The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions

A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease

This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts. D-statistics suggest possible Sub-Saharan introgression into one of the studied genomic regions (10q11). We also found differences in linkage disequilibrium patterns between the two Mediterranean coasts, possibly attributable to differential Sub-Saharan admixture. Our results confirm the potentially important role of human demographic history when performing epidemiological studies.

Population variation of LIN28B in the Mediterranean: Novel markers for microgeographic discrimination

OBJECTIVES

The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival.

METHODS

A total of 1,197 DNA samples were genotyped. The allele frequencies were used to determine the relationship between populations, with data from the 1000 Genomes Project being used for external comparisons. The genotype distributions and the population structure between populations and groups of populations were determined.

RESULTS

The population results indicate a significant degree of variation (F_ST  = 0.043, P < 0.0001). Allele frequencies show significant differences among populations. A hierarchical variance analysis is consistent with a primary differentiation between populations on the North and South coasts of the Mediterranean. This difference is especially evident in the unexpected distribution of the SNP rs221639, which shows one of the highest F_ST (11.5%, P < 0.0001) values described in the Mediterranean region thus far.

CONCLUSION

The population differentiation and the structuring of the genetic variance, in agreement with previous studies, indicate that the SNPs in question are good tools for the study of human populations, even at a microgeographic level. Am. J. Hum. Biol. 28:905-912, 2016. © 2016Wiley Periodicals, Inc.

Determination of arylsulfatase A pseudodeficiency allele and haplotype frequency in the Tunisian population

Arylsulfatase A (ASA) is a lysosomal enzyme involved in the catabolism of cerebroside sulfate. ASA deficiency is associated with metachromatic leukodystrophy (MLD). Low ASA activities have also been reported in a more common condition with no apparent clinical consequences termed ASA pseudo-deficiency (ASA-PD) which is associated with two linked mutations in the ASA gene (c.1049A>G and c.*96A>G). This study aimed to investigate the frequency of the two ASA-PD variants and their linkage disequilibrium (LD) among Tunisians. ASA-PD variants were detected in 129 healthy Tunisians and their frequencies were compared to those described worldwide. The frequency of the PD allele was estimated at 17.4% for the overall sample, with c.1049A>G and c.*96A>G frequencies of 25.6 and 17.4%, respectively. This study also revealed a high LD between the two ASA-PD variants (r(2) = 0.61). Inter-population analysis revealed similarities in the ASA-PD genetic structure between Tunisians and populations from Middle East with c.*96A>G frequencies being the highest in the world. A significant North vs. South genetic differentiation in the ASA-PD frequency was also observed in Tunisian population who seems genetically intermediate between Africans, Middle-Easterners and Europeans. This is the first report on the allele frequency of the ASA-PD in North Africa, revealing a relatively high frequency of the PD allele among Tunisians. This study gives also evidence on the importance of discriminating ASA-PD allele from pathological mutations causing MLD and supporting enzymatic activity testing with both sulfatiduria determination and genetic testing in the differential diagnosis of MLD in the Tunisian population.

Mediterranean Founder Mutation Database (MFMD): Taking Advantage from Founder Mutations in Genetics Diagnosis, Genetic Diversity and Migration History of the Mediterranean Population

The Mediterranean basin has been the theater of migration crossroads followed by settlement of several societies and cultures in prehistoric and historical times, with important consequences on genetic and genomic determinisms. Here, we present the Mediterranean Founder Mutation Database (MFMD), established to offer web-based access to founder mutation information in the Mediterranean population. Mutation data were collected from the literature and other online resources and systematically reviewed and assembled into this database. The information provided for each founder mutation includes DNA change, amino-acid change, mutation type and mutation effect, as well as mutation frequency and coalescence time when available. Currently, the database contains 383 founder mutations found in 210 genes related to 219 diseases. We believe that MFMD will help scientists and physicians to design more rapid and less expensive genetic diagnostic tests. Moreover, the coalescence time of founder mutations gives an overview about the migration history of the Mediterranean population. MFMD can be publicly accessed from http://mfmd.pasteur.ma.

Variability and distribution of COL1A2 (type I collagen) polymorphisms in the central-eastern Mediterranean Basin

BACKGROUND

The most abundant of the collagen protein family, type I collagen is encoded by the COL1A2 gene. The COL1A2 restriction fragment length polymorphisms (RFLPs) EcoRI, RsaI and MspI in samples from several different central-eastern Mediterranean populations were analysed and found to be potentially informative anthropogenetic markers.

AIM

The objective was to define the genetic variability of COL1A2 in the central-eastern Mediterranean and to shed light on its genetic distribution in human groups over a wide geographic area.

SUBJECTS AND METHODS

PCR-RFLP analysis of EcoRI, RsaI and MspI polymorphisms of the COL1A2 gene was performed on oral swab and blood samples from 308 individuals from the central-eastern Mediterranean Basin. The genetic similarities among these groups and other populations described in the literature were investigated through correspondence analysis.

RESULTS

Single-marker data and haplotype frequencies seemed to suggest a genetic homogeneity within the European populations, whereas a certain degree of differentiation was noted for the Egyptians and the Turks.

CONCLUSIONS

The genetic variability in the central-eastern Mediterranean area is probably a result of the geographical barrier of the Mediterranean Sea, which separated European and African populations over time.

The burden of disease in Spain: results from the global burden of disease study 2010

BACKGROUND

We herein evaluate the Spanish population's trends in health burden by comparing results of two Global Burden of Diseases, Injuries, and Risk Factors Studies (the GBD studies) performed 20 years apart.

METHODS

Data is part of the GBD study for 1990 and 2010. We present results for mortality, years of life lost (YLLs), years lived with disability, and disability-adjusted life years (DALYs) for the Spanish population. Uncertainty intervals for all measures have been estimated.

RESULTS

Non-communicable diseases accounted for 3,703,400 (95% CI 3,648,270-3,766,720) (91.3%) of 4,057,400 total deaths, in the Spanish population. Cardiovascular and circulatory diseases were the main cause of mortality among non-communicable diseases (34.7% of total deaths), followed by neoplasms (27.1% of total deaths). Neoplasms, cardiovascular and circulatory diseases, and chronic respiratory diseases were the top three leading causes for YLLs. The most important causes of DALYs in 2010 were neoplasms, cardiovascular and circulatory diseases, musculoskeletal disorders, and mental and behavioral disorders.

CONCLUSIONS

Mortality and disability in Spain have become even more linked to non-communicable diseases over the last years, following the worldwide trends. Cardiovascular and circulatory diseases, neoplasms, mental and behavioral disorders, and neurological disorders are the leading causes of mortality and disability. Specific focus is needed from health care providers and policy makers to develop health promotion and health education programs directed towards non-communicable disorders.

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.

Analysis of HLA-A, -B, -C, -DR, -DQ polymorphisms in the South Tunisian population and a comparison with other populations

BACKGROUND

The Human Leucocyte Antigen (HLA) system is often used as a genetic marker for analysing populations. HLA antigen distribution among the Tunisian population is not well defined because of the lack of a general population study.

AIM

The aim of the present study was to investigate the polymorphism of HLA-A, -B, -C, -DR and -DQ loci in the South Tunisian population.

SUBJECTS AND METHODS

This study has investigated HLA-A, -B, -C, -DR and -DQ polymorphisms in 123 unrelated healthy individuals originating from the south of Tunisia. HLA class I was studied by serology and completed by polymerase chain reaction-sequence specific primer (PCR-SSP). HLA class II was performed using PCR-SSP.

RESULTS

The most common alleles were A-2 (0.2154), B-44 (0.1179), C7 (0.2114), DR4 (0.1626) and DQ2 (0.313). A1-B-8-C7-DR3-DQ2 (2.84%) was the predominant haplotype in this population. Comparisons with data of other worldwide populations based on phylogenetic tree and multidimensional scaling analysis were done. This study suggests that both HLA class I and class II polymorphism specificities demonstrate a high diversity in this South Tunisian population, which reflects ancient and recent admixture with neighbouring populations.

CONCLUSION

The results provide useful information for further studies of Tunisian population evolution, anthropology and for resolving HLA frequencies when searching for HLA-compatible donors in transplantation and for the analysis of disease associations.

North African influences and potential bias in case-control association studies in the Spanish population

Background

Despite the limited genetic heterogeneity of Spanish populations, substantial evidences support that historical African influences have not affected them uniformly. Accounting for such population differences might be essential to reduce spurious results in association studies of genetic factors with disease. Using ancestry informative markers (AIMs), we aimed to measure the African influences in Spanish populations and to explore whether these might introduce statistical bias in population-based association studies.

Methodology/Principal Findings

We genotyped 93 AIMs in Spanish (from the Canary Islands and the Iberian Peninsula) and Northwest Africans, and conducted population and individual-based clustering analyses along with reference data from the HapMap, HGDP-CEPH, and other sources. We found significant differences for the Northwest African influence among Spanish populations from as low as ≈5% in Spanish from the Iberian Peninsula to as much as ≈17% in Canary Islanders, whereas the sub-Saharan African influence was negligible. Strikingly, the Northwest African ancestry showed a wide inter-individual variation in Canary Islanders ranging from 0% to 96%, reflecting the violent way the Islands were conquered and colonized by the Spanish in the XV century. As a consequence, a comparison of allele frequencies between Spanish samples from the Iberian Peninsula and the Canary Islands evidenced an excess of markers with significant differences. However, the inflation of p-values for the differences was adequately controlled by correcting for genetic ancestry estimates derived from a reduced number of AIMs.

Conclusions/Significance

Although the African influences estimated might be biased due to marker ascertainment, these results confirm that Northwest African genetic footprints are recognizable nowadays in the Spanish populations, particularly in Canary Islanders, and that the uneven African influences existing in these populations might increase the risk for false positives in association studies. Adjusting for population stratification assessed with a few dozen AIMs would be sufficient to control this effect.