The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations

Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum

While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the current populations inhabiting Arabia and the impact of their contributions remains a challenging task. We investigate the genetic makeup of the current Yemeni population using 46 whole genomes and 169 genotype arrays derived from Yemeni individuals from all geographic regions across Yemen and 351 genotype arrays derived from neighboring populations providing regional context. Principal Component Analysis shows stratification between Yemen districts but also with respect to nearby populations: Yemeni, other Arabian and Bedouin samples form a continuum towards the populations of the Levant, whereas East Africa and India appear strongly differentiated. This finding is further supported by higher Principal Components, admixture and haplogroup analyses, and F-statistics. Moreover, two-reference linkage disequilibrium decay estimates are most significant for Yemeni admixture from an ancient northern influx (up to 5220BP from Palestine) and East Africa (750BP). We show that the initial gene flow into the Yemeni populations of today came from the rest of Arabia and the Levant, and a less substantial and more recent genetic impact into coastal Yemen from East Africa, particularly.

Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups

BACKGROUND

The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies.

METHODS

The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity.

RESULTS

Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples.

CONCLUSION

The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.

On the Y chromosome of Chennai, Tamil Nadu and the Indian subcontinent

Several migratory waves from various origins along with cultural practices restricting marriages between people of different castes and tribes as well as continued endogamy have led to a complex and diverse society in the Indian subcontinent. Despite being widely represented in genetic studies, several interrogatives remain with regards to India's current genetic constituents and distributions, source populations and population relationships. To identify the forces that may have shaped Indian population's genetic relationships, we undertook a comprehensive comparative study of the Y-chromosomes across India utilizing Y-STR and Y-SNP chromosomal markers using the general population of Chennai in the state of Tamil Nadu as a point of reference. Our analyses identify differences in source populations for different regions within India, unique linguistic characteristics as well as demographic and cultural forces that may have shaped population structure.

A validated LC-MS/MS method for determination of antiviral prodrug molnupiravir in human plasma and its application for a pharmacokinetic modeling study in healthy Egyptian volunteers

A fully validated, simple, rapid and reproducible liquid chromatography-tandem mass spectrometry method was developed to determine NHC (N-hydroxycytidine), the active metabolite of Molnupiravir (MOL) in human plasma; one of the limited treatment options for SARS-CoV-2 in plasma of healthy volunteers. The internal standard (IS) used was ribavirin. The extraction of analyte and IS from plasma was performed using acetonitrile as a solvent for protein precipitation. Agilent Zorbax Eclipse plus C₁₈, 4.6 × 150 mm, (5 µm) was used for chromatographic separation using a mixture of methanol0.2 % acetic acid (5:95, v/v) as a mobile phase that was pumped at a flow rate of 0.9 mL/min. Detection was performed on a triple quadrupole mass spectrometer operating in multiple reaction monitoring (MRM) employing positive ESI interface using API4500 triple quadrupole tandem mass spectrometer system, with the transitions set at m/z 260.10 → 128.10 and 245.10 → 113.20 for NHC and IS respectively. Method validation was performed in accordance with United States FDA bioanalytical guidance. The concentration range of 20.0-10000.0 ng/mL was used to establish linearity via weighted linear regression approach (1/x²). Moreover, the analyzed pharmacokinetic data from twelve Egyptian healthy volunteers were used to develop a population pharmacokinetic model for NHC. The developed model was used to perform simulations and evaluate the current MOL dosing recommendations through calculating the maximum concentration (C_max) "the safety metric" and area under the curve (AUC_0-12 h) "the efficacy metric" for 1000 virtual subjects. Geometric mean ratios (GMR) with their associated 90% confidence intervals (CI) compared to literature values were computed. Geometric means of simulation-based Cmax and AUC0-12 were 3827 ng/mL (GMR = 1.05; 90% CI = 0.96-1.15) and 9320 ng.h/mL (GMR = 1.04; 90% CI = 0.97-1.11), respectively indicating that current MOL dosage can achieve the therapeutic targets and dose adjustment may not be required for the Egyptian population. The developed model could be used in the future to refine MOL dosage once further therapeutic targets are identified.

Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD

The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being  introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.

Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes

Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East.

Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.

The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India

A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Some noteworthy findings of this present analysis include the following: The three most frequent haplogroups detected in the Soliga population are F*, H1 and J2. F*, the oldest (43 to 63 Kya), has a significant frequency bias in favor of Indian tribes versus castes. This observation coupled with the fact that Y-STR haplotypes shared with sub-Saharan African populations are found only in F* males of the Soliga, Irula and Kurumba may indicate a unique genetic connection between these Indian tribes and sub-Saharan Africans. In addition, our study suggests that haplogroup H is confined mostly to South Asia and immediate neighbors and the H1 network may indicate minimal sharing of Y-STR haplotypes among South Asian collections, tribal and otherwise. Also, J2, brought into India by Neolithic farmers, is present at a significantly higher frequency in caste versus tribal communities. This last observation may reflect the marginalization of Indian tribes to isolated regions not ideal for agriculture.

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Hg F*, H1 and J2 of the Soliga population chronicle the demographic history of the Indian tribal communities.

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Frequency bias for F* in Indian tribes may be a result of genetic drift due isolation and low population growth.

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Sharing of Y-STR haplotypes among tribal populations may be indicative of a common source population.

Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population

To obtain refreshed insights into the paternal lineages of Tunisian populations, Y-chromosome diversity was assessed in two populations belonging to an Arab genealogical lineage, Kairouan and Wesletia, as well as in four Tunisian Andalusian populations, Testour, Slouguia, Qalaat-El-Andalous and El Alia. The Arabs from Kairouan revealed 73.47% of E-M81 and close affinities with Berber groups, indicating they are likely arabized Berbers, clearly differentiated from the Arabs from Wesletia, who harbored the highest frequency (71.8%) of the Middle Eastern component ever observed in North Africa. In the Tunisian Andalusians, the North African component largely prevailed, followed by the Middle Eastern contribution. Global comparative analysis highlighted the heterogeneity of Tunisian populations, among which, as a whole, dominated a set of lineages ascribed to be of autochthonous Berber origin (71.67%), beside a component of essentially Middle Eastern extraction (18.35%), and signatures of Sub-Saharan (5.2%), European (3.45%) and Asiatic (1.33%) contributions. The remarkable frequency of T-M70 in Wesletia (17.4%) prompted to refine its phylogeographic analysis, allowing to confirm its Middle Eastern origin, though signs of local evolution in Northern Africa were also detected. Evidence was clear on the ancient introduction of T lineages into the region, probably since Neolithic times associated to spread of agriculture.

The Y chromosome of autochthonous Basque populations and the Bronze Age replacement

Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.

Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population

Background

The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited.

Aim

This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations.

Materials and methods

Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software.

Results and conclusion

One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.

Searching for the roots of the first free African American community

San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise F_ST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions.

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community.

Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population

In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.

Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates

Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067-4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677-20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci.

Genetic Diversity and Low Stratification of the Population of the United Arab Emirates

With high consanguinity rates on the Arabian Peninsula, it would not have been unexpected if the population of the United Arab Emirates (UAE) was shown to be relatively homogenous. However, this study of 1000 UAE nationals provided a contrasting perspective, one of a relatively heterogeneous population. Located at the apex of Europe, Asia, and Africa, the observed diversity could be explained by a plethora of migration patterns since the first Out-of-Africa movement. A strategy to explore the extent of genetic variation of the population of the UAE is presented. The first step involved a comprehensive population stratification study that was instructive for subsequent whole genome sequencing (WGS) of suitable representatives (which is described elsewhere). When these UAE data were compared to previous smaller studies from the region, the findings were consistent with a population that is a diverse and admixed group of people. However, rather than sharp and distinctive clusters, cluster analysis reveals low levels of stratification throughout the population. UAE emirates exhibit high within-Emirate-distance/among-Emirate distance ratios. Supervised admixture analysis showed a continuous gradient of ancestral populations, suggesting that admixture on the south eastern tip of the Arabian Peninsula occurred gradually. When visualized using a unique technique that combined admixture ratios and principal component analysis (PCA), unappreciated diversity was revealed while mitigating projection bias of conventional PCA. We observe low population stratification in the UAE in terms of homozygosity versus separation cluster coefficients. This holds for the UAE in a global context as well as for isolated cluster analysis of the Emirati birthplaces. However, the subtle clustering observed in the Emirates reflects geographic proximity and historic migration events. The analytical strategy used here highlights the complementary nature of data from genotype array and WGS for anthropological studies. Specifically, genotype array data were instructive to select representative subjects for WGS. Furthermore, from the 2.3 million allele frequencies obtained from genotype arrays, we identified 46,481 loci with allele frequencies that were significantly different with respect to other world populations. This comparison of allele frequencies facilitates variant prioritization in common diseases. In addition, these loci bear great potential as biomarkers in anthropological and forensic studies.

The Genetics of Warfarin Dose-Response Variability in Africans: An Expert Perspective on Past, Present, and Future

Coumarins such as warfarin are prescribed for prevention and treatment of thromboembolic disorders. Warfarin remains the most widely prescribed and an anticoagulant of choice in Africa. Warfarin use is, however, limited by interindividual variability in pharmacokinetics and a narrow therapeutic index. The difference in patients' pharmacodynamic responses to warfarin has been attributed to genetic variation in warfarin metabolism and molecular targets (e.g., CYP2C9 and VKORC1) and host-environment interactions. This expert review offers a synthesis of human genetics studies in Africans with respect to pharmacogenetics-informed warfarin dosing. We identify areas that need future research attention or could benefit from harnessing existing pharmacogenetics knowledge toward rational and optimal therapeutics with warfarin in African patients. A literature search was conducted until January 2019. A total of 343 articles were retrieved from nine African countries: Botswana, Ethiopia, Egypt, Ghana, Kenya, South Africa, Sudan, Tanzania, and Mozambique. We found 19 studies on genetics of warfarin treatment specifically among Africans. Genes examined included CYP2C9, VKORC1, CYP4F2, APOE, CALU, GGCX, and EPHX1. CYP2C9*2 and *3 alleles were highly frequent among Egyptians, while rare in other African populations. CYP2C9*5, *8, *9, and *11, and VKORC1 Asp36Tyr genetic variants explained warfarin variability in Africans better, compared to CYP2C9*2 and *3. In Africa, there is limited pharmacogenetics data on warfarin. Therefore, future research and funding commitments should be prioritized to ensure safe and effective use of warfarin in Africa. Lessons learned in Africa from the science of pharmacogenetics would inform rational therapeutics in hematology, cardiology, and surgical specialties worldwide.

Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y-chromosome lineages in the Guadeloupe archipelago

OBJECTIVES

The history of the Caribbean region is marked by numerous and various successive migration waves that resulted in a global blending of African, European, and Amerindian lineages. As the origin and genetic composition of the current population of French Caribbean islands has not been studied to date, we used both mitochondrial DNA and Y-chromosome markers to complete the characterization of the dynamics of admixture in the Guadeloupe archipelago.

MATERIALS AND METHODS

We sequenced the mitochondrial hypervariable regions and genotyped mitochondrial and Y-chromosomal single nucleotide polymorphisms (SNPs) of 198 individuals from five localities of the Guadeloupe archipelago.

RESULTS

The maternal haplogroups revealed a blend of 85% African lineages (mainly traced to Western, West-Central, and South-Eastern Africa), 12.5% Eurasian lineages, and 0.5% Amerindian lineages. We highlighted disequilibria between European paternal contribution (44%) and European maternal contribution (7%), pointing out an important sexual asymmetry. Finally, the estimated Native American component was strikingly low and supported the near-extinction of native lineages in the region.

DISCUSSION

We confirmed that all historically known migratory events indeed left a visible genetic imprint in the contemporary Caribbean populations. The data gathered clearly demonstrated the significant impact of the transatlantic slave trade on the Guadeloupean population's constitution. Altogether, the data in our study confirm that in the Caribbean region, human population variation is correlated with colonial and postcolonial policies and unique island histories.

Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation

Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.

Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world

BACKGROUND

The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components.

AIM

To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages.

SUBJECT AND METHODS

Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed.

RESULTS

Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages.

CONCLUSION

The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.

Ancestry and different rates of suicide and homicide in European countries: A study with population-level data

INTRODUCTION

There are large differences in suicide rates across Europe. The current study investigated the relationship of suicide and homicide rates in different countries of Europe with ancestry as it is defined with the haplotype frequencies of Y-DNA and mtDNA.

MATERIAL AND METHODS

The mortality data were retrieved from the WHO online database. The genetic data were retrieved from http://www.eupedia.com. The statistical analysis included Forward Stepwise Multiple Linear Regression analysis and Pearson Correlation Coefficient (R).

RESULTS

In males, N and R1a Y-DNA haplotypes were positively related to both homicidal and suicidal behaviors while I1 was negatively related. The Q was positively related to the homicidal rate. Overall, 60-75% of the observed variance was explained. L, J and X mtDNA haplogroups were negatively related with suicide in females alone, with 82-85% of the observed variance described.

DISCUSSION

The current study should not be considered as a study of genetic markers but rather a study of human ancestry. Its results could mean that research on suicidality has a strong biological but locally restricted component and could be limited by the study population; generalizability of the results at an international level might not be possible. Further research with patient-level data are needed to verify whether these haplotypes could serve as biological markers to identify persons at risk to commit suicide or homicide and whether biologically-determined ancestry could serve as an intermediate grouping method or even as an endophenotype in suicide research.

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages

BACKGROUND

Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

RESULTS

In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase.

CONCLUSIONS

Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.

Across the Gap: Geochronological and Sedimentological Analyses from the Late Pleistocene-Holocene Sequence of Goda Buticha, Southeastern Ethiopia

Goda Buticha is a cave site near Dire Dawa in southeastern Ethiopia that contains an archaeological sequence sampling the late Pleistocene and Holocene of the region. The sedimentary sequence displays complex cultural, chronological and sedimentological histories that seem incongruent with one another. A first set of radiocarbon ages suggested a long sedimentological gap from the end of Marine Isotopic Stage (MIS) 3 to the mid-Holocene. Macroscopic observations suggest that the main sedimentological change does not coincide with the chronostratigraphic hiatus. The cultural sequence shows technological continuity with a late persistence of artifacts that are usually attributed to the Middle Stone Age into the younger parts of the stratigraphic sequence, yet become increasingly associated with lithic artifacts typically related to the Later Stone Age. While not a unique case, this combination of features is unusual in the Horn of Africa. In order to evaluate the possible implications of these observations, sedimentological analyses combined with optically stimulated luminescence (OSL) were conducted. The OSL data now extend the radiocarbon chronology up to 63 ± 7 ka; they also confirm the existence of the chronological gap between 24.8 ± 2.6 ka and 7.5 ± 0.3 ka. The sedimentological analyses suggest that the origin and mode of deposition were largely similar throughout the whole sequence, although the anthropic and faunal activities increased in the younger levels. Regional climatic records are used to support the sedimentological observations and interpretations. We discuss the implications of the sedimentological and dating analyses for understanding cultural processes in the region.

The Impact of Genetic and Non-Genetic Factors on Warfarin Dose Prediction in MENA Region: A Systematic Review

Background

Warfarin is the most commonly used oral anticoagulant for the treatment and prevention of thromboembolic disorders. Pharmacogenomics studies have shown that variants in CYP2C9 and VKORC1 genes are strongly and consistently associated with warfarin dose variability. Although different populations from the Middle East and North Africa (MENA) region may share the same ancestry, it is still unclear how they compare in the genetic and non-genetic factors affecting their warfarin dosing.

Objective

To explore the prevalence of CYP2C9 and VKORC1 variants in MENA, and the effect of these variants along with other non-genetic factors in predicting warfarin dose.

Methods

In this systematic review, we included observational cross sectional and cohort studies that enrolled patients on stable warfarin dose and had the genetics and non-genetics factors associated with mean warfarin dose as the primary outcome. We searched PubMed, Medline, Scopus, PharmGKB, PHGKB, Google scholar and reference lists of relevant reviews.

Results

We identified 17 studies in eight different populations: Iranian, Israeli, Egyptian, Lebanese, Omani, Kuwaiti, Sudanese and Turkish. Most common genetic variant in all populations was the VKORC1 (-1639G>A), with a minor allele frequency ranging from 30% in Egyptians and up to 52% and 56% in Lebanese and Iranian, respectively. Variants in the CYP2C9 were less common, with the highest MAF for CYP2C9*2 among Iranians (27%). Variants in the VKORC1 and CYP2C9 were the most significant predictors of warfarin dose in all populations. Along with other genetic and non-genetic factors, they explained up to 63% of the dose variability in Omani and Israeli patients.

Conclusion

Variants of VKORC1 and CYP2C9 are the strongest predictors of warfarin dose variability among the different populations from MENA. Although many of those populations share the same ancestry and are similar in their warfarin dose predictors, a population specific dosing algorithm is needed for the prospective estimation of warfarin dose.

On the Bantu expansion

Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.

Human Dispersal Out of Africa: A Lasting Debate

Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.

Mayans: a Y chromosome perspective

In spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR markers.

FINDINGS

overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54. Although the Y-STR data illustrates diversity, this diversity, for the most part, is uniformly distributed among geographically distant Mayan populations. Similar haplotypes among populations, abundance of singletons and absence of population partitioning within networks among Mayan populations suggest recent population expansion and substantial gene flow within the Mayan dominion, possibly due to the development of agriculture, the establishment of interacting City-State systems and commerce.

Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements

Background

The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization.

Results

Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography.

Conclusions

Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks.

Electronic supplementary material

The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.

Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup

The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.

Genetic structure of the Kuwaiti population revealed by paternal lineages

OBJECTIVE

We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape.

METHOD

A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe.

RESULTS

The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST  = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan.

CONCLUSION

Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.

The Duffy blood group system in the Tunisian population

BACKGROUND

Tunisia was described to as genetically heterogenous. Besides the 1% native Berber, the genetically influence of the Europeans seems much larger than that of sub-Saharan populations. Due to their ethnic variability, blood group variants have the potential to support population analyses. The aim of this study was to estimate the Duffy blood group system in this mixed population with enhanced characterization of samples with aberrant expression.

MATERIALS AND METHODS

Standard serological testing for the Duffy antigen was done for 105 Tunisian blood donors. Samples with altered Fy expression underwent DNA sequencing of the DARC, RHD and RHCE genes.

RESULTS

The Fy(a-b+) was the most common phenotype identified in the Tunisian population (38.1%). Five samples with Fy(a-b-) phenotype were determined as FY*02N.01/FY*02N.01 by a homozygous occurrence of the FY*B-67C>T alteration. Another three individuals exhibited a Fy(b+(w))Fy(x) expression, confirmed by a FY*A/FY*02M.01 (n = 1) and a FY*02M.01/FY*02M.01 (n = 2) genotype. RHD and RHCE sequencing (n= 8) revealed altered alleles observed in black populations in 5 samples. One individual with FY*02M.01/FY*02M.01 have the silent 165C>T nucleotide substitution each in the RHD and RHCE gene.

DISCUSSION

The composition of blood group variants determined in this study confirms the genetically proximity of Tunisia to Europe. The small sub-Saharan genetic influence was approved by a limited number of variant samples associated with the black population.

From Arabia to Iberia: A Y chromosome perspective

At different times during recent human evolution, northern Africa has served as a conduit for migrations from the Arabian Peninsula. Although previous researchers have investigated the possibility of the Strait of Gibraltar as a pathway of migration from North Africa to Iberia, we now revisit this issue and theorize that although the Strait of Gibraltar, at the west end of this corridor, has acted as a barrier for human dispersal into Southwest Europe, it has not provided an absolute seal to gene flow. To test this hypothesis, here we use the spatial frequency distributions, STR diversity and expansion time estimates of Y chromosome haplogroups J1-P58 and E-M81 to investigate the genetic imprints left by the Arabian and Berber expansions into the Iberian Peninsula, respectively. The data generated indicate that Arabian and Berber genetic markers are detected in Iberia. We present evidence that suggest that Iberia has received gene flow from Northwest Africa during and prior to the Islamic colonization of 711A.D. It is interesting that the highest frequencies of Arabia and Berber markers are not found in southern Spain, where Islam remained the longest and was culturally most influential, but in Northwest Iberia, specifically Galicia. We propose that Moriscos' relocations to the north during the Reconquista, the migration of cryptic Muslims seeking refuge in a more lenient society and/or more geographic extensive pre-Islamic incursions may explain the higher frequencies and older time estimates of mutations in the north of the Peninsula. These scenarios are congruent with the higher diversities of some diagnostic makers observed in Northwest Iberia.

Arab gene geography: From population diversities to personalized medical genomics

Genetic disorders are not equally distributed over the geography of the Arab region. While a number of disorders have a wide geographical presence encompassing 10 or more Arab countries, almost half of these disorders occur in a single Arab country or population. Nearly, one-third of the genetic disorders in Arabs result from congenital malformations and chromosomal abnormalities, which are also responsible for a significant proportion of neonatal and perinatal deaths in Arab populations. Strikingly, about two-thirds of these diseases in Arab patients follow an autosomal recessive mode of inheritance. High fertility rates together with increased consanguineous marriages, generally noticed in Arab populations, tend to increase the rates of genetic and congenital abnormalities. Many of the nearly 500 genes studied in Arab people revealed striking spectra of heterogeneity with many novel and rare mutations causing large arrays of clinical outcomes. In this review we provided an overview of Arab gene geography, and various genetic abnormalities in Arab populations, including disorders of blood, metabolic, circulatory and neoplasm, and also discussed their associated molecules or genes responsible for the cause of these disorders. Although studying Arab-specific genetic disorders resulted in a high value knowledge base, approximately 35% of genetic diseases in Arabs do not have a defined molecular etiology. This is a clear indication that comprehensive research is required in this area to understand the molecular pathologies causing diseases in Arab populations.

Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing

SNPs from the non-recombining part of the human Y chromosome (Y-SNPs) are informative to classify paternal lineages in forensic, genealogical, anthropological, and evolutionary studies. Although thousands of Y-SNPs were identified thus far, previous Y-SNP multiplex tools target only dozens of markers simultaneously, thereby restricting the provided Y-haplogroup resolution and limiting their applications. Here, we overcome this shortcoming by introducing a high-resolution multiplex tool for parallel genotyping-by-sequencing of 530 Y-SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups. Contrary to previous Y-SNP multiplex tools, our approach covers branches of the entire Y tree, thereby maximizing the paternal lineage classification obtainable. We used a default DNA input amount of 10 ng per reaction but preliminary sensitivity testing revealed positive results from as little as 100 pg input DNA. Furthermore, we demonstrate that sample pooling using barcodes is feasible, allowing increased throughput for lower per-sample costs. In addition to the wetlab protocol, we provide a software tool for automated data quality control and haplogroup classification. The unique combination of ultra-high marker density and high sensitivity achievable from low amounts of potentially degraded DNA makes this new multiplex tool suitable for a wide range of Y-chromosome applications.

Phylogeography of E1b1b1b-M81 haplogroup and analysis of its subclades in Morocco

In this study we analyzed 295 unrelated Berber-speaking men from northern, central, and southern Morocco to characterize frequency of the E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183, and E1b1b1b2a-M165. For this purpose, we typed four biallelic polymorphisms: M81, M107, M183, and M165. A large majority of the Berber-speaking male lineages belonged to the Y-chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1% to 98.5% in all localities sampled. E1b1b1b2-M183 was the most dominant subclade in our samples, ranging from 65.1% to 83.1%. In contrast, the E1b1b1b1-M107 and E1b1b1b2a-M165 subclades were not found in our samples. Our results suggest a predominance of the E1b1b1b-M81 haplogroup among Moroccan Berber-speaking males with a decreasing gradient from south to north. The most prevalent subclade in this haplogroup was E1b1b1b2-M183, for which diffferences among these three groups were statistically significant between central and southern groups.

At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

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Maputo Bantus exhibit close affinities with other West and East African Bantus.

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Traces of Khoisan and Pygmy markers persist in the Maputo Province Bantus.

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R1a1a-M17/M198 in the Maputo Province may represent back or recent migration.

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Linguistic, cultural and genetic heritages are reflected in Maputo's gene pool.

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Admixture and assimilation processes of Bantu elements were region-specific.

Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites

Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.

Population genetics studies continue to debate whether Ashkenazi Levites originated in Europe or the Near East. Here, Rootsi et al. use whole Y-chromosome DNA sequences to unravel the phylogenetic origin of the Ashkenazi Levite and suggest an origin for the Levite founder lineage in the Near East.

Genetic variation and adaptation in Africa: implications for human evolution and disease

Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.

Early back-to-Africa migration into the Horn of Africa

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents

Background

Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.

Results

Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.

Conclusions

The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

Genetic diversity and prevalence of CCR2-CCR5 gene polymorphisms in the Omani population

Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Ocean. In this study, we examined the CCR2-CCR5 haplotypes in Omanis and compared the patterns of genetic diversity with those of other populations. Blood samples were collected from 115 Omani adults and genomic DNA was screened to identify the polymorphic sites in the CCR5 gene and the CCR2V64I mutation. Four minor alleles were common: CCR5-2554T and CCR5-2086G showed frequencies of 49% and 46%, respectively, whereas CCR5-2459A and CCR5-2135C both had a frequency of 36%. These alleles showed moderate levels of heterozygosity, indicating that they were under balancing selection. However, the well-known allele CCR5Δ32 was relatively rare. Eleven haplotypes were identified, four of which were common: HHC (46%), HHE (20%), HHA (14%) and HHF*2 (12%).

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism

Archeological and paleontological evidences point to East Africa as the likely area of early evolution of modern humans. Genetic studies also indicate that populations from the region often contain, but not exclusively, representatives of the more basal clades of mitochondrial and Y-chromosome phylogenies. Most Y-chromosome haplogroup diversity in Africa, however, is present within macrohaplogroup E that seem to have appeared 21 000-32 000 YBP somewhere between the Red Sea and Lake Chad. The combined analysis of 17 bi-allelic markers in 1214 Y chromosomes together with cultural background of 49 populations displayed in various metrics: network, multidimensional scaling, principal component analysis and neighbor-joining plots, indicate a major contribution of East African populations to the foundation of the macrohaplogroup, suggesting a diversification that predates the appearance of some cultural traits and the subsequent expansion that is more associated with the cultural and linguistic diversity witnessed today. The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.

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.