The African contribution to the present‐day population of the Azores Islands (Portugal): Analysis of the Y chromosome haplogroup E

Among the settlers that, from 1432 onwards, arrived to the Azores Islands were individuals of North and sub‐Saharan African origin. A previous study of markers of the Y chromosome revealed that haplogroup E is the second more frequent in the Azores (13%). Since this haplogroup is heterogeneous and may contain subtypes of African or non‐African origin, we analyzed an extended sample of 319 Azoreans, originating from the three groups of islands (Eastern, Central, and Western), to evaluate the African contribution to the present‐day population of the Azores. Samples belonging to the E clade were distributed into six haplogroups, from which the most frequent was E3b1a, representing 47.2% of the E chromosomes (6.3% of the total sample). The sub‐Saharan haplogroup E3a was found in 7.1% of E chromosomes (0.9% of the total), corresponding to the highest frequency reported so far in a Portuguese population. No significant differences were detected in the haplogroup distribution among groups of islands, as well as between Azores and most of other European populations compared. The present‐day representation of sub‐Saharan lineages in Azores, although reduced, is higher than in other Portuguese populations, where the demographic representation of sub‐Saharan slaves is reported as similar. Am. J. Hum. Biol., 2007. © 2007 Wiley‐Liss, Inc.     

High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males

We genotyped 45 biallelic markers and 11 STR systems on the Y chromosome in 201 male Somalis. In addition, 65 sub-Saharan Western Africans, 59 Turks and 64 Iraqis were typed for the biallelic Y chromosome markers. In Somalis, 14 Y chromosome haplogroups were identified including E3b1 (77.6%) and K2 (10.4%). The haplogroup E3b1 with the rare DYS19-11 allele (also called the E3b1 cluster gamma) was found in 75.1% of male Somalis, and 70.6% of Somali Y chromosomes were E3b1, DYS19-11, DYS392-12, DYS437-14, DYS438-11 and DYS393-13. The haplotype diversity of eight Y-STRs ('minimal haplotype') was 0.9575 compared to an average of 0.9974 and 0.9996 in European and Asian populations. In sub-Saharan Western Africans, only four haplogroups were identified. The West African clade E3a was found in 89.2% of the samples and the haplogroup E3b1 was not observed. In Turks, 12 haplogroups were found including J2*(xJ2f2) (27.1%), R1b3*(xR1b3d, R1b3f) (20.3%), E3b3 and R1a1*(xR1a1b) (both 11.9%). In Iraqis, 12 haplogroups were identified including J2*(xJ2f2) (29.7%) and J*(xJ2) (26.6%). The data suggest that the male Somali population is a branch of the East African population - closely related to the Oromos in Ethiopia and North Kenya - with predominant E3b1 cluster gamma lineages that were introduced into the Somali population 4000-5000 years ago, and that the Somali male population has approximately 15% Y chromosomes from Eurasia and approximately 5% from sub-Saharan Africa.     

Y‐chromosome lineages in São Tomé e Príncipe islands: Evidence of European influence

The Y‐chromosome haplogroup composition of the population of São Tomé e Príncipe (STP) archipelago was analyzed using 25 biallelic markers and compared with populations of different origins from Europe, Africa, and the Middle East. Two main Y‐chromosome haplogroups were found: E3a, very common among sub‐Saharans accounts for 84.2% of the paternal lineages and R1b, typical of West Eurasia, represents 8.7% of the overall male population. Nevertheless, we detected in the population of STP a significant heterogeneous distribution of R1b among the two main ethnic groups of the archipelago: Forros (10.3%) and Angolares (6.6%). Together, haplogroups known to be prevalent in West Eurasia reach 12.5% of the chromosomes analyzed unequally distributed among the two groups: Forros present 17.7% while Angolares display only 8.2% of west Eurasian haplogroups. Our findings suggest that, despite its sub‐Saharan genetic background, a relevant contribution of European paternal lineages is present in nowadays STP population. This influence has shown to be stronger in Forros than in Angolares, which could be explained by the social isolation that these have last experienced through their history.Am. J. Hum. Biol. 19:422–428, 2007. © 2007 Wiley‐Liss, Inc.     

The Y-chromosomal Heritage of the Azores Islands Population

The Azores, a Portuguese archipelago located in the north Atlantic Ocean, had no native population when the Portuguese first arrived in the 15th century. The islands were populated mainly by the Portuguese, but Jews, Moorish prisoners, African slaves, Flemish, French and Spaniards also contributed to the initial settlement. To understand the paternal origins and diversity of the extant Azorean population, we typed genomic DNA samples from 172 individuals using a combination of 10 Y‐biallelic markers (YAP, SRY‐1532, SRY‐2627, 92R7, M9, sY81, Tat, SRY‐8299, 12f2 and LLY22g) and the following Y‐chromosomal STR systems: DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385. We identified nine different haplogroups, most of which are frequent in Europe. Haplogroup J* is the second most frequent in the Azores (13.4%), but it is modestly represented in mainland Portugal (6.8%). The other non‐European haplogroups, N3 and E3a, which are prevalent in Asia and sub‐Saharan Africa, respectively, have been found in the Azores (0.6% and 1.2%, respectively) but not in mainland Portugal. Microsatellite data indicate that the mean gene diversity (D) value for all the loci analysed in our sample set is 0.590, while haplotype diversity is 0.9994. Taken together, our analysis suggests that the current paternal pool of the Azorean population is, to a great extent, of Portuguese descent with significant contributions from people with other genetic backgrounds.     

Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation

The analysis of the hypervariable regions I and II of mitochondrial DNA in Portugal showed that this Iberian population presents a higher level of diversity than some neighbouring populations. The classification of the different sequences into haplogroups revealed the presence of all the most important European haplogroups, including those that expanded through Europe in the Palaeolithic, and those whose expansion has occurred during the Neolithic. Additionally a rather distinct African influence was detected in this Portuguese survey, as signalled by the distributions of haplogroups U6 and L, present at higher frequencies than those usually reported in Iberian populations. The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country. This seems to point to different population movements as the main contributors for the two haplogroup introductions. We hypothesise that the recent Black African slave trade could have been the mediator of most of the L sequence inputs, while the population movement associated with the Muslim rule of Iberia has predominantly introduced U6 lineages.     

Analysis of Y-chromosome Variability and its Comparison with mtDNA Variability Reveals Different Demographic Histories Between Islands in the Azores Archipelago (Portugal)

We determined the Y‐chromosomal composition of the population of the Azores Islands (Portugal), by analyzing 20 binary polymorphisms located in the non‐recombining portion of the Y‐chromosome (NRY), in 185 unrelated individuals from the three groups of islands forming the Archipelago (Eastern, Central and Western). Similar to that described for other Portuguese samples, the most frequent haplogroups were R1(xR1b3f) (55.1%), E(xE3a) (13%) and J (8.6%). Principal components analysis revealed a Western European profile for the Azorean population. No significant differences between Azores and mainland Portugal were observed. However, the haplogroup distribution across the three groups of islands was not similar (P<0.003). The Western group presented differences in the frequencies of haplogroups R1, E(xE3a) and I1b2 (27.3%, 22.7% and 13.6%, respectively) when compared to the other two groups. An assessment of the NRY variability, and its comparison with mitochondrial DNA (mtDNA) variability, was further evidence of the differential composition of males during the settlement of the three groups of islands, contrary to what has been previously deduced for the female settlers using mtDNA data.     

Binary and microsatellite polymorphisms of the Y‐chromosome in the Mbenzele pygmies from the Central African Republic

This study analyzes the variation of six binary polymorphisms and six microsatellites in the Mbenzele Pygmies from the Central African Republic. Five different haplogroups (B2b, E(xE3a), E3a, P and BR(xB2b,DE,P)) were observed, with frequencies ranging from 0.022 (haplogroup P) to 0.609 (haplogroup E3a). A comparison of haplogroup frequencies indicates a close genetic affinity between the Mbenzele and the Biaka Pygmies, a finding consistent with the common origin and the geographical proximity of the two populations. The haplogroups P, BR(xB2b,DE,P) and E(xE3a), which are rare in sub‐Saharan Africa but common in western Eurasia, were observed with frequencies ranging from 0.022 (haplogroup P) to 0.087 (haplogroup E(xE3a)). Thirty different microsatellite haplotypes were detected, with frequencies ranging from 0.022 to 0.152. The Mbenzele share the highest percent of microsatellite haplotypes with the Biaka Pygmies. Five out seven haplotypes which are shared by the Mbenzele and Biaka Pygmies belong to haplogroup E3a, which suggests that they are of Bantu origin. The plot based on F_st genetic distances calculated using microsatellite data provides a picture of population relationships which is in part congruent and in part complementary to that obtained using haplogroup frequencies. Finally, the Mbenzele and Biaka Pygmies were found to be markedly more genetically similar using Y‐chromosomal than autosomal microsatellites. We suggest that this could be due to the higher phylogenetic stability of Y‐chromosome and to the effect of the male‐biased gene flow during the Bantu expansion. Am. J. Hum. Biol. 16:57–67, 2004. © 2003 Wiley‐Liss, Inc.     

Genetic characterization of uniparental lineages in populations from Southwest Iberia with past malaria endemicity

Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD—Coruche, Pias, and Alcacer do Sal—to evaluate if their present‐day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty‐five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y‐chromosome markers. Results were then compared with data from other Portuguese and non‐Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub‐Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub‐Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia. Am. J. Hum. Biol. 22:588–595, 2010. © 2010 Wiley‐Liss, Inc.     

Y‐chromosome variation in South Iberia: Insights into the North African contribution

Population of Pedroches Valley, a hypothetical Berber settlement, located in the northwest portion of Córdoba province (Andalusia, Spain), had been analyzed for its Y‐chromosome diversity. Moreover, to contextualize this population, 127 Y‐chromosomes from a general Andalusia sample and a North African Berber community (Marrakech, Morocco) were also typed. For all samples, 24 single nucleotide polymorphisms of the non‐recombining portion of the Y‐chromosome (NRY) were analyzed and those samples described as belonging to E3b1b‐M81 haplogroup were also typed for 16 Y‐chromosome short tandem repeats. Our Analysis showed low levels of North African E3b1b‐M81 haplogroup in the Pedroches Valley population (1.5%), which is a lower contribution than would be expected. This result rejects the hypothesis of a gradual genetic assimilation of Berber settlers during the Islamic period. Am. J. Hum. Biol., 2009. © 2009 Wiley‐Liss, Inc.     

Y-chromosome diversity in Sweden - a long-time perspective

Sixteen Y-chromosomal binary markers and nine Y-chromosome short tandem repeats were analyzed in a total of 383 unrelated males from seven different Swedish regions, one Finnish region and a Swedish Saami population in order to address questions about the origin and genetic structure of the present day population in Sweden. Haplogroup I1a* was found to be the most common haplogroup in Sweden and accounted, together with haplogroups R1b3, R1a1 and N3, for over 80% of the male lineages. Within Sweden, a minor stratification was found in which the northern region V?sterbotten differed significantly (P < 0.05) from the other Swedish regions. A flow of N3 chromosomes into V?sterbotten mainly from Saami and Finnish populations could be one explanation for this stratification. However, the demographic history of V?sterbotten involving a significant male absence during the 17th Century may also have had a large impact. Immigration of young men from elsewhere to V?rmland at the same time, can be responsible for a similar deviation with I1a* haplotypes. Y chromosomes within haplogroup R1b3 were found to have the highest STR variation among all haplogroups and could thus be considered to be one of the earliest major male lineages present in Sweden. Regional haplotype variation, within R1b3, also showed a difference between two regions in the south of Sweden. This can also be traced from historical time and is visible in archaeological material. Overall this Y chromosome study provides interesting information about the genetic patterns and demographic events in the Swedish population.     

Micro-Phylogeographic and Demographic History of Portuguese Male Lineages

The clinal pattern observed for the distribution of Y‐chromosome lineages in Europe is not always reflected at a geographically smaller scale. Six hundred and sixty‐three male samples from the 18 administrative districts of Portugal were typed for 25 Y‐chromosome biallelic and 15 microsatellite markers, in order to assess the degree of substructuring of male lineage distribution. Haplogroup frequency distributions, Analysis of Molecular Variance (AMOVA) and genetic distance analyses at both Y‐SNP and Y‐STR levels revealed a general genetic homogeneity of Portuguese sub‐populations. The traditional division of the country in north, central and south, which is usually considered in studies addressing questions of the genetic variation distribution in Portugal, was not reflected in the Y‐haplotype distribution. Instead, just one sub–region (Alentejo) stood out due to the presence of high diversity levels and a higher number of different lineages, at higher frequencies than in other regions. These results are reconciled with the historical evidence available, assuming that from prehistorical times down to the end of the medieval period this region harboured the most diverse groups of people and, because of economic depression, remained relatively isolated from recent homogenisation movements. The finding of a broadly homogeneous background for the Portuguese population has vast repercussions in forensic, epidemiological and association studies.     

Dissecting the Genetic History of São Tomé e Príncipe: A New Window from Y-Chromosome Biallelic Markers

Twenty biallelic Y chromosome markers were analyzed in Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. While most male lineages belonged to sub-Saharan haplogroups, the component of European origin added up 23.9% in the archipelago. This contrasts with the reported absence of European mtDNA lineages, and the combined findings testify to a strong sex-biased admixture process during the long-lasting colonial period in São Tomé e Príncipe. Furthermore, the male mediated European component was clearly found to be out of proportion to the small demographic impact of the Portuguese on the islands, reflecting high variance in the reproductive success of the individuals that contributed to its peopling.
The male portion of European ancestry was 33.3% in Forros, 27.3% in Tongas and approximately two-fold less, 14.5%, in Angolares. The Angolares also showed the lowest haplogroup diversity and the most reduced number of different haplogroups. The current results reinforce our previous evidence pointing to remarkable restrictions in gene flow between Angolares and other São Tomean inhabitants, in agreement with their considerable isolation and confinement to the south-eastern tip of São Tomé until recently.     

Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes

Background: The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.

Aim: This study aims to investigate genetic variation and the gene pool in North Indians.

Subjects and methods: A total of 32 Y-chromosomal markers in 560 North Indian males collected from three higher caste groups (Brahmins, Chaturvedis and Bhargavas) and two Muslims groups (Shia and Sunni) were genotyped.

Results: Three distinct lineages were revealed based upon 13 haplogroups. The first was a Central Asian lineage harbouring haplogroups R1 and R2. The second lineage was of Middle-Eastern origin represented by haplogroups J2*, Shia-specific E1b1b1, and to some extent G* and L*. The third was the indigenous Indian Y-lineage represented by haplogroups H1*, F*, C* and O*. Haplogroup E1b1b1 was observed in Shias only.

Conclusion: The results revealed that a substantial part of today's North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants. The presence of haplogroup E in Shias, first reported in this study, suggests a genetic distinction between the two Indo Muslim sects. The findings of the present study provide insights into prehistoric and early historic patterns of migration into India and the evolution of Indian populations in recent history.     

Y-chromosome genetic variation in Rio de Janeiro population.

The present-day Brazilian gene pool is known to be the outcome of an admixture process of populations from different origins, mainly Amerindians, Europeans, and Africans. It is also known that in Brazil, a wide variation in the admixture process occurred in different regions of the country or even in different subpopulations from the same region. In the present study, we aimed to characterize the male lineages present in the Rio de Janeiro population, the second most populated of the 26 Brazilian states. A random sample of 127 unrelated males from Rio de Janeiro was typed for 28 Y-chromosome-specific biallelic markers. In total, 17 different haplogroups were defined within our sample, most of them of European ancestry (88.1%). Those of sub-Saharan African origin (E3a) amounted to 7.9%, while only 2 males carried Amerindian lineages (characterized by the presence of an M3 mutation: haplogroup Q3). Using both Y-STR haplotype and Y-SNP haplogroup information, genetic distances were calculated between the subgroup of Rio de Janeiro males carrying European haplogroups and the Portuguese population. Low, nonsignificant, values were obtained. Thus, in contrast with what is observed in their female counterparts, the vast majority of the present Rio de Janeiro male gene pool is of European extraction, while the original Amerindian lineages are residual and much less frequent than the sub-Saharan component resulting from the slave trade. These observations can be interpreted as the signature of the strong gender asymmetry of the admixture processes in colonial systems.     

Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau

The island of Crete, credited by some historical scholars as a central crucible of western civilization, has been under continuous archeological investigation since the second half of the nineteenth century. In the present work, the geographic stratification of the contemporary Cretan Y-chromosome gene pool was assessed by high-resolution haplotyping to investigate the potential imprints of past colonization episodes and the population substructure. In addition to analyzing the possible geographic origins of Y-chromosome lineages in relatively accessible areas of the island, this study includes samples from the isolated interior of the Lasithi Plateau--a mountain plain located in eastern Crete. The potential significance of the results from the latter region is underscored by the possibility that this region was used as a Minoan refugium. Comparisons of Y-haplogroup frequencies among three Cretan populations as well as with published data from additional Mediterranean locations revealed significant differences in the frequency distributions of Y-chromosome haplogroups within the island. The most outstanding differences were observed in haplogroups J2 and R1, with the predominance of haplogroup R lineages in the Lasithi Plateau and of haplogroup J lineages in the more accessible regions of the island. Y-STR-based analyses demonstrated the close affinity that R1a1 chromosomes from the Lasithi Plateau shared with those from the Balkans, but not with those from lowland eastern Crete. In contrast, Cretan R1b microsatellite-defined haplotypes displayed more resemblance to those from Northeast Italy than to those from Turkey and the Balkans.     

Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western Mediterranean

Phylogenetic analysis of mitochondrial DNA (mtDNA) performed in Western Mediterranean populations has shown that both shores share a common set of mtDNA haplogroups already found in Europe and the Middle East. Principal co‐ordinates of genetic distances and principal components analyses based on the haplotype frequencies show that the main genetic difference is attributed to the higher frequency of sub‐Saharan L haplogroups in NW Africa, showing some gene flow across the Sahara desert, with a major impact in the southern populations of NW Africa. The AMOVA demonstrates that SW European populations are highly homogeneous whereas NW African populations display a more heterogeneous genetic pattern, due to an east‐west differentiation as a result of gene flow coming from the East. Despite the shared haplogroups found in both areas, the European V and the NW African U6 haplogroups reveal the traces of the Mediterranean Sea permeability to female migrations, and allowed for determination and quantification of the genetic contribution of both shores to the genetic landscape of the geographic area. Comparison of mtDNA data with autosomal markers and Y‐chromosome lineages, analysed in the same populations, shows a congruent pattern, although female‐mediated gene flow seems to have been more intense than male‐mediated gene flow.     

The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.     

Y chromosomal heritage of Croatian population and its island isolates

Y chromosome variation in 457 Croatian samples was studied using 16 SNPs/indel and eight STR loci. High frequency of haplogroup I in Croatian populations and the phylogeographic pattern in its background STR diversity over Europe make Adriatic coast one likely source of the recolonization of Europe following the Last Glacial Maximum. The higher frequency of I in the southern island populations is contrasted with higher frequency of group R1a chromosomes in the northern island of Krk and in the mainland. R1a frequency, while low in Greeks and Albanians, is highest in Polish, Ukrainian and Russian populations and could be a sign of the Slavic impact in the Balkan region. Haplogroups J, G and E that can be related to the spread of farming characterize the minor part (12.5%) of the Croatian paternal lineages. In one of the southern island (Hvar) populations, we found a relatively high frequency (14%) of lineages belonging to P*(xM173) cluster, which is unusual for European populations. Interestingly, the same population also harbored mitochondrial haplogroup F that is virtually absent in European populations--indicating a connection with Central Asian populations, possibly the Avars.     

The Peopling of Modern Bosnia-Herzegovina: Y-chromosome Haplogroups in the Three Main Ethnic Groups

The variation at 28 Y‐chromosome biallelic markers was analysed in 256 males (90 Croats, 81 Serbs and 85 Bosniacs) from Bosnia‐Herzegovina. An important shared feature between the three ethnic groups is the high frequency of the “Palaeolithic” European‐specific haplogroup (Hg) I, a likely signature of a Balkan population re‐expansion after the Last Glacial Maximum. This haplogroup is almost completely represented by the sub‐haplogroup I‐P37 whose frequency is, however, higher in the Croats (～71%) than in Bosniacs (～44%) and Serbs (～31%). Other rather frequent haplogroups are E (～15%) and J (～7%), which are considered to have arrived from the Middle East in Neolithic and post‐Neolithic times, and R‐M17 (～14%), which probably marked several arrivals, at different times, from eastern Eurasia. Hg E, almost exclusively represented by its subclade E‐M78, is more common in the Serbs (～20%) than in Bosniacs (～13%) and Croats (～9%), and Hg J, observed in only one Croat, encompasses ～9% of the Serbs and ～12% of the Bosniacs, where it shows its highest diversification. By contrast, Hg R‐M17 displays similar frequencies in all three groups. On the whole, the three main groups of Bosnia‐Herzegovina, in spite of some quantitative differences, share a large fraction of the same ancient gene pool distinctive for the Balkan area.     

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages

Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25^* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25^* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25^* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25^* and about half of the few European/west Asian R-P25^* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200–5600 kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.