Afghanistan from a Y-chromosome perspective

Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.     

Y-chromosome haplogroup N dispersals from south Siberia to Europe

In order to reconstruct the history of Y-chromosome haplogroup (hg) N dispersals in north Eurasia, we have analyzed the diversity of microsatellite (STR) loci within two major hg N clades, N2 and N3, in a total sample of 1,438 males from 17 ethnic groups, mainly of Siberian and Eastern European origin. Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago. Median network and variance analyses of STR haplotypes suggest that south Siberian N3a2 haplotypes spread further into Volga-Ural region undergoing serial bottlenecks. In addition, median network analysis of STR data demonstrates that haplogroup N2-A is represented by two subclusters, showing recent expansion times. The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe.     

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.     

Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic

The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat ( Triticum aestivum ) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.     

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.     

A Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y-Chromosome Lineages

The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; ∼17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; ∼31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; ∼10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; ∼37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.     

Y-chromosome variation in Tajiks and Iranians

Aim: The purpose of this study was to characterize Y-chromosome diversity in Tajiks from Tajikistan and in Persians and Kurds from Iran.

Method: Y-chromosome haplotypes were identified in 40 Tajiks, 77 Persians and 25 Kurds, using 12 short tandem repeats (STR) and 18 binary markers.

Results: High genetic diversity was observed in the populations studied. Six of 12 haplogroups were common in Persians, Kurds and Tajiks, but only three haplogroups (G-M201, J-12f2 and L-M20) were the most frequent in all populations, comprising together ～ 60% of the Y-chromosomes in the pooled data set. Analysis of genetic distances between Y-STR haplotypes revealed that the Kurds showed a great distance to the Iranian-speaking populations of Iran, Afghanistan and Tajikistan. The presence of Indian-specific haplogroups L-M20, H1-M52 and R2a-M124 in both Tajik samples from Afghanistan and Tajikistan demonstrates an apparent genetic affinity between Tajiks from these two regions.

Conclusions: Despite the marked similarities between Y-chromosome gene pools of Iranian-speaking populations, there are differences between them, defined by many factors, including geographic and linguistic relationships.     

Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence.

A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.     

Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia

The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across Eurasia. Here we genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526. Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R. Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.     

Y-chromosome polymorphisms define the origin of the Mang, an isolated population in China

The Mang is an isolated population living at the border of Vietnam and China characterized by small stature and a primordial lifestyle. However, the origin of this population remains unclear. To clarify the origin of the Mang and its genetic relationship with other populations, 20 Y-chromosome markers were analyzed, including 12 biallelic markers and eight short tandem repeats (STR) in this population, and the data compared with published data from other populations in eastern Asia. Only three Y-chromosome haplogroups, O2a*-M95, O3d-M7 and O3e-M134, were identified in Mang. Among them, the southern haplogroups O2a*-M95 were most prevalent, with a frequency of 97%. Principal component analysis (PCA) plots showed that Mang clustered with southern populations but not with northern populations. In conclusion, the present study provided evidence for the first time that the Mang population is of southern origin.     

Review of Croatian genetic heritage as revealed by mitochondrial DNA and Y chromosomal lineages

The aim of this review is to summarize the existing data collected in high-resolution phylogenetic studies of mitochondrial DNA and Y chromosome variation in mainland and insular Croatian populations. Mitochondrial DNA polymorphisms were explored in 721 individuals by sequencing mtDNA HVS-1 region and screening a selection of 24 restriction fragment length polymorphisms (RFLPs), diagnostic for main Eurasian mtDNA haplogroups. Whereas Y chromosome variation was analyzed in 451 men by using 19 single nucleotide polymorphism (SNP)/indel and 8 short tandem repeat (STR) loci. The phylogeography of mtDNA and Y chromosome variants of Croatians can be adequately explained within typical European maternal and paternal genetic landscape, with the exception of mtDNA haplogroup F and Y-chromosomal haplogroup P* which indicate a connection to Asian populations. Similar to other European and Near Eastern populations, the most frequent mtDNA haplogroups in Croatians were H (41.1%), U5 (10.3%), and J (9.7%). The most frequent Y chromosomal haplogroups in Croatians, I-P37 (41.7%) and R1a-SRY1532 (25%), as well as the observed structuring of Y chromosomal variance reveal a clearly evident Slavic component in the paternal gene pool of contemporary Croatian men. Even though each population and groups of populations are well characterized by maternal and paternal haplogroup distribution, it is important to keep in mind that linking phylogeography of various haplogroups with known historic and prehistoric scenarios should be cautiously performed.     

Recent Radiation within Y‐chromosomal Haplogroup R‐M269 Resulted in High Y‐STR Haplotype Resemblance

Y‐chromosomal short tandem repeats (Y‐STRs) are often used in addition to Y‐chromosomal single‐nucleotide polymorphisms (Y‐SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y‐STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R‐M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y‐STR haplotypes are still informative beyond high‐resolution Y‐SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West‐European regions of Flanders (Belgium), North‐Brabant and Limburg (the Netherlands) at the highest resolution of the current Y‐SNP tree together with 38 commonly used Y‐STRs. We observed high resemblance of Y‐STR haplotypes between males belonging to different subhaplogroups of haplogroup R‐M269. Several subhaplogroups within R‐M269 could not be distinguished from each other based on differences in Y‐STR haplotype variation. The most likely hypothesis to explain this similarity of Y‐STR haplotypes within the population of R‐M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high‐resolution Y‐SNP typing rather than Y‐STR typing might be more useful to study population genetic patterns in (Western) Europe.     

The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25 000 (95% CI: 21 300–29 000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800–6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.     

Phylogeography of the Y‐chromosome haplogroup C in northern Eurasia

To reconstruct the phylogenetic structure of Y‐chromosome haplogroup (hg) C in populations of northern Eurasia, we have analyzed the diversity of microsatellite (STR) loci in a total sample of 413 males from 18 ethnic groups of Siberia, Eastern Asia and Eastern Europe. Analysis of SNP markers revealed that all Y‐chromosomes studied belong to hg C3 and its subhaplogroups C3c and C3d, although some populations (such as Mongols and Koryaks) demonstrate a relatively high input (more than 30%) of yet unidentified C3* haplotypes. Median joining network analysis of STR haplotypes demonstrates that Y‐chromosome gene pools of populations studied are characterized by the presence of DNA clusters originating from a limited number of frequent founder haplotypes. These are subhaplogroup C3d characteristic for Mongolic‐speaking populations, “star cluster” in C3* paragroup, and a set of DYS19 duplicated C3c Y‐chromosomes. All these DNA clusters show relatively recent coalescent times (less than 3000 years), so it is probable that founder effects, including social selection resulting in high male fertility associated with a limited number of paternal lineages, may explain the observed distribution of hg C3 lineages.     

Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms

We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.     

Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia

Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.

Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.

Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.

Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000?years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000?years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.

Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.     

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.     

Y-chromosome polymorphisms define the origin of the Mang,an isolated population in China

The Mang is an isolated population living at the border of Vietnam and China characterized by small stature and a primordial lifestyle. However, the origin of this population remains unclear. To clarify the origin of the Mang and its genetic relationship with other populations, 20 Y-chromosome markers were analyzed, including 12 biallelic markers and eight short tandem repeats (STR) in this population, and the data compared with published data from other populations in eastern Asia. Only three Y-chromosome haplogroups, O2a*-M95, O3d-M7 and O3e-M134, were identified in Mang. Among them, the southern haplogroups O2a*-M95 were most prevalent, with a frequency of 97%. Principal component analysis (PCA) plots showed that Mang clustered with southern populations but not with northern populations. In conclusion, the present study provided evidence for the first time that the Mang population is of southern origin.     

Multiple founder haplotypes of mitochondrial DNA in Amerindians revealed by RFLP and sequencing

The mitochondrial DNA (mtDNA) of 139 individuals from eight tribes which belong to four linguistic groups of the Brazilian Amazon Region was studied both by RFLP and by sequencing of the D-loop region. RFLP analysis showed that 41 haplotypes (29%) belonged to haplogroup A, 39 (28%) to haplogroup B, 38 (27%) to haplogroup C., 19 (14%) to haplogroup D, and 2 (<2%) could not be assigned to any of the four haplogroups. Among the 92 individuals analyzed by direct sequencing of the D-loop region, we observed 43 different haplotypes defined by 48 polymorphic points, while one haplotype could not be assigned to any of the clusters previously described. Joint analysis of data obtained by RFLP and by sequencing of mtDNA demonstrated that, regardless of the method of analysis, the mtDNA haplotypes of contemporary Amerindians cluster into four groups, similar to those previously described, even though 7% of the total sample or 12% of the haplotypes have discrepancies between results obtained by RFLP and sequencing. In addition to supporting the prevalence of four major haplogroups among contemporary Amerindians, our data are compatible with multiple founder haplotypes in each haplogroup, based on: i) a high prevalence of unusual haplotypes; ii) presence of multiple polymorphic sites shared by different haplogroups; iii) relative differences in nucleotide diversity based on RFLP or sequencing within the different haplogroups.     

The Y-chromosome short tandem repeats variation within haplogroup E3b: evidence of recurrent mutation in SNP.

Haplogroup E3b is defined by a single nucleotide mutation (SNP) in locus M35 and is found at high frequency (more than 35%) in populations from North Africa with a heterogeneous distribution. On the basis of compilation of 553 Y-chromosomes from Europe and 633 from sub-Saharan Africa we selected 130 individuals belonging to haplogroup E3b and characterized subhaplogroups according to the Y-Chromosome Consortium nomenclature. Y-chromosome haplotypes can be defined using short tandem repeats (STR). The use of STRs makes it possible to measure diversity and estimate age coalescence. Significant differences on frequencies of Y-chromosome STR loci were found among the E3b subhaplogroups and the same was observed when haplotype frequencies were considered. Some mutations in SNPs were detected when comparing E3b subhaplogroups with the correspondent STR haplotypes. These results show that the mutation rate for some SNPs could be higher than previously thought and also that it is important to associate both haplotype and haplogroup in Y-chromosome studies.