Page 1 of 7 123 ... LastLast
Results 1 to 10 of 63

Thread: First High quality genomes from the Chinese Late Neolithic and EBA

  1. #1
    Registered Users
    Posts
    935
    Sex

    First High quality genomes from the Chinese Late Neolithic and EBA

    h/t @ Sahaliyan

    中原仰韶至龙山时期古代人群基因组学研究 Population Genetic analysis of Neolithic populations of the Central Plains from the Yangshao and Longshan cultures
    Dissertation authored by Tianjiao Li, 李添骄, University of Jilin

    Link here
    Chinese-language discussion on Ranhaer forum

    Abstract: 摘要:
    河南位于中原中心地区,是我国华夏文明的发祥地。由于该地区史前自然资源丰富且气候适宜、优越的自然条件孕 育了早期的文明。
    The Henan region at the core of the Central Plains of China is where Chinese civilisation began. The excellent natural conditions in this region in prehistory allowed complex societies to receive a head start.

    中原地区的文化血脉连续、序列完整,并同周围地区的文化存在着广泛的交流。百川汇海,各种文化精髓汇聚成中 国古代文明,而这个汇集的中心便是中原地区的仰韶—龙山文化体系。
    The archaeological record and cultural sequence of this region is well known, and demonstrates a history of exchange with surrounding regions. The hundred rivers reach the sea, and the spiritual essence of of many cultures meet within the Yangshao-Longshan cultural sequence of the central plains.

    目前有关 中原地区的仰韶—龙山文化体系的相关资料较为全面,考古学家所主导通过出土的器物和葬俗已经成功推演出文化 迁移的路线。目前关于史前物质文化变迁是否由人群迁移所致尚无定论。 古基因组学以分子生物学为手段,为解决文化变迁是否伴随人群迁移提供遗传学证据。
    The Yangshao-Longshan cultural sequence is described by an extensive literature, with the artifacts and burial styles as discovered by the archaeologists providing a detailed view of cultural change across geographic space. There is currently little agreement as to the role of migration in promoting cultural change. Ancient DNA, as a branch of molecular biology, provides population-genetic evidence that may help to resolve the question as to whether cultural change was accompanied by the migration of people.
    由于中原地区属于暖湿带-亚热带气候,不利于DNA的保存,因此至今尚无有关中原史前人群基因组学的报道。
    As the weather of this region is warm humid temperate to subtropical, DNA preservation is poor, and there is currently no data as to the population-genetic affinities of the ancestors of the people of the Central Plains.

    本研究以仰韶文化时期的晓邬和汪沟遗址,以及龙山文化时期的郝家台和平粮台遗址为研究对象,成功获取17例 样本的全基因组数据。检测出男性样本7例女性样本10例,其中线粒体单倍型类群主要分为B单倍型类群下的B 4d1亚型;D单倍型类群下的D4,D4g2a1,D4b2,D4j1b2,D4e1a和D4b1a亚型; F单倍型类群下的F4a2,F1a1和F2h亚型。以上单倍型均为东亚典型的单倍型,本研究中单倍型D与单 倍型F所占比例较高。
    The current study successfully extracted the whole-genome sequences of 17 individuals from the Shaowu and the Wanggou sites of the Yangshao culture, and the Chijiatai and the Pingliangtai sites of the Longshan culture. They comprise 7 males and 10 females. Among them the mitochondrial DNA sequences fall under B4d1, D4, D4g2a1, D4b2, D4j1b2, D4e1a, D4b1a, and F4a2, F1a1 and F2h, which are typical for East Asian populations. The proportion of mtDNA sequences falling under the D and F clades is relatively high.
    全基因组亲缘关系研究表明,以上17例个体中,来自平粮台遗址的三例个体间存在着相互的一、二级的亲缘关系 。结合这三个样本的年龄,测年数据以及基因组亲缘关系鉴定,本研究成功对这三例个体进行家族树的构建,为研 究龙山时期社会习俗以及社会结构提供了遗传的理论基础。
    Analyses of kinship indicate that, among the 17 samples, 3 from the Pingliangtai site show first and second degree relationships. Using the dating, skeletal ages, and genetic data, we successfully reconstructed the family tree of these samples, which is valuable for understanding the social structure and kinship institutions of the Longshan culture.
    全基因组主成分分析(PCA)表明,河南仰韶和龙山人群与中国现代的汉族人群聚类在一起。
    The PCA indicates that the Yangshao and Longshan samples are close to present-day Han.
    在F3分析中,仰韶和龙山古人群与中国的汉族、畲族、土家族、苗族人群共享较多的等位基因。 以上分析说明新石器中晚期,仰韶与龙山人群遗传组分高度相似,对现代的汉族、畲族、土家族等人群有着遗传贡 献。
    The f3 shared drift between these samples and Han, She, Tujia, and Miao, is relatively high. This shows that, by the late Neolithic, the Yangshao and Longshan gene pools were fairly similar and, and may have contributed to the ancestry of present-day Han, She, Tujia and Miao.

    在人群混合度Admixture分析表明,中原新石器晚期的龙山人群,相比较于新石器中期的仰韶人群,具有 较多南亚的成分,F4的分析也支持了这一结论。
    The Admixture and F4 analyses show that the Longshan population has some admixture from the South, when compared with the Yangshao.

    考古学证据表明河南仰韶文化与龙山文化,无论是文化形式、葬式及葬俗、还是农作物的栽培上都有着明显的差异 。同位素的证据表明,河南龙山时期,北方的粟作农业区与南方稻作农业区存在文化交流,这与我们在遗传学上观 察到龙山人群相对于仰韶人群具有较多的南方遗传成分相一致,即文化的交流伴随了人群的迁徙和混 合。
    Archaeological evidence, whether from subsistence crops, artifact styles, or burials, indicate that clear differences existed between the Yangshao and the Longshan. Isotopic evidence indicates that some exchange existed between the millet-farming north and the rice-farming south during the late neolithic Longshan. This is in keeping with our genetic analyses, showing that cultural change was accompanied by migration and admixture.


    综上所述,本研究首次获得了高质量的中原地区新石器时期古代人类基因组,并为研究提中华文明的起源及发展历 程提供了一个重要的时间、空间节点的参比数据。本研究结果表明,中原(河南)地区仰韶文化和龙山文化时期的 农耕人群其遗传组成具高度相似性且有略微不同,龙山人群相对于仰韶人群具有较多南方遗传成分的流入,为人群 的迁移导致文化交流提供了遗传学证据。
    In summary, the first high quality whole genome sequences from neolithic populations of the central plains show that the Longshan and Yangshao populations were mostly similar, with the Longshan population having some admixture from populations of the south, providing evidence for the role of migration in causing cultural change.

    _________ADMIXTURE analysis:
    Toupload_1.bmp
    The Longshan and Yangshao look fairly generic East Asian. As there is no Tibetan component, only Northeast Asian, Southeast Asian and Siberian, there is no way of telling how West vs East (Tibetan vs Japanese/Devil's Gate) shifted the Yangshao and Longshan samples are.
    There is a small amount of what looks like West Eurasian ancestry in Yangshao (?), need to investigate this in more detail.

    Results continued below:




    Edit: fixed some translation errors
    Last edited by Ryukendo; 05-19-2020 at 03:51 PM.
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

  2. The Following 37 Users Say Thank You to Ryukendo For This Useful Post:

     Agamemnon (05-20-2020),  Alain (05-19-2020),  blackflash16 (05-19-2020),  cpan0256 (05-23-2020),  Dewsloth (05-19-2020),  Dorkymon (05-19-2020),  Ebizur (05-19-2020),  evon (05-21-2020),  Gheg (05-29-2020),  Helen (05-19-2020),  hokkanto (05-20-2020),  Inigo Montoya (05-19-2020),  Jatt1 (05-21-2020),  kolgeh (05-20-2020),  Kulin (05-19-2020),  Lank (05-19-2020),  Max_H (05-21-2020),  Megalophias (05-19-2020),  Michalis Moriopoulos (05-20-2020),  NixYO (05-20-2020),  okarinaofsteiner (05-20-2020),  Onur Dincer (05-29-2020),  perttimp (05-19-2020),  Piquerobi (05-19-2020),  Pribislav (05-19-2020),  R.Rocca (05-19-2020),  Reza (05-29-2020),  Riverman (06-20-2020),  rozenfeld (05-19-2020),  Ruderico (05-21-2020),  Seabass (05-20-2020),  siberoberingian (05-19-2020),  Táltos (05-29-2020),  traject (05-24-2020),  Webb (05-19-2020),  xenus (06-09-2020),  xKeleix (05-19-2020)

  3. #2
    Registered Users
    Posts
    935
    Sex

    Sample details and uniparental haplogroups______:
    Attachment 37655
    Attachment 37656

    Look at the snps! This is pretty good work from Jilin university, great to see!
    O-M117 found in Longshan, second oldest O-M117 after Mogou in the Gansu Neolithic. The Q1a1a is a Chinese, specifically Han-specific clade, also found at the Hengbei site. Looks like it is actually indigenous to North China (not a pastoralist introduction), since the Neolithic at least.


    PCA Analysis______:

    https://imgur.com/a/LIFjy0M

    Attachment 37652

    Yangshao seem to fall in a position similar to Wuzhuangguoliang samples of Wang et. al., but a little bit more Eastern (closer to Japanese and Koreans), where Wzgl are more Western, but this is hard to make out anyway.

    F3 shared drift___:
    Attachment 37653
    Attachment 37654

    The maximal drift is actually shared with modern Koreans, the population overall seems quite Northern and Eastern compared to present-day Han.





    ________________________________________
    Ignoring all the politically-correct language, once we get the sequences the Yangshao may be something like a population between Boshan, Yumin, and Wzgl.
    Last edited by Ryukendo; 05-19-2020 at 06:11 PM.
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

  4. The Following 8 Users Say Thank You to Ryukendo For This Useful Post:

     Agamemnon (05-20-2020),  Jatt1 (05-21-2020),  K33 (05-20-2020),  Megalophias (05-19-2020),  Michalis Moriopoulos (05-20-2020),  okarinaofsteiner (05-20-2020),  Onur Dincer (05-29-2020),  Reza (05-29-2020)

  5. #3
    Registered Users
    Posts
    579
    Sex
    Location
    Belgrade
    Ethnicity
    Slavic
    Nationality
    Serb
    Y-DNA (P)
    PH908>A5913>A22312

    Serbia Montenegro Bosnia and Herzegovina Croatia Split-Dalmatia

  6. The Following 15 Users Say Thank You to Pribislav For This Useful Post:

     Agamemnon (05-20-2020),  Dewsloth (05-19-2020),  Helen (05-19-2020),  hokkanto (05-20-2020),  Jatt1 (05-21-2020),  kolgeh (05-20-2020),  Kulin (05-19-2020),  Lank (05-19-2020),  Megalophias (05-19-2020),  Onur Dincer (05-29-2020),  Principe (05-19-2020),  R.Rocca (05-19-2020),  Riverman (06-20-2020),  Ryukendo (05-19-2020),  siberoberingian (05-19-2020)

  7. #4
    Gold Class Member
    Posts
    1,257
    Sex
    Location
    Pittsburgh, PA
    Ethnicity
    100% European
    Nationality
    American
    Y-DNA (P)
    DF27>Z195>FGC23196
    mtDNA (M)
    U5a1a2a

    United States of America United Kingdom Germany Ireland Scotland Wales
    Quote Originally Posted by Ryukendo View Post
    h/t @ Sahaliyan

    中原仰韶至龙山时期古代人群基因组学研究 Population Genetic analysis of Neolithic populations of the Central Plains from the Yangshao and Longshan cultures
    Dissertation authored by Tianjiao Li, 李添骄, University of Jilin

    Link here
    Chinese-language discussion on Ranhaer forum

    Abstract: 摘要:
    河南位于中原中心地区,是我国华夏文明的发祥地。由于该地区史前自然资源丰富且气候适宜、优越的自然条件孕 育了早期的文明。
    The Henan region at the core of the Central Plains of China is where Chinese civilisation began. The excellent natural conditions in this region in prehistory allowed complex societies to receive a head start.

    中原地区的文化血脉连续、序列完整,并同周围地区的文化存在着广泛的交流。百川汇海,各种文化精髓汇聚成中 国古代文明,而这个汇集的中心便是中原地区的仰韶—龙山文化体系。
    The archaeological record and cultural sequence of this region is well known, and demonstrates exchange with surrounding regions. The hundred rivers reach the sea, and the spiritual essence of of many cultures meet within the Yangshao-Longshan cultural sequence of the central plains.

    目前有关 中原地区的仰韶—龙山文化体系的相关资料较为全面,考古学家所主导通过出土的器物和葬俗已经成功推演出文化 迁移的路线。目前关于史前物质文化变迁是否由人群迁移所致尚无定论。 古基因组学以分子生物学为手段,为解决文化变迁是否伴随人群迁移提供遗传学证据。
    The Yangshao-Longshan cultural sequence is described by an extensive literature, with the artifacts and burial styles as discovered by the archaeologists providing a detailed view of cultural change across geographic space. There is currently little agreement as to the role of migration in promoting cultural change. Ancient DNA, as a branch of molecular biology, provides population-genetic evidence that may help to resolve the question as to whether cultural change was accompanied by the migration of people.
    由于中原地区属于暖湿带-亚热带气候,不利于DNA的保存,因此至今尚无有关中原史前人群基因组学的报道。
    As the weather of this region is warm humid temperate to subtropical, DNA preservation is poor, and there is currently no data as to the population-genetic affinities of the ancestors of the people of the Central Plains.

    本研究以仰韶文化时期的晓邬和汪沟遗址,以及龙山文化时期的郝家台和平粮台遗址为研究对象,成功获取17例 样本的全基因组数据。检测出男性样本7例女性样本10例,其中线粒体单倍型类群主要分为B单倍型类群下的B 4d1亚型;D单倍型类群下的D4,D4g2a1,D4b2,D4j1b2,D4e1a和D4b1a亚型; F单倍型类群下的F4a2,F1a1和F2h亚型。以上单倍型均为东亚典型的单倍型,本研究中单倍型D与单 倍型F所占比例较高。
    The current study successfully extracted the whole-genome sequences of 17 individuals from the Shaowu and the Wanggou sites of the Yangshao culture, and the Chijiatai and the Pingliangtai sites of the Longshan culture. They comprise 7 males and 10 females. Among them the mitochondrial DNA sequences fall under B4d1, D4, D4g2a1, D4b2, D4j1b2, D4e1a, D4b1a, and F4a2, F1a1 and F2h, which are typical for East Asian populations. The proportion of mtDNA sequences falling under the D and F clades is relatively high.
    全基因组亲缘关系研究表明,以上17例个体中,来自平粮台遗址的三例个体间存在着相互的一、二级的亲缘关系 。结合这三个样本的年龄,测年数据以及基因组亲缘关系鉴定,本研究成功对这三例个体进行家族树的构建,为研 究龙山时期社会习俗以及社会结构提供了遗传的理论基础。
    Analyses of kinship indicate that, among the 17 samples, 3 from the Pingliangtai site show a first and second degree relationship. Using the dating, skeletal ages, and genetic data, we successfully reconstructed the family tree of these samples, which is valuable for understanding the social structure and kinship institutions of the Longshan culture.
    全基因组主成分分析(PCA)表明,河南仰韶和龙山人群与中国现代的汉族人群聚类在一起。
    The PCA indicates that the Yangshao and Longshan samples are close to present-day Han.
    在F3分析中,仰韶和龙山古人群与中国的汉族、畲族、土家族、苗族人群共享较多的等位基因。 以上分析说明新石器中晚期,仰韶与龙山人群遗传组分高度相似,对现代的汉族、畲族、土家族等人群有着遗传贡 献。
    The f3 shared drift peaks between these samples and Han, She, Tujia, and Miao. This shows that, by the late Neolithic, the Yangshao and Longshan gene pools were fairly similar and, and may have contributed to the ancestry of present-day Han, She, Tujia and Miao.

    在人群混合度Admixture分析表明,中原新石器晚期的龙山人群,相比较于新石器中期的仰韶人群,具有 较多南亚的成分,F4的分析也支持了这一结论。
    The Admixture and F4 analyses show that the Longshan population has some admixture from the South, when compared with the Yangshao.

    考古学证据表明河南仰韶文化与龙山文化,无论是文化形式、葬式及葬俗、还是农作物的栽培上都有着明显的差异 。同位素的证据表明,河南龙山时期,北方的粟作农业区与南方稻作农业区存在文化交流,这与我们在遗传学上观 察到龙山人群相对于仰韶人群具有较多的南方遗传成分相一致,即文化的交流伴随了人群的迁徙和混 合。
    Archaeological evidence, whether from subsistence crops, artifact styles, or burials, indicate that clear differences existed between the Yangshao and the Longshan. Isotopic evidence indicates that some exchange existed between the millet-farming north and the rice-farming south during the late neolithic Longshan. This is in keeping with our genetic analyses, showing that cultural change was accompanied by migration and admixture.


    综上所述,本研究首次获得了高质量的中原地区新石器时期古代人类基因组,并为研究提中华文明的起源及发展历 程提供了一个重要的时间、空间节点的参比数据。本研究结果表明,中原(河南)地区仰韶文化和龙山文化时期的 农耕人群其遗传组成具高度相似性且有略微不同,龙山人群相对于仰韶人群具有较多南方遗传成分的流入,为人群 的迁移导致文化交流提供了遗传学证据。
    In summary, the first high quality whole genome sequences from neolithic populations of the central plains show that the Longshan and Yangshao populations were mostly similar, with the Longshan population having some admixture from populations of the south, providing evidence for the role of migration in causing cultural change.

    _________ADMIXTURE analysis:
    Toupload_1.bmp
    The Longshan and Yangshao look fairly generic East Asian. As there is no Tibetan component, only Northeast Asian, Southeast Asian and Siberian, there is no way of telling how West vs East (Tibetan vs Japanese/Devil's Gate) shifted the Yangshao and Longshan samples are.
    There is a small amount of what looks like West Eurasian ancestry in Yangshao (?), need to investigate this in more detail.

    Results continued below:
    This article is really interesting. My wife is from Kaifeng, Henan province. I have been through Xingyang, on our way to Louyang to see the Longmen Grottoes and the Kaifeng Museum has an exhibit about the Longshan Culture.

  8. #5
    Registered Users
    Posts
    579
    Sex
    Location
    Belgrade
    Ethnicity
    Slavic
    Nationality
    Serb
    Y-DNA (P)
    PH908>A5913>A22312

    Serbia Montenegro Bosnia and Herzegovina Croatia Split-Dalmatia
    china neolithic.PNG

    EDIT: I added 8 more Longshan samples from Wadian site to the spreadsheet, from another unpublished study. Even though most of them are very low quality, one belongs to one of the three "neolithic superclades" O2a2b1a2a1c-Y20>Y12>CTS2643.

    Source

  9. The Following 9 Users Say Thank You to Pribislav For This Useful Post:

     Agamemnon (05-20-2020),  Helen (05-19-2020),  Lank (05-19-2020),  Megalophias (05-19-2020),  Onur Dincer (05-29-2020),  Principe (05-19-2020),  R.Rocca (05-19-2020),  rms2 (05-19-2020),  Ryukendo (05-19-2020)

  10. #6
    Registered Users
    Posts
    935
    Sex

    Quote Originally Posted by Pribislav View Post
    china neolithic.PNG

    EDIT: I added 8 more Longshan samples from Wadian site to the spreadsheet, from another unpublished study. Even though most of them are very low quality, one belongs to one of the three "neolithic superclades" O2a2b1a2a1c-Y20>Y12>CTS2643.

    Source
    The source link doesn't work, could you post again?
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

  11. #7
    Registered Users
    Posts
    579
    Sex
    Location
    Belgrade
    Ethnicity
    Slavic
    Nationality
    Serb
    Y-DNA (P)
    PH908>A5913>A22312

    Serbia Montenegro Bosnia and Herzegovina Croatia Split-Dalmatia
    Quote Originally Posted by Ryukendo View Post
    The source link doesn't work, could you post again?
    Try this one:

    http://www.ranhaer.com/forum.php?mod...read&tid=39732

    Summary:

    http://www.ranhaer.com/data/attachme....png.thumb.jpg

  12. The Following 2 Users Say Thank You to Pribislav For This Useful Post:

     Onur Dincer (05-29-2020),  Ryukendo (05-19-2020)

  13. #8
    Registered Users
    Posts
    109
    Sex
    Omitted
    Ethnicity
    Mostly Chinese
    Nationality
    USA

    United States of America China
    Quote Originally Posted by Ryukendo View Post
    Sample details and uniparental haplogroups______:
    Attachment 37655
    Attachment 37656

    Look at the snps! This is pretty good work from Jilin university, great to see!
    O-M117 found in Longshan, second oldest O-M117 after Mogou in the Gansu Neolithic. The Q1a1a is a Chinese, specifically Han-specific clade, also found at the Hengbei site. Looks like it is actually indigenous to North China (not a pastoralist introduction), since the Neolithic at least.


    PCA Analysis______:

    https://imgur.com/a/LIFjy0M

    ________________________________________
    Ignoring all the politically-correct language, once we get the sequences the Yangshao may be something like a population between Boshan, Yumin, and Wzgl.

    What do the bold colored shapes represent? I'm guessing the yellow diamonds are Han_HGDP (which is a more southern-shifted Han Chinese reference population)?

  14. #9
    Registered Users
    Posts
    547
    Sex

    Quote Originally Posted by okarinaofsteiner View Post
    What do the bold colored shapes represent? I'm guessing the yellow diamonds are Han_HGDP (which is a more southern-shifted Han Chinese reference population)?
    The legend reads, in Chinese:

    Red circles = 仰韶 (Yangshao)
    Green squares = 龙山 (Longshan)
    Yellow diamonds = 汉族 (Han people)

    Or are you wondering whether Ryukendo is privy to more precise information regarding the origins of these "Hanzu" individuals?

  15. The Following 3 Users Say Thank You to Ebizur For This Useful Post:

     Agamemnon (05-20-2020),  okarinaofsteiner (05-21-2020),  Onur Dincer (05-29-2020)

  16. #10
    Registered Users
    Posts
    90
    Sex

    The M134 sample in Henan Longshan sample is actually wrong,it's pre-F915.And the NO sample in Longshan is N-M1819

  17. The Following User Says Thank You to sahaliyan For This Useful Post:

     Ryukendo (05-20-2020)

Page 1 of 7 123 ... LastLast

Similar Threads

  1. Replies: 14
    Last Post: 05-31-2020, 10:12 AM
  2. Replies: 382
    Last Post: 04-29-2020, 10:10 PM
  3. Replies: 41
    Last Post: 05-31-2018, 11:36 PM
  4. Replies: 2
    Last Post: 03-29-2017, 06:29 PM
  5. Replies: 2
    Last Post: 10-10-2015, 09:39 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •