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Modern North Africans' recent origin is outside Africa
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[QUOTE]Originally posted by Troll Patrol # Ish Gebor: [QB] I find it ironic that they used the same photo collage as on Mathilda's web blog, 2008. https://mathildasanthropologyblog.files.wordpress.com/2008/07/moroccan-moors2.jpg Anyway, I am trying to understand David Coma claims he made on Henn's publication, on which he took part, ...: [QUOTE] Sequences from the mitochondrial DNA (mtDNA) control region were analyzed in nine European and West Asian populations. They showed low genetic heterogeneity when compared to world populations. However, a Caucasoid population tree displayed a robust east-west gradient. Within-population diversity (ascertained through various parameters) and mean pairwise differences declined from east to west, in a pattern compatible with ancient population migration and expansion from the Middle East. Estimated expansion times indicate a Paleolithic event with important differences among populations according to their geographical position and thus a slower tempo than previously believed. The replacement of Neanderthals by anatomically modern humans, fully compatible with the present results, may have been a slower and more complex process than cultural change suggests.[/QUOTE]--David Coma et al. Hum Genet. 1997 Apr;99(4):443-9. Mitochondrial DNA variation and the origin of the Europeans. http://www.ncbi.nlm.nih.gov/pubmed/9099831 [QUOTE] After an intensive bibliographic search, we compiled all the available data on allele frequencies for classical genetic polymorphisms referring to North African populations and synthesized the data in an attempt to reconstruct the populations' demographic history using two complementary methods: (1) principal components analysis and (2) genetic distances represented by neighbor-joining trees. In both analyses the main feature of the genetic landscape in northern Africa is an east-west pattern of variation pointing to the differentiation between the Berber and Arab population groups of the northwest and the populations of Libya and Egypt. Moreover, Libya and Egypt show the smallest genetic distances with the European populations, including the Iberian Peninsula. The most plausible interpretation of these results is that, although demic diffusion during the Neolithic could explain the genetic similarity between northeast Africa and Europe by a parallel process of gene flow from the Near East, a Mesolithic (or older) differentiation of the populations in the northwestern regions with later limited gene flow is needed to understand the genetic picture. The most isolated groups (Mauritanians, Tuaregs, and south Algerian Berbers) were the most differentiated and, although no clear structure can be discerned among the different Arab- and Berber-speaking groups, Arab speakers as a whole are closer to Egyptians and Libyans. By contrast, the genetic contribution of sub-Saharan Africa appears to be small. [/QUOTE]--David Coma et al. Hum Biol. 1997 Jun;69(3):295-311. Population history of north Africa: evidence from classical genetic markers. http://www.ncbi.nlm.nih.gov/pubmed/9164042 [QUOTE] Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations-that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit. [IMG]http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288373/bin/AJHGv65p1623fg1.jpg[/IMG] [i]Parsimony network relating the haplogroups defined by 10 of the unique-event polymorphisms analyzed. Arrowheads indicate the derived states, as inferred or established by typing nonhuman primates (Jobling and Tyler-Smith 1995; Jobling et al. 1996, 1997; Hurles et al. 1998). Blackened circles are proportional to haplogroup frequency, and unblackened circles indicate haplogroups detectable but not found in our set of 129 Y chromosomes from northwestern Africa.[/i] [/QUOTE]--David Coma et al. Am J Hum Genet. 1999 Dec;65(6):1623-38. Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. http://www.ncbi.nlm.nih.gov/pubmed/10577916 [QUOTE] The eight short tandem repeat (STR) polymorphic systems mapping on the male-specific region of the human Y chromosome, DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393, were typed in four populations from northwest (NW) Africa (Moroccan Arabs, southern Moroccan Berbers, Saharawis and Mozabites). Allele frequency distributions showed statistically significant differences for all loci among all the populations except for DYS19. Complete typing was obtained for 185 chromosomes, which showed 74 different haplotypes. The two most frequent haplotypes were found in 16.2% and 15.1% of the individuals, although the latter was almost exclusively found in the Mozabites. Locus and haplotype informativeness were measured by means of the gene diversity (D). The haplotype diversity ranged from 0.856 (Mozabites) to 0.967 (southern Moroccan Berbers). For some loci, allele frequencies in NW Africans were clearly different from those in Europeans. The most common NW African haplotype was found only in one individual out of a total of 494 Europeans typed for the whole STR set. Thus, NW African and European Y chromosomes are clearly differentiated. [/QUOTE]--David Coma et al. Int J Legal Med. 2000;114(1-2):36-40. Y chromosome STR haplotypes in four populations from northwest Africa. http://www.ncbi.nlm.nih.gov/pubmed/11197625 [QUOTE]An analysis of 11 I Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans, Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting a strong genetic barrier matching the geographical Mediterranean Sea barrier. The restriction to gene flow may be attributed to the navigational hazards across the Straits, but cultural factors must also have played a role. Some degree of gene flow from sub-Saharan Africa can be detected in the southern part of North Africa and in Saharawi and Southeastern Moroccans, as a result of a continuous gene flow across the Sahara desert that has created a south-north cline of sub-Saharan Africa influence in North Africa. Iberian samples show a substantial degree of homogeneity and fall within the cluster of European-based genetic diversity. [/QUOTE]Hum Genet. 2000 Oct;107(4):312-9. Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. [QUOTE] BACKGROUND: Various populations have contributed to the present-day gene pool of Morocco, including the autochthonous Berber population, Phoenicians, Sephardic Jews, Bedouin Arabs and sub-Saharan Africans. OBJECTIVE: The primary objective of the study was to complete a genetic description of the Berber-speaking population in the Souss region of southern Morocco, based on mitochondrial DNA (mtDNA) sequence analysis. SUBJECTS AND METHODS: The first hypervariable segment of the mtDNA control region was sequenced in a sample of 50 individuals from the Souss Valley, and the results compared with the extensive body of data available on mtDNA sequence variation in Europe and sub-Saharan Africa. RESULTS: Thirty-four different sequences were found: an estimated 68% of the sequences occurred throughout Europe, West Asia and North Africa, 26% originated in sub-Saharan Africa, and 6% belonged to the North African specific haplogroup U6. The Souss Valley mtDNA sequences indicated the presence of two populations which expanded at different times: the West Eurasian sequences in the Souss sample had a smaller average number of pairwise differences than pairs of sub-Saharan sequences. CONCLUSION: Detailed knowledge of the possible geographic origin of each sequence facilitated an interpretation of both internal diversity parameters and between-population relationships. The sub-Saharan admixture in the Souss Valley matched the south-north cline of sub-Saharan influence in North Africa, also evident in the genetic distances of North African populations to Europeans and sub-Saharan Africans [/QUOTE]--David Coma et al. Ann Hum Biol. 2001 May-Jun;28(3):295-307. Human mitochondrial DNA sequence variation in the Moroccan population of the Souss area. http://www.ncbi.nlm.nih.gov/pubmed/11393336 [QUOTE]Berbers live in groups scattered across North Africa whose origins and genetic relationships with their neighbours are not well established. The first hypervariable segment of the mitochondrial DNA (mtDNA) control region was sequenced in a total of 155 individuals from three Tunisian Berber groups and compared to other North Africans. The mtDNA lineages found belong to a common set of mtDNA haplogroups already described in North Africa. Besides the autochthonous North African U6 haplogroup, a group of L3 lineages characterized by the transition at position 16041 seems to be restricted to North Africans, suggesting that an expansion of this group of lineages took place around 10500 years ago in North Africa, and spread to neighbouring populations. Principal components and the coordinate analyses show that some Berber groups (the Tuareg, the Mozabite, and the Chenini-Douiret) are outliers within the North African genetic landscape. This outlier position is consistent with an isolation process followed by genetic drift in haplotype frequencies, and with the high heterogeneity displayed by Berbers compared to Arab samples as shown in the AMOVA. Despite this Berber heterogeneity, no significant differences were found between Berber and Arab samples, suggesting that the Arabization was mainly a cultural process rather than a demographic replacement. [/QUOTE]]--David Coma et al. Ann Hum Genet. 2004 May;68(Pt 3):222-33. Mitochondrial DNA heterogeneity in Tunisian Berbers. http://www.ncbi.nlm.nih.gov/pubmed/15180702 [QUOTE]Mitochondrial DNA (mtDNA) lineages of 232 individuals from 12 Central Asian populations were sequenced for both control region hypervariable segments, and additional informative sites in the coding region were also determined. Most of the mtDNA lineages belong to branches of the haplogroups with an eastern Eurasian (A, B, C, D, F, G, Y, and M haplogroups) or a western Eurasian (HV, JT, UK, I, W, and N haplogroups) origin, with a small fraction of Indian M lineages. This suggests that the extant genetic variation found in Central Asia is the result of admixture of already differentiated populations from eastern and western Eurasia. Nonetheless, two groups of lineages, D4c and G2a, seem to have expanded from Central Asia and might have their Y-chromosome counterpart in lineages belonging to haplotype P(xR1a). [b]The present results suggest that the mtDNA found out of Africa might be the result of a maturation phase, presumably in the Middle East or eastern Africa, that led to haplogroups M and N, and subsequently expanded into Eurasia, yielding a geographically structured group of external branches of these two haplogroups in western and eastern Eurasia, Central Asia being a contact zone between two differentiated groups of peoples.[/b] [/QUOTE]--David Coma et al. Eur J Hum Genet. 2004 Jun;12(6):495-504. Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. [QUOTE] [b]Africa is the homeland of humankind and it is known to harbour the highest levels of human genetic diversity. However, many continental regions, especially in the sub-Saharan side, still remain largely uncharacterized (i.e. southwest and central Africa).[/b] Here, we examine the mitochondrial DNA (mtDNA) variation in a sample from Angola. The two mtDNA hypervariable segments as well as the 9-bp tandem repeat on the COII/tRNA(lys) intergenic region have allowed us to allocate mtDNAs to common African haplogroups. Angola lies in the southern end of the putative western branch of the Bantu expansion, where it met the local Khoisan populations. Angolan mtDNA lineages show basically a Bantu substrate with no traces of Khoisan lineages. Roughly, more than half of the southwestern mtDNA pool can be assigned to west Africa, approximately 25% to central Africa and a significant 16% to east Africa, which points to the western gene pool having contributed most to the mtDNA lineages in Angola. We have also detected signals of extensive gene flow from southeast Africa. Our results suggest that eastern and western Bantu expansion routes were not independent from each other, and were connected south of the rainforest and along the southern African savannah. In agreement with historical documentation, the analysis also showed that the Angola mtDNA genetic pool shows affinities with the African lineages from Brazil, the main American destination of the slaves from Angola, although not all lineages in Brazil can be accounted for by the Angolan mtDNA pool. [/QUOTE]--David Coma et al. Hum Genet. 2004 Oct;115(5):439-47. Epub 2004 Sep 1. Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola. [QUOTE] A more recent geographically restricted enrichment of the African maternal gene pool was shown to have occurred during the early Upper Paleolithic, [b]when populations carrying mtDNA clades M1 and U6 arrived to north and northeast Africa from Eurasia, hardly penetrating the sub-Saharan portion of the continent, except Ethiopia.13,14[/b] Therefore, the current sub-Saharan mtDNA gene pool is overwhelmingly a rich mix of L0 and L105 clades, found at varying frequencies throughout the continent.15 [/QUOTE]--David Coma et al. The Dawn of Human Matrilineal Diversity The American Journal of Human Genetics 82, 1130–1140, May 2008 http://www.sciencedirect.com/science/article/pii/S0002929708002553 [QUOTE] The hypervariable region-1 and four nucleotide positions (10400, 10873, 12308, and 12705) of the coding region of mitochondrial DNA (mtDNA) were analyzed in 441 individuals belonging to eight populations (Daba, Fali, Fulbe, Mandara, Uldeme, Podokwo, Tali, and Tupuri) from North Cameroon and four populations (Bakaka, Bassa, Bamileke, and Ewondo) from South Cameroon. All mtDNAs were assigned to five haplogroups: three sub-Saharan (L1, L2, and L3), one northern African (U6), and one European (U5). Our results contrast with the observed high frequencies of a Y-chromosome haplogroup of probable Asian origin (R1*-M173) in North Cameroon. As a first step toward a better understanding of the evident discrepancy between mtDNA and Y-chromosome data, we propose two contrasting scenarios. The first one, here termed "migration and asymmetric admixture," implies a back migration from Asia to North Cameroon of a population group carrying the haplotype R1*-M173 at high frequency, and an admixture process restricted to migrant males. The second scenario, on the other hand, temed "divergent drift," implies that modern populations of North Cameroon originated from a small population group which migrated from Asia to Africa and in which, through genetic drift, Y-chromosome haplotype R1*-M173 became predominant, whereas the Asian mtDNA haplogroups were lost.[/QUOTE]--David Coma et al. Brief communication: mtDNA variation in North Cameroon: lack of Asian lineages and implications for back migration from Asia to sub-Saharan Africa. Am J Phys Anthropol. 2005 Nov;128(3):678-81. http://www.ncbi.nlm.nih.gov/pubmed/15895434 [QUOTE] Interindividual variation of human mitochondrial DNA has been extensively studied over the last two decades, and its usefulness for reconstructing evolutionary relationships of extant populations has been proved. However, some mitochondrial lineages still need to be studied using a combination of larger and tailored datasets and increased level of resolution in order to shed light on their origin and on the processes underlying their present distribution. In this study, we analyze the phylogeny of the L1c haplogroup of human mitochondrial DNA using sequence data from hypervariable regions 1 and 2 obtained from 455 individuals (extracted from a total sampling of 2542 individuals) belonging to sub-Saharan African and African-American populations. We propose a substantial revision of L1c phylogeny, by introducing one new sub-haplogroup (L1c4), two new L1c1 clades (L1c1b and L1c1c), and by reassigning the previous L1c1a1 sequences to a clade which we termed L1c5. The new phylogeny encompasses distinct lineages with different evolutionary histories. In fact, based on population frequency, internal variation and mismatch distribution, we propose that L1c1b, L1c1c and L1c2 originated in Bantu ancestors, whereas L1c1a, L1c4 and L1c5 evolved among Western Pygmies. The population structure of L1c is not comparable to any known mitochondrial or, even, Y-chromosomal haplogroup, and challenges the current view that most of mtDNA variation in Pygmies might reflect admixture with Bantu or a persistence of plesiomorphic characters. In fact, the unique feature of the L1c is that it retains a signature of a phase common to the ancestors of the Bantu and Western Pygmies, while encompassing some specific sub-clades which can indicate their divergence. This allowed us to attempt a phylogenetically based assessment of the evolutionary relationships between the two groups. Taking into consideration estimates of the time to the most recent common ancestor of L1c and its clades together with archaeological and paleoclimatological evidence, we propose that the ancestors of Bantu and Western Pygmies separated between 60 and 30 kya. [/QUOTE]--David Coma et al. Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. http://www.ncbi.nlm.nih.gov/pubmed/17107816 [/QB][/QUOTE]
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