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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

本帖最后由 Ryan 于 2014-2-10 10:01 编辑

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Maanasa Raghavan etc.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12736.html
本帖最后由 sahaliyan 于 2013-11-21 16:53 编辑

论坛没有谁比萨某还无私的了

Mal'ta.pdf (503.46 KB)

三界无安,犹如火宅。众苦充满,甚可怖畏
                            --------《法华经》
是以法从心生。名因法立
                      ------------《宗镜录》
2# sahaliyan 先存一份,好歹也是阿堵物。
附件太大提供不了,想要的请私信
三界无安,犹如火宅。众苦充满,甚可怖畏
                            --------《法华经》
是以法从心生。名因法立
                      ------------《宗镜录》
The mtDNA sequences of MA-1 and
DV-14 share only the three basal mutations inside hg U with each other, and do not
belong toany known modern branch of hg U.

Of these, 138 are in the derived and 5 in the ancestral state,
placing MA-1 as a lineage basal to hg R. With only a few exceptions characterized
below, all other informative positions in MA-1 are in the ancestral state, further
supporting the phylogenetic positioning of MA-1 on the tree.
三界无安,犹如火宅。众苦充满,甚可怖畏
                            --------《法华经》
是以法从心生。名因法立
                      ------------《宗镜录》
It is a little misleading to call this boy  "european" because he had dark brown eyes and dark skin (Table SI 14).  It actually reaffirmed that the european treats (blue eyes and fair skin) developped much later and the early modern humans in europe are probably dark skinned people.
很有料的paper,要仔細看一會兒。Ma的Y染:
Y_Malta.png
2013-11-22 10:24
目前在復旦已經停止對外的收費服務,只做科硏項目。測試可以找源基因 www.yoogene.com 。
新浪微博@polyhedron
微信公衆号fenzirenleixue
這麼看MA-1的Y染色體是R(xR1, R2)下的一個支系了。
Y染色體:O3 M134+ M117-
mtDNA:D5a2
估计是R诞生不久的分支。
O3a3c* (M134+, M117-)
MA-1與現代各地人群樣本在常染色體PCA上的遺傳關係。
pca.png
treemix.png
Y染色體:O3 M134+ M117-
mtDNA:D5a2
本帖最后由 Ryan 于 2013-11-25 18:34 编辑

在我看来,这样的常染色体的相似状态,与之前推测的Y染色体单倍群的扩散过程没有冲突:  在距今~2.4万年的时候,P的下游 Q&R 刚刚诞生,他们很可能作为同一个人群生活在同一个区域(南西伯利亚)。LGM来临,有一部分R的下游(R1b),向西部和南部扩散,称为后来遍布西欧亚和非洲的R1b的来源。而LGM 之后,Q向东部扩散,最后进入美洲和东亚。R1a1则是 LGM之后才缓慢向西部扩散的,他们的扩散可能伴随着浅色素基因的扩散。(南亚高频的R2在中亚也普遍可见,其诞生与中亚偏西南方向的可能是存在的。)

西方人恐怕难以接受 父系 R是从中亚诞生的吧,这意味这他们绝大部分人有“亚洲血统”。 但就文章来说,声称"contemporary western Eurasians had a more north-easterly distribution 现代西欧亚人群在远古时期在东方的分布范围比原来以为的要广阔得多 ", "western Eurasian genetic signatures in modern-day Native Americans 西欧亚遗传标记在现代美洲土著中",不是有违事实吗?

不过,从另一个讲,如果作者说“现代西欧亚人的大部分常染色体成分可以追溯到史前的南西伯利亚人群”,这文章恐怕也很难发表吧。
1

评分次数

本帖最后由 baiyueren 于 2013-11-25 20:31 编辑
在我看来,这样的常染色体的相似状态,与之前推测的Y染色体单倍群的扩散过程没有冲突:  在距今~2.4万年的时候,P的下游 Q&R 刚刚诞生,他们很可能作为同一个人群生活在同一个区域(南西伯利亚)。LGM来临,有一部分 ...
Ryan 发表于 2013-11-25 18:33
我基本同意兰海兄的观点,但是从Y树来看,MA-1的R类型有独有的35个位点突变,所以R的实际年龄保守估计应该近3万年,如果再考虑突变速率低估的话,应该还要久远一些。

还有补充一点,就是这个马尔塔男孩实际代表的是被LGM灭绝的Y-R*,mt-U*类型,暗示LGM前存在过R的分支类型是相当多的。结合田园洞的mt-B*类型来看,现在大规模扩散的很多Y和mt类型,可能只是众多存在过的分支之中的极少数LGM幸存者而已。
NRY: O2a1c1a1a1a1a1a1-002611,F11,F17,F856,F1495(源自粤西云浮)
mtDNA:B4d1(源自浙北慈溪)
百越人的人类学文集 http://blog.sina.com.cn/baiyueren
本帖最后由 baiyueren 于 2013-11-25 20:52 编辑

还有就是田园洞人的常染与现代东亚和美洲人都有共享成分,这很容易理解,因为美洲常见的Y-C和mt-A/B/C/D都是来自东亚北上的成分。
但是马尔塔男孩和美洲人有常让共享成分就很出人意料了!这部分共享成分只能解释成Y-C和mt-A/B/C/D到来之前的西伯利亚土著成分,也就是与现代美洲人的Y-Q和极少量mt-X有关的早期土著组分。这样看来,美洲土著人的常染比他们显然经历过瓶颈效应的Y和mtDNA包含更多古老年代的信息。
NRY: O2a1c1a1a1a1a1a1-002611,F11,F17,F856,F1495(源自粤西云浮)
mtDNA:B4d1(源自浙北慈溪)
百越人的人类学文集 http://blog.sina.com.cn/baiyueren

美国土著居民有西伯利亚的根

http://radiovr.com.cn/2013_11_25/252824735/
美国土著居民有西伯利亚的根

由俄罗斯、英国、丹麦、美国和瑞典人组成的国际科学小组确定 了美国土人-印地尼安人和西伯利亚居民之间的遗传联系。

研究证明欧亚西部居民后代在最寒冷的的冰川时期散布在比以前 设想的更朝东的地区。科学家们著文指出:在某段时期西方的欧洲人 和东方的亚洲人杂居,结果出现了在遥远的南北美洲居住的种群。

研究是以俄罗斯最大的博物馆之一-彼得堡埃尔米塔什博物馆保存 的男孩遗骸DNA的分析为基础进行的。这是今天保存的现代人的最古 老的遗骸之一。男孩生于二万四千年前-旧石器时代晚期,地点在西 伯利亚南部贝加尔湖附近。

按初步分析结果,男孩属于所谓的单倍型类群U。以前认为旧石器 时代只在欧洲和亚洲西部,而不是在亚洲东部能发现这种人。此后科 学家们又有了新的意外发现:更准确的分析证明这个古代男孩的一些 DNA元素只在现代印地尼安人的DNA中存在。

这种意外发现的原因在于:冰川时期东亚的一部份人向北迁移。 他们在西伯利亚地区碰到了从西欧东迁的人们,两种部族混合了。结 果,他们共同的后代迁移到了美洲。

以前科学家也曾说过美洲土人有亚洲的根。新的研究弄清了这些 遥远历史进程的地理和遗传图景。现在己清楚西伯利亚人的祖先是 谁,并且知道美洲的印地尼安人是他们的后代。
本帖最后由 natsuya 于 2013-11-28 18:28 编辑

Eurogenes: http://eurogenes.blogspot.tw/201 ... eolithic-human.html

Mal'ta男孩的常染組成,其最接近的現代人群成分,的確是南亞特點的綠色(37%),接著是歐洲特點的藍色(34%),然後是美洲土著特點的橘色(16%),北亞-愛斯基摩特點的粉紅色(10%),更值得注意的是巴布亞(Papuans)特點的紫色(4%)。因為P和M的親緣關係剛確認,因此父系R的Mal'ta男孩與現代以父系M為主的巴布亞人共享微量常染組成,十分引人注目。

At K = 9, MA-1 is composed of five genetic components of which the two major ones make up ca. 70% of the total. The most prominent component is shown in green and is otherwise prevalent in South Asia but does also appear in the Caucasus, Near East or even Europe. The other major genetic component (dark blue) in MA-1 is the one dominant in contemporary European populations, especially among northern and northeastern Europeans. The co-presence of the European-blue and South Asian green in MA-1 can be interpreted as admixture of the two in MA-1 or, alternatively, MA-1 could represent a proto-western Eurasian prior to the split of Europeans and South Asians. This analysis cannot differentiate between these two scenarios. Most of the remaining nearly one third of the MA-1 genome is comprised of the two genetic components that make up the Native American gene pool (orange and light pink). Importantly, MA-1 completely lacks the genetic components prevalent in extant East Asians and Siberians (shown in dark and light yellow, respectively). Based on this result, it is likely that the current Siberian genetic landscape, dominated by the genetic components depicted in light and dark yellow (Figure SI 6), was formed by secondary wave(s) of immigrants from East Asia.

Mal'ta.png
Y染色體:O3 M134+ M117-
mtDNA:D5a2
Eurogenes: http://eurogenes.blogspot.tw/201 ... eolithic-human.html

Mal'ta男孩的常染組成,其最接近的現代人群成分,的確是南亞特點的綠色(37%),接著是歐洲特點的藍色(34%),然後是美洲土著特點的橘色(16% ...
natsuya 发表于 2013-11-28 18:13
我不这么认为,因为这种巴布亚成份在南亚很常见,在高加索人种大举南下之前只会更常见。这只是南亚成份之一。
O3a3c* (M134+, M117-)
我不这么认为,因为这种巴布亚成份在南亚很常见,在高加索人种大举南下之前只会更常见。这只是南亚成份之一。
hercules 发表于 2013-11-28 21:05
謝謝提醒,你說的可能性不小,該種在巴布亞人群(Papuans)當中幾乎100%的紫色成分,的確普遍微量見於南亞人群(South Asia)的樣本。
Mal'ta.png
Y染色體:O3 M134+ M117-
mtDNA:D5a2
但是马尔塔男孩和美洲人有常让共享成分就很出人意料了!这部分共享成分只能解释成Y-C和mt-A/B/C/D到来之前的西伯利亚土著成分,也就是与现代美洲人的Y-Q和极少量mt-X有关的早期土著组分。这样看来,美洲土著人的常染比他们显然经历过瓶颈效应的Y和mtDNA包含更多古老年代的信息。
baiyueren 发表于 2013-11-25 20:49
支持此論點。
Y染色體:O3 M134+ M117-
mtDNA:D5a2
从常染来看,马尔塔男孩还是更接近布鲁沙斯基人,只是其中的淡蓝色西亚成分要换成蓝色欧洲成分,而黄色东亚成分要换成橘黄色美洲成分。我估计在体质特征上也会很接近现代的布鲁沙斯基人,可能肤色发色还是相当浅的。
NRY: O2a1c1a1a1a1a1a1-002611,F11,F17,F856,F1495(源自粤西云浮)
mtDNA:B4d1(源自浙北慈溪)
百越人的人类学文集 http://blog.sina.com.cn/baiyueren
从常染来看,马尔塔男孩还是更接近布鲁沙斯基人,
[baiyueren 发表于 2013-11-28 23:31
布鲁沙斯基人的Y 中就有 R1a1,R2 和 R*.    很可能,马尔他男孩代表的族群的父系,正是被布鲁沙斯基人继承了。值得深究。
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