natsuya 发表于 2013-12-24 16:39


本帖最后由 Ryan 于 2013-12-27 19:04 编辑

Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis et al.

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.


natsuya 发表于 2013-12-24 16:40

baiyueren 发表于 2013-12-25 12:39


natsuya 发表于 2013-12-26 12:04

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

This Lazaridis et al. pre-print is quite a Christmas present for those of us with a passion for European genetic origins and history. It's the first study to fully sequence genomes of pre-Neolithic Europeans and report their Y-chromosome haplogroups.

Five out of the five successfully tested forager Y-chromosomes belonged to haplogroup I, which probably won't come as a surprise to many people, as this was always the main candidate for Europe's Paleolithic paternal marker. Interestingly, three of the results fell into haplogroup I2a1b, and none into the presently more common I1.

What this suggests is that I1 expanded after the Mesolithic and replaced most of the I2a1b across Northwestern Europe. I'd say these were mostly expansions from North-Central Europe, although recent chatter on the web suggests that two distinct I1 lineages might have arrived in North-Central Europe from Eastern Europe at different times.

All of the forager mtDNA sequences belonged to haplgroups U2 and U5, which is line with past results, and again not very surprising.

However, the genome-wide results are not as straightforward. The basic upshot is that Northern Europeans are mostly of indigenous European hunter-gatherer origin, while Southern Europeans are largely derived from Neolithic farmers of mixed European and Near Eastern origin. But the authors identify three ancestral populations from their stats (WHG, EEF and ANE), and four meta-populations from the available ancient data (WHG, EEF, ANE and SHG). I found that somewhat confusing at first, but maybe that's just me? In any case, here are brief summaries of each of these groups:

West European Hunter-Gatherer (WHG): this ancestral component is based on an 8,000 year old forager from the Loschbour rock shelter in Luxembourg (one of the individuals mentioned above belonging to I2a1b). The WHG meta-population includes the Loschbour sample and two Mesolithic individuals from the La Brana Cave in Spain. However, the WHG component peaks today near the Baltic, among Lithuanians at almost 50%.

Early European Farmer (EEF): apparently this is a hybrid component, the result of mixture between "Basal Eurasians" and a WHG-like population from somewhere in Europe, possibly the Balkans. It's based on a 7,500 year old farmer from the Linearbandkeramik (LBK) culture from Stuttgart, Germany, but today peaks at just over 80% among Sardinians. Apart from the Stuttgart sample, the EEF meta-population includes Oetzi the Iceman and a Neolithic Funnelbeaker farmer from Sweden.

Ancient North Eurasian (ANE): this is the twist in the tale, a component based on a 24,000 year old, Y-DNA R* Upper Paleolithic forager from South Central Siberia, known as Mal'ta boy or MA1. This component was very likely present in Southern Scandinavia since at least the Mesolithic (see the summary of SHG below), but only seems to have reached Western Europe after the Neolithic. In Europe today it peaks among Estonians at just over 18%, and, intriguingly, reaches a similar level among Scots. However, numbers weren't given for Finns, Russians and Mordovians, who, according to one of the maps, also carry very high ANE, but their results are confounded by more recent Siberian admixture (see the discussion on the European outliers below). The ANE meta-population includes Mal'ta boy as well as a late Upper Paleolithic sample from Central Siberia, dubbed Afontova Gora-2 (AG2).

Scandinavian Hunter-Gatherer (SHG): this is a meta-population made up of Swedish Mesolithic and Neolithic forager samples from Motala and Gotland, respectively. It's a more easterly variant of WHG, with probable ANE admixture.

Below are arguably the two most important figures from the paper: a) the three-way mixture model that is a statistical fit to the data, and b) a plot of the proportions of ancestry from each of the three inferred ancestral populations. As per above, East Baltic populations are the most WHG, which is somewhat curious, because they mostly carry Y-DNA R1a and N1c1.

natsuya 发表于 2013-12-26 12:05

本帖最后由 Ryan 于 2013-12-27 18:38 编辑

The concept of the Basal Eurasian ancestral population is a novel one and very interesting. At this point it's a purely statistical concept, and will need to be confirmed with ancient DNA from the Middle East. But ADMIXTURE clusters that are specific to Sardinians (usually termed "Mediterranean" in my own analyses) are always quite distinct in terms of Fst genetic distances from most other West Eurasian clusters, except those that peak among Saudi Arabians and some Bedouins. I wonder whether this is due to an inflated level of ancestry from the Basal Eurasians? And were they perhaps the proto-Mediterraneans?
"原欧亚始祖人群"是一个很有意思的新概念。目前,它只是一个统计学上的概念,需要与远古的中东地区的古DNA来比较和确定。但ADMIXTURE 的聚类分析显示,撒丁岛人群(我称之为地中海人群)在Fst距离上,总是远离其他西部欧亚人群,除了与一些在沙特阿拉伯和贝都因人中出现峰值的成分。我想,这是否正式因为“原欧亚始祖人群”的混入导致? 他们是否可能就是“原始地中海人群”?

Nevertheless, if not for the ANE, we'd simply have a two-way mixture model between indigenous European foragers and migrant Near Eastern farmers, at least for most Europeans anyway. Moreover, the seemingly late arrival of ANE in much of Europe is fascinating, because it's yet another smoking gun for a major genetic upheaval across the continent during the Copper Age (aka. Late Neolithic/Early Bronze Age). Interestingly, archeological data suggest that this was also the period which saw the introduction of new social organization and perhaps Indo-European languages across most of the continent. None of this was lost on the authors of the paper, but it appears they'd rather be cautious pending more ancient genomic data, because they chose not to explicitly mention the Indo-Europeans.

This study raises two questions that are important to address in future research. A first is where the EEF picked up their WHG ancestry. Southeastern Europe is a candidate as it lies along the geographic path from Anatolia into central Europe, and hence it should be a priority to study ancient samples from this region. A second question is when and where ANE ancestors admixed with the ancestors of most present-day Europeans. Based on discontinuity in mtDNA haplogroup frequencies in Central Europe, this may have occurred during the Late Neolithic or early Bronze Age ~5,500-4,000 years ago35. A central aim for future work should be to collect transects of ancient Europeans through time and space to illuminate the history of these transformations.

The absence of Y-haplogroup R1b in our two sample locations is striking given that it is, at present, the major west European lineage. Importantly, however, it has not yet been found in ancient European contexts prior to a Bell Beaker burial from Germany (2,800-2,000BC)12, while the related R1a lineage has a first known occurrence in a Corded Ware burial also from Germany (2,600BC)13. This casts doubt on early suggestions associating these haplogroups with Paleolithic Europeans14, and is more consistent with their Neolithic entry into Europe at least in the case of R1b15, 16. More research is needed to document the time and place of their earliest occurrence in Europe.Interestingly, the Mal’ta boy belonged to haplogroup R* and we tentatively suggest that some haplogroup R bearers may be responsible for the wider dissemination of Ancient North Eurasian ancestry into Europe, as their haplogroup Q relatives may have plausibly done into the Americas17.
在我们的两个地点的样本中,没有发现R1b。这对目前这一西欧的主要支系来说,是一个打击。重要的是,到目前为止还没有在比德国的Bell Beaker墓葬更早的遗址中发现这一类型。 而对于相关的R1a,目前在德国Corded Ware 的墓葬中发现的样本是最早的。这些结果不支持之前的认识,即R1a和R1b是欧洲的旧石器时代的父系类型,反而支持这些类型是在新石器时代以后才进入欧洲的--至少对于R1b1来说是可以肯定的。需要更多的证据来说明它们在欧洲出现的时间和地点。有意思的是,马尔他男孩 属于R*。这让我们不免怀疑正是有一部分父系为R的人群把ANE(原始北部欧亚人群)的成分带入了欧洲,就像他们的Q系亲族把Q系带入欧洲一样。

No doubt, a lot of people will now be wondering about the ultimate source of the ANE that apparently rushed into Europe during the advent of the metal ages. The Siberian steppe will probably be the favored option for many, since this is where Mal'ta boy and Afontova Gora-2 came from. But I think the source was Eastern Europe.
毫无疑问,很多人现代开始考虑ANE(原始北部欧亚人群)的最初来源,后者看起来是青铜时代和铁器时代进入欧洲的。其来源很有可能是西伯利亚草原,因为现在我们知道Mal'ta boy and Afontova Gora-2就活动在那里。但我认为,ANE的来源是东欧。

First of all, as already mentioned, it seems that ANE was present in Sweden during the Mesolithic (Figure S12.7 shows around 19% ANE in the Motala12 sample). Secondly, despite the ANE and WHG being classified as separate ancestral and meta-populations, the differences between them appear to be clinal rather than discrete, which I think can be seen in the ADMIXTURE and PCA results from the study (see here and here). Thus, I'd expect a lot more ANE in Eastern Europe during the Mesolithic than in Scandinavia. Thirdly, it's likely that the ancestors of modern Uralic speakers were in Siberia very early, possibly during the Mesolithic, and they were probably East Eurasians, which ANE is not.
首先,正如之前已经提到的,看起来ANE的成分出现在中石器时代的瑞典(图 S12.7 显示Motala12样本有约19% 的ANE成分)。其次,尽管ANE和WHG被划分为独立的人群集团,两者之间的差异看起来是种群内的(连续状态),而不是不连续的。因此,我预测在东欧将会找到更多的ANE,而不是在斯堪的纳维亚。第三点,现代乌拉尔语人群的祖先很早以前是生活在西伯利亚的,可能一直延续到中石器时代。他们可以被认定是 “东欧亚人群”,而 ANE不可以。

Indeed, continuing with that third point, the paper identified two sets of genetic outliers within Europe, due to relatively recent Near Eastern and Siberian admixtures, respectively. Moreover, this Siberian admixture came from a population more closely related to present-day East Asians than to ANE.

While our three-way mixture model fits the data for most European populations, two sets of populations are poor fits. First, Sicilians, Maltese, and Ashkenazi Jews have EEF estimates beyond the 0-100% interval (SI13) and they cannot be jointly fit with other Europeans (SI12). These populations may have more Near Eastern ancestry than can be explained via EEF admixture (SI13), an inference that is also suggested by the fact that they fall in the gap between European and Near Eastern populations in the PCA of Fig. 1B. Second, we observe that Finns, Mordovians, Russians, Chuvash, and Saami from northeastern Europe do not fit our model (SI12; Extended Data Table 3). To better understand this, for each West Eurasian population in turn we plotted f4(X, Bedouin2; Han, Mbuti) against f4(X, Bedouin2; MA1, Mbuti), using statistics that measure the degree of a European population’s allele sharing with Han Chinese or MA1 (Extended Data Fig. 7). Europeans fall along a line of slope >1 in the plot of these two statistics. However, northeastern Europeans fall away from this line in the direction of Han. This is consistent with Siberian gene flow into some northeastern Europeans after the initial ANE admixture, and may be related to the fact that Y-chromosome haplogroup N30, 31 is shared between Siberian and northeastern Europeans32, 33 but not with western Europeans. There may in fact be multiple layers of Siberian gene flow into northeastern Europe after the initial ANE gene flow, as our analyses reported in SI 12 show that some Mordovians, Russians and Chuvash have Siberian-related admixture that is significantly more recent than that in Finns (SI12).
当使用三重混合模式时,大部分欧洲人群的数据符合与这个模式,但有两组人群则不太符合于这个模式。第一组是西西里人,马耳他人和德系犹太人。他们的ANE成分超过0-100%的(置信?)区间,并且无法和其他欧洲人相一致。这些人群可能拥有更多的近东祖先,这可以解释为来自EEF的混合。这种解释也符合与以下事实:在PCA图中,他们落在欧洲人和近东人群之间。第二组是芬兰人,摩尔多瓦人,俄罗斯人,楚瓦什人和萨米人。他们来自东北欧,均不合符于三重混合模式。为了更好地理解这一点,我们对每一个欧洲西部人群进行散布图分析(f4(X, Bedouin2; Han, Mbuti) against f4(X, Bedouin2; MA1, Mbuti))。使用的数据是每一个欧洲人群和汉族或者MA1的共享位点比例(Extended Data Fig. 7)。在这项分析中,欧洲人沿一条斜率大于1的斜线分布。但是,上述东北欧人群在与汉族相反的方向上远离这条线。这与以下图景吻合:即在ANE混入欧洲之后,以后来自西伯利亚的遗传成分进入部分东北欧人群。并且很可能与Y染色体单倍群N相关。这种单倍群同时在西伯利亚人群和东北欧人群中出现,但在西部欧洲人群没有。在ANE的成分混入欧洲之后,西伯利亚的遗传成分混入东北欧人群可能存在多个层次。这是因为,我们的分析显示(SI 12),部分摩尔多瓦人,俄罗斯人和楚瓦什人的西伯利亚成分,明显早于芬兰人。

The authors are actually referring to the Kargopol Russians from the HGDP in that quote. But from my own analyses with a wide variety of Eastern European samples, I know that other Russians are much more similar to Belorussians, Ukrainians and Estonians in regards to the levels of Siberian admixture they carry.

So what could be the cause of this relatively recent Siberian gene flow into Northeastern Europe? The best bet is the Uralic expansion and, for the Chuvash and Mordovians, perhaps also the Turkic expansion. Based on latest linguistic research, the pre-proto-Uralics appear to have expanded at some point from Siberia into the Volga-Ural region, in far eastern Europe. During the Bronze Age the Uralics proper then expanded from the Volga-Ural both back to the east and also west, as far as the Baltic (see here).

This of course means that there are more than three ancestral populations for present-day Europeans, albeit not all of them influenced all Europeans. In any case, it's very clear that to learn all the details about the peopling of Europe, these sorts of studies really need to start focusing on the large swath of land that stretches from present-day Poland to the Urals. In other words, Eastern Europe.

I was also going to discuss the genetically inferred pigmentation of the ancient individuals, but at this stage there's not much to discuss. The Loschbour forager possibly had blue eyes (50% chance), but dark hair and relatively swarthy skin. On the other hand, the Stuttgart farmer definitely had dark eyes and hair, but light skin. I wonder if this swarthy hunter-gatherer skin complexion has anything to do with the fact that today lots of people from around the Baltic tan really well?
我也很想讨论一下 这些远古人类个体的基因数据所见的色素问题。但现在这个阶段能够讨论的数据还很少。卢森堡的采集者可能有蓝色的眼睛(50%概率),但他的头发是黑色的,肤色可能较深的。而另一方面,Stuttgart的农人有深色的眼睛和头发,但肤色是比较浅的。现代波罗的海人群的黄褐色的肤色,我很怀疑这些深肤色的采集狩猎者,与前者是否真的有什么关联?


Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, bioRxiv, Posted December 23, 2013, doi: 10.1101/001552

Ryan 发表于 2013-12-26 13:20

本帖最后由 Ryan 于 2013-12-26 13:23 编辑

在上面增加了一部分翻译。看来欧洲的专业学者,已经开始讨论 R1b和R1b在很晚的时候才进入欧洲的这种可能性了。这对于认识早期欧洲的历史是有帮助的,有一些成见需要重新考虑了。


natsuya 发表于 2013-12-26 13:22


natsuya 发表于 2013-12-26 13:50

A new preprint on the bioRxiv reports ancient DNA from a Mesolithic European hunter-gatherer from Luxembourg whose mtDNA was published a few years ago and a Neolithic European LBK farmer from Germany, as well as several Mesolithic hunter-gatherers from Sweden.

The Luxembourg sample is similar to the IberianLa Brana samples and the Swedish Mesolithic samples are similar to Swedish Neolithic hunter-gatherers. The LBK farmer is similar to Oetziand a Swedish TRB farmer and to Sardinians. The authors also study the recently publishedMal'ta Upper Paleolithic sample from Lake Baikal and find that it is part of an "Ancient North Eurasian" population that also admixed into West Eurasians on top of the Neolithic/Mesolithic mix.

It seems that the estimates go all the way to "almost pure" Early European farmer ancestry but "West European Hunter-Gatherer" and "Ancient North Eurasian" ancestry isn't found unmixed in any modern populations. The model seems to agree with Raghavan et al. that Karitiana are "Mal'ta"-admixed but also finds the most basal Eurasian ancestry in the European Neolithic farmer. The authors write:
The successful model (Fig. 2A) also suggests 44 ± 10% “Basal Eurasian” admixture into the ancestors of Stuttgart: gene flow into their Near Eastern ancestors from a lineage that diverged prior to the separation of the ancestors of Loschbour and Onge. Such a scenario, while never suggested previously, is plausible given the early presence of modern humans in the Levant25, African-related tools made by modern humans in Arabia26, 27, and the geographic opportunity for continuous gene flow between the Near East and Africa28The Swedish/Luxembourg Mesolithic hunter-gatherers are all mtDNA-haplogroup U and Y-chromosome haplogroup I, so again no R1a/R1b in early European samples.

An interesting finding is that the Luxembourg hunter-gatherer probably had blue eyes (like a Mesolithic La Brana Iberian, a paper on which seems to be in the works) but darker skin than the LBK farmer who had brown eyes but lighter skin. Raghavan et al. did not find light pigmentation in Mal'ta (but that was a very old sample), so with the exception of light eyes that seem established for Western European hunter-gatherers (and may have been "darker" in European steppe populations, but "lighter" in Bronze Age South Siberians?), the origin of depigmentation of many recent Europeans remains a mystery. Ancient DNA continues to surprise at every turn.

一个有意思的发现是卢森堡古采集狩猎人可能有蓝色的眼睛(和中石器时代的伊比利亚半岛的La Brana 人一样,相关文章应在准备中),但比 LBK农人的肤色更深。LBK农人有褐色的眼睛,但肤色更浅。Raghavan et al. 没有在马尔他男孩身上发现浅色素基因(这个样本的年代确实太古老)。因此,除了蓝色眼睛可以推测是起源自西欧采集狩猎人外(欧洲草原居民的肤色更深,而青铜时代南西伯利亚人的肤色更浅?),欧洲人群的浅色素来源仍然是个谜。 古DNA实在是处处都有惊喜啊。

natsuya 发表于 2013-12-26 13:52

West European Hunter-Gatherer (WHG): this ancestral component is based on an 8,000 year old forager from the Loschbour rock shelter in Luxembourg (one of the individuals mentioned above belonging to I2a1b). The WHG meta-population includes the Loschbour sample and two Mesolithic individuals from the La Brana Cave in Spain. However, the WHG component peaks today near the Baltic, among Lithuanians at almost 50%.
natsuya 发表于 2013-12-26 12:04年前的盧森堡獵人Y染色體屬於I2a1b。

natsuya 发表于 2013-12-26 13:59

An interesting finding is that the Luxembourg hunter-gatherer probably had blue eyes (like a Mesolithic La Brana Iberian, a paper on which seems to be in the works) but darker skin than the LBK farmer who had brown eyes but lighter skin. Raghavan et al. did not find light pigmentation in Mal'ta (but that was a very old sample), so with the exception of light eyes that seem established for Western European hunter-gatherers (and may have been "darker" in European steppe populations, but "lighter" in Bronze Age South Siberians?), the origin of depigmentation of many recent Europeans remains a mystery. Ancient DNA continues to surprise at every turn.
natsuya 发表于 2013-12-26 13:50值得注意的是,Dienekes提及古代DNA研究顯示,8000年前的盧森堡獵人(Y屬於I2a1b)的眼睛可能是藍色的,就如同伊比利半島La Brana中石器獵人的藍色眼睛。但該盧森堡獵人的膚色較歐洲LBK新石器農民的膚色更深,因此今日歐洲人的淺膚色可能並非來自歐洲土著獵人。
再者,先前對2萬多年前西伯利亞Mal'ta男孩(Y屬R*; mt屬U)的膚色基因作分析,並無發現淺膚色基因。

baiyueren 发表于 2013-12-26 14:11

本帖最后由 baiyueren 于 2013-12-26 14:15 编辑

值得注意的是,Dienekes提及古代DNA研究顯示,8000年前的盧森堡獵人(Y屬於I2a1b)的眼睛可能是藍色的,就如同伊比利半島La Brana中石器獵人的藍色眼睛。但該盧森堡獵人的膚色較歐洲LBK新石器農民的膚色更深,因此今日歐洲人的淺膚色可能並非來自歐洲土著獵人。
natsuya 发表于 2013-12-26 13:59


natsuya 发表于 2013-12-26 14:13

本帖最后由 natsuya 于 2013-12-26 14:16 编辑

The Swedish/Luxembourg Mesolithic hunter-gatherers are all mtDNA-haplogroup U and Y-chromosome haplogroup I, so again no R1a/R1b in early European samples.
natsuya 发表于 2013-12-26 13:50古代DNA分析顯示,瑞典&盧森堡中石器狩獵者的mtDNA皆是單倍群U,而其Y染色體皆是單倍群I(其中之一是I2a1b)。目前的歐洲早期樣本尚未發現R1a/R1b。但我認為R1a/R1b應是歐洲中石器獵人一員,僅是未測到,推測當時R1a/R1b可能並非已經廣佈的類型。

baiyueren 发表于 2013-12-26 14:19

本帖最后由 baiyueren 于 2013-12-26 14:36 编辑

古代DNA分析顯示,瑞典&盧森堡中石器狩獵者的mtDNA皆是單倍群U,而其Y染色體皆是單倍群I(其中之一是I2a1b)。目前的歐洲早期樣本尚未發現R1a/R1b。但我認為R1a/R1b應是歐洲中石器獵人一員,僅是未測到,推測當時R1a/R ...
natsuya 发表于 2013-12-26 14:13

baiyueren 发表于 2013-12-26 14:21

本帖最后由 baiyueren 于 2013-12-26 14:35 编辑


反恐 发表于 2013-12-26 14:29


baiyueren 发表于 2013-12-26 14:50

本帖最后由 baiyueren 于 2013-12-26 14:55 编辑

反恐 发表于 2013-12-26 14:29

天天向上 发表于 2013-12-26 14:55

本帖最后由 天天向上 于 2013-12-26 14:56 编辑

依我看,古希腊人多半是黑头发黝黑皮肤的,跟现代希腊人无异。古希腊受印欧人影响的主要在语言、文化和原始宗教方面。而且据说希腊语从语言分类角度来看还不是很典型的印欧语。而在艺术方面,早期印欧人艺术水准远 ...
baiyueren 发表于 2013-12-26 14:50现代希腊人都靠近西北欧了,要不其实是斯拉夫的说法从何而来

性手枪 发表于 2013-12-26 18:26

17# 天天向上

天天向上 发表于 2013-12-26 19:11

17# 天天向上
性手枪 发表于 2013-12-26 18:26希腊人的白化是在火鸡之上的,火鸡的白化又是在新疆之上的,这一点是没有问题的

198401 发表于 2013-12-27 08:23

Lochsbour : U5b1a
Motala 1 & 3: U5b1a
Motala 2 & 12: U2e1
Motala 4 & 6: U5a2d
Motala 9: U5a2

Lochsbour: I2a1b*(xI2a1b1, I2a1b2, I2a1b3)
Motala 2: I*(xI1, I2a2,I2a1b3)
Motala 3: I2*(xI2a1a, I2a2, I2b)
Motala 6: uncertain (L55+ would make it Q1a2a but L232- forces it out of Q1)
Motala 9: I*(xI1)
Motala 12: I2a1b*(xI2a1b1, I2a1b3)
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