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Friday, June 16, 2017

Cypriot Y-chromosomes (Heraclides et al. 2017)

Over at PLoS ONE at this link. Note the fairly high levels of Y-haplogroups R1a and/or R1b in many of the Greek and Turkish populations in the figure below. Much of this might be of fairly recent European (mostly Slavic) and Central Asian (Turkic nomad and Ottoman) provenance, but I'd say some of it has to date back to the Bronze Age, and potentially to the expansions of the Proto-Anatolians, Proto-Armenians and Proto-Greeks into the Balkans and Anatolia from the Pontic-Caspian steppe. Emphasis is mine:

Abstract: Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7–8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.


Y-haplogroup frequencies within GCy and TCy can be found in S6 Table. Y-haplogroup frequencies of Cypriots, Greeks, and Turks, as well as other surrounding populations can be found in Fig 1 (as well as S7 Table). GCy and TCy showed very similar frequencies for the major Y-haplogroups, differentiating both from Greek and Turkish sub-populations (Fig 3). The most frequent major Y-haplogroup subclade in both GCy and TCy was J2a-M410 (23.8% and 20.3% among GCy and TCy, respectively), followed by E-M78 (12.8% Vs 13.9%) and G2-P287 (12.5% Vs13.7%). R1b-M343 was found in higher frequency among GCy (11.9%) than TCy (6.8%), while the same applies for E-M123 (13.1% Vs 6.3%). Finally, haplogroup, although in much lower frequencies than the aforementioned haplogroups, haplogroup I2 was somewhat higher among TCy (6.8%), than among GCy (2.3%), while haplogroup J2b was higher among GCy (5.8%) than TCy (1.8%). Other, less common haplogroups (i.e. I1, R1a, L, and T) showed similar frequencies (in the range of 1–5%) between GCy and TCy.

One additional difference between GCy and TCy was the presence of moderate numbers of East Eurasian (primarily Central Asian) Y-haplogroups and small numbers of North African Y-haplogroups among TCy but not among GCy. The frequency of East Eurasian haplogroups among TCy was C-M130 (0.5%), H-L901 (0.3%), N-M231 (2.4%), O-M175 (0.8%) and Q-M242 (1.3%), reaching a total of 5.6%, but only totalling 0.6% among GCy. North African haplogroups (E-M81, E-V38) were only found among TCy (2.1%) (S6 and S7 Figs).

A major feature differentiating Cypriots from Greeks, is the much lower frequency of haplogroups I (2.9% GCy, 7.3% TCy, ~10–21% mainland Greeks) and R1a (2.9% GCy, 3.2% TCy, ~10–22% mainland Greeks) among the former. All differences in haplogroup frequencies between populations were statistically significant (Fisher’s Exact test, p<0.001).


In terms of Y-haplogroup distribution, Cypriots (GCy and TCy) show substantial differences from Greeks, characterized by much lower frequency of haplogroups I2, R1a, and R1b in the former. These haplogroup differences indicate differential migrations into Cyprus and mainland Greece, at different points in history and prehistory. I2 is considered the major haplogroup among Mesolithic European Hunter-Gatherers[60], who apparently were either absent from Cyprus or were totally diluted (nearly extinguished) by subsequent migrations. Although the exact origins and migratory patterns of R1a and R1b are still under rigorous investigation, it seems that they are linked to Bronze Age migrations from the Western Eurasian Steppe and Eastern Europe into Southern (including Greece) and Western Europe[61]. Apparently, such migrations (especially as regards R1a) into Cyprus were limited.

Additionally, the Greek population has received considerable migrations during the Byzantine era and the Middle Ages from other Balkanic populations, such as Slavs[62,63], Aromanians (Vlachs)[64], and Albanians (Arvanites)[65,66]. The former, is very likely to have increased R1a frequencies among Greeks. In fact, Fig 3 (also S7 Table) indicate that R1a increases gradually with increasing latitude in Greece. There is no historical evidence for such migrations into Cyprus during the same period.

Heraclides A, Bashiardes E, Fernández-Domínguez E, Bertoncini S, Chimonas M, Christofi V, et al. (2017) Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots. PLoS ONE 12(6): e0179474.


Ryan said...

I wish there was more on the specific subclades.

Davidski said...

I was referring to the pie charts, not to the PCA. I haven't even looked at the PCA yet.

In any case, all of that R1a/R1b can't be younger than the Bronze Age. Some of it has to date back to the Eneolithic and Bronze Age, no matter what the subclades are.

Anthro Survey said...


I second that. They aren't.

They'd be more useful with resolved y-haplogroup subclades, but even then, with stuff like potential drift and bottleneck scenarios in action, it is a very crude method to assess population relationships. Nevertheless, I realize that the presence/presence of certain haplogroups, in a very binary sense, can prove to be useful breadcrubs in tracking population changes over time. Just ask Gioiello!

Rob said...

& Dave
I was referring to the PCA not your comment on pie charts
But now that you bring it up: 90% of R1b in turkey is probably Z2013. But there's no way of telling when it arrived there (unless we have a decent amount of NGS moderns with a calculated local TMrCA ). In other words, Z2013 could have arrived from Yamnaya, or with the post-K/A movements through Armenia, or which Proto historic peoples from the Balkans. IIRC Aram suggested the second scenario was most consistent with the data.

Obviously 90% of R1a in Greece came with 'Slavs', so I'm not sure why you're pretending to be confused there.

Davidski said...

In other words, Z2013 could have arrived from Yamnaya, or with the post-K/A movements through Armenia, or which Proto historic peoples from the Balkans. IIRC Aram suggested the second scenario was most consistent with the data.

Seems unlikely.

Obviously 90% of R1a in Greece came with 'Slavs', so I'm not sure why you're pretending to be confused there.

If you say so, but even if true, which I doubt that it is, then where did the rest of the R1a come from, especially on Crete?

Rob said...

@ Dave

RE: Z2103: What 'seems unlikely" ?

"If you say so, but even if true,"

Of course it's true. It was published in Underhill and also evident in the ftDNA R1a database .

"When where did the rest of the R1a come from, especially on Crete?"

There is little "the rest" to account for. in the Underhill study, 100% of mainland Greek R1a is nestled within younger Balto-Slavic caldes. Heck, some of it is even M458.

Same deal with Crete. Of a total of 10%, 1% is Z93, the rest "B-Sl" clades. IIRC there is a local peak in lasithi plateau, perhaps one of the many re-settlements of Sklavenes within the Byzantine Empire.

Davidski said...

Well, considering ancient DNA from the steppe and Caucasus, it's not very parsimonious not to consider Yamnaya as the most likely source of Z2103 in West Asia.

And I'm not sure if the Greek R1a sample set in the last Underhill et al. paper was exactly exhaustive.

By the way, Alexandros has posted here in the past, but he won't be posting in this thread, which is fair enough. But for anyone commenting here, please note that this paper has a very specific goal, which is comparing the paternal ancestry of Greek and Turkish Cypriots, and anything beyond that is a bonus.

Gioiello said...

@ Anthro Survey
"Just ask Gioiello!"

I thank you for asking me, but of course it is very difficult to interprete haplotypes without the help of SNPs, and we have had many disproves recently from haplotypes of the Ligurian stock, but I'd say that also a presence of recent Italian haplotypes in Ciprus shouldn't be discarded. Perhaps venetian Bragadin, before being skinned from Turks, had the time to entertain himself with some woman of the island. We discussed a lot if the haplotype with fractionate DYS385b were from Vandals of Northern Africa or decisively from Italy. The fact that it is present both amongst Cypriots and Turks is in favour of this solution rather than due to Northern Africans, being those haplotypes more amongst Turks but very rare amongst Greeks.

Rob said...

@ Dave
I don't think you understood my point
I'm not saying that Z2103 isn't ultimately from Yamnaya; but I'm pointing out that we don't know if it came to Anatolia *directly* from Yamnaya in 2600 BC, or at a later stage via an intermediary location. So it was just a comment on your hypothesis of "at least Bronze Age".

Skordo said...

The R1A in the lasithi plateau is from the resettlement of the area by the venetians as evacuating the rebellious local population and brought Greeks in from peloponesse, obviously hellenized slavs

Rob said...

Ok thanks. Yes I suspected it was something possibly later on than the initial wave of Slavic migrations.

Romulus said...

What I get from looking at these frequencies is that J2a, J2B, and EM78 do not look like Neilithic Haplogroups.

Davidski said...

And this is why Southeastern Europeans cluster between the Near East and the rest of Europe.

Antoni Małkowski said...

Pamięta jeszcze tak niedawno obecność R1a w Norwegii tłumaczono sprowadzeniem Słowian przez Wikingów I1.

AWood said...

Whatever haplogroups are encapsulated in the "Other" may have arrived with the Turks, as this seems to be mostly absent from SE Europe. The "Other" category also seems higher in the TCy sample.

EastPole said...

New paper on mtDNA:

“Mitogenomic diversity in Russians and Poles”

“As a result, we have observed an episode of rapid population growth starting from ~4.3 kya (95% CI: 2.9-5.8 kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists [41,42]. It is noteworthy that the evolutionary ages of most mtDNA lineages specific to eastern and central Europeans (mtDNA subclades described within haplogroups H5, U2e, U3, U4, U5 [5,7,9]) were calculated to approximately 4 kya (from 2.3 to 5.9 kya), thus corresponding to population expansions of the Corded Ware culture (also known as the Battle-Axe culture), which flourished 5.2-3.8 kya in eastern and central Europe [43]”

Samuel Andrews said...

I'll post about that mtDNA paper later.

Samuel Andrews said...

Son of a bitch, I can't get access to those new mitogenomes. But I was able to get access to somewhat newly published Estonian mitogenomes.

Right now I have a big collection of mitogenomes from Denmark, Finland, Sardinina, Basque country, Iran, Egypt, Pakistan, and now Estonia.

Gioiello said...

Of course this isn't the way to do an inquire to-day in the time of the NGS. These haplotypes are tested for only a few SNPs and not all (some has been tested for only M343) and the attribution of the haplotype is based upon old calculators with pretty no meaning now, but I can say that only in Greek Cypriots there is an haplotype older than M269 (it seems that there isn't any R-M73): ID078, ID081, ID098, ID342. They are very likely (even though some key markers lack) R-L389* and if someone would know the origin of the Jewish R-L389
97835 Samuel Ofen, b. ±1660 Budapest Hungary R-P25
13 23 14 11 12-13 12 13 12 13 13 29 15 9-9 11 11 25 15 18 28 13-14-14-16 11 11 18-23 15 17 20 15 36-39 14 11 11 8 15-16 8 10 10 8 10 10 12 19-21 16 10 12 12 12 8 11 27 21 14 11 11 13 13 11 12 11 33 15 9 15 11 28 27 19 13 10 12 12 11 9 12 11 10 11 11 32 12 13 24 14 10 10 18 15 20 13 22 16 11 15 25 12 24 17 10 14 16 9 12 11
he should very likely test these haplotypes from Greek Cypriots.

Gioiello said...

We already knew that Cyprus had some samples of R1a-M420, perhaps YP4141, (and I spoke a lot about that), but that they are found only in Turkish Cypriots now and not in Greek Cypriots makes us think that they may have come recently with Turks.

Samples HT169 and HT245. said...

Completely useless study without any subclade analysis: haplogroups like J1 and J2 in Italy match the ones in the rest of Europe and are widely different from those of MENA regions. This hints that one single event spread those haplos and adddition basal Eurasian admixture in the European continent.

Further quotes from the study:

"If the high genetic affinity observed between Cypriots and Calabrian Italians is assumed to be true, it could be explained by the fact that South Italy has been a part of the ancient Greek world for centuries (Magna Graecia) and Calabria in particular has been settled by Achaean Greeks during the 8th and 7th cent. B.C [as Cyprus was, a few centuries back[67]]. Thus the high genetic affinity between Calabrians and Cypriots could be a result of a common ancient Greek (Achaean) genetic contribution to both populations."

"However, despite the very low genetic differentiation between Cypriots, Calabrian Italians, and Lebanese, the former appear to differentiate, in terms of Y-haplogroup frequencies, both from Middle Eastern (including Lebanese) and from Southeast European Mediterranean (including South Italians) populations. The main feature distinguishing Cypriots from Lebanese and other Middle Easterners included in our analysis is their much lower frequency of haplogroup J1. This observation clearly suggests that although Cypriots and Lebanese share common paternal roots, the latter received a substantial influx from populations high in J1, probably during the early Arab conquest era (7th cent. AD)."

"The separation of Cypriots from Southeast European Mediterranean populations included in our analysis is brought about by the much lower frequency in the former of haplogroups I2, R1a and R1b. South Italians in particular, although relatively low in haplogroups I2 and R1a, have a substantial proportion of haplogroup R1b (Fig 3). This difference suggests that although Calabrian Italians share primarily common paternal genetic roots with Cypriots, there has been an influx of populations high in R1b, which affected South Italy much more than Cyprus. With the lack of ancient DNA data from either region, it is difficult to disentangle the origins of this differentiation."

Cypriots are the closest living population to the Copper Age Anatolians who migrated into Europe during the early Bronze Age. Those groups mixed with proto-Italo-Celtic R1b carriers from the Unetice culture forming modern Calabrians. Modern Lebanese have a massive amount of recent Arabian admixture which separates them from both Cypriots and SE Europeans.

mooreisbetter said...

When people, including otherwise intelligent people and scientists, estimate the mechanisms for gene flow around the Mediterranean, they tend to greatly diminish the effects of Roman migration. I am talking centuries of OUTFLOW from the Italian peninsula: soldiers, merchants, and colonies. In this post, I explained how certain Mediterranean similarities are due to that outflow:

Here, it is entirely possible that the Cypriot similarities to certain South Italians are due to both ancient Greek colony outflow towards Italy, but also Roman soldier outflow during the early Imperial era. During that era, most Roman soldiers were Lucanians (modern Basilicata/North Calabria).

mooreisbetter said...

A quick note on the stats of this study that I noticed.

They sampled 3023 Italians and 3 Italians had haplo similarities to Cypriots. 3, or 0.9%.

Then, they sampled like 100 Israelis and 200 Egyptians, and were like, nope - didn't find any similarities.

They then use this 0.9% similarity to make the rather sweeping conclusion, "Cypriots are intermediately between Lebanon and Italy."

Now I DO NOT doubt that is true, but from a scientific perspective, this appears to be, "have conclusions, need data."

Would have been much more responsible to have similar sample sizes. With ANY sample, anywhere, if you go big enough, you'll find something close to matches -- and 0.9% of 3000 is hardly anything to write home about.

And the "no matches" in 100 people we happened to find? Pretty bad, scientifically...

Tobus said...

moore: 3/3023 = 0.099% (say 0.1), not 0.9%, so your point is nearly an order of magnitude stronger.

At that ratio, in 100 sample we'd expect ~0.1 matches, in 200 we'd expect ~0.2.. so getting 0 is *exactly* in line with expectations... the frequency in Israeli/Egyptians could be double that of Italians and we'd still expect 0 matches in sample sizes that small.

Davidski said...

Sounds like you guys are exaggerating something. This is the quote that I highlighted in the post...

Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.

So their argument is based on all of the data. said...

Needless to say, Y-STR analysis is vastly inferior to the Y-SNP one....

Cypriot genes said...

Just a note from one of the co-authors to clarify some grey areas. The specific study comprised of 3 separate analyses involving the comparison between Cypriots (GCy and TCy) and surrounding populations:

1. Y-STR data: Pairwise genetic distances (Rst)

2. Y-STR data: Shared haplotypes (17/17 STR matches, AmpFLSTR® Yfiler®)

3. Y-haplogroup data: Generally low resolution SNP data.

The conclusion that Cypriots are in the middle of a genetic continuum between the Levant (particularly Lebanon) and SE Europe (particularly Calabria) comes specifically from the first analysis listed above and not from the latter two. In particular, the second analysis is designed to detect recent shared ancestry between the different populations rather than deep shared roots. Therefore, the lack of shared haplotypes between Cypriots and South Italians does not at all disproof the common ancestral roots between the two populations, which are quite evident in the Rst based analysis (Table 2, S12 Table). Analysis 3 on the other hand, is very sensitive to even minor differences in haplogroup frequencies and thus with their higher frequencies in haplogroup R1b (South Italians) and J1 (Lebanese) they both differentiate substantially from Cypriots in the PCA plot. As discussed in the paper and also highlighted by David in this post, the purpose of the study was not to present a comprehensive genetic analysis of the Eastern Mediterranean based on deep haplogroup sub-clades, but simply to answer a very relevant question which remained unanswered up to this day, that is do Greek Cypriots and Turkish Cypriots derive from the same local source population, or do they derive primarily from the corresponding gene pools of the mainland (Greece and Turkey, respectively). Based on the findings of the paper, the answer is clearly the former. Hope you enjoy reading..

Matthew Siwak said...

Hi Davidski, could I email you a couple questions in regards to how to read and understand the eurogenes k13 admixture proportions report? I'm very green to genetics and am trying to research something.
please help.
Matthew @

Gioiello said...

@ Cypriot genes

I understand that it may be a question of funds, and very likely you did the best you could, but we ask other answers from the tests now. I understand also your intention to demonstrate that Turks arrived later and Turks of Anatolia descend above all from previous people, but only answers at the deepest level of SNPs may be reliable. I tried to give some of them in my analyses, asked from Anthro Survey. I always read the papers, but this time I looked only at some haplotypes and made some hypotheses. For instance for the fractionate DYS385b, which is very likely R1b1a2-U152-Z142...S23458, having Greek Cypriots and Turkish Cypriots two very different haplotypes, we'd be glad to understand how and when those haplotypes arrived in Cyprous, and they may have had two very different ways. Argiedude and me are inquiring that haplotype from 2011 on, and later I found many samples also in Italy. The whole answers are made of many little answers but possibly verified at the deepest level, otherwise we risk to see the night where all the cows are black.

MfA said...

4 (1.2%) E-FGC18401 in Greek Cypriots (ID 123, ID 127, ID 201, ID 239), the locations are unknown. Previously it's been found in a Greek-Cypriot from Amnochostos (NE Cyprus) at Voskarides et al., 2016.

Davidski said...

@Matthew Siwak

You'll find a lot of useful posts, including one specifically on the K13, here...

I can't add much to what I've already said there.

Arza said...

@ EastPole
New paper on mtDNA

Historians: Slavs were a small tribe that suddenly expanded in the middle of the first millennium CE.

mtDNA: Slavic population was expanding rapidly starting from 4.3kya, 2kya growth started to decelerate (Figure 2.).

Clearly there is a conspiracy of Turboslavic nucleotides.

Matthew Siwak said...

Thanks! I know its probably the wrong forum to bring these things to the table for help. Basically I ran the k13 model with my raw dna and came up with a heritage not found on ancestry or ftDNA. Amerindian. I also don't quite know how to read the model. Basically ive found my biological father who will be doing a paternity test but in the mean time disclaims the fact I'm his child probably due to the fact he has 2 generations of metis and treaty (parents, grandparents with the exception of his father who was is Caucasian).
Through using GEDmatch I see I have multiple chromosomes with small percentages of Amerindian. Could this be a hint that I'm correct in thinking it came from him? I'm guessing its not and paternity test is the only solution but Id like to use those facts to convince him that it doesn't matter if he has 2 generations of native, that genetics could have easily not passed those traits down since its such a small dilution.
so can someone tell me if I'm reading the results correctly?

Chromosome 4
Amerindian 1.0
snps evaluated = 10596

theres 9 chromosomes with numbers up to 3.0

does this mean from the snps tested, %1 belong to Amerindian dna?
Sorry I'm so green to genetics, I tried reading the blogs from Davidski but i'd understand greek before I understood genetics hahaha!
Thanks guys

Davidski said...

@Matthew Siwak

You need to join a genetic genealogy forum and have someone experienced in reading these sorts of tests in the context of genetic genealogy, not just population genetics, give you feedback.

Matthew Siwak said...

Thanks, suggestions?

Davidski said...

Joshua Lipson said...

Principe at Anthrogenica says Y6923, the slightly larger of the 2 large Ashkenazi E-M34 subclades, has shown up in 2 Turkish Cypriots and 1 Greek Cypriot. Based on STRs run through Nevgen. Huge if true, as the subclade has otherwise only ever been confirmed in one Puerto Rican with possible Converso roots.

Gioiello said...

@ Joshua Lipson

"Principe at Anthrogenica says Y6923, the slightly larger of the 2 large Ashkenazi E-M34 subclades, has shown up in 2 Turkish Cypriots and 1 Greek Cypriot. Based on STRs run through Nevgen. Huge if true, as the subclade has otherwise only ever been confirmed in one Puerto Rican with possible Converso roots".

E-Y6923 Y6935 * Y6942 * Y6928+29 SNPs 4600 ybp, TMRCA CI 95% 2100 1050 ybp"formed 5400 ybp, TMRCA 1550 ybp
Also this is a Jewish line with a MRCA after the diaspora. Bottleneck as Jews like to think or introgression? See what I said above about the possible R-L389*.