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Thursday, February 11, 2016

Greek-Cypriot Y-chromosomes


Open access at Investigative Genetics:

Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization.

Results: Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.

Conclusions: Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.

Voskarides et al., Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements, Investigative Genetics, 20167:1, DOI: 10.1186/s13323-016-0032-8

49 comments:

Roy King said...

Thanks! This paper took six years of arduous effort from start to publication--this is pretty sobering for those who complain that academics are slow to write up results. Cyprus clearly is a repository for very early "Neolithic" Y haplogroup G lineages, as well as the receptacle for J2 lineages that likely arrived later and carried much CHG rich autosomal ancestry.

Joshua Lipson said...

Not enough discussion of E-M34. Frequency in Greek Cypriots: 10%. Frequency in Ashkenazi Jews: 10%.

Roy King said...

Yes, Joshua, I agree with you--E-M34 is very important. We also found J2a-Z489 which is frequent among Ashkenazi Jews as well. It is possible that Cyprus formed part of the founding population of Ashkenazi Jews. Autosomally, there is nearness from the PC plots.

Joshua Lipson said...

http://jewishdna.net/

^ which of the above haplotypes corresponds to/falls under Z489?

Rob said...

Nice paper, Roy

I;ve not yet read it in detail, but a retention of G2 and pre-bronze Age J2 subgroups would make sense in Aegean islands parts of Greece, where the Copper Age 'collapse' was not felt, but rather a steady trajectory of population growth occurred, culminating in southern Greece and Aegean islands 'overshadowing' the north by the Bronze Age. (during the early Neolithic, most of the demic growth was in northern Greece - which was tied in with the Balkan Neolithic cultures based in the riverine valleys)

Romulus said...

Not sure what to make of those R1b clades.

Rob said...

@ Rom

"Not sure what to make of those R1b clades. "

5% are Z2105 -derived. That makes sense to me, suggesting little nomadic influence
The other 2% are 'western' type M412 lineages. Could have arrived any time. Was Cyprus ever under Crusaders ?

AWood said...

When you evaluate just the 574 Cypriot haplotypes you arrive at about 11.7% R1b. if you include the 629 Cypriots, you arrive just under 11%. There are a small handful of P312+ and U152+ Cypriots in this sample, I have also seen a U106+ haplotype in the public FTDNA database. It's difficult to pinpoint origins of the more downstream branches of R1b on this island when so many of the men derive from historical immigrants, the many non-R1b guys included.

AWood said...

The determination of R1b-L277 on the NE of the island, in contrast to the lack of it on the western side is revealing. The team is likely onto something. More SNP resolution on the Turkish data included in the overall analysis would have been revealing, at least with respect to R1b.

Krefter said...

Most or almost most Y DNA is G2a2, E1b1b1, and J2a1. J2b1, R1b1a2-M269(xM412), and J1a2b-pag8 also have a strong presence.

Krefter said...

Here's a pretty detailed presentation of the Greek-Cypriot Y DNA results.

https://docs.google.com/spreadsheets/d/1Uluf6piB27T2s2Y1agmoaTQX45mwYpkFDN9AtPLms3k/edit#gid=1071440317

J2a1 and E1b1b1 take up 46% of Y DNA. E1b1b1 and J2a1 overwhelmed G2a2 in the Aegean after 4000 BC. 59% is J2a1+E1b1b1+G2a2. Most J2a1 is; J2a1b and J2a1h. Most G2a is G2a2 and most G2a2 is G2a2b. E1b1b1 is pretty evenly broke up between E1b1b1a1b1a-V13, E1b1b1a1b2-V22, and E1b1b1b2a1-M34.

Kotais had J2a, but he didn't have J2a1, which looks like the dominate form of J2a in all moderns.

Davidski said...

Would love some ancient genomes from Mesolithic Anatolia and the Fertile Crescent.

We'll be treading water to a large extent until we get those.

Gökhan said...


The Eastern part of Cyprus, the Ammochostos (also known as Famagusta) R1b (17,21% at Famagusta, %10,78 at overall Cyrpus), L and J1a (9,84% at Famagusta, 6,5% at overall Cyprus) frequencies are higher then rest of the region and lower at J2a. Higher frequencies at L and J1 understandable as far as Famagusta looks toward the Levant shores. But what i noticed that %24 of R1bs in Famagusta are M412 and its subsclades which is known as West European clade. In my opinion the reason of that increase is Frenk-Lusignan refugess who exiled from jarusalem to Cyprus tok place after the Salahaddin victory in Jarusalem. Many of the cruseders had moved to Famagusta in Cyrpus after that defeat and they proceed thier kingdom at Famagusta.

The second interesting issue is the high J2a percentage in Paphos where is far west side of Cyprus. 29,5% of Paphos seems J2a and 11,43% are J2b. Thats kind a record. Interestingly R1a have the highest percentage there according to rest of the island: 8,87% which is almost 2 times of island average. Interestingly R1a and R1b frequencies in pahos are equal and R1b in Paphos is the lowest frequency in entire island although Paphos looks toward the west; Europe...

Rob said...

Dave

Unfortunately, to date, no Mesolithic skeletons/ bodies from Anatolia have been found. So we'll be treading water for quite some time

Davidski said...

Seriously?

Rob said...

Yes, (as of last November)
So to the Levant we look

Labayu said...

I’m an archaeologist in Israel. There are a lot of human remains here from all time periods, but almost nothing is happening with them. None of the heads of major excavations follow the research regularly discussed here (that I know of). There isn’t much incentive for them career wise either, because publicly attaching your name to working with human remains is likely to incite disruptions to your work – like an angry mob of guys with crazy beards dressed in black hats and suits. And even though those guys are a relatively small minority, their political parties are needed for the ruling coalition to maintain power, which gives them disproportionate political power. So we always use a code word when dealing with human remains. On top of that, there are all sorts of academic rivalries which means everyone is reluctant to share information. When I first came here from the US, I was trying to get the varies excavation heads more interested in this research, but the result in most cases of them realizing that I knew something about it, was them becoming even less likely to talk to me. I know there are some unpublished mtDNA results that may not come to light until the final excavation reports are done, which could be several years or more.

Some Late Bronze remains from an excavation I’m working on were recently sent to Australia, but no skull, so I doubt there will be any autosomal DNA. At UC San Diego, there are the remains of 287 Iron Age Edomite individuals from southern Jordan. Last I heard, the head of the excavation Tom Levy was considering having some DNA analysis done, but I don’t know if anything ever came of it. For there to be significant progress, I think it’s going to take researchers from outside Israel contacting the heads of the excavations. I’m not well connected to any excavations that are pre-Bronze Age though, so if that’s already happened, I wouldn’t know.

Nirjhar007 said...

If we are mostly concerned on the Indo-European issue , the best spot is Kurdistan-Syria area to start with.

Alberto said...

Pinhasi's site has 2 samples from Early Neolithic Israel (Tel Roim West) listed, so at least we might see those at some point.

https://sites.google.com/site/pinhasierc/home/samples

Though for the mysterious Basal Eurasian putative population we'd probably need older samples, from Antelian to Kebaran periods (but no idea if there are human remains from those periods in any good preservation state).

Gioiello said...


Of course this kind of papers based upon the STRs are destined to fail without history and aDNA. Roy King was he who found Greeks in Alalia (Corsica) not knowing that Greeks were defeated from Etruscans and Carthaginians and settled after at Velia (Campania, Italy) as very likely he ignored the historuy of Jews in Cyprus. Anyway a progress there is: many caveats, the use of the two MR for the STRs and above all inviting to wait for aDNA. Fortunately that no one spoke of an origin of hg. R1b from Middle East after the findings of Samara: now they think that this haplogroup arrived in Cyprus with the Indo-European Hittites, i.e. from Europe. Interesting are the STRs samples, which I'll study very carefully.
Anyway I could say more about hg.R than the other hgs . It seems that Cyprus was a recipient of hgs from everywhere, just from the 2 R-M415*: one is R-L389- (A012) found in Asia and the other is R-L389+ (N080), the ancestor of all the subclades: highest variance in Italy. Also the R-U152 have come very likely from Venetians, there is also an R-U152-Z142 (DYS385b=13.2), I discovered with the great Argiedude and we wrote a lot on www.worldfamilies.net. One sample from Liguria is processed now. Also 1 R-M269 with DYS385=12-14 of the Sardinian type and so on.

Nirjhar007 said...

Gioiello,
Nice to see you again. I do have question for you, which region in Europe show the highest amount of SNP variance of M-269?. Is it in Italy?.

Karl_K said...

@Nirjhar007

"If we are mostly concerned on the Indo-European issue , the best spot is Kurdistan-Syria area to start with."

Great idea. This is probaably the most logical place to start for the Indo-European issue!

I would even personally volunteer to go to Syria to pick up some samples, but I have this other thing I have to do.

Nirjhar007 said...

Like what?.

Gioiello said...

Nirjhar, I had some problem with my old PC (very likely contaminated from viruses) and wasn't able to contact this blog. Now I have a new PC, and it is possible again. If you understand R-M269*, I think that the best tree is that of Sergey Malyshev (smal) on the R1b-M269 (P312- U106-) DNA Project, better also than the YFull tree, which uses only the samples submitted, whereas smal may use all the samples tested from FTDNA, which are much more. You can see there that R-M269* has an old subclade PF7563- found in Anatolia, but amongst the PF7563+ the Italian and Sardinian ones are the most part. So far only a Jewish subclades with 19 SNPs in common, but as always with a MRCA after the diaspora, thus it could be introgressed too. Perhaps you know that in my theory of an Italian or European Refugium are just the upstream subclades in favour of it ( R-V88, R-V88-M18-, R-V88-V35, now also R-M335, some old R-M73 to be tested, till the R-L51 subclades, but also my R-L23-Z2110 old in Western Europe more that 7200 years because tested with FGC and not Big Y, that are at the base of my theory. I consider the rare R-L23 found in Russia as descendants of Western European hunter-gatherers, like the R1a-M420 descendants. Yes, as to your Indian R-Z94 subclades, I think that they came from Eastern Europe with the Indo-European satem languages. Of course I think that the centum ones came from Italy or nearby, perhaps Ceentral Europe.

AWood said...

@Gokhan,

Nice summary, but an inconsistency is your claim about "Crusaders". Most definitely other haplogroups existed amongst "Crusaders" of 1100AD+. Not a single I1 or I2-M223 in Cyprus (G-P303, E-V13, J2 were also present amongst 1100AD west Euros too). That's not realistic if you're assuming west European input within that timeframe.

Gökhan said...

@AWood you are right that we should consider I2-M223 too as far as West European medevial clades are concerned. But you are wrong that there are 8 I-M436 in the study. And 5 of them in Famagusta (%62 of all I2a2 samples). There are 22 I2 in study in whole island. 8 of them is I-M436 which might be M223 and 5 in famagusta!!! Due to they didnt test M233 and any STR of I samples we can not comment if they are M233 actualy. But question is why those M436 samples condensed on Famagusta? In famagusta I2 frequency is 1.5 times of overall Cyprus. I will not insist that they are the footprints of Crusaders but i just brainstorming that those stats might be evidence of the Cruseder input in East Cyprus.

On the other hand you are right that there are not any single I1 in study. But i dont think that it will prove or disprove something as far as its not so common haplogroup in west european especial in france and italy

Eren said...

@ROB @Davidski:

According to this source, 16.000 year old Hunter-Gatherer samples from Direkli Cave in south-eastern Turkey are already in the labs in the US.
http://www.dailysabah.com/nation/2014/09/09/dna-analysis-on-human-bones-to-give-clues-about-anatolian-peoples-gene-structure

AWood said...

@Gokhen

Maybe it is Turkish migration, and the P312/U152 is a legacy of the Celts. Alternatively, I wouldn't rule out some Luwians and Hittites belonging to downstream branches of R1b like P312/U152.

Gaspar said...

@Gökhan said...

"we should consider I2-M223 too as far as West European medevial clades are concerned. But you are wrong that there are 8 I-M436 in the study. And 5 of them in Famagusta (%62 of all I2a2 samples). "

The area of Famgusta and its fortress was "ruled " even under frankish rule of Cyprus by firstly Genovese and then Venetians governments.
The Venetians since they also ruled Istria and Dalmatia for over 500 years, which is where I2a is found in abundance, would IMO, be the source of this marker in eastern Cyprus, as well as , as the paper noted the G2-L497 north-italians

FrankN said...

One point to consider is that the term copper stems from aes cyprium, "Cypriote ore". Cyprus was the dominating copper producer during the early Bronze Age, exporting up to Sweden. Later on, its relevance diminished in favour of continental (Slovakia, Tirol), Sardinian and Iberian sources, but it still remained the key supplier of the East Mediterranean, including Egypt and the Levante.

This role surely brought about immigration of all kinds, from miners / metalworkers (Caucasian/ Balkans, for the longer tradition there?), to traders from all directions, and others just attracted by the island's prosperity.

http://www.mnh.si.edu/exhibits/cyprus/early-bronze.html
"Beginning in about 2400 BC, prospectors from Anatolia explored the island for copper. They brought new ways of building houses, cooking, spinning, and weaving. They also brought cattle and the ox-drawn plow, creating an agricultural revolution. Plows opened up new terrain for farming, leading to a boom in food production and a rapid increase in population."

Before that point, Cyprus appears to only have been sparsely populated. There may even have been two periods with hardly any population, namely (a)before 4500 BC and (b) around 4000 BC. After both, radical cultural shifts become visible that could point at new immigrants.
http://what-when-how.com/ancient-europe/copper-age-cyprus-consequences-of-agriculture-5000-2000-b-c-ancient-europe/

The "copper belt" is located in W. Cyprus, as a circle formed by the foothills of the Troodos mountains where uplift has exposed copper-rich strata to the surface. While mining already started during the CA, evidence for Cypriote copper export is only available from the early 2nd millenium BC. During EBA and MBA, Cyprus appears to have mainly been a commodity exporter. Local bronze-making picks up significantly in the LBA (after 1200 BC) and is being linked to inflow of Aegean Greeks.
The Politikos Phorades smelting site in WC Cyprus shows four distinct phases of operation: (I) CA (30-25th cBC, stry finds), (II) EBA from ca. 2000 BC, (III) MBA, from the 16th into the 14th cBC, (IV) LBA after 1200 BC. Possibly, that phase ended around 900 BC before activity picked up again during the IA (7-5th cBC). At least until the LBA, the site only produced matte, an intermediate smelter still containing some 25% sulphur. Secondary smelting, refinement, and producing stadardised ingots for export took place in the large coastal towns.
http://www.academia.edu/1179089/The_Archaeology_of_Late_Bronze_Age_Copper_Production_Politiko_Phorades_on_Cyprus

While probably not all those coastal towns have been excavated yet, they seem to concentrate in the SW, which makes sense for the proximity to the copper mines. However, there were other centers as well. The most significant during the LBA seems to have been Enkomi on the East Coast. For the MBA, Kalavasos-Ayios Dhimitrios, at the center of the South Coast, seems to have played a major role for trade with Egypt, the Levante and Ugarit.
http://antiquity.ac.uk/projgall/urban338/

How that archeological record might fit the genetic results reported I leave others here to sort out.

FrankN said...

As an addition, her something on IA Cyprus:
http://www.ucl.ac.uk/sargon/essentials/countries/cyprus/

"To the Assyrians, it [Cyprus] was known as Ya' Adnana or Yadnana, the "island of Adnana". The inscriptions of Sargon II of Assyria stress that this name was entirely unknown to his predecessors. Indeed, when Cyprus had been part of the international trade and diplomatic network of the Late Bronze Age, in which Assyria had also participated, it had been known as Alašiya. The new name links the island and its inhabitants to the Sea Peoples of the dnn (known from Egyptian sources of c. 1200 BC), the dnnym inhabiting the nearby Cilician coast (according to local alphabetic inscriptions from the 8th century BC) and Homer's Danaoi."

So, the takeover rather came from Cilician than Aegean Greeks, which could explain some of the Anatolia-like DNA.

Also interesting is the discussion on the linkage of Cyprus to Tyre and later the Assyrians:
"The names of seven of the ten rulers of Yadnana mentioned here [a 680-669 building inscription from Nineveh] can be explained as Greek: Akestor of Idalion, Philagoras of Chytroi, Etewandros of Paphos, Damasos of Kourion, Admetos of Tamassos, Onasagoras of Ledrai and Buthytes of Marion. The names of the remaining three rulers can be explained as West Semitic, possibly Phoenician."

One of those Semites ruled Qarti-hadasti (= "Carthage", meaning "new town" in Phoenician). If the kings' names weren't sufficient, a Phoenician "new town" is obvious signal for sizeable demic expansion from the Levante.

Amichai said...

I honestly don't see how the fact Cypriots and Jews have 10% E-M34 indicates a recent common ancestor. The TMRCA of it is 15200 ybp.

Alexandros said...

Roy (and colleagues) thanks for the study; David thanks for posting.

This is indeed a thorough investigation of Greek Cypriot paternal ancestry, with an overall robust methodology and analysis. In a nutshell, the main findings of the paper in my opinion are:

1. The persistence of apparently Neolithic G2a subclades allover the island, despite numerous migrations and occupations throughout history and prehistory.

2. The clear sign of an extensive migration (metallurgy-related) from Anatolia to Cyprus throughout the Bronze age, introducing, predominantly, haplogroup J2a and new subclades of G2a, and to a lesser extent R1b, to the island.

3. Very low frequencies of haplogroups I and R1a, indicating very minimal contribution from continental Europe to the Cypriot patrilineages.

Despite the thorough analysis and very interesting findings, there are a few disappointments:

• There is a surprising lack of interpretation of the E1b1b results, which appears to be the predominant haplogroup in Cyprus. The 10% E-M34 is just ignored??

• Also, regarding E-V13, the authors very nicely show that the evidence indicates a predominantly Greek origin and also indicate that a large proportion of J2a in Cyprus may also be of Greek origin. How can the authors explain however the very low frequency of I2 and especially R1a in Cyprus? This is somewhat paradoxical, unless we accept that Iron Age Greeks who migrated to Cyprus, were mainly of E-V13/J2a origin (+R1b, G2a) but very low in I2 and R1a. This would make ancient Greeks quite different from modern Greeks, who have substantial frequencies of both I2 and R1a. More discussion is warranted there.

• The comparison with modern Greeks and Turks is quite disappointing (PCA plot, fig. 3). There are several published studies reporting Y-haplogroups from Greece and many of these were ignored. Also, the Cinnioglu, King, et al Anatolia paper contains 9 Turkish sub-populations, so why reduce these to just 3 in this paper?

Alexandros said...

@Gökhan

I agree with you that the evidence from this paper suggests a minor contribution from western Europe to the area of Ammochostos (Famagusta) in Eastern Cyprus and yes you are right that this is most likely of Franksih/Venetian/Genoese origin. When the Ottoman Turks defeated the Venetians and occupied Famagusta in 1571 after a 1-year siege (https://en.wikipedia.org/wiki/Siege_of_Famagusta), the western Europeans living there were forced to either leave the island or convert to Islam and stay. Apparently some of these people did stay. These people however might have already mixed with the local Greek Cypriot population leaving a minor western genetic European legacy.

As I mentioned in my previous post however, based on this study, continental European paternal ancestry is very low in Cyprus, compared to other Mediterranean islands such as Crete and Sicily.

Gioiello said...

For doing hypotheses from the STRs data, we should be sure about them. I haven't yet examined all these samples, only the R1b, and when I studied similar studies I found numerous mistakes, astonishingly the R-L51 in a paper on Balkans which were R1b1a2-L23 “Balkan cluster”. For instance the sample 316, Li117 isn't of course an R-M269 but very likely an R1a.

Gioiello said...

Amichai, I didn't write that, because everyone would think that I am against Jews. Glad that you wrote that, with a nickname which seems Jewish. For saying everything then, the pretension of Roy King that J2a-Z489 are “Jewish” is as always wrong, being this haplogroup above all Italian in its oldest samples, and being Jews the recent subclade under Y15238, with a MRCA not older that 1000 years, thus very likely introgressed.

Gioiello said...

@ Davidski

There are also two wonderful samples R-M459-YP1272* (N088 and P058):

R-M459L120/M516/PF6236 * PF6168/F1545 * CTS10042/PF6207/M754+43 SNPs formed 18200 ybp, TMRCA 14400 ybp info
R-M459*
R-YP1272 YP1301 * YP1293 * YP1302+75 SNPs formed 14400 ybp, TMRCA 3900 ybp info
id:YF02892TUN [TN-11]
id:YF02130BLR

Gioiello said...

@ Gioiello
"For instance the sample 316, Li117 isn't of course an R-M269 but very likely an R1a."

It is very likely that it isn't R1b-M269 but neither R1a, but I1*.

Slumbery said...

Alexandros

"Also, regarding E-V13, the authors very nicely show that the evidence indicates a predominantly Greek origin and also indicate that a large proportion of J2a in Cyprus may also be of Greek origin. How can the authors explain however the very low frequency of I2 and especially R1a in Cyprus? This is somewhat paradoxical, unless we accept that Iron Age Greeks who migrated to Cyprus, were mainly of E-V13/J2a origin (+R1b, G2a) but very low in I2 and R1a. This would make ancient Greeks quite different from modern Greeks, who have substantial frequencies of both I2 and R1a. More discussion is warranted there."

R1a is supposed to be mainly of Slavic origin is modern Greeks, isn't it? Also I2 is under 10% in most of Greece, not as dominant as up North. It is surely older here than R1a, but its frequency could have increased parallel with the arrival of R1a in Medieval times.

Also even modern Greeks are dominantly E-V13/J2a. If Bronze Age Greeks were a little more so that does not make a lot of difference, neither should come as a surprise.

Gioiello said...

@ Gioiello

"It is very likely that it isn't R1b-M269 but neither R1a, but I1*"...

or G2a.

Alexandros said...

@ Gioiello

Thanks for the info on specific samples, but from where do you get these predictions? Are you running one of the online Y-STR based haplogroup predictors?

Alexandros said...

@Slumbery

Northern Greeks have frequencies of haplogroups I2 and R1a in excess of 15% each (thus total R1a+I2 of 30%). I agree that some of this might be of Slavic origin, but surely it cannot be all, otherwise 1 in 3 Greeks should be considering themselves as Slavs (at least paternally).

Only Bronze age and Iron age DNA from Greece will solve this issue. Let's hope that day is approaching..

Gioiello said...

@ Alexandros

The Y predictors are usefull when we have many markers and within an average range of the modal. I use my experience above all of the R1b haplogroup. Of course it isn't always possible when the markers are a few, just because the STRs aren't always reliable. It happens that they fail sometimes. The motive DYS389I=12 (or 13) DYS392=14 DYS389II= +15 makes us think to an R1b-L23-L277, but with a friend of mine it failed, and we are testing him for R-U152-L20 c/o www.yseq.net, because the L277 SNPs failed. Thus we may do some hypotheses, but after we need SNPs for being certain.

ben-canaan said...

@Amichai,

I agree that this doesn't suggest a common origin for Ashkenazim (or any Jews, for that matter) and Cypriots within the last 2-3,000 years. Just an interesting illustration of the deep history of Levantine Y-DNA distribution patterns. Moderately common among Jews, Palestinians, Jordanian Bedouins, and Cypriots, but rather uncommon among Syrians, Lebanese, and Anatolians. Has seemed like a likely vector of the proto-Semitic expansion, but the distribution in Cyprus (along w/surprisingly high frequency among Kurds, and ancient presence in Armenia) and TMRCA paint a more complicated picture.

I'm only bringing up Ashkenazi E-M34 in particular because the sample size (http://jewishdna.net/) is beyond argument, and the rate of ca. 10% has been replicated several times.

Gioiello said...

"@ Alexandros

The Y predictors are usefull when we have many markers and within an average range of the modal. I use my experience above all of the R1b haplogroup. Of course it isn't always possible when the markers are a few, just because the STRs aren't always reliable. It happens that they fail sometimes. The motive DYS389I=12 (or 13) DYS392=14 DYS389II= +15 makes us think to an R1b-L23-L277, but with a friend of mine it failed, and we are testing him for R-U152-L20 c/o www.yseq.net, because the L277 SNPs failed. Thus we may do some hypotheses, but after we need SNPs for being certain"

The sample has been confirmed to be L20 from www.yseq.net.

Alexandros said...

Thanks Gioiello,

Any ideas about the significance of the presence of this subclade in Cyprus? From a brief search I see that despite being rare, it has been found in relatively high frequencies in Italy. It was also found in Britain, Scandinavia and other places.

Also, could you please share a few things about 'www.yseq.net'? What type of raw data do you send there? What kind of results do they provide? Thanks!

Gioiello said...

@ Alexandros

Did you mean the sample 316 Li 117?
1) First of all, I have to say that frequently these peer reviewed papers are wrong about the assignement of the haplogroups, thus all what they say and conclude is invalidated. One researcher should get a sufficient knowledge of the haplotypes for alarming when a SNP test could be wrong. I have written tons of letter about the wrong SNP tests of the FTDNA. The fact is that these scholars are newbies about that and many other things. I didn't studied deeply this haplotype, but if you say that it is diffused in Italy and some country of Western Europe, I wouldn't have difficulties to say that very likely it came from the “Italian Refugium”. Hg. G is very old in Italy. This could be the first step for a deep SNP tests.
2) www.yseq.net is the firm, it seems no profit, of Thomas Krahn. You know that he had an own firm before passing to FTDNA and created this after having being fired from FTDNA, just when FTDNA promoted Big Y, whereas TK was an expert of SNPs above all. They offer many SNP test, more than 20000 (and now also many panel), at a low cost (17,50 dollars each SNP): they are fast and reliable and at a price which is the half of FTDNA. I used and use their work frequently. TK is also in the FGC, with Justin Low and others (I did also their Full Genome), and I didn't understand at which point they are truly in competition with FTDNA or if the money is pretty the same. I am 100% confident in the TK work, whereas I am not all in the FTDNA one.
3) We'll see next which of these hypotheses of mine will be true, for instance if FTDNA will release again its BAM file for YFull or not and if FGC will become the most important firm with its Full Genome 15X at about 800 dollars, with the BAM file of the Y, the mt and all the autosome at 98% of my Full Genome 30x, reliable also for medical predictions.

Simon_W said...

@Gioiello

Thanks for the link to yseq.net, really a cool service! I've been waiting endlessly for FTDNA to offer a test for YP401, but it doesn't seem like they are going to offer it anytime soon. Which is really strange, because there is no doubt that this SNP marks a node and a clade downstream of R1a-Z287, as can be seen on yfull.org. Great I could order it now on yseq.net!

TheNewPossibility said...

Where can I find these samples R-M459-YP1272* (N088 and P058)? Are they in the supplementary materials? Could anyone with access to this data provide info on them and STR values? Thank you