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Post by djoser-xyyman on Aug 6, 2014 21:11:57 GMT -5
I always speculated that MtDNA Haplogroup H has an African origin basd upon the geographic pattern.
Toronni and Achilli BS their way into popularity with their hypothesis of hg-H having an Iberian origin. The Refugia Theory. Of course this is fast falling out of favor and popularity. Ennaffa proposed an Arabia/Near East for H1 but and African origin for H3….based upon diveristy. Achilli et al did their work(based upon frequency). The dataset for Africans were not as complete as it is now. The current dataset rules OUT Europe as the origin og hg-H.
I always said that frequency is NOT the end all of origin. H has an African origin. See my therad on ESR. Haplotype diversity and up-stream clades are much better indicators. As it stands right now, all evidence included, Africa has the edge over Arabia for hg-H origin. Why?
The recent work by Kefi(2014) will even further help resolve that question. From her abstract both H1 and H3 seem to have an AFRICAN origin.
Time will tell. The lies cannot be upheld much longer. Everyone has a "DNA machine"
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Post by djoser-xyyman on Aug 6, 2014 21:12:33 GMT -5
Since pre-history SSA “owned” the Nile while African Amazigh dominated Sahara regions and points West. And “Arabia/Yemen is an extension of Africa”. Don’t believe me? DNATribes confirmed that also. The Geographic dominance. --------------- Quote: The two leading principal components displayed in Figure 2 capture 47.9% and 26.9% of the variance showing a well-defined separation between Mediterranean African populations and sub- Saharan populations (Fig 2a). There is a clear cluster of North African populations comprised of Libyans, Moroccans, and Tunisians. The Nile River marks another boundary of mtDNA differentiation within Africa, linking Egypt, Ethiopia and Kenya but also extending through to Yemen. Yemenis and Saudis both associate strongly with Egyptians, whereas the Jordanian, Lebanese, Palestinian, and Syrian populations clustered together. Thus, the Arabian Peninsula population clusters were relatively differentiated from the more northern Levantine populations. Mitochondrial DNA Haplogroups showing significant contributions to the principal components include H, L3, L2, L0, V, L1, M, J, U, T, K, HV, and R0. The principal vectors for HV, T, K, J, and U point almost directly at the Levantine cluster (Fig 2a). H marks Western Europe and is a significant contributor to Libyan Sahara and Mali mtDNA diversity. L2 and L3 frequencies distinguish the populations of Kenya, Niger, Burkina Faso, Mali, Tunisia, and Libyan Sahara, with a decrease in frequencies of L haplotypes from Kenya through Saudi Arabia.
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Post by djoser-xyyman on Aug 6, 2014 21:13:46 GMT -5
IIRC Ennaffa had the age of these sub-clades much young eg H-11-H-21 at about 11kyo. Irregradless the fact is the distribution pattern concur with Roostalu et al. H-11-H21 predominates in the Arabian region while H1-H6 predominates in Western Europe compared to the Arabian region. On the other hand North Africa has an appreciable frequency of BOTH groups of sub-clades. Significance? North Africa was either the recipient of both European AND Arabian female gene flow or North Africa was the source population for both Europe and the Arabian region(sounds like Basal Eurasian SNP to me). Again, this is where Kefi’s paper will help clarify things.
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Post by djoser-xyyman on Aug 6, 2014 21:14:54 GMT -5
On Table S2 –
“H Haplotypes classified” means the “quantity' not “different type" of haplotypes. Essentially the 510(IP) means the sum of the haplotypes. It does NOT mean there are 510 different haplotypes in Iberia!! Do the math.
That is why quoting frequency alone is very mis-leading and deceptive. Most haplotypes could be exactly the SAME within Iberia. You need to dive deeper.
That is why spreadsheet S1 is where the “rubber hits the road” as I pointed out. Now once you understand that take it one step further and look at the data closely. Match-up the “unique” haplotypes, H*, between populations. Clearly, H*, between Arabia and North Africa is different. In the levant it is virtually absent except for, yeah, Jordan. But the population sampled with is Jordan is …you guessed it….Bedoiuns.
That is why Ennaafa concluded North Africa is NOT a subset of Arabia. Their H* and most other haplotypes do NOT match. She said “ Lack exclusivity”. Meaning Arabians did not back-migrate into North Africa. Islamic or otherwise.
As for Iberia, you your self agree that they carry signal of expansion FROM Africa.
I did look at the other supplementals but I dismissed them because S3 and S2 were meaningless for the discussion.
This is not rocket science.
Kefi et al (2014) is no longer needed.
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Post by djoser-xyyman on Aug 6, 2014 21:15:57 GMT -5
I was just about to touch on Table1 that Sage posted. Looking closely at hHG +- se3 , TuB is at 85+-3. Significance?
That is Gene haplogroup diversity. This African group carry the highest diversity.
BTW- NA on the whole is lower because of the low values of Saharawis and Mau.
The two African groups exceed Both IP and AP. NE is the least.
To sum it up. Two North African groups carry the highest diveristy(hHG). And Unclassified H, H*, is highest North Africa.
Edit: Oh! The Saharawi's and Mau carry the highest frequency of pre-H/HV. (Pillars of Hercules) meaning they are an older population albeit Berbers. They, Saharawis also carry a high freqiency of YDNA R-V88 but their SNP data profile is 100% African, O% European!!! Meaning?!
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Post by djoser-xyyman on Aug 6, 2014 21:16:34 GMT -5
Henn, Ennafaa etc all agree that the "Arab" invasion was cultural and did NOT involve movement of people.
Why do you keep repeating that nonsense. Deceptive.
---
Edit(added)- Good thinking by Lioness on the Table3 break down. I looked at that already and dismissed it. Why? HT, HTu %HTu is again misleading. Why? Within a Haplogroup there may be several haplotypes. ie more mutations within a HG.
That is why I went back to the unclassified, H*(in Supp 1) and the hHG+-se3 in Table 1 Sage posted.
This combined with the Exclusivity of H* in Africa and NE/AP gives Africa the edge.
But nice try!
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Post by djoser-xyyman on Aug 6, 2014 21:17:35 GMT -5
Significance?
There are only two scenarios that could explain the current geographic distribution observed for hg-H with the current diversity pattern from Arabia, North Africa and then Europe.
Either
1. Arabians AND Europeans BOTH back-migrated and settled in North Africa 2. Africans dispersed (from a central source) into Arabia and Iberia/Europe.
a. Within Europe there is a decrease in cline from West To East b. Arabia lacks the presence of specific clades of hg-H. ditto for Europe. c. North Africa has appreciable frequency of BOTH clade absent EITHER in Arabia or Europe. d. Ennaafa – observed the above details.
So as I said, Arabian AND European women back-migrated to North Africa or Africa was the source of the dispersal.
So what does the SNP tell us? Oh!....I forgot!....”basal Eurasian”! big picture fellas! big picture!
DNATribes, :Lazaridis and a few new resreach papers have confirmed this?
Giving you “space” have worked out. Now you have recognized hsubHG/ (hHG ± se),. You will figure it out. I will give more space. You will get there. You are well on your way.
Hint. Why is Tunisia almost 10 points higher(85%) than either Arabia/NE or IP.
Uber Africa!
------------ Quote The hsubHG/ (hHG ± se), figure for * NA is 74 ± 2 * AP is 76 ± 3 * NE is 72 ± 3
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Post by djoser-xyyman on Aug 6, 2014 21:18:11 GMT -5
Why is Tunisia almost 10 points higher(85%) than either Arabia/NE or IP.
Uber Africa!
------------ Quote The hsubHG/ (hHG ± se), figure for * NA is 74 ± 2 * AP is 76 ± 3 * NE is 72 ± 3 Moroccan Berbers 79 ± 3 Tunisian Ber 85 ± 3
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Use your head man! Don’t you find it odd/fascinating that BOTH jump off point to Europe has the highest (hHG ± se), Morocco and Tunisia are, what, 2000 miles away??!!! The Berbers have the highest. THEY ARE THE OLDEST POPULATION IN NORTH AFRICA. May be as old an the San, pygmies and Nilo-Saharans. Older t han the Bantus.
Further.
So what does the IBD tell us. Mesolithic African migrants to Europe. Henn et al What does the Archeology tell us. Mesolithic Africans to Europe. sources cited What does the Anthropology tell us Paleolithic/Mesolithic African to Europe. What does aDNA cattle tell us ….Mesolithic African cattle to Europe ..sources cited What does Sergi tell us… Mesolithic Africans to Europe ..source cited
In the Table you keep posting… Moroccan Berbers and Tunisian Berbers, two African populations, about 2000miles away, have the highest (hHG ± se), of ALL populations including NE/AP. These two populations are the closest region to “jump off’ point to Europe. The population with the next highest (hHG ± se), is AP, about, what 4000 miles way from Tunisia and 6000miles away from Morocco. The next highest is the NE, even lower than Iberia/Europe. The Balkans, Turkey etc do not even compare. . Significane? They were NOT the path of migration. .
I got this covered!!
I got this covered!!
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Post by djoser-xyyman on Aug 6, 2014 21:18:59 GMT -5
What Ennaafa has done is the typical Eurocentric data manipulation. Eg in Table 3 she did not show a comparason between the SAH and TUB to Iberians. Which would have been very important for her premise. Instead she grouped North Africans when it was convenient to her to make her point. But some of us are unto her game.
These are the same SAH who carry ***zero*** European SNP/AIM but carry mt-DNA hg-H AND the paragroup hg-V(Pillars of Hercules…..). Significance. SAH were MtDNA hg-H long long long before European probably existed.
Beyoku, Am I right with Table 3? We are back to my TunisianB and your Saharawis again. What is up with these two populations?
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Post by djoser-xyyman on Aug 6, 2014 21:19:26 GMT -5
The Jordanian population where Ennaafa got her “Near East” dataset from …. González et al. 2008.
Background: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations.
Aim: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations. Subjects and methods: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.
Results: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.
Conclusion: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area. ---
Classes will continue at a later date.
These Euros. I know all their games. Time you do to. You have been at this long enough.
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Post by djoser-xyyman on Aug 6, 2014 21:20:02 GMT -5
To those who have a problem with “my”Bedoiuns s in the the Levant. What the author is saying is that the genetic composition of the Bedoiuns are identical to Africans(North/South). They are the founder population IN the Levant. Get it! got it! Most of present population in the Levant are new to the area. These same Bedoiuns also mirror the peoples of Southern Arabia. That is why it is extremely important to look at the sub-populations being sampled.
I KNOW ALL THEIR GAMES.
Oh! These Bedoiuns are the closest match to aDNA recently discovered in the Neolithic peoples of the Levant. Sources cited. On ESR. I got this.!
So Beyoku/AMRTU – see why Sardinia and the Bedoiuns are so important when sampling. -------- Quote: and its(Bedoiun) south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest Africa --------
The Bediouns are the last remaining pocket of “Africa” remaining in the Levant. The “proxy”.
Where Am I going with this? To those who are having difficulty following the thread. The NE peoples who are significant carriers of the h Haplotype being discussed here are …….Jordanians. Jordanians, more specifically – Jordanians Bedoiuns, carry the hg-H haplotypes. The other Levant populations Syrians, Lebanese etc do not carry appreciable amounts of hg-H haplotypes.
My buddy missed that one.
Henn et al did the exact same thing with her infamous “back-migration” paper. She chose Qatar as her “Middle East” population rep. After close examination, outside of Yemen, Qatar is the most Africanized population outside of Africa. The genetic makeup of Qatar is identical to Sahara/Sahel region. An admixture of North Africans and SSA
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Post by djoser-xyyman on Aug 6, 2014 21:20:40 GMT -5
Y-DNA R1?
You don't get it, do you? R-M269 is NOT the genetic counter-part to mtDNA hg-H. Current aDNA shows that hg-H entered Europe 5000y!!! ahead of R-M269 by about 4000years. Achilli got it wrong.
Kefi aDNA observed hg-H in Africa since 12,000YA!!!!!
The enigma is the Western European male line, yes. Enough data has not been disclosed as yet. But Clearly the male line was NOT present in Europe until about the bronze age.
I believe(this is a conjecture), that R-V88 geographic pattern holds the clue to break this wide open.
Three Africanize populations carry a high frequency R-V88...outside of Canmeroon and SSA.
1. Saharawis 2. Siwa Berbers and 3. ...you guessed in.... my Bedoiuns of the Levant.
Significance? Exit points OUT Africa.
But I am getting ahead of myself!
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Post by djoser-xyyman on Aug 8, 2014 7:56:00 GMT -5
Here is something very interesting that we may have oover looked in the discussion. Sage touched on it earlier.
---------- From HOLOCENE HUMAN PEOPLING OF LIBYAN SAHARA Molecular analysis of maternal lineages in ancient and extant populations of Fezzan CLAUDIO OTTONI
Haplogroup V frequencies Only in the populations which present the highest frequencies of the H-CRS haplotype, the frequency of haplogroup V was observed too (Table 3.6). The highest values were found in the Berber groups, particularly in those characterized by a high frequency of the haplotype H-CRS (Matmata, 16.33%; Souss Berbers, 10%; Mozabiti, 8.2%; Moroccan Berbers, 6.25%), with the exception of Sened. It is worth noting that non Berber groups, i.e. Tunisians and Algerians, despite the high frequencies of H-CRS, DO NOT SHOW ANY V LINEAGE.
------------------
How does it relate?
Haplogroup V. Haplogroup V is closely related to haplogroup H: they are two sister groups /paragroupsthat originated from a common ancestor (Torroni et al. 1998). Haplogroup V has a much more LIMITED GEOGRAPHICAL DISTRIBUTION than haplogroup H, and is mainly observed in Northwest Europe and North Africa: it reaches high frequencies in some Iberian populations, and is also very common among the Berbers of North Africa.
Western Eurasian lineages: H1 and V. Complete mtDNA sequencing carried out on five H1 Tuareg individuals, indicates a certain degree of DIVERSIFICATION of H1 lineages in Northern Africa. In fact, they are all different and tend to cluster in Northern African specific sub-haplogroups. It supports the hypothesis of an early arrival at the beginning of the Holocene of the H1 lineages in Northern Africa, this being a consequence of the Post-Glacial expansion from the Iberian Peninsula. Furthermore, the topology of the tree, that is characterised by many haplotypes departing directly from the root, clearly reflects the star-like structure of the haplogroup H1. This is an evidence of the expansion event that involved the H1 lineages at the beginning of the Holocene, as previously reported in literature (Pereira et al. 2001, Achilli et al. 2004, Roostalu et al. 2006).
As regards the V lineages, no genealogical was carried out. Nevertheless it is worth noting that the HVS-I haplotype 16189-16298 is shared with six sequences from Europe, three of which are from a Basque sample (Richards et al. 2000). We think that it is a further significant proof of the linkage between the West-Eurasian lineages in Northern Africa and the Post-Glacial expansion from the Iberian refuge
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Post by Ish Gebor on Jun 21, 2016 2:37:46 GMT -5
--Brotherton P1, Haak W, Templeton J, Nat Commun. 2013;4:1764. doi: 10.1038/ncomms2656. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. www.ncbi.nlm.nih.gov/pubmed/23612305
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Post by Ish Gebor on Jun 21, 2016 2:39:09 GMT -5
--Laura R. Botiguéa,1, Brenna M. Henn et al
Gene flow from North Africa contributes to differential human genetic diversity in southern Europe (July 16, 2013)
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