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Tocharian_2 发表于 2014-6-6 13:58

The complete genome sequence of a 45,000-year-old modern human from Eurasia

[i=s] 本帖最后由 Ryan 于 2014-6-6 14:06 编辑 [/i]

SMBE 2014 Ancient Genomics

[url=https://mcidublin.conference-services.net/reports/template/onetextabstract.xml?xsl=template/onetextabstract.xsl&conferenceID=3958&abstractID=811773]https://mcidublin.conference-ser ... 8&abstractID=811773[/url]

"We have sequenced to high coverage the genome of a femur recently discovered near Ust-Ishim in Siberia. The bone was directly carbon-dated to 45,000 years before present. Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians. The over-all amount of genomic admixture from Neandertals is similar to that in present-day non-Africans and there is no evidence for admixture from Denisovans. However, the size of the genomic segments of Neandertal ancestry in the Ust-Ishim individual is substantially larger than in present-day individuals. From the size distribution of these segments we estimated that this individual lived about 200-400 generations after the admixture with Neandertals occurred. The age of this genome allows us to directly assess the mutation rate in the different compartments of the human genome. These results will be presented and discussed."

一统浆糊 发表于 2014-6-6 19:50

值得期待。

一统浆糊 发表于 2014-6-6 22:02

大胆预测一下:此君Y会是F下今天没有的一支,MT会是U下今天没有的一支。跟MA-1一样,此君没有直系后代。

cpan0256 发表于 2014-6-23 13:06

网上可以搜到的信息比一楼的会议报告摘要里的多一些。但是文章还没有出,Y单倍型还没有公布。mtDNA单倍群类型据网上听过Fu Qiaomei一次有关讲演的人说是R。

我的三个印象。(1)测序的平均覆盖率是42倍。(2)按今天的人的数据,mtDNA单倍型M和N在距今50000-59000年前成为人群中的成分。因为R是N之下的分支,所以45000年前的R与此相符合。(3)按这人的DNA来估计,与尼人的混合发生在他的331加减99代以前,距今50000-60000年。按今天的人(French, Sardinian, Han, Dai, Karitiana)的数据,简单假定有过一次混合,估计出的时间区间比较宽,距今37000-86000年。

下面是几个链接。
Svante Paabo在美国国立卫生研究院(NIH)的一次有关讲演:
[url=http://www.youtube.com/watch?v=M7VdRKQuAa8]http://www.youtube.com/watch?v=M7VdRKQuAa8[/url]
如果接不通,也许下面的链接可用:
[url=http://dienekes.blogspot.com/2014/04/svante-paabo-talk-at-nih.html]http://dienekes.blogspot.com/201 ... bo-talk-at-nih.html[/url]
[url=http://aratta.wordpress.com/2014/04/14/svante-paabo-talk-at-nih]http://aratta.wordpress.com/2014/04/14/svante-paabo-talk-at-nih[/url]
美国国立卫生研究院关于这次讲演的报导:
[url=http://nihrecord.nih.gov/newsletters/2014/05_23_2014/story1.htm]http://nihrecord.nih.gov/newsletters/2014/05_23_2014/story1.htm[/url]

有人在听Fu Qiaomei的一次有关讲演时做的一页笔记:
[url=http://snag.gy/IzthP.jpg]http://snag.gy/IzthP.jpg[/url]

Ust-Ishim, 按谷歌翻译是俄罗斯,鄂木斯克州,乌斯季 - 伊希姆区,不知准不准。

Yungsiyebu 发表于 2014-6-23 14:15

大体与石叶工业的传播吻合,找不到考古学依据的沿海迁徙理论,渐渐被古dna证据冲散。

hercules 发表于 2014-6-23 15:04

种种特点听起来很像basal Eurasian,与今天的欧亚人种相差均远。

wolfgang 发表于 2014-6-23 15:08

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392299&ptid=28540]6#[/url] [i]hercules[/i] [/b]未必是basal Eurasian,也有可能走向东亚的一个小分支。

natsuya 发表于 2014-6-23 15:36

[quote]Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians.
[size=2][color=#999999]Tocharian_2 发表于 2014-6-6 13:58[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=389240&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]這段話的意思好像是說,該古人的遺傳組成,與今日歐洲人及亞洲人的共祖群體關係密切,不知道這共祖群體是不是指K-M526,包括K2a(NO)及K2b(M、S、P等支系)。

[b]Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia:[/b]
[url=http://www.ranhaer.com/thread-28528-1-1.html]http://www.ranhaer.com/thread-28528-1-1.html[/url]


[img]http://www.ranhaer.com/attachments/forumid_97/1406051617feaa2d36a95169d1.png.thumb.jpg[/img]

ranger 发表于 2014-6-23 15:56

是不是就是那个田园洞人的全序?这个会有Y吗?

Tocharian_2 发表于 2014-6-23 16:11

[quote]是不是就是那个田园洞人的全序?这个会有Y吗?
[size=2][color=#999999]ranger 发表于 2014-6-23 15:56[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392310&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]

"We have sequenced to high coverage the genome of a femur recently discovered near [b]Ust-Ishim in Siberia[/b]"

ranger 发表于 2014-6-23 16:15

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392315&ptid=28540]10#[/url] [i]Tocharian_2[/i] [/b]不好意思,没注意到,{:8_197:}

wolfgang 发表于 2014-6-23 16:32

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392306&ptid=28540]8#[/url] [i]natsuya[/i] [/b]如果这具古尸是和Y-C1相关的话,也会是和现代欧洲和东亚人群密切相关,但显然不会是主流。

hercules 发表于 2014-6-23 17:37

[quote]這段話的意思好像是說,該古人的遺傳組成,與今日歐洲人及亞洲人的共祖群體關係密切,不知道這共祖群體是不是指K-M526,包括K2a(NO)及K2b(M、S、P等支系)。

Improved phylogenetic resolution and rapid diversif ...
[size=2][color=#999999]natsuya 发表于 2014-6-23 15:36[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392306&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]常染色体方面的,未必与Y贴合。我觉得与今天高加索地区和西亚一带人最接近

hercules 发表于 2014-6-23 17:48

[quote]大体与石叶工业的传播吻合,找不到考古学依据的沿海迁徙理论,渐渐被古dna证据冲散。
[size=2][color=#999999]Yungsiyebu 发表于 2014-6-23 14:15[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392289&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]{:8_192:}

hercules 发表于 2014-6-23 17:48

[quote]大体与石叶工业的传播吻合,找不到考古学依据的沿海迁徙理论,渐渐被古dna证据冲散。
[size=2][color=#999999]Yungsiyebu 发表于 2014-6-23 14:15[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392289&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]{:8_192:}

natsuya 发表于 2014-6-23 18:09

[quote]常染色体方面的,未必与Y贴合。我觉得与今天高加索地区和西亚一带人最接近
[size=2][color=#999999]hercules 发表于 2014-6-23 17:37[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392326&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]的確,看摘要更可能是講常染色體的共祖,Y不見得吻合。比較耐人尋味的,他說歐洲人和亞洲人的共祖群體成分,但沒有提到中東人和非洲人,是不是說這個共祖群體的常染影響主要融入歐洲人和亞洲人。

natsuya 发表于 2014-6-23 18:12

[quote] 8# natsuya 如果这具古尸是和Y-C1相关的话,也会是和现代欧洲和东亚人群密切相关,但显然不会是主流。
[size=2][color=#999999]wolfgang 发表于 2014-6-23 16:32[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392318&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]Yes,摘要應該是講常染影響,Y可能不能完全對應。

天天向上 发表于 2014-6-23 19:27

[quote]的確,看摘要更可能是講常染色體的共祖,Y不見得吻合。比較耐人尋味的,他說歐洲人和亞洲人的共祖群體成分,但沒有提到中東人和非洲人,是不是說這個共祖群體的常染影響主要融入歐洲人和亞洲人。
[size=2][color=#999999]natsuya 发表于 2014-6-23 18:09[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392334&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]只要是和亚洲对比,欧洲学者默认中东北非就是欧洲成分

hercules 发表于 2014-6-23 20:56

[quote]的確,看摘要更可能是講常染色體的共祖,Y不見得吻合。比較耐人尋味的,他說歐洲人和亞洲人的共祖群體成分,但沒有提到中東人和非洲人,是不是說這個共祖群體的常染影響主要融入歐洲人和亞洲人。
[size=2][color=#999999]natsuya 发表于 2014-6-23 18:09[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=392334&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
这也未必吧,要注意这是四五万年前的古DNA,即使他所在人群没有发展成欧亚人,他仍有可能比现代的欧亚人更接近欧亚人的祖先。

cpan0256 发表于 2014-10-23 02:29

文章正式发表了。

Genome sequence of a 45,000-year-old modern human from western Siberia

Nature 514, 445-449 (23 October 2014)  doi:10.1038/nature13810
Received 15 May 2014 Accepted 29 August 2014 Published online 22 October 2014

Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola & Svante Pääbo

Abstract
We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before - or simultaneously with - the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10-9 to 0.6 × 10-9 per site per year, a Y chromosomal mutation rate of 0.7 × 10-9 to 0.9 × 10-9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10-8 to 3.2 × 10-8 per site per year based on the age of the bone.


全文和附件:[url=http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html]http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html[/url]
[url=http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf]http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf[/url]

cpan0256 发表于 2014-10-23 07:26

一篇关于此文章的短新闻附带有第一和倒数第四作者的一张照片:

[url=http://news.harvard.edu/gazette/story/2014/10/new-evidence-on-neanderthal-mixing/]http://news.harvard.edu/gazette/story/2014/10/new-evidence-on-neanderthal-mixing/[/url]

Ryan 发表于 2014-10-23 08:00

The Ust’-Ishim sequence mitochondrial   shares  a  common  ancestor  with  the  sequencesfrom  154  individuals belonging to the R haplogroup (0.88 posterior support).  (Figure S8.1). The Ust’-Ishim individual carries the following substitutions that define the R haplogroup (compared to rCRS sequence) : 73G, 263G, 750G, 1438G, 2706G, 3107d, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G as well as one specific substitution not seen in any presentday population (rCRS pos: 16150). Further, it lacks any of the additional substitutions that  define  subclades  of  haplogroup  R,  suggesting  that  it  is  related  to  the  mtDNA [b][color=blue]ancestral to present-day haplogroup R[/color][/b].

Haplogroup  R  is  a  large  and  diverse  haplogroup  and  represents  the  most  common macro-haplogroup in West Eurasia. The 6 most common European haplogroups (H, V, J, T, U, K) 7, and half of the most common eastern Eurasian mtDNA haplogroups 8,9 belong to the R haplogroup. Though the phylogeny is not strongly supported, the Ust’-Ishim mtDNAappears to be most closely related to the [color=blue][b]direct R sub-clades R*[/b][/color](P,B,  F,  T,  J)  which  are  also  found  among  Papuans,  indigenous  Australians, and mainland Eurasians.

Ryan 发表于 2014-10-23 08:01

The Ust’-Ishim  Y  chromosome  sequence  clusters  with  the  K(xLT) haplogroup.  The Ust’-Ishim  sequence  shares all the  mutations  common  to  the  K  macrohaplogroup and has one additional specific mutation rs2033003/M526 which defines the group
K(xLT) (Figure S9.1,  blue part). The Ust’-Ishim Y-chromosome carries no additional mutations belonging to any of the sub-haplogroups of [b][color=blue]K(xLT)[/color][/b]; however, there are 6 additional mutations that are not observed in the 23 present-day humans to which we compare. K(xLT)  currently has a 54% frequency in Eurasia (Lippold et al. 2014, bioRxiv doi: 10.1101/001792).

Ryan 发表于 2014-10-23 08:03

We used the Ust’-Ishim radiocarbon date of 45,000 years asa calibration point to estimate the Ychromosome mutation rate.

With  the  strict  clock  model  and  the constant size model, we estimate a mutation rate of [color=blue][b]0.76 ×10-9[/b][/color] substitutions per site per year (95% HPD: [color=blue][b]0.67-0.86 ×10-9[/b][/color]). This estimate is consistent with the mutation rate of [color=blue][b]0.82 x 10-9[/b][/color](95% CI: [color=blue][b]0.72 - 0.92 ×10-9[/b][/color]) estimated in reference 5
which used the first settlement of the Americas as a  calibration  point,  and is  in  the  range  of  the  other  published  estimate 6 of  1.0 × 10−9 mutations/nucleotide/year (95% CI: 3.0×10−10– 2.5×10−9) based on sequencing of a deep-rooting pedigree. The mutation rate is higher than that used by Mendez et al. (2013) 7.

Ryan 发表于 2014-10-23 08:22

According to this paper, K-M9 is ~50k (47k-55k) years old.

ranger 发表于 2014-10-23 08:31

[quote]According to this paper, K-M9 is ~50k (47k-55k) years old.
[size=2][color=#999999]Ryan 发表于 2014-10-23 08:22[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405921&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]不错,这对K系的年龄是一个很好的校正。我很好奇[align=center]Ust’-Ishim的来源是南亚,还是东南亚,根据以往得文献,C,K系于4.5-5万年已经到了东南亚华莱士线以东的地区。[/align]

Yungsiyebu 发表于 2014-10-23 11:34

K(xLT)。。。

所以,诸如沿海大迁徙,东南亚起源,这种毫无考古依据的推测,出了一两例古DNA,就不会有人再提了。

imvivi001 发表于 2014-10-23 13:09

[quote] ...The Ust’-Ishim Y-chromosome carries no additional mutations belonging to any of the sub-haplogroups of [b][color=blue]K(xLT)[/color][/b]; however, there are 6 additional mutations that are not observed in the 23 present-day humans to which we compare.
[size=2][color=#999999]Ryan 发表于 2014-10-23 08:01[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405917&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]
也有可能是[b][color=blue]K(xLT)[/color][/b]某一个现在已经灭绝的支系~

Ryan 发表于 2014-10-23 16:27

Yes. It should be marked as K*(xLT).  

It had been mentioned that Ust'-Ishim Man have "6 additional mutations that are not observed in the 23 present-day humans".  So, just as Mal'ta Boy, Ust' Ishim Man's paternal lineage have its own special SNPs, but it vanished in the history.

I consider that his lineage is only one of numerous of K-M9's sublineages. Please notice the time gap:  K-M9 is about 50k years old (or older slightly to 52k years) and Ust' Ishim Man is only one of M9's descendants after 5000 (or 7k years) years.

Yungsiyebu 发表于 2014-10-23 20:20

我还是老话,就分子人类学这种刚刚研究了皮毛而已的新兴学科,不要听风就是雨,人群迁徙轨迹还是要重点考虑传统手段,有人骨,观察颅骨形态学变化(至少和常染色体特征有很好的吻合性),没有人骨也要看器物证据,一种与人骨特征变化和石器文化变化毫无吻合度可言的理论,几乎可以不用当回事。

wolfgang 发表于 2014-10-23 23:54

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405988&ptid=28540]30#[/url] [i]sahaliyan[/i] [/b]没什么要重新考虑的,出非洲人群到印度后迅速分南北两线迁徙,开始北线人群的发展不逊于南线。但是随着小冰期的到来,北线人群被重创,南线人群取得了优势,现在这个世界的主流单倍群O,N,Q,R都来自于南线。

wolfgang 发表于 2014-10-23 23:58

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405977&ptid=28540]29#[/url] [i]Ryan[/i] [/b]嗯,这个K*看起来是从K的根部直接分出来的。看起来K人群在印度有一次大爆发,然后迅速向各处迁徙。

wolfgang 发表于 2014-10-24 00:01

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405993&ptid=28540]32#[/url] [i]sahaliyan[/i] [/b]这个其实是意料中的。按照以前的估计,这个北线人群和现代欧洲人群并没有太多的交集。

hercules 发表于 2014-10-24 07:58

[quote]仅仅诞生5000年就到了西伯利亚?这样看来南线迁徙理论确实问题重重,需要重新考虑了
[size=2][color=#999999]sahaliyan 发表于 2014-10-23 18:39[/color] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405988&ptid=28540][img]http://www.ranhaer.com/images/common/back.gif[/img][/url][/size][/quote]美洲人3000年就跑到了火地岛,岂不是更牛逼?

xfcookey 发表于 2014-10-24 08:18

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=406019&ptid=28540]36#[/url] [i]hercules[/i] [/b]真有这事?是时间估算是错的还是“跑”这件事有问题?还是那些人真“牛”?

ranger 发表于 2014-10-24 09:06

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=405917&ptid=28540]23#[/url] [i]Ryan[/i] [/b]这似乎说明Ust‘-Ishim和其他K-M526系人群分离较早,K-M526南亚起源的可能性也很大,在K-M526产生不久,正好一个小间冰期,Ust’-Ishim向北发展,而其他k-M526向东南亚发展,但[align=center]Ust’-Ishim无法[/align][align=center]躲避随后的冰期,最后灭绝。[/align]

Yungsiyebu 发表于 2014-10-24 13:16

一、南线,石器文化不支持任何东南亚砾石工业北上的说法。
二、北线,石叶工业的扩散以及在向细石器文化过渡中,一直不存在断层现象。

被冻死是想当然的。事实上,4万年前后,南太平洋地区有没有现代人还是一打问号的问题,比如蒙戈湖人就不是。

Yungsiyebu 发表于 2014-10-24 14:29

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=406059&ptid=28540]39#[/url] [i]Yungsiyebu[/i] [/b]

wolfgang 发表于 2014-10-24 15:18

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=406067&ptid=28540]40#[/url] [i]Yungsiyebu[/i] [/b]Ust‘-Ishim的常染也很原始,没有占明显优势的成分,只能说南亚成分最多,巴布亚和东亚成分次之。这和马尔他男孩是有本质区别的,甚至和田园洞人相比也是如此。

wolfgang 发表于 2014-10-24 15:26

[b] [url=http://www.ranhaer.com/redirect.php?goto=findpost&pid=406059&ptid=28540]39#[/url] [i]Yungsiyebu[/i] [/b]马尔他男孩的分子生物学证据和考古物证是决定性的,其他任何一种考古学证据目前都没有这种决定性。马尔他男孩的Y是R*,而R是和印尼地区的某些P更接近,mtDNA是U,常染接近南亚和欧洲,而遗址中的大蛇崇拜显示了这是一次从热带亚热带地区的快速迁徙。

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