Classical polymorphisms in Berbers from Moyen Atlas (Morocco): genetics, geography, and historical evidence in the Mediterranean peoples

Digging into the admixture strata of current-day Canary Islanders based on mitogenomes

The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.

Differential mutational profiles of familial Mediterranean fever in North Africa

Familial Mediterranean fever (FMF) is a recessive autoinflammatory disease, mainly occurring in the eastern Mediterranean. In these populations, the five FMF founder mutations are differently distributed. In Algeria, the FMF-causing variants remain poorly explored. This retrospective study aims to report the mutational profile of Algerian FMF patients and to compare it with North African FMF patients. One hundred eighty-three unrelated patients clinically suspected of FMF were recruited from various Algerian hospitals (2007-2015) and tested for mutations in exon 10 of MEFV gene. Molecular analysis identified 144 mutant alleles among 87 of 183 patients (47.5%). p.M694I was the most prevalent pathogenic allele, accounting for 63.2% of mutant alleles, followed by p.M694V and p.M680I occurring with a same frequency (14.5%). Others, p.A744S (6.2%) and p.I692del (1.3%), are less frequent. Interestingly, p.M694I was the most recurrent in patients with renal AA-amyloidosis. Our results provide the first genetic data on FMF in Algeria, demonstrating the predominance of p.M694I and the absence of p.V726A, compared to other North African countries (Morocco, Tunisia, and Egypt). In conclusion, North African FMF patients display differential mutational profiles that may result from the difference in ethnic origin and the genetic heterogeneity among these populations.

Spatial principal component analysis points at global genetic structure in the Western Mediterranean

Many studies have tackled the existence of a genetic barrier in the Strait of Gibraltar between Iberian and North African populations, often with controversial conclusions. Here, we address this issue using a collection of Western Mediterranean populations and two dimensionality reduction methods: principal component analysis (PCA) and spatial PCA (sPCA). Our four different data sets consisted of (i) 16 polymorphic Alu insertions in 12 populations; (ii) 35 single-nucleotide polymorphisms in 13 populations; (iii) 13 short tandem repeats in 11 populations; and (iv) all 64 markers in 9 populations. In all PCA plots, South European and North African samples were visually distinguishable along the first PC. Several smaller clusters were also identifiable, especially on the African side of our geographical setting. sPCA indicated a single global structure for each of the marker sets and no local structures. These results are more compatible with a clinal distribution of allele frequencies rather than with abrupt changes, suggesting that isolation-by-distance, rather than a barrier to gene flow, is a more likely mechanism of genetic differentiation in the Western Mediterranean. An alternative/complementary explanation is progressive introgression from North African to Southwestern European populations.

Usefulness of autosomal STR polymorphisms beyond forensic purposes: data on Arabic- and Berber-speaking populations from central Morocco

BACKGROUND

This work describes, for the first time, the profile of Middle Atlas Berbers and Arabic-speaking central Moroccans for 15 autosomal STR loci widely used in forensic sciences.

AIM

The main objectives were to determine the degree of heterogeneity among different Moroccan samples to identify geographic or linguistic patterns and to evaluate the usefulness of forensic STRs in anthropological studies.

SUBJECTS AND METHODS

Blood samples were collected from 71 Arabic-speakers and 75 Berbers from the regions of Doukkala (central-west coast) and Khenifra (Middle Atlas), respectively. The AmpFlSTR Identifier kit was used to genotype 15 autosomal STR in both samples.

RESULTS

Middle Atlas Berbers showed slightly higher genetic variation values compared to Arabic-speakers, both in the number of alleles and heterozygosity. In order to assess population relationships, data from Morocco, Algeria, Tunisia, Libya, Egypt, Kuwait, Qatar, Palestine, Syria, South-Spain and Turkey were included in the analysis. Within Morocco, genetic distances followed a clear geographic pattern. In the Arabic-speaking sample the genetic proportion of 'Arabian' admixture was estimated in 13%.

CONCLUSION

The low value of admixture suggests that the Arabization of Morocco had a reduced demographic impact, which should be taken with caution because it is based on autosomal STRs with low inter-population variation levels.

Polymorphisms influencing muscle phenotypes in North-African and Spanish populations

AIM

The purpose of this study was to determine the allelic and genotypic frequency distribution of the C34T mutation in the muscle isoform of the adenosine monophosphate deaminase 1 (AMPD1) gene and of the missense substitution K153R in the myostatin (GDF8) gene in one Spanish and two North African populations.

METHOD

One sample of 98 individuals was genotyped from the South of Spain (Alpujarra) and two samples from Morocco (77 Berbers and 78 Arabs).

RESULTS

The frequency of the AMPD1 C34T mutation was lower in Berbers (0.071) compared with the Alpujarra cohort (0.153, p = 0.018). The GDF8 K153R substitution showed little variability among the three cohorts.

CONCLUSIONS

Studies with larger cohorts and other ethnic groups are needed to corroborate that there does not exist any major variability in the genotype distribution of genes associated with muscle phenotypes in the South-Eastern Mediterranean area.

Genetic differences among North African Berber and Arab-speaking populations revealed by Y-STR diversity

Y-chromosome STR polymorphisms are inherited in a haploid state which makes them a powerful tool for easy tracing of paternal lineage and for use in human population evolutionary studies. North-African Y chromosomal diversity has traditionally been studied in order to find genetic and geographic associations as well as to test how natural and cultural barriers have affected the degree of genetic flow not only within North Africa but also in a wider Mediterranean context. The degree of Berber/Arab genetic differentiation in the Moroccan population has been tested for a complete set of forensic markers as sixteen Y-chromosomal short tandem repeats (STRs) (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1). The results suggest considerable population heterogeneity in North Africa.

Human genetic differentiation across the Strait of Gibraltar

BACKGROUND

The Strait of Gibraltar is a crucial area in the settlement history of modern humans because it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this strait constitutes a barrier to gene flow, as previous results were highly variable depending on the genetic locus studied. The present study evaluates the impact of the Gibraltar region in reducing gene flow between populations from North-Western Africa and South-Western Europe, by comparing formally various genetic loci. First, we compute several statistics of population differentiation. Then, we use an original simulation approach in order to infer the most probable evolutionary scenario for the settlement of the area, taking into account the effects of both demography and natural selection at some loci.

RESULTS

We show that the genetic patterns observed today in the region of the Strait of Gibraltar may reflect an ancient population genetic structure which has not been completely erased by more recent events such as Neolithic migrations. Moreover, the differences observed among the loci (i.e. a strong genetic boundary revealed by the Y-chromosome polymorphism and, at the other extreme, no genetic differentiation revealed by HLA-DRB1 variation) across the strait suggest specific evolutionary histories like sex-mediated migration and natural selection. By considering a model of balancing selection for HLA-DRB1, we here estimate a coefficient of selection of 2.2% for this locus (although weaker in Europe than in Africa), which is in line with what was estimated from synonymous versus non-synonymous substitution rates. Selection at this marker thus appears strong enough to leave a signature not only at the DNA level, but also at the population level where drift and migration processes were certainly relevant.

CONCLUSIONS

Our multi-loci approach using both descriptive analyses and Bayesian inferences lead to better characterize the role of the Strait of Gibraltar in the evolution of modern humans. We show that gene flow across the Strait of Gibraltar occurred at relatively high rates since pre-Neolithic times and that natural selection and sex-bias migrations distorted the demographic signal at some specific loci of our genome.

Screening for Alpha 1 antitrypsin deficiency in Tunisian subjects with obstructive lung disease: a feasibility report

Background

AATD is one of the most common inherited disorders in the World. However, it is generally accepted that AATD in North African populations is not a risk factor for lung and/or liver disease, based on a number of small studies. We therefore planned a screening study for detection of AATD in patients with OLD in a cohort of patients from Kairouan in central Tunisia. Methods: One hundred twenty patients with OLD (asthma, emphysema, COPD) were enrolled in the screening programme. Laboratory diagnosis for AATD was performed according to current diagnostic standards.

Results

We found that 6/120 OLD patients carried an AAT deficient allele, 1 PI*MZ, 1 PI*MPlowel, 3 PI*MMmalton, 1 PI*MMwurzburg.

Conclusion

this pilot study demonstrated that alleles related to deficiency of AAT are not absent in the Tunisian population, and that rare AATD variants prevailed over commonest PI*Z variant. These results would support a larger scale screening for AATD in Tunisia.

X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)

Background

Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome.

Results

A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea.

A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area.

Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza.

Conclusion

Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.

Study of GM immunoglobulin allotypic system in Berbers and Arabs from Morocco

The GM immunoglobulin allotype polymorphism was investigated in four Moroccan populations: three Berber groups from Khenifra (Middle Atlas), Amizmiz (High Atlas), and Bouhria (Beni Snassen) and one Arabic-speaking sample from the Doukkala area (Abda, Chaouia, Doukkali, and Tadla districts in south-central Morocco). In order to characterize the genetic relationships between the populations, our results were compared with those obtained for other North African groups (from Morocco, Algeria, Tunisia, and Niger) and for Middle-East Africans, sub-Saharans, and Southwest Europeans. Based on GM haplotype frequencies, Factorial Correspondence Analyses, F(ST) significance testing, and hierarchical analyses of variance were performed. Our results reveal that Moroccan populations have heterogeneous GM profiles with high frequencies of GM haplotypes in Europeans (from 76% for Doukkala to 88% for Bouhria) and relatively high frequencies of GM haplotypes in sub-Saharans (from 11% for Bouhria to 23% for Amizmiz). The genetic diversity observed among Moroccans is not significantly correlated with either geographic or linguistic differentiation. In spite of their cultural and historical differentiation, we did not discover any significant genetic differences between Berbers and Arabic-speakers from Morocco. However, when large geographical areas are considered, our population samples are integrated in the North African GM variation, significantly distant from sub-Saharan groups but with a close relationship with Southwest European populations.

Genetic relationships among Berbers and South Spaniards based on CD4 microsatellite/Alu haplotypes

BACKGROUND

CD4 STR/Alu haplotype diversity, both for its qualitative and quantitative properties, has been widely used in molecular anthropology to clarify the degree of genetic relationships among human populations.

AIM

CD4 STR/Alu variation was studied in two West Mediterranean samples, Andalusians from La Alpujarra region on the north side of the Gibraltar Strait and Berbers from the south, to ascertain the pattern of affinities between them.

SUBJECTS AND METHODS

Alu and microsatellite alleles were tested in 99 Andalusians from La Alpujarra region (Southeast Spain) and 124 Middle Atlas Berbers (Morocco).

RESULTS

Two new combinations of Alu and STR alleles (75(+) and 80(-)) were found in Berbers. The CD4 STR/Alu haplotype distribution in South Spaniards is similar to that of other Europeans, the only special feature is the slight presence of the 90(+) and 130(+) typical Sub-Saharan haplotypes. The Berber sample is characterized by a high number of different haplotypes (18) with intermediate heterozygosity values (0.846) in comparison with other North African groups, and by a high frequency of the 110(-) combination that has been proposed as representative of an ancient Northwest African population.

CONCLUSION

A geographical gradient of Sub-Saharan gene contribution has been detected in North Africa. The Middle Atlas Berbers showed an intermediate value in comparison with the high and low values found in Mauritanians and Moroccan Berbers, respectively. The analysis of the CD4 STR/Alu haplotype variation failed to indicate any particular relationship between South Spaniards and North Africans.

Exploring northeast African metric craniofacial variation at the individual level: A comparative study using principal components analysis

A principal components analysis was carried out on male crania from the northeast quadrant of Africa and selected European and other African series. Individuals, not predefined groups, were the units of study, while nevertheless keeping group membership in evidence. The first principal component seems to largely capture "size" variation in crania from all of the regions. The same general morphometric trends were found to exist within the African and European crania, although there was some broad separation along a cline. Anatomically, the second principal component captures predominant trends denoting a broader to narrower nasal aperture combined with a similar shape change in the maxilla, an inverse relation between face-base lengths ("projection") and base breadths, and a decrease in anterior base length relative to base breadth. The third principal component broadly describes trends within Africa and Europe: specifically, a change from a combination of a relatively narrower face and longer vault, to one of a wider face and shorter vault; it shows the northeast quadrant Africans along a cline with the other Africans. Stated in relative terms, the northeastern Africans tend to exhibit narrower bases in relationship to more projecting faces, and broader nasal areas than Europeans, although there is range of variation. Relative to the other African groups, they have narrower nasal areas and narrower faces in relationship to vault length. The crania from the northeast quadrant of Africa collectively demonstrate the greatest pattern of overlap with both Europeans and other Africans. Variation was found to be high in all series but greatest in the African material as a whole. Individuals from different geographical regions frequently plotted near each other, revealing aspects of variation at the level of individuals that is obscured by concentrating on the most distinctive facial traits once used to construct "types." The high level of African interindividual variation in craniometric pattern is reminiscent of the great level of molecular diversity found in Africa. These results, coupled with those of Y chromosome studies, may help generate hypotheses concerning the length of time over which recent craniometric variation emerged in Africa.