Pallantides
07-16-2012, 05:09 PM
A little more than a year ago, I noticed (http://dienekes.blogspot.no/2011/05/east-asian-and-african-shift-of-west.html) an interesting pattern in North Europeans: they all tended to be shifted towards East Asians in PCA plots:
http://1.bp.blogspot.com/-oBE7kJoLnU4/UAGg2SV9zDI/AAAAAAAAFAo/NzXX9j5voSA/s1600/waeu_yri_chb_blowup2.png
With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).
The same pattern could also be observed in the arrangement of the ancestral components inferred by the Dodecad Project (http://dodecad.blogspot.no/2012/01/k12b-and-k7b-calculators.html). The "Atlantic_Baltic" component, which is modal in Northern Europeans, exhibits lowered genetic divergences to the East Eurasian components (Siberian / East_Asian) relative to the "Southern" component which is modal (in Europe) in Southern Europeans.
http://1.bp.blogspot.com/-tIQmmTLI5QA/UAGhuOAsMnI/AAAAAAAAFAw/s4P1uXbxzwU/s1600/fst.png
The fact that Southern European populations were shifted towards the African side relative to Northern European ones across an African-Asian projection, was interpreted by Moorjani et al. (2011) (http://dienekes.blogspot.no/2011/04/sub-saharan-admixture-in-west-eurasian.html) as evidence of African admixture. As I noted at the time, this entailed the assumption that Northern European populations did not have East Asian admixture, which would also produce the observed pattern:
However, this is clearly a case of seeing the glass half full. The authors prefer the hypothesis that some Caucasoid groups have African ancestry, although the hypothesis that other Caucasoid groups have East Asian ancestry can equally well explain the observed pattern. Indeed, both hypotheses may explain the phenomenon they observe.
It now appears that some of the co-authors of the above paper have realised this, and have detected Central/East Asian admixture in northern Europeans. Writing in the supplement (http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature11258-s1.pdf) of the recent Reich et al. (2012) (http://dienekes.blogspot.no/2012/07/reconstructing-origin-of-native.html) paper, we read this important aside:
A complication in computing this statistic is that Native American, Siberian, and East Asian populations are not all equally genetically related to West Eurasian populations, as we can see empirically from 4 Population Tests of the proposed tree (Yoruba, (French, (East Asian, Native American))) failing dramatically whether the East Asian population is Han, Chukchi, Naukan and Koryak. The explanation for this is outside the scope of this study (it has to do with admixture events in Europe, as we explain in another paper in submission). In practice, however, it means that we cannot simply use a European population like French to represent West Eurasians in Equation S3.2, since if we do this, Equation S3.2 may have a non-zero value for a Native American population, even without recent European admixture.
To address this complication, we took advantage of the fact that east/central Asian admixture has affected northern Europeans to a greater extent than Sardinians (in our separate manuscript in submission, we show that this is a result of the different amounts of central/east Asian-related gene flow into these groups). To quantify this, we computed the statistic f4(San, West Eurasian; Pop1, Pop2) for West Eurasian = Sardinian and West Eurasian = French, and for 24 Siberian and Native American populations (Pop1 and Pop2) (Figure S3.2). Figure S3.2 shows a scatterplot for all 190=20?19/2 possible pairs of these populations. Within nonArctic Native populations, and within Arctic populations (East Greenland Inuit, Chukchi, Naukan and Koryak), the statistics are close to zero, consistent with their being (approximate) clades relative to West Eurasians. In contrast, there are deviations from zero when the comparisons are between non-Arctic Native and Arctic populations, with non-Arctic Native populations showing consistent evidence of being genetically closer to West Eurasians.
David Reich has hinted about ancient admixture in Europeans before (http://dienekes.blogspot.no/2011/10/ichg-2011-webcast.html), and is apparently working (http://dienekes.blogspot.no/2012/06/smbe-2012-abstracts-part-ii.html) on the South Asian admixture event. It would appear that the new works might be using the newer techniques employed in the Reich et al (2012) paper, which allows one to consider multiple admixture events rather than the more simple ones of Reich et al. (2009) (http://www.nature.com/nature/journal/v461/n7263/abs/nature08365.html) and Moorjani et al. (2011) that considered only two ancestral populations.
I will, of course, eagerly wait the publication of the mentioned manuscript, but it appears that this is not the only piece of evidence of gene flow from Central Asia into Europe. In an SMBE 2012 abstract (http://dienekes.blogspot.no/2012/06/smbe-2012-abstracts-part-ii.html) by Palstra et al. we read:
Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa. A further evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both long-term presence and admixture in more recent historical times.
Neither of these two upcoming pieces of work mention the timing of the Central Asian element in Europe:
One possibility is that the Mesolithic Europeans were Asian-shifted themselves (http://dienekes.blogspot.no/2012/06/mesolithic-iberians-la-brana-arintero.html).
Another one would relate it to the emerging ancient mtDNA picture of deep penetration (http://dienekes.blogspot.no/2012/07/population-strata-in-west-siberian.html) of Mongoloid elements into west Eurasia at the dawn of history, although the western limit of this penetration has not been conclusively ascertained.
Finally, the elements may be a legacy of the Bronze Age Indo-European invasion of Europe (http://dienekes.blogspot.no/2012/07/bronze-age-indo-european-invasion-of.html), piggy-backing on the spread of the latter from their eastern homeland
In two of the existing models of how the latter event took place (the Armenian plateau hypothesis of Gamkrlidze and Ivanov and the Bactria Sogdiana hypothesis of Johanna Nichols), the Indo-Europeans followed separate streams from their eastern homeland into Europe, with some groups following a path north of the Black and Caspian seas, while others followed a southern path from Anatolia to the Balkans. The northern dispersal route would have brought them into contact with the mixed Caucasoid/Mongoloid population of West Siberia and Eastern Europe, and they may have carried some of this DNA across their sweep over Northern Europe.
http://2.bp.blogspot.com/-vIj-JQm6mv0/UAGnVEsYoUI/AAAAAAAAFA8/9Qhs0DMOLC8/s1600/epicenter.pnghttp://4.bp.blogspot.com/-ODGH0_cr_jk/UAGoPUPH8tI/AAAAAAAAFBE/stw13S3Jz_g/s1600/indo_european_migation.jpg
My own working hypothesis would derive the earliest Proto-Indo-Europeans with groups living in Neolithic eastern Anatolia and northern Mesopotamia. There are details to be fleshed out, such as when this group of people reached the Balkans (pending ancient DNA from the region), and how they interfaced with the populations living in the north of the Black and Caspian seas (e.g., via a trans-Caucasus movement or a counterclockwise spread around the Caspian).
We will know soon enough how and when Northern Europeans ended up with an extra slice of Central/East Asian ancestry. Things are looking good for our understanding of events in Eurasian prehistory.
http://dienekes.blogspot.no/2012/07/hints-of-eastcentral-asian-admixture-in.html
http://1.bp.blogspot.com/-oBE7kJoLnU4/UAGg2SV9zDI/AAAAAAAAFAo/NzXX9j5voSA/s1600/waeu_yri_chb_blowup2.png
With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).
The same pattern could also be observed in the arrangement of the ancestral components inferred by the Dodecad Project (http://dodecad.blogspot.no/2012/01/k12b-and-k7b-calculators.html). The "Atlantic_Baltic" component, which is modal in Northern Europeans, exhibits lowered genetic divergences to the East Eurasian components (Siberian / East_Asian) relative to the "Southern" component which is modal (in Europe) in Southern Europeans.
http://1.bp.blogspot.com/-tIQmmTLI5QA/UAGhuOAsMnI/AAAAAAAAFAw/s4P1uXbxzwU/s1600/fst.png
The fact that Southern European populations were shifted towards the African side relative to Northern European ones across an African-Asian projection, was interpreted by Moorjani et al. (2011) (http://dienekes.blogspot.no/2011/04/sub-saharan-admixture-in-west-eurasian.html) as evidence of African admixture. As I noted at the time, this entailed the assumption that Northern European populations did not have East Asian admixture, which would also produce the observed pattern:
However, this is clearly a case of seeing the glass half full. The authors prefer the hypothesis that some Caucasoid groups have African ancestry, although the hypothesis that other Caucasoid groups have East Asian ancestry can equally well explain the observed pattern. Indeed, both hypotheses may explain the phenomenon they observe.
It now appears that some of the co-authors of the above paper have realised this, and have detected Central/East Asian admixture in northern Europeans. Writing in the supplement (http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature11258-s1.pdf) of the recent Reich et al. (2012) (http://dienekes.blogspot.no/2012/07/reconstructing-origin-of-native.html) paper, we read this important aside:
A complication in computing this statistic is that Native American, Siberian, and East Asian populations are not all equally genetically related to West Eurasian populations, as we can see empirically from 4 Population Tests of the proposed tree (Yoruba, (French, (East Asian, Native American))) failing dramatically whether the East Asian population is Han, Chukchi, Naukan and Koryak. The explanation for this is outside the scope of this study (it has to do with admixture events in Europe, as we explain in another paper in submission). In practice, however, it means that we cannot simply use a European population like French to represent West Eurasians in Equation S3.2, since if we do this, Equation S3.2 may have a non-zero value for a Native American population, even without recent European admixture.
To address this complication, we took advantage of the fact that east/central Asian admixture has affected northern Europeans to a greater extent than Sardinians (in our separate manuscript in submission, we show that this is a result of the different amounts of central/east Asian-related gene flow into these groups). To quantify this, we computed the statistic f4(San, West Eurasian; Pop1, Pop2) for West Eurasian = Sardinian and West Eurasian = French, and for 24 Siberian and Native American populations (Pop1 and Pop2) (Figure S3.2). Figure S3.2 shows a scatterplot for all 190=20?19/2 possible pairs of these populations. Within nonArctic Native populations, and within Arctic populations (East Greenland Inuit, Chukchi, Naukan and Koryak), the statistics are close to zero, consistent with their being (approximate) clades relative to West Eurasians. In contrast, there are deviations from zero when the comparisons are between non-Arctic Native and Arctic populations, with non-Arctic Native populations showing consistent evidence of being genetically closer to West Eurasians.
David Reich has hinted about ancient admixture in Europeans before (http://dienekes.blogspot.no/2011/10/ichg-2011-webcast.html), and is apparently working (http://dienekes.blogspot.no/2012/06/smbe-2012-abstracts-part-ii.html) on the South Asian admixture event. It would appear that the new works might be using the newer techniques employed in the Reich et al (2012) paper, which allows one to consider multiple admixture events rather than the more simple ones of Reich et al. (2009) (http://www.nature.com/nature/journal/v461/n7263/abs/nature08365.html) and Moorjani et al. (2011) that considered only two ancestral populations.
I will, of course, eagerly wait the publication of the mentioned manuscript, but it appears that this is not the only piece of evidence of gene flow from Central Asia into Europe. In an SMBE 2012 abstract (http://dienekes.blogspot.no/2012/06/smbe-2012-abstracts-part-ii.html) by Palstra et al. we read:
Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa. A further evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both long-term presence and admixture in more recent historical times.
Neither of these two upcoming pieces of work mention the timing of the Central Asian element in Europe:
One possibility is that the Mesolithic Europeans were Asian-shifted themselves (http://dienekes.blogspot.no/2012/06/mesolithic-iberians-la-brana-arintero.html).
Another one would relate it to the emerging ancient mtDNA picture of deep penetration (http://dienekes.blogspot.no/2012/07/population-strata-in-west-siberian.html) of Mongoloid elements into west Eurasia at the dawn of history, although the western limit of this penetration has not been conclusively ascertained.
Finally, the elements may be a legacy of the Bronze Age Indo-European invasion of Europe (http://dienekes.blogspot.no/2012/07/bronze-age-indo-european-invasion-of.html), piggy-backing on the spread of the latter from their eastern homeland
In two of the existing models of how the latter event took place (the Armenian plateau hypothesis of Gamkrlidze and Ivanov and the Bactria Sogdiana hypothesis of Johanna Nichols), the Indo-Europeans followed separate streams from their eastern homeland into Europe, with some groups following a path north of the Black and Caspian seas, while others followed a southern path from Anatolia to the Balkans. The northern dispersal route would have brought them into contact with the mixed Caucasoid/Mongoloid population of West Siberia and Eastern Europe, and they may have carried some of this DNA across their sweep over Northern Europe.
http://2.bp.blogspot.com/-vIj-JQm6mv0/UAGnVEsYoUI/AAAAAAAAFA8/9Qhs0DMOLC8/s1600/epicenter.pnghttp://4.bp.blogspot.com/-ODGH0_cr_jk/UAGoPUPH8tI/AAAAAAAAFBE/stw13S3Jz_g/s1600/indo_european_migation.jpg
My own working hypothesis would derive the earliest Proto-Indo-Europeans with groups living in Neolithic eastern Anatolia and northern Mesopotamia. There are details to be fleshed out, such as when this group of people reached the Balkans (pending ancient DNA from the region), and how they interfaced with the populations living in the north of the Black and Caspian seas (e.g., via a trans-Caucasus movement or a counterclockwise spread around the Caspian).
We will know soon enough how and when Northern Europeans ended up with an extra slice of Central/East Asian ancestry. Things are looking good for our understanding of events in Eurasian prehistory.
http://dienekes.blogspot.no/2012/07/hints-of-eastcentral-asian-admixture-in.html