|
Post by djoser-xyyman on Sept 26, 2014 13:20:25 GMT -5
Phylogeny and genetic structure of Tunisian populations and their position within Mediterranean - Rym Kefi 2014
Compared to 4206 mtDNA sequences from Mediterranean populations, 354 different sequences were observed in Tunisia, among them 234 WERE UNIQUE. The distribution of unique sequences is higher in the North of Tunisia (number of unique sequences (N139), than in the South (N86). The highest value is observed in Capital Tunis (N36). These values were corrected by the number of individuals in each sample and results from this study showed that among Mediterranean populations, significantly Tunisia (10.2%) contain the highest frequency of unique sequences. On the second position we found populations from Galicia (GAL, 3.4%), Northern Greece (GNG, 3.3%), Alexandria (ALX, 2.8%) and Turkey (TUR, 2.2%). Thirdly, frequencies of unique sequences in populations from Greece (GRE), Italia (SIC, ITS), Spain (AND, CAT), Egypt (EGY) and Palestine (PAL) ranged from 1–2%, while the remaining Mediterranean populations contains values of unique sequences under the level of 1% (Figure 2).
Genetic structure of the Tunisian population
The analysis of the genetic diversity of the Tunisian population and the dispersal distribution of haplogroup frequencies were summarized in (Table 3, Figure 1, Supplementary material Appendices A, C, D). The mtDNA genetic pool of Tunisian populations contains three components: Eurasian lineages (H, HV, U (excepted U6), T, J, V, K, N, R, U5, I, W, X), Sub-Saharan lineages (L0, L1, L2, L3) and North African lineages (U6 and M1). The exception was observed in two Southern Berber populations from Jerba and Chenini-Douiret where the North African component was absent. The Eurasian lineages are predominant in all Tunisian populations, with the exception of the Southern Berbers from Bou Saaˆd where the percentage of the Eurasian lineages was equivalent to the percentage of the Sub-Saharan lineages (43% and 44% respectively). The Eurasian lineages range from 43% in the population of Bou Saaˆd to 87% IN BERBERS FROM JERBA.
Phylogeny of Tunisian with Mediterranean populations The FST matrix relating the 61 Mediterranean populations including the 16 Tunisian populations was reported in Supplementary material Appendices G, H. Comparison of FST values from pairs of populations revealed that most Tunisian samples displayed significant differences with European populations. The highest FST values (0.38271) were observed between Chenini-Douiret from Southern Tunisia and Galicia from Iberian Peninsula. The phenogram based on the resulting FST matrix (Figure 5A) displayed three clusters. The first (I) was composed by six Tunisian populations with different ethnic origins clustered with populations from Libya, Morocco and Egypt. The second group was composed by seven Tunisian populations with different ethnic origins clustered with populations from Algeria Morocco and Egypt. The third group was mainly composed by European and Near Eastern populations. Only one Tunisian population from Jerba Berbers (JEB) belonged to the third group. According to the phenogram (Figure 5A) and MDS plots (Figure 5B), populations
of Chenini-Douiret and Bou Saaˆd from Tunisia, Mozabites from Algeria and Fazzan Al Awaynat from Libya were outliers. IN ORDER TO REFINE THE POSITION OF TUNISIANS WITHIN MEDITERRANEAN POPULATIONS we pooled all Tunisian populations into one group (TUN), with the exception of the outliers CHO and SAB. Statistical analyses are shown in Supplementary material Appendices I, J. Phylogenetic and MDS analysis showed that Tunisians occupied central position in the NJ tree and the MDS plots (Figures 6, 7) between North Africans and Near Eastern populations. According to the matrix of significance, Tunisians are significantly distant from the majority of European populations EXCEPT POPULATIONS FROM SARDINIA, CORSICA, TUSCANY AND SOME SPANISH POPULATIONS (VAL, BAS, MIN, CHU).
The present phylogenetic study and the AMOVA analysis deduced that there are no differences between the three ethnic Tunisian groups: Arabs, Berbers and Andalusians. In fact, in the phenogram and the MDS plots, one cluster could contain populations from different ethnic groups and there is no specific cluster for one ethnic group (Figure 4). This means that the previous ethnic studies using uniparental markers (mtDNA and Y chromosome) (Cherni et al., 2005, 2009; Ennafaa et al., 2011; Loueslati et al., 2006) and autosomal markers (Ancestry Informative SNP panel) (Khodjet-el-Khil et al., 2011).
|
|
|
Post by djoser-xyyman on Sept 26, 2014 13:20:49 GMT -5
Comparisons at the haplotypic level revealed that Tunisia and in particular Capital Tunis encompassed the highest frequency of unique sequences among the Mediterranean populations (Figure 1). THIS WAS THE FIRST INVESTIGATION ON UNIQUE SEQUENCE IN THE MEDITERRANEAN AREA. Capital Tunis harbors also the highest diversity parameters and the higher number of haplogroups in Tunisia (Table 2, Table 3). The higher variability of Capital Tunis might be the result of both migration waves in ancient and recent times by the effect of exodus of rural populations to the urban areas.
Outliers from Mediterranean populations
It is noteworthy that two Southern Tunisian Berber groups from Chenini-Douiret (CHO) and Bou Saaˆd (SAB) were genetically distant from the majority of the Tunisian populations. CHO and SAB behaved as outliers (Figures 4, 5). CHO harbored the highest Eurasian component in Tunisia (87%) whereas SAB harbored the lowest one (43%). Both CHO and SAB presented low values of haplotype diversity (CHO: H¼0.939±0.017 and SAB: H¼0.897±0.033). This pattern of variation is most probably explained by the intense drift and endogamy undergone by the isolated groups (Ben Halim et al., 2012; Bittles, 2005). Previous studies suggested that Mozabites from Algeria (Macaulay et al., 1999) and Chenini-Douiret from Tunisia (Fadhlaoui-Zid et al., 2004) were outliers compared to North African populations. Our phylogenetic study confirmed this observation in the Mediterranean region and highlighted two other out groups: Bou Saaˆd (SAB) from Tunisia and Fezzan Al Awayanat (FAL) from Libya (Figure 5).
Tunisians position among Mediterranean populations
The phylogenetic analysis showed a dispatched pattern of Tunisians among Mediterranean populations (Figure 5). Tunisian populations were localized within North African populations with the exception of Jerba Berbers which are clustered with Sardinians(Italy) and Valencians(Spain). The genetic proximity of Jerba Berbers with Sardinians and Valencians might be the result of concomitant higher Eurasian component, lower frequency of Sub-Saharan haplogoups, absence of North African lineages and lower value of MNP (in the range of most European populations (Supplementary material Appendix K). When we pooled all Tunisian populations (with and without outliers: CHO and SAB) in one sample, we found that Tunisians occupied a central position in the phylogenetic tree, between North African and Near Eastern populations (Figures 6 and 7, Supplementary material Appendices I, J, L, M). This position may be explained by the impact of the different waves of migration since the Paleolithic period.
|
|
|
Post by djoser-xyyman on Sept 26, 2014 13:21:16 GMT -5
Conclusions
Our results suggested that neither geographical location nor ethnic origins have a major role in the mtDNA genetic background of the Tunisian population. The high genetic heterogeneity of the Tunisian population is accentuated by the presence of high frequency of unique haplotypes and by the presence of two outliers. Each Tunisian locality presents its own genetic specificity and cannot represent on it self the general Tunisian population.
|
|
|
Post by djoser-xyyman on Sept 26, 2014 13:26:19 GMT -5
I know this may be gibberish to some of your reading this but let me try to explain it with a picture. As they say “a picture tells a thousand words”. This is the first study of it’s kind. I have been calling for this comparison for years. Finally it is here. It was behind the paywall but now it is free…at least the pre-print.
The chart (picture) Fig 2. shows the relationship between mtDNA unique Haplotypes, shared Haplotypes amongst Mediterranean populations. Unique means – it is found ONLY within that population. Shared meaning…it is shared amongst populations.
So…this is very simple. …if a population is migrating from one region to the next you would expect to see some genes stay behind and others move/migrate on ie demic diffusion. In other words the “new” population will be a subset of the source population. More unique genetic markers(haplotypes) will remain BEHIND since those migrating on will be a “sub-set” of the source population. The source population will carry older and unique haplotypes NOT found in the younger population.. Keep in mind mutation does not cease so there may new haplotypes that may occur in the younger population, but those will be very infrequent.
So look at the chart…what do you see? Answer – the regions with the highest frequency of UNIQUE Haplotypes are 1. Tunisia/Sicily /Sardinia 2. Egypt/Greece/Levant 3. Morroco/Iberia
Turkey is an outlier
THESE ARE THE THREE EXIT POINTS [b}TO[/b] EUROPE FROM AFRICA. BOOOYAAA!!!!
This chart demonstrates two things
1. It debunks Achilli nonsense about hg-H originating IN Iberia from a Refugia 2. There were THREE exit points from Africa.
Tunisia is NOT the central African source. That source still needs to be sampled OR they are buried in the deserts of the Sahara.
|
|
|
Post by djoser-xyyman on Sept 26, 2014 13:26:50 GMT -5
Picture to come
|
|
|
Post by djoser-xyyman on Sept 26, 2014 20:15:30 GMT -5
|
|
|
Post by djoser-xyyman on Oct 1, 2014 10:54:02 GMT -5
A few posters sent me PM asking about the new Kefi paper.
Here is the link. It is in ResearchGate. Google – proof article_Kefi et al 2014_confidential. It should come up.
If not I can upload .
|
|
|
Post by djoser-xyyman on Dec 31, 2019 16:20:51 GMT -5
Phylogeny and genetic structure of Tunisian populations and their position within Mediterranean - Rym Kefi 2014
|
|