September 27, 2009

Y chromosomes of Saudi Arabia

From the paper:
The recent resolutions of the CDEF-M168 tripartite structure to the bipartite DE-YAP and CF-P143 [16, 31] extends the conversation regarding the early successful colonization of Eurasia. While several scenarios remain potentially possible the most parsimonious model is the most prudent. This model proposes the successful colonization of Eurasia by migration(s) of populations containing precursor Y-chromosome founder macrohaplogroup CDET-M168 and basal mtDNA L3 representatives. Regions near but external to northeast Africa, like the Levant or the southern Arabian Peninsula could have served as an incubator for the early diversification of non-African uniparental haplogroup varieties like Y chromosome DE-YAP*, CF-P143* and mtDNA M and N molecular ancestors. These would have spread globally and diversified over time and space. This model would imply that both CF-P143 and the DEYAP evolved nearby but outside Africa. One DE-YAP* ancestor would have spread to Asia and evolved to haplogroup D while another DE-YAP* returned to northeast Africa and evolved into hg E.

The paper unfortunately uses the faulty "evolutionary mutation rate" for Y-STRs, hence its age estimates are wrong and should be roughly divided by 3.

This correction brings the age of Saudi Arabian J1-M267 to ~2,000BC, which corresponds exactly with the inferred linguistic divergence of the most populous clade of Semitic which includes Ugaritic, Aramaic, Arabic, and Hebrew. I have little doubt that the modality of J1 among Semitic populations such as Arabs or Jews can be traced to the Bronze Age expansion of Semitic populations from southwestern Asia.

Related: Y chromosome population structure in Arabian peninsula

BMC Genetics 2009, 10:59doi:10.1186/1471-2156-10-59

Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions

Khaled K. Abu-Amero et al.

Abstract

Background

Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci.

Results

Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n=2) and J-M304* (n=3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 +/- 1.9 ky) is similar to that obtained previously for Yemen (11.3 +/- 2) but significantly older that those estimated for Qatar (7.3 +/- 1.8) and UAE (6.8 +/- 1.5).

Conclusions

The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.

Link

16 comments:

German said...

The authors claim that "it is well documented that, in the Palaeolithic, at least three clades (X1, U6, M1) derived respectively from the three main Eurasian macrohaplogroups (N, R, M) came back to North Africa from Asia."

One of their references is Reidla 2003 on the worldwide distribution of X mtDNA lineages. However Reidla 2003 treat X1 as an outgroup for X2 to which all X sequences outside of Africa and some North African sequences belong. Reidla 2003 leave open a possibility that X1 is actually a subset of X2 as there could have been mutational reversals on X1 sequences in two positions (Reidla 2003, 1181). I wonder if Abu-Amero et al. reassert that X1 derived from X2 was actually the case. This would indeed create a consistent pattern whereby Africa absorbed descendants from N, R and M macrohaplogroups.

Dirk said...

Unfortunately, there are some statements in the paper which are inconsistent with the phylogenetic tree:

"a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers."

"Only 27 of the 67 binary markers analyzed were informative in defining the haplogroup census of the Saudi Arabian sample (Table 1). The following 40 polymorphisms (...M215, ... M78, M81, M123,...) were observed at ancestral allele status in the sample set."

"E1b1b1a3* V22 0.64
E1b1b1b* M81 -
E1b1b1c1* M34 4.46"

How come M215 is "ancestral" when downstream derived mutations were found?

No M81 derived Y-chromosomes were found, so the statement about M81 is correct.

However, how can M78 and M123 be "ancestral", if downstream derived mutations were found?

Also the table lists V22 as - in Egypt, apparently the authors are unaware of Cruciani's work?!

I hope these errors are due to a lack of proofreading, and not due to a lack of understanding of the phylogenetic tree.

Also, please report haplotypes for all investigated Y-chromosomes.

argiedude said...

Also, please report haplotypes for all investigated Y-chromosomes.

XLS file (haplotype data)

;)

Ponto said...

Dienekes certainly has a problem with J-M267!

Age estimations must be reduced by three. How do you justify that? I guess on prejudice and the belief in your religious beliefs. Age estimation are just that, estimations. The age estimates for J-M267 are mostly based on the Paleolithic/Neolithic paradigm with a little bit of history chucked in. Every schoolchild knows about the Pheonicians or the Muslim takeover in Southern Europe. I go by the results of scientific studies not the Bible or school book histories. J-M267 in Europeans, Anatolians, and Ethiopians is more genetically diverse any in any group of Middle Easterners barring Kurds and Iranians. The idea of an origin in the depths of Arabia is not proven, neither is a birth among speakers of Semitic languages. The Ethiopians are the only highly genetically diverse J-M267 who speak a Semitic language. Even Tunisians are more highly diverse than Omani Arabians. All the theories to fit beliefs of a "Semitic" origin to J-M267 or its origin point in Peninsula Arabia or its age manufactured or doctored to fit in with the Neolithic paradigm have all been proved wrong. J-M267 was in Europe, Anatolia, North Africa and the Canary Islands long before Shem or any other pre Semite or proto Arab.

Studies of Arabians have shown that J-M267 is of Northern Middle Eastern origin, is older in Egyptians, and Lebanese Arabs than in the true Arabs whether Kahtani or Adnani by their mythohistory. A proper age for Arabian J-M267 would be more likely of the same age as Neolithic age settlements in Europe, that is 7,000 years old or younger. Arabian haplogroups are skewed due to their peculiar emphasis on male lineages, and breeding practices, or put it another way, they are highly inbred on the male side. Yemenis in particular are especially inbred.

It is very likely that no Y chromosome haplogroup found in Europe dates back before the Neolithic age. You may want to hold on to your Paleolithic/Neolithic paradigm for population continuation in Europe, and the idea that the Middle East had no Paleolithic past and its haplogroups are very recent in origin, but most results are proving you wrong.

Dienekes said...

Age estimations must be reduced by three. How do you justify that? I guess on prejudice and the belief in your religious beliefs.

Er, I wrote a whole series of blog posts where I justify it with a rational criticism of the "evolutionary rate". If you have any problem with my analysis, question that, rather than bring up red herrings.

Ponto said...

Oh I have read it my friend. Just as I hope what you want to achieve in the Greek elections pays off for you. You'll have a hard time getting all those Middle Easterners, and ex Soviet Russians/Ukrainians out of Greece.

I read what you write, it doesn't mean I accept it as either right mathematically or scientifically when you do your aging exercises. I just let you rabbit on like some Jeremiah. I don't give a fig if you think R1b is Paleolithic rather than as I consider, Neolithic like all the other haplogroups in Europe or that J1 is pure Middle Eastern Wog and of recent vintage and totally due to horrid Jews or dirty, mad Arabs. You have your beliefs and I go by science. It seems your beliefs keep getting a kick in the rear end by most scientific studies. J1 among Jews is quite old, J1 among Arabians is much younger. I am going by higher genetic diversity. Portuguese and Italian Europeans, yes they are darkies I suppose, have older J1 than any Semites including the Ethiopians. Your neighbours from you in nearby Asia, the Anatolian Turks have older J1 than any Arabs or Jews. That is how the cookie crumbles. R1b gets older the further east you go in Europe. Armenian R1b is older than any European R1b. They must really burn up the anti Armenians. So the Central Asian R1b has been suffocated by Mongolian Chinese. There is an awful lot of them you know. The Uighurs certainly know the effects of the Chinese as do the Tibetans and other minorities in Greater China. That annihilation of haplogroups is a symptom of colonialism. In Africa the Bantu speakers (Colonialists) swamped the older haplogroups and dominated the whole sub Saharan continent of Africa. Europe is not unusual in that R1b has dominated and lead to the extinction of older preexisting haplogroups.

You want to prove the Caucasoid, Europid origin of Greeks or whatever Levantine looking peoples from the Pillars of Hercules all the way to the Indian Ocean use SNPs which show conclusively the geographical origins of people as either European, Middle Eastern, North African or South Asian rather than go on about sex chromosomes haplogroups which prove nothing much at all, and are totally subject to such recent things as disease as in the Black Death or Syphilis or breeding practices where having children from your cousin or closer relatives is normal or the result of invasion. USA and Australia illustrate how invasions can alter haplogroups that existed in those continents. Europe's invasions took place much earlier i.e from 10 kya.

Good luck with you election hopes.

Dienekes said...

I read what you write, it doesn't mean I accept it as either right mathematically or scientifically when you do your aging exercises. I just let you rabbit on like some Jeremiah.

It also doesn't mean that I give a rat's ass what you think if you don't put your verbiage into cold hard numbers.

Good luck with you election hopes.

Thanks, but your Greek needs work.

argiedude said...

Age estimations must be reduced by three. How do you justify that? I guess on prejudice and the belief in your religious beliefs.

I agree with Dienekes. Zhivotovsky's effective mutation rate dealt with very small populations where genetic drift was a big issue, but since then has been misused by geneticists in studies of R1a, or E1b1a (the Bantu expansion), where the populations involved where several orders of magnitude greater.

How do you justify that? I guess on prejudice and the belief in your religious beliefs.

pure Middle Eastern Wog

they are darkies

You're projecting onto someone else what you yourself are obsessed about.

your beliefs keep getting a kick in the rear end by most scientific studies

Boy, was that ill timed. The recent U4/U5 ancient mtdna studies of north Europe were a giant victory in favor of the farmer expansion theory.

terryt said...

"the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found".

By now that should be no surprise to anyone. However I'd remind several people here that whenever I've previously claimed the Great Southern Migration Route is myth the opposition has been quite vehement.

"This model proposes the successful colonization of Eurasia by migration(s) of populations containing precursor Y-chromosome founder macrohaplogroup CDET-M168 and basal mtDNA L3 representatives".

Again, this has promoted quite vehement opposition whenever I've previously pointed that just two mtDNA and perhaps just one Y-chromosome haplogroup emerged from Africa.

"while another DE-YAP* returned to northeast Africa and evolved into hg E".

Same again, whenever I've remarked that this seems to be what happened. Thanks Dienekes.

Andrew Lancaster said...

Terryt: Concerning "macrohaplogroup CDET-M168 and basal mtDNA L3 representatives" you mention that it "has promoted quite vehement opposition whenever I've previously pointed that just two mtDNA and perhaps just one Y-chromosome haplogroup emerged from Africa".

Such opposition is not surprising. This 1 Y haplogroup and 2 mt haplogroups (I presume you mean M and N) actually include nearly all named haplogroups found in modern humanity.

People really need to stop treating haplogroups as fixed units which can be compared. Every individual is in many haplogroups at once. There are no fixed levels of clade.

Best Regards
Andrew

terryt said...

"Every individual is in many haplogroups at once".

How do you make that out? Most of us have only one type of mtDNA in our cells and men have just one Y-chromosome. Haplogroups are determined by each of these so surely every individual must belong to just one haplogroup. I agree that every individual is in many other genetic groupings at once.

"This 1 Y haplogroup and 2 mt haplogroups (I presume you mean M and N) actually include nearly all named haplogroups found in modern humanity".

In fact virtually all of them outside Africa, and many within that continent. And that fact is very interesting on its own. We're not really descended from any sort of migration out of Africa. It's just that most of us are descended from just one man and two women who moved out at some time. What they did and where they lived before their descendants spread around most of the world is a bit of a mystery but some certainly reached India fairly early on. But this study suggests they did not go through Saudi Arabia, perhaps they went through the Levant.

Creative said...

"Might be of interest."

Mediterranean Moisture Source for an Early-Holocene Humid Period in the Northern Red Sea.

http://epic.awi.de/Publications/Arz2003a.pdf

Andrew Lancaster said...

Terryt:

1. When I wrote,

"Every individual is in many haplogroups at once".

For example, every person in Y haplogroup E1b1b1a2 is also in E1b1b1a, E1b1b1, E1b1b, E1b1, E1b, E1, DE-YAP, CT-M168.

As a mitchondrial example, all people in M and N are also in L3, and so on.

2. When you wrote...

"We're not really descended from any sort of migration out of Africa. It's just that most of us are descended from just one man and two women who moved out at some time."

This is really very incorrect, but again it is a common error. These dominate male lines and female lines are just dominant amongst lines of ancestry which go purely through men, and purely through mothers respectively. For every one of us this represents an infinitesimal amount of all the lines of ancestry we have.

terryt said...

Creative. Thanks for the link.

Andrew. I understand what you were getting at now. Everyone belongs to a wider clade than just the end one. However all non-African mtDNA traces back to just two L3s. My complaint, as I suspect is yours, is that this has been mis-interpreted.

"For every one of us this represents an infinitesimal amount of all the lines of ancestry we have".

I agree totally with that. In fact if we could each write our individual pedigree we would find a list of more than a million names just 20 generations ago. I've written on the subject if you're interested:

http://humanevolutionontrial.blogspot.com/2009/06/human-evolution-on-trial-pedigrees.html

I would argue that most of us have genes that didn't originate in Africa at all. Well, if they originate more recently that H. erectus. Humans are a product of movements back and forth around the world since H. erectus first emerged.

Andrew Lancaster said...

Terryt that makes more sense. The wording is important though. I can tell you a lot of people read these things on line and get very bizarre ideas from things which were quickly written.

Unknown said...

Thank goodness for this study, a more rationale take on j1e origins.