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fjnj 发表于 2016-6-21 06:39

Ancient DNA from Himalayan Arc

[i=s] 本帖最后由 Ryan 于 2016-7-6 02:00 编辑 [/i]

doi: 10.1073/pnas.1520844113 open access

[color=Blue]Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc[/color]
Choongwon Jeonga,

Abstract

The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×–7.25×, mean 2.16×) and mitochondrial genomes (20.8×–1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150–1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.




http://www.pnas.org/content/113/27/7485.abstract

This is the first ancient DNA from East Asia and interestingly, the Y haplogroups are M117 and D.

Yungsiyebu 发表于 2016-6-21 08:38

第二例肯定的古代m117样本,和第一例古代D样本。

Yungsiyebu 发表于 2016-6-21 08:53

[i=s] 本帖最后由 Yungsiyebu 于 2016-6-21 09:03 编辑 [/i]

额,这个好啊,是二代测序数据,7x覆盖率,理论上可以分下游。数据是否公开下载,大家关注一下。
Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc

CHOONGWON JEONG1, ANDREW T. OZGA2, DAVID WITONSKY1, HELENA MALMSTROM3, MATTIAS JAKOBSSON3, CECIL M. LEWIS2, MARK ALDENDERFER4, ANNA DI. RIENZO1 and CHRISTINA WARINNER2.
1Department of Human Genetics, University of Chicago, 2Department of Anthropology, University of Oklahoma, 3Department of Evolutionary Biology, University of Uppsala, 4Department of Anthropology, University of California, Merced

April 16, 2016 11:15, A 602  

The high altitude transverse valleys (> 3000 masl) of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of hypoxia, cold stress, and resource scarcity. The modern populations of these valleys share cultural and linguistic affinities with peoples found today on the Tibetan plateau, and it is commonly assumed that these modern peoples are the descendants of the earliest inhabitants of these valleys. However, this assumption has been challenged by archaeological and osteological evidence that suggests that these valleys were originally populated from areas other than the Tibetan plateau, some of which are found at low elevation. Importantly, long-term inhabitants of the Tibetan plateau are known to have evolved genetic adaptations to hypoxia, including selection of an EGLN1 allele that is rare in lowlanders. Therefore, migrants into these valleys would have been at a disadvantage relative to pre-existing adapted populations. To investigate the peopling and early population history of this dynamic high altitude contact zone, we obtained low-coverage genome-wide sequences (0.04-0.65x, mean 0.25x) and high coverage mitochondrial sequences (20.8-77.8x, mean 46.4x) from eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3150-1250 BP. We demonstrate that the region is characterized by long-term stability of the population genetic make up despite marked changes in cultural remains. Genome-wide markers, mitochondrial haplotypes, and high altitude adaptive alleles suggest a high altitude East Asian origin for prehistoric Himalayan populations.

Yungsiyebu 发表于 2016-6-21 11:21

[i=s] 本帖最后由 Yungsiyebu 于 2016-6-21 11:37 编辑 [/i]

NCBI上的原始数据还没有发出来,非常期待,看看细分后的结果是什么。

[url=http://www.pnas.org/content/early/2016/06/16/1520844113]http://www.pnas.org/content/early/2016/06/16/1520844113[/url]

Data deposition: Metagenomic DNA sequences have been deposited in the NCBI Short Read Archive (SRA) (project accession no. SRP065070 and sample accession nos. SRR2751055–SRR2751058, SRR2751060–SRR2751063, SRR2751066–SRR2751067, SRR2751070, SRR2751142, SRR2751148, SRR2751152, SRR3222643, SRR3222649, SRR3222655, SRR3222659, SRR3222661, SRR3222664, SRR3222686, SRR3222749, SRR3222758, SRR3222765, and SRR3222772).
常染色体分析,基本同质,看不出M117样本D样本有什么差异,与现代藏族最为接近。
母系结果,都是东方类型。

父系样本,覆盖率挺不错,y-dna 5900万位点中,3个m117样本1200-1500万之间,以往经验,这个足够细分到最细端了。期待数据公开。

Yungsiyebu 发表于 2016-6-21 11:45

我还是老话,3000年前后,一例尼泊尔样本,就可以测到M117+,而其它地区,除了内蒙古山戎组,至今没有肯定的样本,我相信这个绝不是偶然现象。

Yungsiyebu 发表于 2016-6-21 12:03

一组古人基因组数据。

wolfgang 发表于 2016-6-21 12:18

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482069&ptid=33941]8#[/url] [i]sahaliyan[/i] [/b]
能将山戎和喜马拉雅地区联系起来的古文明不正是仰韶么?甚至没有另外一种可能。

Yungsiyebu 发表于 2016-6-21 12:28

没人任何证据支持F5主要支系在青铜时代前后走向地理意义上的扩张,这是我们目前基于全部证据看到的事实。

hercules 发表于 2016-6-21 12:34

[quote]没人任何证据支持F5主要支系在青铜时代前后走向地理意义上的扩张,这是我们目前基于全部证据看到的事实。
[size=2][color=#999999]Yungsiyebu 发表于 2016-6-21 12:28[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482082&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]也没有任何证据反对啊。

Yungsiyebu 发表于 2016-6-21 12:51

[quote]证据是支持的,M117下面在青铜时期以后扩张的大簇有哪几个,比例多少?北方M117达到15%,只有F316是在2000多年前扩张的,其他似乎分化都很远,不支持青铜扩张模式,反倒吻合新石器农民扩张模式,所以支系零碎而散,每 ...
[size=2][color=#999999]sahaliyan 发表于 2016-6-21 12:46[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482087&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
完全想当然。

hercules 发表于 2016-6-21 12:51

[quote]证据是支持的,M117下面在青铜时期以后扩张的大簇有哪几个,比例多少?北方M117达到15%,只有F316是在2000多年前扩张的,其他似乎分化都很远,不支持青铜扩张模式,反倒吻合新石器农民扩张模式,所以支系零碎而散,每 ...
[size=2][color=#999999]sahaliyan 发表于 2016-6-21 12:46[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482087&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]你说的这不是一回事。

imvivi001 发表于 2016-6-21 13:51

非常有意思,希望尽早看到关中地区仰韶古人的DNA检测结果~

imvivi001 发表于 2016-6-21 14:36

[quote]不仅关中,河南西部,晋南也颇为值得关注,当然这些地方可能各有区别,不过值得关注
[size=2][color=#999999]sahaliyan 发表于 2016-6-21 13:54[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482115&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
估计豫西晋南在仰韶中后期也是比较混杂了~

wanhuatong 发表于 2016-6-21 18:34

[i=s] 本帖最后由 wanhuatong 于 2016-6-21 18:37 编辑 [/i]

竟然还真让我说中了,还真发现了D!虽然是在西藏。希望有更早期的遗址能够被测量

nfz 发表于 2016-6-21 19:48

与考古符合,克什米尔早就发现仰韶型农具,而且还是在梅尔加赫扩张之前的

nfz 发表于 2016-6-23 06:25

看错时间抱歉,3000年前已经接近佛教时代,对仰韶的成分几乎不提供任何信息了。貌似根据现代分布,在克什米尔盆地使用仰韶石刀者是O2a,也就是带给所有印度语支中的para-munda成分来源的这种可能性还大于M117
印度史有种观点认为奥义书,及后来的佛教、耆那教等反吠陀思潮都是受影响于铁器时代快速砍伐森林导致的与完全不同宗教背景的当地人的接触倒是与此有关

隔壁老王 发表于 2016-6-23 16:32

[quote]我还是老话,3000年前后,一例尼泊尔样本,就可以测到M117+,而其它地区,除了内蒙古山戎组,至今没有肯定的样本,我相信这个绝不是偶然现象。
[size=2][color=#999999]Yungsiyebu 发表于 2016-6-21 11:45[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482066&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
这个论调多次被驳斥的体无完肤,还在继续歪曲,脸皮够厚。

1、大山前遗址样本为灰坑,灰坑不是本部落成员。

2、夏家店上层是不是山戎,目前还不是定论。

3、中原地区的遗址基本都没有大量测过,就歪曲成了其他地方没有M117。

4、很多O3未测M117的点,比如陶寺的一例M134。

Yungsiyebu 发表于 2016-6-23 19:11

数据已经出来了,着手分析。

[url]http://www.ncbi.nlm.nih.gov/sra/?term=SRP065070[/url]

guwei0001 发表于 2016-6-23 20:44

[i=s] 本帖最后由 guwei0001 于 2016-6-23 20:47 编辑 [/i]

[quote]我还是老话,3000年前后,一例尼泊尔样本,就可以测到M117+,而其它地区,除了内蒙古山戎组,至今没有肯定的样本,我相信这个绝不是偶然现象。
[size=2][color=#999999]Yungsiyebu 发表于 2016-6-21 11:45[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482066&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
M117超过一万五千年了,敢情一万多年里他们只在这些地方转。

Yungsiyebu 发表于 2016-6-23 23:08

[quote]
M117超过一万五千年了,敢情一万多年里他们只在这些地方转。
[size=2][color=#999999]guwei0001 发表于 2016-6-23 20:44[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482326&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]


R好几万岁了,但的确在青铜时代前后基本才溜达到欧洲。这个不是想当然的东西,要看证据说话。

guwei0001 发表于 2016-6-24 09:24

[quote]


R好几万岁了,但的确在青铜时代前后基本才溜达到欧洲。这个不是想当然的东西,要看证据说话。
[size=2][color=#999999]Yungsiyebu 发表于 2016-6-23 23:08[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482341&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]你这个例子正说明了y的流动性强。

Yungsiyebu 发表于 2016-6-24 14:14

[i=s] 本帖最后由 Yungsiyebu 于 2016-6-24 14:19 编辑 [/i]

[quote]你这个例子正说明了y的流动性强。
[size=2][color=#999999]guwei0001 发表于 2016-6-24 09:24[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482370&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
所以,不可能万年不变。中原的确古今基因组成变化的十分剧烈,线粒体大量证据已经支持,Ydna的初步证据同样支持。M117最似这种变化因素的代表标记之一。

guwei0001 发表于 2016-6-24 16:43

[quote]
所以,不可能万年不变。中原的确古今基因组成变化的十分剧烈,线粒体大量证据已经支持,Ydna的初步证据同样支持。M117最似这种变化因素的代表标记之一。
[size=2][color=#999999]Yungsiyebu 发表于 2016-6-24 14:14[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=482413&ptid=33941][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]

[url=http://www.docin.com/touch_new/preview_new.do?id=374375000][color=#0066cc]http://www.docin.com/touch_new/preview_new.do?id=374375000[/color][/url]
试论客省庄二期文化

作者认为:庙底沟二期--->客省庄二期——>齐家文化

Yungsiyebu 发表于 2017-2-2 23:00

[i=s] 本帖最后由 Yungsiyebu 于 2017-2-2 23:12 编辑 [/i]

最古老的C1样本,基本分出来了,应当是CST1642下的Z26030。O2a2b1a1a6b1a
[url=http://pan.baidu.com/s/1jIBeZzS]http://pan.baidu.com/s/1jIBeZzS[/url]

核对ing。

文献还一例男性样本M240,因为数据质量比较差,文献没有做分型,大家可以试试。应当是F/K下的分支,但不确定是不是O。

[url=http://pan.baidu.com/s/1o84lrqa]http://pan.baidu.com/s/1o84lrqa[/url]

txt文档是通过samtool由Bam直接转换过来的,比较大,可以用ultraedit打开查阅。

Yungsiyebu 发表于 2017-2-4 12:37

[url]http://pan.baidu.com/share/link?shareid=2407448977&uk=788735098[/url]

BAM文件。

Enkhjargalan 发表于 2017-8-6 16:57

[i=s] 本帖最后由 Enkhjargalan 于 2017-8-6 17:17 编辑 [/i]

2例古尼泊尔样本snp数据,本来要分析出str的,因降解太厉害只有一例样本得出STR数据,数据附链接。[url=http://pan.baidu.com/s/1qYBcWos]http://pan.baidu.com/s/1qYBcWos[/url]

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