journal "River Valleys Shaped the Maternal Genetic Landscape of Han Chinese" https://academic.oup.com/mbe/article/36/8/1643/5423190?login=true#138348886, there were 4 Han Chinese samples whom maternal haplogroups belong to D1j1. There were from Heilongjiang, Jilin, Zhejiang, and Jiangsu province. https://www.yfull.com/mtree/D1j1/ Could D1j and it's downstream D1j1 still be prevalent in Eastern and North Eastern Asia or there were the few rare cases?

Shuzam87
04-04-2021, 12:17 PM
A76LA8QJ2IRV Heilongjiang D1j1
73G 152C 263G 444G 449C 471C 479G 504C 507C 508G 750G 980C 1438G 2080C 2706G 3010A 4123G 4254C 4336C 4395G 4769G 4802C 4883T 4884G 5157T 5165T 5178A 6176C 7028T 7421G 7961C 7963G 7972G 8393T 8409T 8412C 8413G 8414T 8419C 8425G 8566G 8633G 8701G 8704G 8860G 8946G 9540C 9545G 10398G 10400T 10873C 10942G 11719A 11875C 11878C 11893G 12400G 12705T 13659C 13773G 14299C 14497G 14634C 14668T 14766T 14783C 15040T 15043A 15301A 15317A 15323A 15326G 15388C 15394C 15562G 15737A 15748C 15754T 15757G 15758G 15851G 15852C 15874G 16223T 16276C 16311C 16362C 16368C

A76LA8Q62SRI Jiangsu D1j1
73G 152C 263G 444G 449C 471C 479G 504C 507C 508G 750G 980C 1420C 2080C 2706G 3010A 4123G 4254C 4336C 4395G 4742C 4769G 4802C 4883T 4884G 5157T 5165T 5178A 5788C 6176C 7028T 7421G 7961C 7963G 7972G 8409T 8412C 8413G 8414T 8419C 8425G 8566G 8633G 8701G 8704G 8860G 8946G 9540C 9854C 9855G 10398G 10400T 10873C 10942G 11719A 11875C 11878C 11893G 12362T 12363T 12370T 12400G 12705T 13032G 13047G 13659C 13773G 14497G 14634C 14668T 14766T 14783C 15040T 15043A 15301A 15317A 15323A 15326G 15388C 15394C 15562G 16192T 16206C 16223T 16276C 16311C 16316G 16318T 16362C

A76LA8J1TT10 Jilin D1j1
73G 152C 263G 750G 1438G 2706G 3010A 4769G 4883T 5178A 7028T 8393T 8409T 8414T 8701G 8702T 8704G 8860G 9540C 9855G 10398G 10400T 10873C 11719A 12705T 13711A 13713T 13879C 14668T 14783C 15043A 15300C 15301A 15326G 16126C 16192T 16223T 16311C 16316G 16362C

A76LA8FYPE7I Zhejiang D1j1
73G 152C 263G 750G 1438G 2706G 3010A 3996T 4409C 4769G 4883T 5153G 5178A 7028T 8414T 8701G 8704G 8860G 9078C 9540C 10398G 10400T 10873C 11719A 12705T 14668T 14766T 14783C 14956C 14968C 15043A 15301A 15326G 16098G 16223T 16311C 16362C

Howard23
04-07-2021, 07:03 AM
According to the supplmentart material of the journal "River Valleys Shaped the Maternal Genetic Landscape of Han Chinese" https://academic.oup.com/mbe/article/36/8/1643/5423190?login=true#138348886, there were 4 Han Chinese samples whom maternal haplogroups belong to D1j1. There were from Heilongjiang, Jilin, Zhejiang, and Jiangsu province. https://www.yfull.com/mtree/D1j1/ Could D1j and it's downstream D1j1 still be prevalent in Eastern and North Eastern Asia or there were the few rare cases?

I don't know how to estimate the TMRCA between these samples.

Max_H
04-13-2021, 12:50 PM
A76LA8QJ2IRV Heilongjiang D1j1
73G 152C 263G 444G 449C 471C 479G 504C 507C 508G 750G 980C 1438G 2080C 2706G 3010A 4123G 4254C 4336C 4395G 4769G 4802C 4883T 4884G 5157T 5165T 5178A 6176C 7028T 7421G 7961C 7963G 7972G 8393T 8409T 8412C 8413G 8414T 8419C 8425G 8566G 8633G 8701G 8704G 8860G 8946G 9540C 9545G 10398G 10400T 10873C 10942G 11719A 11875C 11878C 11893G 12400G 12705T 13659C 13773G 14299C 14497G 14634C 14668T 14766T 14783C 15040T 15043A 15301A 15317A 15323A 15326G 15388C 15394C 15562G 15737A 15748C 15754T 15757G 15758G 15851G 15852C 15874G 16223T 16276C 16311C 16362C 16368C

A76LA8Q62SRI Jiangsu D1j1
73G 152C 263G 444G 449C 471C 479G 504C 507C 508G 750G 980C 1420C 2080C 2706G 3010A 4123G 4254C 4336C 4395G 4742C 4769G 4802C 4883T 4884G 5157T 5165T 5178A 5788C 6176C 7028T 7421G 7961C 7963G 7972G 8409T 8412C 8413G 8414T 8419C 8425G 8566G 8633G 8701G 8704G 8860G 8946G 9540C 9854C 9855G 10398G 10400T 10873C 10942G 11719A 11875C 11878C 11893G 12362T 12363T 12370T 12400G 12705T 13032G 13047G 13659C 13773G 14497G 14634C 14668T 14766T 14783C 15040T 15043A 15301A 15317A 15323A 15326G 15388C 15394C 15562G 16192T 16206C 16223T 16276C 16311C 16316G 16318T 16362C

A76LA8J1TT10 Jilin D1j1
73G 152C 263G 750G 1438G 2706G 3010A 4769G 4883T 5178A 7028T 8393T 8409T 8414T 8701G 8702T 8704G 8860G 9540C 9855G 10398G 10400T 10873C 11719A 12705T 13711A 13713T 13879C 14668T 14783C 15043A 15300C 15301A 15326G 16126C 16192T 16223T 16311C 16316G 16362C

A76LA8FYPE7I Zhejiang D1j1
73G 152C 263G 750G 1438G 2706G 3010A 3996T 4409C 4769G 4883T 5153G 5178A 7028T 8414T 8701G 8704G 8860G 9078C 9540C 10398G 10400T 10873C 11719A 12705T 14668T 14766T 14783C 14956C 14968C 15043A 15301A 15326G 16098G 16223T 16311C 16362C

Could that be due to some sort of old "back migration" from Beringia to East Asia (as some people have variously proposed) or is it more likely due to older shared ancestry?

Ebizur
04-13-2021, 01:59 PM
I think the assignment of those Chinese mitochondrial haplotypes to haplogroup D1j1 is erroneous.

They do seem to belong to haplogroup D (5178A 16362C) > haplogroup D4 (3010A 8414T 14668T), but I do not recognize them as belonging to any well-known subclade of haplogroup D4.

Shuzam87
04-14-2021, 06:14 AM
I think the assignment of those Chinese mitochondrial haplotypes to haplogroup D1j1 is erroneous.

They do seem to belong to haplogroup D (5178A 16362C) > haplogroup D4 (3010A 8414T 14668T), but I do not recognize them as belonging to any well-known subclade of haplogroup D4.

The quality of these samples does not seem that great appearently

Howard23
04-15-2021, 01:54 AM
Could that be due to some sort of old "back migration" from Beringia to East Asia (as some people have variously proposed) or is it more likely due to older shared ancestry?

Every evidence has many interpretations, which one is more reasonable? In my opinion, D1j is a subclad of D1, and D1j of Mongolia is the evidence of out of America, because it is more natural to let most people stay in the same place and let a few people cross the geographical barrier.

Howard23
04-15-2021, 02:12 AM
I think the assignment of those Chinese mitochondrial haplotypes to haplogroup D1j1 is erroneous.

They do seem to belong to haplogroup D (5178A 16362C) > haplogroup D4 (3010A 8414T 14668T), but I do not recognize them as belonging to any well-known subclade of haplogroup D4.

I got another…
https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajpa.20923



Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American
Noboru Adachi Ken‐ichi Shinoda Kazuo Umetsu Hirofumi Matsumura
First published: 24 October 2008
https://doi.org/10.1002/ajpa.20923
Citations: 60

Abstract
Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre‐) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.

Megalophias
04-15-2021, 03:18 AM
The reported Jomon D1a was corrected to D4h2. https://anthrogenica.com/showthread.php?13287-D1-mtDNA-Jomon-and-Native-American-genetic-affinity

I can't find any details for the Slab Grave sample, so I am not 100% sure it is reliable. Ebizur is right about the Han Chinese ones, they do not share the defining mutations of D1.

American mt hg A2 extends into Asia, mostly in Chukotka but further at low frequencies, even Taimyr in one study IIRC. D1j though seems to be mostly if not exclusively South American, and Mongolia is pretty far, so it would be surprising to find it there.

Max_H
04-15-2021, 01:11 PM
Every evidence has many interpretations, which one is more reasonable? In my opinion, D1j is a subclad of D1, and D1j of Mongolia is the evidence of out of America, because it is more natural to let most people stay in the same place and let a few people cross the geographical barrier.

If so, when do you propose this migration happened then?

Howard23
04-16-2021, 03:48 AM
If so, when do you propose this migration happened then?

The TMRCA of D1j is about 10,000 years. I noticed that most of the Y haplotypes of Ulaanzuuk/Slab Grave culture are Q-M120, and there is a Peruvian sample separated from Chinese branch 6000 years ago on Q-M120 tree, so I roughly estimated that this population left America about 6000 years ago. However, the above samples of D1 have been questioned, so the Slab-Grave D1j may also be a misunderstanding.

Max_H
04-17-2021, 10:48 AM
The TMRCA of D1j is about 10,000 years. I noticed that most of the Y haplotypes of Ulaanzuuk/Slab Grave culture are Q-M120, and there is a Peruvian sample separated from Chinese branch 6000 years ago on Q-M120 tree, so I roughly estimated that this population left America about 6000 years ago. However, the above samples of D1 have been questioned, so the Slab-Grave D1j may also be a misunderstanding.

Q-M120 is not uncommon in northern China (I know it's relatively high in Shandong for example and I think something like 3-5% in the north overall) It has only been found once in the Americas and specifically in that Peruvian sample. Is the distribution not odd if it was a back migration from the Americas? You'd expect to see it more in the north too,unless there was population replacement.

rock
04-18-2021, 05:01 PM
I think the assignment of those Chinese mitochondrial haplotypes to haplogroup D1j1 is erroneous.

They do seem to belong to haplogroup D (5178A 16362C) > haplogroup D4 (3010A 8414T 14668T), but I do not recognize them as belonging to any well-known subclade of haplogroup D4.

They are chip genotype samples, not mtDNA full sequencing samples, so the mutation accuracy is not high. not surprise assigned to wrong haplogroups.

Howard23
04-19-2021, 04:21 AM
Q-M120 is not uncommon in northern China (I know it's relatively high in Shandong for example and I think something like 3-5% in the north overall) It has only been found once in the Americas and specifically in that Peruvian sample. Is the distribution not odd if it was a back migration from the Americas? You'd expect to see it more in the north too,unless there was population replacement.

I don't know much about that Peruvian sample. Maybe I misjudged his family history. The population distribution may be affected by the survivor bias, because native Americans suffered from the "post Columbian" crisis, while those who left America in the early days thrived. There is no general algorithm to determine where the origin is. Most of the descendants of Q-M120 are in China, but Chinese scholars do not emphasize that the origin of Q-M120 is in China.



We reconstructed a highly revised phylogenetic tree of haplogroup Q-M120 with age estimates. Additionally, we performed a comprehensive phylogeographic analysis of this lineage including 15,007 samples from 440 populations in eastern Eurasia. Results: We revealed an ancient connection of this lineage with populations in Siberia. However, this paternal lineage experienced an in-situ expansion between 5,000 and 3,000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2,000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.


https://wx1.sinaimg.cn/orj360/9c9dbb25ly1gpos8lker6j22zl0m3e1y.jpg

Shuzam87
05-12-2021, 06:09 AM
I just found out one of the East Pamir Kyrgyz samples MF522876 (EPK151) from "Mitochondrial Genomes Uncover the Maternal History of the Pamir Populations" was also assigned to D1j1.
https://www.ncbi.nlm.nih.gov/nuccore/MF522876.1?report=fasta

Shuzam87
05-12-2021, 06:28 AM
deleted

Shuzam87
05-12-2021, 06:28 AM
I think the assignment of those Chinese mitochondrial haplotypes to haplogroup D1j1 is erroneous.

They do seem to belong to haplogroup D (5178A 16362C) > haplogroup D4 (3010A 8414T 14668T), but I do not recognize them as belonging to any well-known subclade of haplogroup D4.

Actually these 4 samples couldn't be assigned to D1j1 missing the C15868T mutation but could still be assigned to D1j matching the T152C and T16311C mutations.
https://www.yfull.com/mtree/D1j/

Ebizur
05-12-2021, 07:31 AM
Actually these 4 samples couldn't be assigned to D1j1 missing the C15868T mutation but could still be assigned to D1j matching the T152C and T16311C mutations.
https://www.yfull.com/mtree/D1j/As Megalophias has written in a comment on the first page of this thread (https://anthrogenica.com/showthread.php?23479-mt-D1j-the-hallmark-of-Native-America-was-found-in-slab-grave-in-Mongolia&p=765892&viewfull=1#post765892), the Han Chinese mitochondrial haplotypes that you have presented do not share the defining mutations of haplogroup D1: the Han haplotypes exhibit neither a C2092T nor a T16325C transition.

Ebizur
05-12-2021, 07:45 AM
I just found out one of the East Pamir Kyrgyz samples MF522876 (EPK151) from "Mitochondrial Genomes Uncover the Maternal History of the Pamir Populations" was also assigned to D1j1.
https://www.ncbi.nlm.nih.gov/nuccore/MF522876.1?report=fastaThe mtDNA of EPK151 (GenBank ID MF522876), who is an ethnic Kyrgyz from Taxkorgan, Xinjiang, China, has already been placed on the YFull mtree under haplogroup D4j1b* (https://www.yfull.com/mtree/D4j1b/).

Shuzam87
05-16-2021, 10:54 AM
Interestingly I found a Chueta sample (CHU64) which was assigned to D1j from Majorca (Balearic Islands, Spain) in this article:
“Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas” https://www.nature.com/articles/s41598-020-78487-9#Sec1

Howard23
05-17-2021, 03:17 AM
Interestingly I found a Chueta sample (CHU64) which was assigned to D1j from Majorca (Balearic Islands, Spain) in this article:
“Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas” https://www.nature.com/articles/s41598-020-78487-9#Sec1

CHU64 D1j 16223T 16242T 16311C 16325C 16362C 73G 152C 235G 263G 309.1C 315.1C 489C

This sample has a 16325C transition, but no C2092T, does it a real D1? @Ebizur @Megalophias

Ebizur
05-17-2021, 12:25 PM
CHU64 D1j 16223T 16242T 16311C 16325C 16362C 73G 152C 235G 263G 309.1C 315.1C 489C

This sample has a 16325C transition, but no C2092T, does it a real D1? @Ebizur @MegalophiasThose data should be from Supplementary Table 3 ("Mitochondrial D-loop haplotypes and haplogroups of the 104 Chueta samples (EMPOP*: EMP00672), classified according to HaploGrep2 (Build 17, PhyloTree)") of J. F. Ferragut, C. Ramon, J. A. Castro, et al. (2020), "Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas," Scientific Reports (2020) 10:21428.

In that study, only the D-loop of the mtDNA has been sequenced: "The mitochondrial DNA control region, or D-loop (16024-576), was amplified with two overlapping fragments using mtDNA-specific primers (L15997, H016 and L16555, H639)38. The amplified product was purified with the MBS Spin PCRapace kit (Invitek, Berlin, Germany), and subsequent sequencing reactions were carried out using the BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems), following the manufacturers’ procedures. Finally, products were run in an ABI prism 3130 analyser." (There is an exception for the mtDNA of six Chuetas whose mtDNA belonged to haplogroup R0a+60.1T: "Moreover, the entire mtDNA molecule was sequenced for six Chueta samples belonging to the modal haplogroup R0a + 60.1 T. Amplification of the whole molecule was carried out by 19 overlapping fragments, and the sequencing strategy used 31 smaller fragments, primers, and specifications as described in Ramos et al. [41,42]. When Chueta specific mutations were identified in the complete mtDNA molecule, the status of such nucleotide positions was interrogated in the rest of the samples belonging to the haplogroup.")

The C2092T transition that marks haplogroup D1 is located outside the hypervariable regions of the D-loop of mtDNA, so that locus should not have been sequenced by the authors of the present study.

CHU64 does exhibit 16325C (the only marker of haplogroup D1 located within the sequenced regions of mtDNA) as well as 152C, 16242T, and 16311C (every one of which is a marker of haplogroup D1j), so this individual most likely does belong to mtDNA haplogroup D1j. I suppose that this individual most likely should be a matrilineal descendant of a migrant from South America subsequent to the Iberian colonization of that continent; the sporadic occurrence of mtDNA haplogroups of American or East/Southeast Asian (e.g. Filipino) origin among present-day people in Spain and Portugal has been noted previously, and mtDNA haplogroups of African origin also have been found regularly (although with quite low frequency overall) among present-day people in those countries.

Shuzam87
06-07-2021, 10:18 PM
The oldest D1j sample has now been found in sample LLP.S2.E1 at the Laguna de los Pampas site in the Argentinian Pampas during the Initial Early Holocene (calibrated date is in between 10,223–9,764) period according to the new journal “Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America”

https://doi.org/10.1016/j.isci.2021.102553