Major admixture in India took place ~4.2-1.9 thousand years ago (Moorjani et al. 2013)

A new paper on the topic of Indian population history has just appeared in the American Journal of Human Genetics. In previous work it was determined that Indians trace their ancestry to two major groups, Ancestral North Indians (ANI) (= West Eurasians of some kind), and Ancestral South Indians (ASI) (= distant relatives of Andaman Islanders, existing today only in admixed form). The new paper demonstrates that admixture between these two groups took place ~4.2-1.9 thousand years ago.

The authors caution about this evidence of admixture:

It is also important to emphasize what our study has not shown. Although we have documented evidence for mixture in India between about 1,900 and 4,200 years BP, this does not imply migration from West Eurasia into India during this time. On the contrary, a recent study that searched for West Eurasian groups most closely related to the ANI ancestors of Indians failed to find any evidence for shared ancestry between the ANI and groups in West Eurasia within the past 12,500 years3 (although it is possible that with further sampling and new methods such relatedness might be detected). An alternative possibility that is also consistent with our data is that the ANI and ASI were both living in or near South Asia for a substantial period prior to their mixture. Such a pattern has been documented elsewhere; for example, ancient DNA studies of northern Europeans have shown that Neolithic farmers originating in Western Asia migrated to Europe about 7,500 years BP but did not mix with local hunter gatherers until thousands of years later to form the present-day populations of northern Europe.15, 16, 44 and 45

This is of course true, because admixture postdates migration and it is conceivable that the West Eurasian groups might not have admixed with ASI populations immediately after their arrival into South Asia. On the other hand, a long period of co-existence without admixture would be against much of human history (e.g., the reverse movement of the Roma into Europe, who picked up European admixture despite strong social pressure against it by both European and Roma communities, or the absorption of most Native Americans by incoming European, and later African, populations in post-Columbian times). It is difficult to imagine really long reproductive isolation between neighboring peoples.

Such reproductive isolation would require a cultural shift from a long period of endogamy (ANI migration, followed by ANI/ASI co-existence without admixture) to exogamy ~4.2-1.9kya (to explain the thoroughness of blending that left no group untouched), and then back to fairly strict exogamy (within the modern caste system). It might be simpler to postulate only one cultural shift (migration with admixture soon thereafter, with later introduction of endogamy which greatly diminished the admixture.

The authors cite the evidence from neolithic Sweden which does, indeed, suggest that the neolithic farmers this far north were "southern European" genetically and had not (yet) mixed with contemporary hunter-gatherers, as they must have done eventually. But, perhaps farmers and hunters could avoid each other during first contact, when Europe was sparsely populated. It is not clear whether the same could be said for India ~4 thousand years ago with the Indus Valley Civilization providing evidence for a large indigenous population that any intrusive group would have encountered. In any case, the problem of when the West Eurasian element arrived in India will probably be solved by relating it to events elsewhere in Eurasia, and, in particular, to the ultimate source of the "Ancestral North Indians".

It is also possible that some of the ANI-ASI admixture might actually pre-date migration. At present it's anyone's guess where the original limes between the west Eurasian and ASI worlds were. There is some mtDNA haplogroup M in Iran and Central Asia, which is otherwise rare in west Eurasia, so it is not inconceivable that ASI may have once extended outside the Indian subcontinent: the fact that it is concentrated today in southern India (hence its name) may indicate only the area of this element's maximum survival, rather than the extent of its original distribution. In any case, all mixture must have taken place somewhere in the vicinity of India.

A second interesting finding of the paper is that admixture dates in Indo-European groups are later than in Dravidian groups. This is demonstrated quite clearly in the rolloff figure on the left. Moreover, it does not seem that the admixture times for Indo-Europeans coincide with the appearance of the Indo-Aryans, presumably during the 2nd millennium BC: they are much later. I believe that this is fairly convincing evidence that north India has been affected by subsequent population movements from central Asia of "Indo-Scythian"-related populations, for which there is ample historical evidence. So, the difference in dates might be explained by secondary (later) admixture with other West Eurasians after the arrival of Indo-Aryans. Interestingly, the paper does not reject simple ANI-ASI admixture "often from tribal and traditionally lower-caste groups," while finding evidence for multiple layers of ANI ancestry  in several other populations.

My own analysis of Dodecad Project South Indian Brahmins arrived at a date of 4.1ky, and of North Indian Brahmins, a date of 2.3ky, which seems to be in good agreement with these results.

The authors also report that "we find that Georgians along with other Caucasus groups are consistent with sharing the most genetic drift with ANI". I had made a post on the differential relationship of ANI to Caucasus populations which seems to agree with this, and, of course, in various ADMIXTURE analyses, the component which I've labeled "West Asian" tends to be the major west Eurasian element in south Asia.

Here are the estimated admixture proportions/times from the paper:

Sadly, the warm and moist climate of India, and the adoption of cremation have probably destroyed any hope of studying much of its recent history with ancient DNA. On the other hand, the caste system has probably "fossilized" old socio-linguistic groups, allowing us to tell much by studying their differences and correlating them with groups outside India.

Coverage elsewhere: Gene Expression, HarappaDNA
Related podcast on BBC.

AJHG doi:10.1016/j.ajhg.2013.07.006

Genetic Evidence for Recent Population Mixture in India

Priya Moorjani et al.

Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy.

Link

Roma origins once more (Moorjani et al. 2012)

I had first noticed that this new paper by Moorjani et al. was referenced by Loh et al., and it has now been posted on arXiv. In the last week, a couple of other papers on the same topic (Mendizabal et al. on autosomal DNA and Rai et al. on a Y-chromosome founder lineage) have also appeared.

All three studies appear to converge on NW India as the place of origin of the European Roma, and on a recent admixture between this "Proto-Roma" population and Europeans. It will be interesting to see if there are any substantial differences between Moorjani et al. and Mendizabal et al. in the reconstruction of Roma origins. There is also an appendix on updates to rolloff and other topics of a technical nature that ought to be useful to readers irrespective of their interest in this particular population.

It'll probably take me a while to digest everything in this paper, but I will make one quick observation after (virtually) leafing through the article; the observation that {CEU, ANI} form a clade with Adygei as an outgroup is used to infer admixture proportions. I recently had a blog post on the differential relationship of ANI to Caucasus populations, in which I showed that while D(CEU, Adygei; South Asian, Onge) was positive, and significant in some cases -- indicating CEU being more closely related to ANI (Ancestral North Indians) than Adygei -- the reverse was the case for D(CEU, Georgian/Lezgin; South Asian, Onge).

A second observation was inspired by the following figure:

High IBD sharing with Romanians makes sense, because there is good evidence (e.g., presence of Y-haplogroup E-V13) that the Roma picked up European ancestry in the Balkans. So, I'm fairly sure that we are seeing a real signal that the Roma have Romanian-like recent European ancestors. But, we ought to be vigilant, because it is possible that some Romanians may have Roma ancestry too!  This was the case in a couple of individuals from the Romanian sample of Behar et al. (2010).

This is a more general issue: IBD sharing occasionally involves strictly -or mostly- unidirectional gene flow,  e.g., sharing between European and African Americans largely went EA->AA way, so an AA sharing with a EA more often than not involves EA->AA gene flow.

But, in other cases, the direction of gene flow is more obscure (so, e.g., sharing between German, Magyar, and Slavic speakers, and Jews in the old Austro-Hungarian Empire). This issue often comes up in the genealogical community, with a typical example being a couple of individuals (let's call them Klaus and Mikolaj) discovering a shared IBD segment, and Klaus thinking he's found a Polish ancestor, and Mikolaj a German one.

In any case, as the authors themselves note it will be interesting to use more European reference populations, and this might indicate whether they picked up European ancestry in one particular region, carrying it with them as they expanded into the Balkans and beyond, or whether they picked it up by interacting with different host populations (e.g., Greek Gypsies with Greeks, Romanian Gypsies with Romanians, and so on).


arXiv:1212.1696 [q-bio.PE]

Reconstructing Roma history from genome-wide data

Priya Moorjani et al.

The Roma people, living throughout Europe, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1000-1500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry-deriving from a combination of European and South Asian sources- and that the date of admixture of South Asian and European ancestry was about 850 years ago. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which we hypothesize was followed by a major demographic expansion once the population arrived in Europe.

Link

rolloff and ALDER analysis of Turks

I carried out rolloff analysis of the Behar et al. (2010) sample of Turks together with the sample of Uzbeks from the same, and the Yunusbayev et al. (2011) sample of Armenians. A --geno 0.03 flag was applied for merging and SNPs available in the Rutgers recombination map for Illumina chips were used.

The exponential decay can be seen below:

The signal of admixture seems pretty clear and extends up to several cM. Of course, as always, this does not mean that exactly these two populations mixed to form the Turks sample, but it does mean that they are reasonable standins.

The jackknife gives an admixture time estimate of 27.622 +/- 5.348 generations or 800 +/- 160 years, which of course makes perfect historical sense as it is a date between the first arrival of the Seljuks in Anatolia and the final consolidation of power by the Ottomans. Note also that this probably applies principally to this particular sample (which I believe is from Cappadoccia) and there were perhaps different admixture dynamics elsewhere.

I had started this analysis before the announcement of ALDER, but since it is very fast, I decided to give it a go as well. Below is the raw output:




                    *** Admixture test summary ***

Weighted LD curves are fit starting at 1.45 cM

Pre-test: Does Turks have a 1-ref weighted LD curve with Armenians_Y?
   1-ref decay z-score:    0.09
   1-ref amp_exp z-score: -0.01
                                  NO: curve is not significant

Pre-test: Does Turks have a 1-ref weighted LD curve with Uzbeks?
   1-ref decay z-score:    6.56
   1-ref amp_exp z-score:  5.02
                                  YES: curve is significant

Does Turks have a 2-ref weighted LD curve with Armenians_Y and Uzbeks?
   2-ref decay z-score:    5.61
   2-ref amp_exp z-score:  5.58
                                  YES: curve is significant

Do 2-ref and 1-ref curves have consistent decay rates?
   1-ref Armenians_Y - 2-ref z-score:                  0.01   ( 13%)
   1-ref Uzbeks - 2-ref z-score:                       0.69   ( 11%)
   1-ref Uzbeks - 1-ref Armenians_Y z-score:          -0.00   ( -1%)
                                  YES: decay rates are consistent

Test FAILS (z=5.58, p=2.4e-08) for Turks with {Armenians_Y, Uzbeks} weights

DATA: failure 2.4e-08 Turks Armenians_Y Uzbeks 5.58 -0.01 5.02 13% 23.92 +/- 4.26 0.00002930 +/- 0.00000525 27.18 +/- 302.36 -0.00000082 +/- 0.00013129 26.84 +/- 4.09 0.00002316 +/- 0.00000461

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

The age estimate appears to be very similar, and most curves appear to be significant, except the one with Armenians_Y. This makes good sense. From Loh et al. (2012):

Also, if a reference A' shares some of the same admixture history as C or is simply very closely related to C, the pre-test will typically identify long-range correlated LD and deem A' an unsuitable reference to use for testing admixture.

In our case, A'=Armenians and C=Turks. We can be fairly sure that Armenians lack the same admixture history as Turks (because they were not affected by Central Asian Turkic invasions), but we can try a 1-ref analysis of Armenians with Uzbeks to substantiate it. The admixture lower bound estimate is a huge interval 7.6 +/- 88.2 and the jackknife is unable to estimate the admixture time. Thus, more plausibly, the second explanation applies, and because Armenians_Y are very closely related to Turks, they are deemed as an inappropriate reference to test admixture.

Finally, the lower bound of the admixture fraction for Turks with an Uzbek reference is estimated as:

Mixture fraction % lower bound (assuming admixture): 29.8 +/- 4.0

This is a very interesting number. We can be fairly sure that Central Asian Turkic people who invaded Anatolia carried with them an East Eurasian component, but in what proportion to their West Eurasian one? The East Eurasian element in Turks has been rather consistently estimated at ~5-7% with various methods, so perhaps this formed the minority element in the Turkic people who arrived in Anatolia. 

On the other hand, this case is rather muddled by the occurrence of by-directional gene flow: Uzbeks may have West Eurasian ancestry of ultimate West Asian origin, just as Turks have Central Asian ancestry. And, indeed, when we estimate the admixture fraction of Uzbeks with the Turks as a reference, we obtain:

Mixture fraction % lower bound (assuming admixture): 46.7 +/- 2.4

The age estimate for this is ~16 +/- 2 generations = 460 +/- 60 years. Very similar time estimates appear when Armenians are used as a West Eurasian reference. So, this might indicate that the Uzbek population was formed by admixture after the Anatolian Turks were so formed.

I see no easy way to solve the problem of estimating admixture proportions when both extant populations have been both donors and recipients of gene flow, but in any case, these numbers are something to think about.

Analysis of Turks with a variety of Turkic and East Asian populations

I subsequently formed a new dataset by merging the sample of Turks with a variety of Turkic and East Asian populations (same procedure for SNP choice).

For the calendar year calculation, I arbitrarily set the birthdate of the modern sampled individuals at 1980; I have no idea on the age profile of the individuals comprising the Behar et al. sample of Turks. I have also used a mindis=0.5cM which facilitated the convenient automated extraction of the dates from the ALDER output and also gave a level playing field for all the reference populations. The age picked by ALDER using its own adaptive threshold did not usually differ from the reported one by more than a few generations.

The results indicate two things:

• The % of admixture depends on the choice of population, with highest amount using Uzbeks  as a reference, and lowest using the far Asian populations from China. This indicates our uncertainty regarding the East/West Eurasian-ness of the people who settled in Anatolia.
• Admixture times, on the other hand appear to be fairly constant and appear to frame an important watershed moment of Anatolian history, the Battle of Manzikert which paved the way for the eventual Turkification of the peninsula. The Turkmen sample appears as an outlier in this respect, which might indicate that limited migration of Turkmen tribes may have occurred at a later date.

rolloff analysis of Lezgins as Sardinian+Burusho

I have carried out rolloff analysis of Lezgins, a Northeast Caucasian population that is of particular interest due to it being modal for the "Dagestan" component whose long-distance relationships with Western Europe and South Asia have triggered a great deal of followup investigation on my part.

The Lezgins are also interesting for other reasons: they may be one of the populations related to the Kura-Araxes culture; they possess a high frequency of Y-haplogroup R1b, so they may be related to the migration that brought this haplogroup into Europe from West Asia.

In my previous analysis of the French using the same reference populations, I speculated that their signal of admixture may involve admixture between a Sardinian-like and a West Asian population in Asia itself circa 7,000 years ago, followed by a later expansion into Europe. And, in my analysis of Lithuanians and Ukrainians, I discovered a somewhat less "old" signal of admixture involving South Asian+North European references with a mean value of 5.5-6.3ky for the various population pairs.

The exponential fit for the Lezgins can be seen below:

The admixture time estimate is 198.773 +/- 70.649 generations or 5,760 +/- 2,050 years. This is not very precise, but seems consistent with the two phenomena described above. It also seems to contrast with the much younger signal for Armenians.

An estimate of the admixture time for Finns

Using a similar procedure as in my recent post on the Baltic (Update II), I used 15 FIN individuals from the 1000 Genomes together with 12 Nganasans from Rasmussen et al. (2010) as reference populations, and 15 other FIN individuals to estimate admixture LD in a rolloff analysis. Three outlier Nganasan individuals (GSM558800, GSM558802, GSM558807) were removed.

The estimated time of admixture is 86.095 +/- 10.187 generations, or 2500 +/- 300 years. It corresponds rather well to the beginning of the Iron Age in northern Europe.

As I mention in my previous post, there is evidence for intrusive cultures (Battle Axe and Seima Turbino) converging on the area from different directions during the preceding Bronze Age. If the above date is accurate, it will suggest a rather late admixture event between the Europeoid and Siberian elements of Finns. The former may have included both the descendants of Mesolithic European hunter-gatherers and intruders from Central Europe (Corded Ware/Battle Axe); the latter may have included both Comb Ceramic and the descendants of the Seima Turbino metallurgists.

The Indo-European invasion of the Baltic

In some recent posts, I showed that South Asian populations (North Indian Brahmins, South Indian Brahmins) can be seen as mixtures of West Eurasian and South Indian populations, but also that West Eurasians (Bulgarians, Greeks, Armenians, and French) can be seen as mixtures of South Asian and Sardinian populations.

This may seem strange, but can be explained if we understand how f3-statistics and rolloff actually work. These methods do not require pure or unadmixed ancestral populations, but exploit allele frequency differences in the reference populations together with either (i) allele frequencies in the mixed population, in the case of f3-statistics, or (ii) admixture linkage disequilibrium in the mixed population, in the case of rolloff.

If a and b are allele frequencies in two ancestral populations A and B that mix, then:

• The frequency of a will shift towards b if A experiences gene flow from B
• The frequency of a will randomly shift if A experiences gene flow from an "outgroup" population
• The frequency of a will shift towards b if A experiences gene flow from a third population that is geographically and genetically intermediate between A and B

An application to the Europe-South Asia cline

I took the following set of populations, and calculated all 1,365 possible f3-statistics:

"FIN30"         "Lithuanians"   "Russian"       "Pathan"        "Balochi"       "North_Kannadi" "Polish_D"      "Russian_D"     "Mixed_Slav_D"  "Bulgarian_D"   "Serb_D"        "Ukrainian_D"   "Belorussian"   "Bulgarians_Y"  "Ukranians_Y"

In the following table, I report the lowest Z-scores for each target population (third column). So, for example, Polish_D can be seen as a mixture of Lithuanians and Balochi. Only negative scores are indicative of admixture. I highlight in bold the significant negative scores (Z less than -3)


Lithuanians North_Kannadi FIN30 0.001606 0.000259 6.193 280043
Ukrainian_D Belorussian Lithuanians 0.00078 0.000299 2.614 268493
Lithuanians North_Kannadi Russian -0.002738 0.000248 -11.045 279965
North_Kannadi Polish_D Pathan -0.006959 0.000229 -30.344 280220
North_Kannadi Bulgarians_Y Balochi -0.003636 0.000246 -14.781 281604
Pathan Ukrainian_D North_Kannadi 0.033802 0.000623 54.237 271858
Lithuanians Balochi Polish_D -0.001171 0.000178 -6.581 279519
Lithuanians Pathan Russian_D -0.001829 0.000166 -11.026 280658
Lithuanians Pathan Mixed_Slav_D -0.001715 2e-04 -8.594 277635
Lithuanians Balochi Bulgarian_D -0.001247 0.000313 -3.979 272342
Lithuanians Balochi Serb_D -0.00091 0.000377 -2.416 270807
Lithuanians Balochi Ukrainian_D -0.002222 0.000358 -6.211 270399
Lithuanians Balochi Belorussian -0.000897 0.00027 -3.325 273076
Balochi Polish_D Bulgarians_Y -0.001198 0.000185 -6.481 279632
Lithuanians Balochi Ukranians_Y -0.001727 0.000187 -9.236 278677

It is clear, that what I have described holds here: European populations appear like mixtures of Lithuanians and South Asians; conversely, South Asian populations appear like mixtures of Europeans and North Kannadi.

This does not mean that the populations that appear unadmixed (FIN30, Lithuanians, North_Kannadi, and Serbs) are in fact so, for at least two reasons:

1. The f3 statistic confirms, but does not reject the presence of admixture; in particular, it fails to find real admixture in highly drifted populations
2. The f3 statistics exploits allele frequency correlations between populations: but the North Kannadi and Lithuanians/Finns occupy opposite ends of the studied cline, so their lack of signal of admixture may be due to the non-existence of populations that are even more unadmixed than themselves.

In the case of South Indians, we are completely sure that this is the case. Reich et al. (2009) managed to show this not because there are any unadmixed Ancestral South Indians (ASI) left, but because they exploited the existence of the Onge, an isolated group from the Andaman Islands that was a sister group to the ASI. So, we can be fairly sure that southern Indians themselves have West Eurasian-like admixture, even the ones that are at the end of the West Eurasia-South India cline on its southern end.

The problem is: there is no isolated group of unadmixed Europeans left in existence that might serve a similar proxy function as the Onge did for South Asians.

Enter Pickrell et al. (2012) to the rescue. In that paper, the authors studied admixture in the Khoe-San of South Africa. Now, many of the Khoe-San sub-groups appeared to be admixed, but the "Juj'hoan North" population appeared to be at the "end of the cline": it's impossible to detect admixture in them using alelle frequency differences, because, quite simply, there are no populations that are less unadmixed than them: they're as pure descendants of "Ancestral Bushman" as exist on the earth today.

But, the clever thing is, that we don't have to detect admixture only using allele frequency differences, but also using admixture LD, i.e., by exploiting the correlation between linkage disequilibrium (the co-inheritance of physically separated markers on a chromosome) and allele frequency differences between populations. Pickrell el al. were able to do this not by conjuring up a more unadmixed population than the "Juj'hoan North" one available to them, but by splitting up that population, and using one half to find allele frequency differences, and the other half to detect admixture LD.

Admixture LD signal in Lithuanians

Using the aforementioned idea, I set out to see whether Lithuanians, who occupy the European end of the Europe-South Asia cline present such a signal of admixture LD. I used the Lithuanian_D sample from the Dodecad Project and the Balochi HGDP sample as reference populations (to calculate allele frequency differences), and the Behar et al. (2010) Lithuanians for admixture LD. There were only ~300k SNPs usuable in this set, but sufficient to detect the signal of admixture LD:

The admixture time estimate is 200.350 +/- 61.608 generations, or 5,810 +/- 1790 years. This is not very precise, probably because of the small number of SNPs and individuals used, but it certainly points to the Neolithic-to-Bronze Age for the occurrence of this admixture. The date is certainly reminiscent of the expansion of the Kurgan culture out of eastern Europe, or, the later Corded Ware culture of northern Europe.

So, it may well appear that at least some of the people participating in these groups of cultures, were indeed influenced by the Indo-Europeans as they expanded from their West Asian homeland. These intruders mixed with eastern Europeans who vacillated during the late Neolithic between a northern Europeoid pole akin to Mesolithic hunter gatherers from Gotland and Iberia, and a widely dispersed Sardinian-like population that is in evidence at least in the Sweden-Italian Alps-Bulgaria triangle. The gradual appearance of non-mtDNA U related lineages in Siberia and Ukraine is most likely related to this phenomenon.

It would seem that the Proto-Indo-Europeans mixed with different substrata in the four directions of their expansion: Sardinian-like people in southern Europe, Lithuanian-like people in northern Europe, South Indian-like people in South Asia, and East Eurasians in Siberia and east central Asia. Extant groups are descendants of divergent Neolithic population groups, brought closer together (genetically) because of variable admixture with the PIE population and its early offshoots.

Conclusion

There are mutual signals of admixture across a Europe-South Asia cline: Europeans appear to be mixed with South Asians, and South Asians appear to be mixed with Europeans. The simplest explanation for this pattern involves expansion of a third, geographically and genetically intermediate population that affected both Europe and South Asia. We can use the signal of admixture LD to prove that this expansion affected some of the most unadmixed populations in Europe (e.g., Lithuanians), just as it did the most unadmixed populations of India (e.g., Dravidians).

It will be interesting to use these techniques to study signals of admixture in other "end of the line" populations such as Sardinians, South Indians, etc.

UPDATE I (rolloff analysis of Poles):

I have carried out rolloff analysis of my 25-strong Polish_D sample using Lithuanians and Pathans as references:

The signal is fairly distinct, and corresponds to 149.296 +/- 38.783 generations or 4330 +/- 1120 years. I am guessing that either the different reference population (Pathans vs. Balochi), or, more likely the increased number of target individuals (25 vs. 10) have contributed to the narrowing down of the uncertainty. It will be interesting to explore this signal further with more population pairs.

UPDATE II (rolloff analysis of Finns):

I have also used the 1000 Genomes Finnish sample (FIN) in a similar manner as Lithuanians, using 15 individuals to estimate allele frequency differences, and 15 ones for admixture LD, and using the Pathans as a South Asian reference population. There is a clear signal of admixture:

This dates to 104.967 +/- 14.797 generations, or 3,040 +/- 430 years. Finland came under the influence of both Europeans (and likely Indo-Europeans) during the Bronze Age period (a mixture of Battle Axe with local Comb Ceramic seems to have occurred), as well as likely non-European (and likely Uralic) intrusions during the same time frame, as part of the Seima-Turbino phenomenon. It will be interesting to repeat this analysis with an East Eurasian reference population to isolate potential signals of admixture dating to either the Comb Ceramic or Seima-Turbino episodes of migration.

(Note; added Oct 14): I carried out rolloff analysis using Nganassans as suggested in the above paragraph here.

UPDATE III (rolloff analysis of Ukrainians):

I have used the Yunusbayev et al. sample of Ukrainians, and estimated its admixture time using Lithuanians and Balochi as reference populations:

The admixture time estimate is 191.078 +/- 35.079 generations, or 5,540 +/- 1,020 years. It seems very similar to that in Lithuanians, with a smaller standard error, perhaps on account of either the larger number of SNPs or larger number of individuals.

It is tempting to associate this admixture signal with the Maikop culture which appeared at around this time. Assuming that North_European/West_Asian (or Lithuanian-like and Balochi-like) gene pools existed north and south of the Pontic-Caspian-Caucasus set of geographical barriers, then the Maikop culture which shows links to both the early Transcaucasian culture and those of Eastern Europe would have been an ideal candidate region for the admixture picked up by rolloff to have taken place. There are, of course, other possibilities.

UPDATE IV (rolloff analysis of Lithuanians with Pathan reference):

I repeated the first analysis of this post, but this time, I used Pathans, rather than Balochi as a reference population:

The admixture time estimate of 217.501 +/- 51.170 generations, or 6,310 +/- 1,480 years appears to be similar with the original estimate of 5,810 +/- 1790 years, so it does not appear that the use of Balochi or Pathan as a reference population much affects this result.

rolloff analysis of North Indian Brahmins as Orcadian+North Kannadi

In a previous experiment, I tested the Dodecad Project South Indian Brahmin sample (Iyer and Iyengar) using Orcadians and North Kannadi as reference populations. In the current one, I use the same references to investigate admixture in the Uttar Pradesh Brahmins included in the Metspalu et al. (2011) dataset. A total of 473,837 SNPs are used in this experiment.

I first verified that f3(Brahmins_from_Uttar_Pradesh_M; Orcadian, North_Kannadi) is negative, using qp3Pop:

 Source 1 Source 2 Target f_3 std. err Z SNPs
 result: Orcadian North_Kannadi Brahmins_from_Uttar_Pradesh_M -0.007882 0.000359 -21.951 463297

The exponential fit can be seen below:

The estimated age is 79.706 +/- 9.197 generations, or 2,310 +/- 270 years.

This is about a thousand years younger than the signal observed for the South Indian Brahmin group. A possible explanation has to do with the fact that South Indian Brahmins migrated to South India, and hence did not intermarry with successive waves of invaders into India in historical times. Uttar Pradesh, on the other hand, received multiple invasions from the direction of Central Asia:

Most of the invaders of North India passed through the Gangetic plains of what is today Uttar Pradesh. Control over this region was of vital importance to the power and stability of all of India's major empires, including the Maurya (320–200 BC), Kushan (100–250 CE), Gupta (350–600 CE), and Gurjara-Pratihara (650–1036 CE) empires.[11] Following the Huns invasions that broke the Gupta empire, the Ganges-Yamuna Doab saw the rise of Kannauj.[12] During the reign of Harshavardhana (590–647 CE), the Kannauj empire reached its zenith.[12]

It will be interesting to see whether a young admixture signal also exists in my 5-strong sample of Jatts, since that population has traditions of "Scythian" origins.

rolloff analysis of Bulgarians as Sardinian+Pathan

Continuing my rolloff experiments, I have taken the Yunusbayev et al. sample of Bulgarians. This is interesting because of the recent evidence of a Sardinian-like individual from Iron Age Bulgaria, and also as a complement to a similar analysis on the Greeks. Bulgarians are Slavic speaking, but their ethnogenesis owes a great deal to the Bulgars, adding another potential element of complication. However, the paucity of East Eurasian admixture in Bulgarians, together with their Slavic language, probably suggests that this element represented a small elite that did not have a substantial role in the genetic formation of the Bulgarian population.

The top f3 statistics can be seen below:

Kshatriya_M Sardinian Bulgarians_Y -0.003813 0.000295 -12.918 237507
Velamas_M Sardinian Bulgarians_Y -0.003783 0.000285 -13.287 238276
Piramalai_Kallars_M Sardinian Bulgarians_Y -0.003693 0.000306 -12.061 238106
Kanjars_M Sardinian Bulgarians_Y -0.003643 0.000298 -12.227 237838
GIH30 Sardinian Bulgarians_Y -0.003638 0.000259 -14.028 240548
North_Kannadi Sardinian Bulgarians_Y -0.00355 0.000317 -11.187 237882
Muslim_M Sardinian Bulgarians_Y -0.003542 0.000333 -10.632 236964
Chamar_M Sardinian Bulgarians_Y -0.003505 0.000303 -11.585 238882
INS30 Sardinian Bulgarians_Y -0.003467 0.000264 -13.153 240279
Dharkars_M Sardinian Bulgarians_Y -0.003452 0.000309 -11.155 238211
Brahmins_from_Uttar_Pradesh_M Sardinian Bulgarians_Y -0.003448 0.000278 -12.42 238041
Indian_D Sardinian Bulgarians_Y -0.003411 0.000256 -13.308 241225
Iyer_D Sardinian Bulgarians_Y -0.003364 0.000291 -11.568 237509
Jatt_D Sardinian Bulgarians_Y -0.003327 0.000289 -11.513 236735
Pathan Sardinian Bulgarians_Y -0.003212 0.000239 -13.444 240969
Iyengar_D Sardinian Bulgarians_Y -0.003209 0.000308 -10.416 236840
Dusadh_M Sardinian Bulgarians_Y -0.003181 0.000313 -10.172 237512
Sindhi Sardinian Bulgarians_Y -0.003094 0.000239 -12.919 241268
Balochi Sardinian Bulgarians_Y -0.002804 0.00024 -11.686 240924

To maximize the number of SNPs and number of individuals, I used the Sardinian+Pathan pair as reference populations. 509,395 SNPs were used for this experiment. The exponential fit can be seen below:

There was a technical issue with the jackknife which I am currently investigating, but the mean time of the admixture was estimated at 126.83004 generations, or 3,680 years. This is similar to the value of 3,850 years I obtained on the Greek sample.

If this date is accepted, then the interesting issue is why an individual from Bulgaria was Sardinian-like during the Iron Age. Possibly, either this individual was Sardinian-like in the broad sense, despite having  minority West Asian admixture, or a few centuries after the admixture event, there was still an uneven distribution of the constituent elements, with most individuals still predominantly Sardinian-like. Given that the indigenous element was probably most numerous, so only part of it would have the opportunity to admix with the intrusive West Asian-like population, and this influence would spread to the population-at-large over time.

In any case, this evidence, such as it is, appears consistent with my idea about a Bronze Age invasion of Europe from Asia.

Naturally, only a broad sampling of ancient DNA variation from the Balkans, perhaps targeting different sites, cultures, times, social status, and physical types will be sufficient to track the early appearance of an intrusive population.

rolloff analysis of South Indian Brahmins as Armenian+Chamar

The first analysis of this population showed that there were negative f3(Brahmin; X, Y) signals when X were a variety of West European, Balkan, and West Asian population, and Y either the Chamar or North Kannadi. In the first analysis I used Orcadians and North Kannadi. I have now carried out a new rolloff analysis on 470,559 SNPs, using Armenians_Y and Chamar_M as the reference populations.

The exponential fit can be seen below.

The admixture date is 142.814 +/- 15.010 generations, or 4,140 +/- 440 years, which seems to correspond quite well with commonly accepted dates for the formation of Indo-Iranian.

I have previously observed that:

These patterns can be well-explained, I believe, if we accept that Indo-Iranians are partially descended not only from the early Proto-Indo-Europeans of the Near East, but also from a second element that had conceivable "South Asian" affiliations. The most likely candidate for the "second element" is the population of the Bactria Margiana Archaeological Complex (BMAC). The rise and demise of the BMAC fits well with the relative shallowness of the Indo-Iranian language family and its 2nd millennium BC breakup, and has been assigned an Indo-Iranian identity on other grounds by its excavator. As climate change led to the decline and abandonment of BMAC sites, its population must have spread outward: to the Iranian plateau, the steppe, and into South Asia, reinforcing the linguistic differentiation that must have already began over the extensive territory of the complex.

Quite possibly, as the West Asian element began mixing with the Sardinian-like population in Greece, another branch of the Indo-Europeans made its appearance east of the Caspian, in the territory of the BMAC, admixing with South Asian-like populations. Thus, it might seem that the Graeco-Aryan clade of Indo-European broke down during the Bronze Age, with one branch heading off to the Balkans, and another to the east. 

This scenario would also explain how the likely J2-bearing population associated with the earliest Proto-Indo-Europeans may have acquired the contrasting pattern I have previously described: the western (cis-Caspian) population would have admixed with R1b-bearers who occupy the "small arc" west and south of the Caspian, while the eastern (trans-Caspian) populations would have admixed with R1a-bearers who occupy the "large arc" in the flatlands north and east of the Caspian. It would also explain how the "western" branch (Graeco-Armenian) would have picked up Sardinian-like "Atlantic_Med" admixture, which is absent in the "eastern" Indo-Iranian branch.

At the same time, this scenario would explain the lack of "North European" admixture in the "western" branch (since this was shielded by the Caucasus and Black Sea from the northern Europeoids who may have lived north of these barriers), and explain it in the "eastern" branch (since the BMAC agriculturalists were in contact with presumably northern Europeoid groups inhabiting the steppelands, unhindered by any major physical barriers). (The relative absence of this admixture in the Graeco-Armenian branch may be advanced on the strength of its absence in Armenians, the evidence of a Sardinian-like Iron Age individual from Bulgaria, and the historical-era timing of admixture for the Greek population.)

It would be interesting to carry out similar experiments on Iranian groups, to see if they, too, present a similar pattern of admixture.

rolloff analysis of Greeks as Sardinian+Brahui

In a previous experiment, I showed that Greeks can be seen as composites of two alternate sets: either a Sardinia-South Asia mix, or a North European-Near East mix. I first studied the latter, which provided a historical-period estimate for the admixture time. I now turn to the former, and use Sardinians and Brahui as parental populations. This complements previous analyses on Armenians and French using similar reference populations. Since I used the Balochi and Burusho in the two previous experiments, I decided this time to use the Brahui, which is the third population which presents a significant f3(Greek; Sardinian, Brahui) signal along the Europe-West Asia axis.

473,174 SNPs were used in total. The exponential fit can be seen below.

The jackknife estimate is 132.890 +/- 35.527 generations, or 3,850 +/- 1030 years. This spans the entirety of the Helladic period, with the mean being close to two often-cited dates for the "coming of the Greeks", corresponding to the destructions at the EHIII/MH boundary (c. 2100BC), and the spread of "Minyan ware" at c. 1900BC, although an earlier or later date is certainly possible.

(An alternative interpretation would relate the earliest Greeks to a Sardinian-like European population and the Asian component to a Luwian-like Anatolian population responsible for the well-known -nth and -ss toponyms in the Aegean.)

A signal of West Asian admixture during the Bronze is certainly consistent with my musings on the spread of metallurgy from the east during this time.

Armenians as Phrygian colonists, or, rolloff analysis of Armenians as a mixture of Sardinians+Balochi

I analyze the Yunusbayev et al. Armenians_Y sample in a similar manner as the South Indian Brahmins. The 30 lowest f3 statistics are:

Sardinian Velamas_M Armenians_15_Y -0.00349 0.000264 -13.23 239451
Sardinian Piramalai_Kallars_M Armenians_15_Y -0.003213 0.00028 -11.484 239389
Sardinian GIH30 Armenians_15_Y -0.002983 0.00023 -12.986 241310
Balochi Sardinian Armenians_15_Y -0.002837 0.000193 -14.681 241698
Sardinian Sindhi Armenians_15_Y -0.002794 0.000203 -13.757 241928
Sardinian Muslim_M Armenians_15_Y -0.002761 0.000295 -9.351 238639
Indian_D Sardinian Armenians_15_Y -0.002743 0.000224 -12.226 241916
Sardinian Kanjars_M Armenians_15_Y -0.002727 0.000281 -9.722 239240
Iyer_D Sardinian Armenians_15_Y -0.002718 0.000263 -10.322 238943
Brahui Sardinian Armenians_15_Y -0.002715 0.000196 -13.882 241885
Sardinian Dusadh_M Armenians_15_Y -0.002666 0.000281 -9.502 238994
Sardinian INS30 Armenians_15_Y -0.00265 0.000237 -11.162 240965
Iyengar_D Sardinian Armenians_15_Y -0.002624 0.000297 -8.847 238564
Sardinian Dharkars_M Armenians_15_Y -0.002501 0.000267 -9.359 239505
Sardinian North_Kannadi Armenians_15_Y -0.002463 0.000288 -8.545 239278
Sardinian Chamar_M Armenians_15_Y -0.002445 0.000275 -8.904 240102
Sardinian Kshatriya_M Armenians_15_Y -0.002372 0.000267 -8.897 239047
Pathan Sardinian Armenians_15_Y -0.00224 0.000199 -11.264 241759
Sardinian Brahmins_from_Uttar_Pradesh_M Armenians_15_Y -0.002189 0.00025 -8.774 239395
Jatt_D Sardinian Armenians_15_Y -0.001806 0.000273 -6.608 238465
Cypriots Kanjars_M Armenians_15_Y -0.001699 0.00026 -6.547 238237
Cypriots Velamas_M Armenians_15_Y -0.001642 0.000275 -5.965 238392
Cypriots Muslim_M Armenians_15_Y -0.001618 0.000279 -5.798 237762
Cypriots Dusadh_M Armenians_15_Y -0.001611 0.000279 -5.779 238096
GIH30 Cypriots Armenians_15_Y -0.001608 0.000223 -7.216 239819
Iyer_D Cypriots Armenians_15_Y -0.001562 0.000251 -6.217 238012
Sindhi Cypriots Armenians_15_Y -0.001544 0.000209 -7.383 240276
Cypriots North_Kannadi Armenians_15_Y -0.001464 0.000276 -5.298 238273
Cypriots Kshatriya_M Armenians_15_Y -0.001438 0.00026 -5.534 238076

I carried out rolloff analysis using the Balochi and Sardinians as references, for a total of 510,844 SNPs. Note that the Burusho were not used in this experiment, because they were culled due to more than 5% East Eurasian admixture, as per the followed procedure. 

The Balochi are very similar to the Burusho otherwise, and this also gives me the opportunity to see a Sardinian+Balochi population pair to complement a previous analysis of French as Sardinian+Burusho, which presented an f3 signal of quite similar intensity. The exponential fit is seen below.

The jackknife gives an age estimate of 113.194 +/- 14.674 generations, or 3,280 +/- 430 years, assuming a generation length of 29 years.

I had somewhat expected the Armenians to show a more recent signal of admixture than the French, as they lived much closer to the boundary of Europe and Asia, and may have had more opportunity to admix between Sardinian-like populations of Europe and "West Asian"-like populations of Asia.

But, the inferred date also raises another possibility. Herodotus says of the Armenians who were part of the army of King Xerxes:

the Armenians were equipped like Phrygians, being Phrygian colonists" (7.73)

Now, the Phrygians became masters of Central Anatolia during the tumultuous events near the end of the Bronze Age (12th century BC), following the collapse of the Hittite Empire. And, their ancestral homeland was in Thrace. And, there is fairly good evidence that Armenian is the closest language related to Greek within the Indo-European language family. And, we have some tantalising evidence that even during the Iron Age, the population of Thrace was Sardinian-like. And, the Armenians do contrast with their Caucasian neighbors in possessing ~10% of the Sardinian-like Atlantic_Med component that South and Northeast Caucasians lack.

All of the above combine to make a pretty compelling story. Could it be that Armenians preserve a legacy of admixture between a linguistically Indo-European speaking, genetically Sardinian-like population, which arrived in Asia Minor from the Balkans at the end of the Bronze Age, finally settling in the Armenian Highlands, and mixing with the local people they encountered?

The plot thickens. And, this is, certainly, a question that can be answered by ancient DNA research, e.g., by comparing the genomes of historical Phrygians and Armenians with those from Hittite-era, or earlier Anatolians.

rolloff analysis of South Indian Brahmins

Populations with 5+ individuals and which belonged no more than 5% in African or East Eurasian components at K=7 were retained. South Indian Brahmins were combined from the Iyer_D and Iyengar_D datasets of the Dodecad Project. Other populations were from the current version of the Old World dataset used for the K7b/K12b calculators.

The lowest f3 statistics were the following:

English_D North_Kannadi South_Indian_Brahmin -0.006119 0.000339 -18.06 236533
North_Kannadi Orkney_1KG South_Indian_Brahmin -0.005987 0.000311 -19.223 237162
Irish_D North_Kannadi South_Indian_Brahmin -0.005958 0.000317 -18.817 237023
British_Isles_D Chamar_M South_Indian_Brahmin -0.005931 0.000334 -17.757 237112
Dutch_D North_Kannadi South_Indian_Brahmin -0.005914 0.00034 -17.416 236008
British_Isles_D North_Kannadi South_Indian_Brahmin -0.005914 0.000342 -17.273 236064
North_Kannadi Baleares_1KG South_Indian_Brahmin -0.005878 0.000367 -16.012 235743
German_D North_Kannadi South_Indian_Brahmin -0.005838 0.000306 -19.048 237156
Georgian_D North_Kannadi South_Indian_Brahmin -0.005827 0.000366 -15.924 235091
CEU30 North_Kannadi South_Indian_Brahmin -0.005818 0.000315 -18.461 237266
Greek_D North_Kannadi South_Indian_Brahmin -0.005812 0.000314 -18.527 237028
Orcadian North_Kannadi South_Indian_Brahmin -0.005807 0.000329 -17.649 236669
Austrian_D North_Kannadi South_Indian_Brahmin -0.005803 0.000371 -15.659 235187
North_Kannadi Pais_Vasco_1KG South_Indian_Brahmin -0.005796 0.000337 -17.193 235754
British_D North_Kannadi South_Indian_Brahmin -0.005794 0.000336 -17.243 236613
Mixed_Germanic_D North_Kannadi South_Indian_Brahmin -0.005778 0.000344 -16.794 236047
French North_Kannadi South_Indian_Brahmin -0.005773 0.000312 -18.493 237461
North_Kannadi Cornwall_1KG South_Indian_Brahmin -0.00577 0.000306 -18.846 237375
Armenians Chamar_M South_Indian_Brahmin -0.005759 0.000279 -20.674 238398
Orkney_1KG Chamar_M South_Indian_Brahmin -0.005757 0.000287 -20.042 238463
Hungarians North_Kannadi South_Indian_Brahmin -0.005756 0.000311 -18.482 237196
Serb_D North_Kannadi South_Indian_Brahmin -0.005751 0.000371 -15.499 235625
Iraq_Jews Chamar_M South_Indian_Brahmin -0.005742 0.000303 -18.968 237341
Greek_D Chamar_M South_Indian_Brahmin -0.005736 0.000293 -19.57 238374
North_Kannadi Aragon_1KG South_Indian_Brahmin -0.005733 0.000347 -16.526 235610
Armenians_15_Y Chamar_M South_Indian_Brahmin -0.005723 0.000293 -19.5 237884
German_D Chamar_M South_Indian_Brahmin -0.005719 0.000294 -19.483 238514
Orcadian Chamar_M South_Indian_Brahmin -0.005701 0.000305 -18.707 237880
French_Basque North_Kannadi South_Indian_Brahmin -0.005698 0.000333 -17.104 237119

Links between Western Europe and South Asia have turned up in many of the Project's analyses (e.g., the West European in Dodecad v3, or the Gedrosia component in K12b, or even earlier the "Dagestan" component in both West Europe and South Asia). 

Of course, we don't have to imagine a migration all the way from the the British Isles to South Asia, anymore than we may imagine a migration from South America to Europe to explain the strong negative f3(European; Karitiana, Sardinian) signals previously detected. I don't know what to make of this tendency to minimize f3 for the "longest possible clines". 

In any case, I carried out rolloff analysis using Orcadians and North_Kannadi. This is not the strongest signal, but it is very close to it, and also has the twin advantages of involving public data (so the analysis can be repeated) and a large number of SNPs, which were 466,644 in total. The fit can be seen below:

This appears to be excellent visually. The inferred date from the jackknife is 110.155 +/- 11.345 generations, or 3,190 +/- 330 years, assuming as always a generation length of 29 years.

The obvious candidate for this admixture signal is of course the arrival of the Indo-Aryans into South Asia. 

rolloff analysis of French as a mixture of Sardinian+Burusho

I obtain f3(French; Sardinian, Burusho) = -0.002652 (Z=-13.541) on the basis of 446,917 SNPs. This is the strongest signal of admixture in the French that involves a population that is high on the "West_Asian" component whose influence I have been investigating.

I thus carried out rolloff analysis using the French as a target population and the Sardinians and Burusho as reference populations. The exponential fit can be seen below:

The jackknife gives 239.556 +/- 50.553 generations for this admixture, which corresponds (assuming a generation length of 29 years) to 6,950 +/- 1,470 years.

Analysis of autosomal DNA from the Tyrolean Iceman and a Neolithic TRB farmer from Sweden have revealed an absence of the West Asian ancestral component and a Sardinian-like Neolithic population c. 5ka in Europe. This population may have extended to at least to the Balkans in space and down to the Iron Age in time.

In my opinion, the simplest explanaton for the evidence is that the admixture picked up by rolloff took place in West Asia itself c. 7ka, and then this population begun its movement into Europe at some post-5ka time period.

Importantly, the K=12 Caucasus component appears as a mixture of the K=7 West_Asian and Southern components. The former (West_Asian) is the most important one in the Burusho, and the latter (Southern) is the most important one in Sardinians.

European Neolithic farmers, of presumably West Asian origin only possessed Y-haplogroup G2a out of the wide variety of haplogroups found in West Asia today. They also lacked the West_Asian component which is modal in West Asia today. There is also physical anthropological evidence from Greece and Anatolia, for an introduction of new population elements during the Bronze Age.

These facts combine to make me believe that there were population movements across West Asia which preceded the Indo-European invasion of Europe during late pre-history. That event is then best seen as an extension of a broader Eurasian phenomenon that affected substantially both the western parts of Asia and Europe.

Taking all the evidence into account, I hypothesize that:

• a "Southern"/"Atlantic_Med"/Sardinian-like population substratum existed in West Asia, and this spawned the early European Neolithic.
• a new "West_Asian"/Burusho-like population arrived from the east, perhaps associated with the Halaf/Hassuna cultures, or from some other unknown center of dispersal in the Transcaucasus or Iran. Mobility may have been encouraged post-8.2 kiloyear event.
• these two elements began mixing ~7 thousand years ago in West Asia
• the admixed population expanded at some post-5ka period into Western Europe.

This scenario is also compatible with the lack of "Southern"/"Atlantic_Med" influences in the Indian subcontinent and Central Asia: if the West_Asian component originated to the east of the Sardinian-like population then it would not have the opportunity to incorporate "Southern" elements in its eastern expansion.

(Obviously, more rolloff analyses are needed to study these ideas; the current one took about ~3 days, which was a little faster than I expected.)

Related (?): Is Burushaski Indo-European?

Image credit: Don Perrault (source)

rolloff analysis of North European admixture in Greeks.

One of the signals of admixture in my recent post on the Greeks on the crossroads of Eurasia was between north European and Near Eastern populations, with several pairs of such populations showing a significant negative f3(Greek_D; North European, Near Eastern) statistic. I used rolloff to estimate the date of this admixture.

Note that rolloff assumes a pulse model of admixture, whereby the two populations mix at a point in time, rather than experience gene flow over a protracted period. This may not be applicable in the case of Greeks, since gene flow may have occurred repeatedly throughout history. Also, rolloff estimates admixture times in the absence of very accurate ancestral populations, by exploiting allele frequency differences between them. So, for the first example below, with Finnish_D and Yemen_Jews as reference populations, which showed the most negative f3 statistic, this does not mean that Greeks are the product of admixture between Finns and Yemen Jews, but rather that allele frequency differences between these two populations reflect a contrast between North Europeans and Near Eastern populations, which may, presumably map, to the west Eurasian cline of diminishing Near Eastern "Neolithic" ancestry.

This experiment was performed on a set of 292,223 SNPs, and using the Rutgers map for Illumina chips. The first plot is using Finnish_D and Yemen_Jews as references. The fit does not visually appear extremely convincing, perhaps due to a smaller number of SNPs, or to the aforementioned deviation from the pulse admixture model.

(NB: I used the expfit.sh script with default parameters to do the exponential fit/plotting; note that negative weighted correlation points are not visible in the produced output)

The jackknife estimate of this admixture is 87.849 +/- 20.254 generations, or, assuming a generation length of 29 years, into 2,550 +/- 590 years.

The second plot uses Polish_D and Saudis as references:

The jackknife gives 67.235 +/- 22.148 generations, or 1950 +/- 640 years. The fit seems to capture the rise of the exponential for smaller cM genetic distances reasonably well.

Recently, Graham and Coop used fastIBD to identify a signal of possible Slavic admixture in the Balkans dating to the medieval period, using a similar generation time of 30 years. That method uses shared IBD segments between populations, so it may be limited to uncovering the most recent signal of admixture. Another piece of evidence comes from an abstract in ASHG 2012, according to which an Iron Age individual from Bulgaria was Sardinian-like. Since the Iron Age starts at the conclusion of the 2nd millennium BC, it might seem that a northern European element -whether present or not- had not admixed yet with the people who lived in the Balkans at the time. This seems to parallel the situation in two other earlier locations (c. 5ka in the Tyrolean Iceman and Gok4 Swedish TRB farmer), in which the North_European component was absent, although we cannot yet exclude its absence from the Iron Age Bulgarian, since a little such admixture might still leave an individual mostly Sardinian-like. Finally, levels of the North_European component in Greek individuals seem fairly variable, and this might indicate that levels of this element of ancestry had not had sufficient time to even out in the population.

(A different possibility is that the admixture signal reflects admixture of a Near Eastern kind. I consider this less likely, since there is evidence of "Southern" and "Southwest Asian" ancestry (in the K7b/K12b sense) already in Neolithic Europe.)

More research on the issue is certainly needed, but a first reading of the evidence suggests that this type of admixture may reflect events that took place during the historical period of Greek history.

Each of these experiments took about 1.5 days to complete. I am currently running another set of experiments with ~2-fold more SNPs, and assuming that finishes in good time, I may re-visit the question addressed in this post, to see if standard errors decrease and/or time estimates change with denser coverage.