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Population relationships in the Mediterranean revealed by autosomal genetic data (Alu and Alu/STR compound systems).
González-Pérez et al.
Am J Phys Anthropol. 2009 Nov 16.
The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub-Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans-Mediterranean interchanges. Two specific Alu/STR combinations-CD4 110(-) and DM 107(-)-detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples.
Posts: 2007 | From: Washington State | Registered: Oct 2006
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quote:Originally posted by Evergreen: Population relationships in the Mediterranean revealed by autosomal genetic data (Alu and Alu/STR compound systems).
González-Pérez et al.
Am J Phys Anthropol. 2009 Nov 16.
The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub-Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans-Mediterranean interchanges. Two specific Alu/STR combinations-CD4 110(-) and DM 107(-)-detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples.
A detailed survey of the E-M78 Y-chromosome haplogroup (Cruciani et al., 2007) indicates the Northeast African origin of this variant and its involvement in trans-Mediterranean migrations from North Africa to Europe during the last 13,000 YBP.
As for individual populations, the sub-Saharan gene flow in North Africa based on the Alu data collection ranges between 6 and 17% (Table 3), except the Siwa Berbers where that influence was negligible. Admixture values based on Alu/STR combinations indicate that sub- Saharan flow in North Africa ranged from 16% (North East Moroccan Berbers) to 35% (remaining samples) with the exception of Siwa Berbers who showed the highest admixture value (51%).
Concerning Northern Mediterraneans, the gene flow from sub-Saharan Africa was inappreciable for Alu markers and swung from 6 to 15% for the Alu/STR.
Interestingly, data from mtDNA and Y-chromosome estimates of sub-Saharan gene flow in North Africa are similar to that obtained from our Alu loci set, a value also concordant with that corresponding to Mozabites in the recent survey of Li et al. (2008) based on more than 500,000 SNPs.
Nevertheless, our findings include indirect indicators of the gene flow that occurred throughout the Mediterranean region. In Northern Mediterraneans, traces from sub-Saharan African genes were detected through admixture analysis suggesting continuous contacts among both Mediterranean shores as it has been also described in other reports. The fact that these traces have been detected in the entirety of the northern shore, from Spain (10%) to Turkey (9.4%), reinforces the hypothesis that gene flow in this region is probably linked to the first ancient trans-Mediterranean navigations and that has been maintained and homogenized through enduring slave trade that prevailed until the end of the 17th century (Olesa-Mun˜ ido, 1968), rather than merely reflecting the Islamic expansions of the 8th to 15th centuries.Posts: 2007 | From: Washington State | Registered: Oct 2006
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^^ Haven't finished reading all the text yet but a few things stand out.
1)) How come they choose the Ivory Coast for their "sub Saharan" sample? Big parts of Mali, Chad, Niger are closer to their Berber samples. Why jump over these to go to Ivory Coast? Could it be that these Saharan populations might have yielded results that they didn't want?
2)) They make the usual sample from the FAR NORTH of Egypt near the Libyan border. Now where else have we seen such "representative" sampling?
Great quote on the Siwa Berbers of Egypt who show more Sub-Saharan influences than other populations. It deserves a repeat: [quote]:
"Admixture values based on Alu/STR combinations indicate that sub-Saharan flow in North Africa ranged from 16% (North East Moroccan Berbers) to 35% (remaining samples) with the exception of Siwa Berbers who showed the highest admixture value (51%)." --Gonzalez et al on the Siwa (Egyptian Oasis) Berbers. "Population Relationships in the Mediterranean Revealed by Autosomal Genetic Data" 2009
3) Speaking of which can you or someone else give a quick rundown on how they do this "admixture analysis" and how accurate it is?
Posts: 5905 | From: The Hammer | Registered: Aug 2008
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As for individual populations, the sub-Saharan gene flow in North Africa based on the Alu data collection ranges between 6 and 17% (Table 3), except the Siwa Berbers where that influence was negligible.
Admixture values based on Alu/STR combinations indicate that sub- Saharan flow in North Africa ranged from 16% (North East Moroccan Berbers) to 35% (remaining samples) with the exception of Siwa Berbers who showed the highest admixture value (51%).
There are two ways of approaching this piece: the "negligible influence" in the "individual" Siwa sample suggests that they were deemed to have shared-TMRCA markers with "Sub-Saharan" groups, even after factoring in "Sub-Saharan gene flow".
The "admixture analysis" finds on the other hand, suggest that notwithstanding the autochthonous state of the Siwa gene pool, considerable subsequent gene flow had also occurred. The question then becomes: Are the two observations contradictory? It will boil down to the specifics of microsatellite nucleotide patterns and distribution.
quote: In Northern Mediterraneans, traces from sub-Saharan African genes were detected through admixture analysis suggesting continuous contacts among both Mediterranean shores as it has been also described in other reports. The fact that these traces have been detected in the entirety of the northern shore, from Spain (10%) to Turkey (9.4%), reinforces the hypothesis that gene flow in this region is probably linked to the first ancient trans-Mediterranean navigations and that has been maintained and homogenized through enduring slave trade that prevailed until the end of the 17th century (Olesa-Mun˜ ido, 1968), rather than merely reflecting the Islamic expansions of the 8th to 15th centuries.
True enough.
quote:Originally posted by zarahan:
3) Speaking of which can you or someone else give a quick rundown on how they do this "admixture analysis" and how accurate it is?
"Admixture analysis" is a pair-wise quantitative [and comparative] application that relies on the select markers that were tested for starters, and thereof, the differences between them both molecularly and distribution-wise per sample. It is generally accompanied by calculations for Fst distances.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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What's the scoop on the Siwa Berbers? Various web pages say that the Siwa Oasis has been occupied at least 10,000 years.
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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^Based on available data that has come to my attention, "Berber" expansion occurred from eastern Sahel or lower confines of the Sahara, perhaps in the region straddling between greater Egypt and Sudan, at about 5 ky ago or so. This would have applied to the ancestors of the Siwa group as well.
To me, the below maybe contradictory, having not yet read the study in its entirety.
As for individual populations, the sub-Saharan gene flow in North Africa based on the Alu data collection ranges between 6 and 17% (Table 3), except the Siwa Berbers where that influence was negligible.
Admixture values based on Alu/STR combinations indicate that sub- Saharan flow in North Africa ranged from 16% (North East Moroccan Berbers) to 35% (remaining samples) with the exception of Siwa Berbers who showed the highest admixture value (51%).
...but I have noted, as to how I would approach the matter, as a preliminary assessment. Either the Siwa must have accumulated Alu markers that further evolved, having shared the same TMRCAs as the "sub-Saharan" counterparts, or the said markers are reflective of external gene flow. However, there is a problem with the latter reckoning, as we know that sections of coastal northwest African "Berbers" have substantial external ancestry from neighboring north regions; yet, according to the above:
As for individual populations, the sub-Saharan gene flow in North Africa based on the Alu data collection ranges between 6 and 17%
So, I'm inclined to go with the idea that the Siwa Alu insertion markers are derivatives that share their immediate TMRCAs with those of "sub-Saharan" counterparts. As such, "sub-Saharan gene flow" influence would seem negligible. In sections of coastal northwest African "Berbers" the "sub-Saharan African" Alu markers vs those from external gene flow would be more acute, because the external examples would have likely undergone additional step TMRCAs, separating them from the "sub-Saharan African" counterparts.
Question: Have you completed reading the study; what did you learn from it, as it relates to the question surrounding the Siwa?
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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posted
Still have to wade thru several pages of small font- sort of a compressed type file. Hit me up email for details.
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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^zarahan, I left you a private message. Looking forward to your response.
-------------------- The Complete Picture of the Past tells Us what Not to Repeat Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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In keeping with pointing out the recurring theme of the lingering onto outdated or outmoded and subjective concepts by the authors of the present study, the following serves as further example:
Concerning Northern Mediterraneans, the gene flow from sub-Saharan Africa was inappreciable for Alu markers and swung from 6 to 15% for the Alu/STR haplotypes data calculations. When gene flow in Northern Mediterraneans was tested, taking Central Europe and Southern Mediterraneans as parental populations, the results were statistically inconsistent, indicating the limited power of our markers to discriminate gene flow within Caucasoid populations. Nonetheless, the distributions of frequencies for the Mediterranean haplotypes CD4 110(-) and DM 107(-) (Fig. 4A,B) are suggestive of gene flow processes across this geographical region.
-------------------- The Complete Picture of the Past tells Us what Not to Repeat Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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This is one of the few studies if any that have Siwan Y-DNA samples:
"E-M81 was found in only one Siwi(1%)"
"Siwa Berber shave a similar frequency(6%) of this haplogroup, but other sub-Saharan haplogroups(e.g.B-M109 andE-V6) have been observed at high frequencies: about 60% on the whole(these haplogroup sare very rare north of the Sahara)"
"Relative high microsatellite diversity in Siwa Berbers suggests that their presence cannot be ascribed to recent bottleneck or recent founder effect"
Posts: 2463 | From: New Jersey USA | Registered: Dec 2007
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posted
^^ nice ref, showing how diverse the Berbers are. I will pull that study you mention.
Also Explorer's blog breaks it down comprehensively including the use of so-called "representative" samples, and many other shaky points made by Gonzalez et al. above.
-------------------------------------- from Exp blog:
"One issue that stands out like a sore thumb, is the comprehensiveness of the authors' so-called "sub-Saharan" collection; see:
In search of new insights into these questions, this study analyzes a relevant set of Mediterranean populations including eight European samples (from Spain, France, Greece, and Turkey), seven from North Africa (Morocco, Algeria, and Egypt), plus two samples from Central Europe (Germany) and sub-Saharan Africa (Ivory Coast) as external references.
Granted, the Ivory Coast sample is representative of sub-Saharan gene pool, but it only serves as a part of that gene pool, not the whole of it. It is highly questionable that this Ivory Coast sample will contain all that that is present in sub-Saharan Africa, as opposed to giving a snapshot of what is present in sub-Saharan Africa. Furthermore, what purpose does it serve, to ignore populations situated between Ivory Coast and those in the northern African territories sampled? Common sense intimates, that such an undertaking will ensure more abrupt changes in DNA marker distribution trends; but then again, the authors could be gunning for just that." ------------------------------- end quote
Some in recent threads have argued that certain blood types like A2 are "reserved" markers for "Caucasain" presence in North Africa but it turns out that these "reserved" blood types show up in black Berbers as well. The Siwa would be 'black' Berbers', but I had never heard of the Flitta of Algeria, until recently. (quote)
"A remarkable isolate is that of the Flittas who live at Zemmora, southeast of Oran, and have a long history of fierce resistance to successive rulers of Algeria.. Their ABO frequencies are unique, with 18 per cent of A2 genes, the highest frequency known except in the Lapps of northern Scandinavia. The total A gene frequency reaches the high level of 30 per cent, and M at 57 per cent is also well above the general North Africa level. The presence of 26 per cent of cDe shows considerable Negro admixture, presumably long ago. The high A2 frequency remains a mystery—it is presumably the result of genetic drift or natural selection.." -- D'Adamo (2009) "Subgroups of Type A."
-------------------- Note: I am not an "Egyptologist" as claimed by some still bitter, defeated, trolls creating fake profiles and posts elsewhere. Hapless losers, you still fail. My output of hard data debunking racist nonsense has actually INCREASED since you began.. Posts: 5905 | From: The Hammer | Registered: Aug 2008
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This is one of the few studies if any that have Siwan Y-DNA samples:
"E-M81 was found in only one Siwi(1%)"
"Siwa Berber shave a similar frequency(6%) of this haplogroup, but other sub-Saharan haplogroups(e.g.B-M109 andE-V6) have been observed at high frequencies: about 60% on the whole(these haplogroup sare very rare north of the Sahara)"
"Relative high microsatellite diversity in Siwa Berbers suggests that their presence cannot be ascribed to recent bottleneck or recent founder effect"
Yeah, I'd seen that publication a few years back, and it was in fact discussed here some time back. In that particular sample, the E-M81 was relatively low, but it is not the first time E-M81 has been implicated in the Siwa. It is widely written in published journal that frequencies of E-M81 are far greater in northwestern Africa than eastern, but the older coalescence ages of the Siwa examples, gave legs to the estimation that the E-M81 mutation first emerged in eastern Sahara or nearby Sahel areas. The substantial frequencies in northwestern Africa is attributed to a founder effect situation and genetic drift.
Indeed, the Siwa are known candidates of deep-root African markers, as noted above. This is in line with my estimation of the Siwa sample of the present study, in that, some of that "sub-Saharan" character of their gene pool, may actually be telltale signs of their autochthonous ancestry [i.e. African origin] in the Sahel area, but that through the ethnogenesis of the Siwa, their gene pool had since evolved within-population, therefore differentiating their gene pool from its original pattern. This may in part explain the different pattern of the Siwa Alu distribution from the lone sub-Saharan example, although it is important to note here again, that that lone sub-Saharan sample is from the Ivory Coast. Undoubtedly, the Ivory Coast pattern will be distinct from those of groups in central and eastern Sahel. So, the Ivory Coast sample as "representative" of "sub-Saharan" gene pool, although it still serves an educational value at some level, is not an accurate estimation of reality.
Posts: 7516 | From: Somewhere on Earth | Registered: Jan 2008
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